MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Journal of Bimolecular NMR' source. Thu, 09 Feb 2012 14:07:53 +0100 http://www.medworm.com/index.php?rid=5671990&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22314702%26dopt%3DAbstract We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and (13)C(β) chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of β-turns: I, II, I', II' and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and β-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5671990 Wed, 08 Feb 2012 05:00:00 +0100 5671990 http://www.medworm.com/index.php?rid=5671989&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22314703%26dopt%3DAbstract We describe a relaxation violated coherence transfer approach where the relaxation of multiple-quantum (1)H-(13)C methyl coherences during the relaxation delay period is quantified. The NMR experiment and the associated fitting procedure that models the time-dependence of the signal build-up, are applicable to the characterization of side-chain order in [(13)CH(3)]-methyl-labeled, highly deuterated protein systems up to ~100 kDa in molecular weight. The feasibility of extracting reliable measures of side-chain order is experimentally verified on methyl-protonated, perdeuterated samples of an 8.5-kDa ubiquitin at 10°C and an 82-kDa Malate Synthase G at 37°C. PMID: 22314703 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5671989 Wed, 08 Feb 2012 05:00:00 +0100 5671989 http://www.medworm.com/index.php?rid=5671988&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22314704%26dopt%3DAbstract Authors: Gorbatyuk VY, Schiller MR, Gorbatyuk OI, Barwinski M, Hoch JC PMID: 22314704 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5671988 Wed, 08 Feb 2012 05:00:00 +0100 5671988 http://www.medworm.com/index.php?rid=5671987&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22314705%26dopt%3DAbstract Authors: Lehtivarjo J, Tuppurainen K, Hassinen T, Laatikainen R, Peräkylä M Abstract While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein (1)H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (N... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5671987 Wed, 08 Feb 2012 05:00:00 +0100 5671987 http://www.medworm.com/index.php?rid=5618947&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22252483%26dopt%3DAbstract We present here a procedure to analyze and correct the calibration of (13)C NMR data of RNAs. Our procedure uses five (13)C chemical shifts as a reference, each of them found in a narrow shift range in most datasets deposited in the Biological Magnetic Resonance Bank. In 49 datasets we could evaluate the (13)C calibration and detect errors or inconsistencies in RNA (13)C chemical shifts based on these chemical shift reference values. More than half of the datasets (27 out of those 49) were found to be improperly referenced or contained inconsistencies. This large inconsistency rate possibly explains that no clear structure-(13)C chemical shift relationship has emerged for RNA so far. We were able to recalibrate or correct 17 datasets resulting in 39 usable (13)C datasets. 6 new datasets fr... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5618947 Wed, 18 Jan 2012 05:00:00 +0100 5618947 http://www.medworm.com/index.php?rid=5618946&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22252484%26dopt%3DAbstract Authors: Löhr F, Reckel S, Karbyshev M, Connolly PJ, Abdul-Manan N, Bernhard F, Moore JM, Dötsch V Abstract Obtaining NMR assignments for slowly tumbling molecules such as detergent-solubilized membrane proteins is often compromised by low sensitivity as well as spectral overlap. Both problems can be addressed by amino-acid specific isotope labeling in conjunction with (15)N-(1)H correlation experiments. In this work an extended combinatorial selective in vitro labeling scheme is proposed that seeks to reduce the number of samples required for assignment. Including three different species of amino acids in each sample, (15)N, 1-(13)C, and fully (13)C/(15)N labeled, permits identification of more amino acid types and sequential pairs than would be possible with previously publishe... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5618946 Wed, 18 Jan 2012 05:00:00 +0100 5618946 http://www.medworm.com/index.php?rid=5595342&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22228480%26dopt%3DAbstract We present reduced dimensionality (RD) 3D HN(CA)NH for efficient sequential assignment in proteins. The experiment correlates the (15)N and (1)H chemical shift of a residue ('i') with those of its immediate N-terminal (i - 1) and C-terminal (i + 1) neighbors and provides four-dimensional chemical shift correlations rapidly with high resolution. An assignment strategy is presented which combines the correlations observed in this experiment with amino acid type information obtained from 3D CBCA(CO)NH. By classifying the 20 amino acid types into seven distinct categories based on (13)C(β) chemical shifts, it is observed that a stretch of five sequentially connected residues is sufficient to map uniquely on to the polypeptide for sequence specific resonance assignments. This method is exe... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5595342 Sat, 07 Jan 2012 05:00:00 +0100 5595342 http://www.medworm.com/index.php?rid=5557865&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22203187%26dopt%3DAbstract We describe here, adaptation of the HNN pulse sequence for multiple nuclei detection using two independent receivers by utilizing the detectable (13)C(α) transverse magnetization which was otherwise dephased out in the conventional HNN experiment. It enables acquisition of 2D (13)C(α)-(15)N sequential correlations along with the standard 3D (15)N-(15)N-(1)H correlations, which provides directionality to sequential walk in HNN, on one hand, and enhances the speed of backbone assignment, on the other. We foresee that the implementation of dual direct detection opens up new avenues for a wide variety of modifications that would further enhance the value and applications of the experiment, and enable derivation of hitherto impossible information. PMID: 22203187 [PubMed - as supplied by p... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5557865 Wed, 28 Dec 2011 05:00:00 +0100 5557865 http://www.medworm.com/index.php?rid=5557866&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22200887%26dopt%3DAbstract Authors: Redfield AG Abstract Improvements are described in a shuttling field-cycling device (Redfield in Magn Reson Chem 41:753-768, 2003), designed to allow widespread access to this useful technique by configuring it as a removable module to a commercial 500 MHz NMR instrument. The main improvements described here, leading to greater versatility, high reliability and simple construction, include: shuttling provided by a linear motor driven by an integrated-control servomotor; provision of automated bucking magnets to allow fast two-stage cycling to nearly zero field; and overall control by a microprocessor. A brief review of history and publications that have used the system is followed by a discussion of topics related to such a device including discussion of some future appli... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5557866 Tue, 27 Dec 2011 05:00:00 +0100 5557866 http://www.medworm.com/index.php?rid=5544567&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22193860%26dopt%3DAbstract Authors: Wagner G PMID: 22193860 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5544567 Fri, 23 Dec 2011 05:00:00 +0100 5544567 http://www.medworm.com/index.php?rid=5525761&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22167466%26dopt%3DAbstract Authors: Orts J, Bartoschek S, Griesinger C, Monecke P, Carlomagno T Abstract Low-affinity ligands can be efficiently optimized into high-affinity drug leads by structure based drug design when atomic-resolution structural information on the protein/ligand complexes is available. In this work we show that the use of a few, easily obtainable, experimental restraints improves the accuracy of the docking experiments by two orders of magnitude. The experimental data are measured in nuclear magnetic resonance spectra and consist of protein-mediated NOEs between two competitively binding ligands. The methodology can be widely applied as the data are readily obtained for low-affinity ligands in the presence of non-labelled receptor at low concentration. The experimental inter-ligand NOEs ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5525761 Wed, 14 Dec 2011 05:00:00 +0100 5525761 http://www.medworm.com/index.php?rid=5525760&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22167467%26dopt%3DAbstract Authors: Linser R Abstract For micro-crystalline proteins, solid-state nuclear magnetic resonance spectroscopy of perdeuterated samples can provide spectra of unprecedented quality. Apart from allowing to detect sparsely introduced protons and thereby increasing the effective resolution for a series of sophisticated techniques, deuteration can provide extraordinary coherence lifetimes-obtainable for all involved nuclei virtually without decoupling and enabling the use of scalar magnetization transfers. Unfortunately, for fibrillar or membrane-embedded proteins, significantly shorter transverse relaxation times have been encountered as compared to micro-crystalline proteins despite an identical sample preparation, calling for alternative strategies for resonance assignment. In this ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5525760 Wed, 14 Dec 2011 05:00:00 +0100 5525760 http://www.medworm.com/index.php?rid=5525762&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22160811%26dopt%3DAbstract Authors: Kleckner IR, Foster MP Abstract Molecular dynamics are essential for life, and nuclear magnetic resonance (NMR) spectroscopy has been used extensively to characterize these phenomena since the 1950s. For the past 15 years, the Carr-Purcell Meiboom-Gill relaxation dispersion (CPMG RD) NMR experiment has afforded advanced NMR labs access to kinetic, thermodynamic, and structural details of protein and RNA dynamics in the crucial μs-ms time window. However, analysis of RD data is challenging because datasets are often large and require many non-linear fitting parameters, thereby confounding assessment of accuracy. Moreover, novice CPMG experimentalists face an additional barrier because current software options lack an intuitive user interface and extensive documentation. H... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5525762 Sun, 11 Dec 2011 05:00:00 +0100 5525762 http://www.medworm.com/index.php?rid=5525764&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22138787%26dopt%3DAbstract We present here a (1)H-detected 3D (H)CCH experiment for assignment of backbone and sidechain proton resonances. Resolution is significantly improved by employing simultaneous (13)CO and (13)Cβ J-decoupling during evolution of the (13)Cα chemical shift. In total, ~90% of the (1)Hα-(13)Cα backbone resonances of chicken α-spectrin SH3 could be assigned. PMID: 22138787 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5525764 Sun, 04 Dec 2011 05:00:00 +0100 5525764 http://www.medworm.com/index.php?rid=5525763&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22143941%26dopt%3DAbstract Authors: Krähenbühl B, Hofmann D, Maris C, Wider G Abstract A five-dimensional (5D) APSY (automated projection spectroscopy) HCNCH experiment is presented, which allows unambiguous correlation of sugar to base nuclei in nucleic acids. The pulse sequence uses multiple quantum (MQ) evolution which enables long constant-time evolution periods in all dimensions, an improvement that can also benefit non-APSY applications. Applied with an RNA with 23 nucleotides the 5D APSY-HCNCH experiment produced a complete and highly precise 5D chemical shift list within 1.5 h. Alternatively, and for molecules where the out-and-stay 5D experiment sensitivity is not sufficient, a set of out-and-back 3D APSY-HCN experiments is proposed: an intra-base (3D APSY-b-HCN) experiment in an MQ or in a TROSY... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5525763 Sun, 04 Dec 2011 05:00:00 +0100 5525763 http://www.medworm.com/index.php?rid=5472067&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22131165%26dopt%3DAbstract We describe a robust approach for alleviating such difficulties, by using proteins selectively labeled with an equimolar mixture of (2R, 3S)-[β-(13)C; α,β-(2)H(2)] Cys and (2R, 3R)-[β-(13)C; α,β-(2)H(2)] Cys, but otherwise fully deuterated. Since either one of the prochiral methylene protons, namely β2 (proS) or β3 (proR), is always replaced with a deuteron and no other protons remain in proteins prepared by this labeling scheme, all four of the expected NOEs for the β-protons across disulfide bonds could be measured without any spin diffusion interference, even with long mixing times. Therefore, the NOEs for the β2 and β3 pairs across each of the disulfide bonds could be observed at high sensitivity, even though they are 25% of the theoretical maximum for each pair. With the NO... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5472067 Thu, 01 Dec 2011 05:00:00 +0100 5472067 http://www.medworm.com/index.php?rid=5472068&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22124680%26dopt%3DAbstract Biomass production of site selective (13)C/ (15)N nucleotides using wild type and a transketolase E. coli mutant for labeling RNA for high resolution NMR. J Biomol NMR. 2011 Nov 29; Authors: Thakur CS, Luo Y, Chen B, Eldho NV, Dayie TK Abstract Characterization of the structure and dynamics of nucleic acids by NMR benefits significantly from position specifically labeled nucleotides. Here an E. coli strain deficient in the transketolase gene (tktA) and grown on glucose that is labeled at different carbon sites is shown to facilitate cost-effective and large scale production of useful nucleotides. These nucleotides are site specifically labeled in C1' and C5' with minimal scrambling within the ribose ring. To demonstrate the utility of this labeling approach, the new sit... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5472068 Tue, 29 Nov 2011 05:00:00 +0100 5472068 http://www.medworm.com/index.php?rid=5472069&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22105305%26dopt%3DAbstract Authors: Nand D, Cukkemane A, Becker S, Baldus M Abstract Solid-state Nuclear Magnetic Resonance can provide detailed insight into structural and dynamical aspects of complex biomolecules. With increasing molecular size, advanced approaches for spectral simplification and the detection of medium to long-range contacts become of critical relevance. We have analyzed the protonation pattern of a membrane-embedded ion channel that was obtained from bacterial expression using protonated precursors and D(2)O medium. We find an overall reduction of 50% in protein protonation. High levels of deuteration at H(α) and H(β) positions reduce spectral congestion in ((1)H,(13)C,(15)N) correlation experiments and generate a transfer profile in longitudinal mixing schemes that can be tuned to spe... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5472069 Tue, 22 Nov 2011 05:00:00 +0100 5472069 http://www.medworm.com/index.php?rid=5472070&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22089526%26dopt%3DAbstract Authors: Thakur CS, Dayie TK Abstract Selective isotopic labeling provides an unparalleled window within which to study the structure and dynamics of RNAs by high resolution NMR spectroscopy. Unlike commonly used carbon sources, the asymmetry of (13)C-labeled pyruvate provides selective labeling in both the ribose and base moieties of nucleotides using Escherichia coli variants, that until now were not feasible. Here we show that an E. coli mutant strain that lacks succinate and malate dehydrogenases (DL323) and grown on [3-(13)C]-pyruvate affords ribonucleotides with site specific labeling at C5' (~95%) and C1' (~42%) and minimal enrichment elsewhere in the ribose ring. Enrichment is also achieved at purine C2 and C8 (~95%) and pyrimidine C5 (~100%) positions with minimal labeling... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5472070 Thu, 17 Nov 2011 05:00:00 +0100 5472070 http://www.medworm.com/index.php?rid=5411995&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22083880%26dopt%3DAbstract Authors: Gledhill JM, Wand AJ Abstract Sparse sampling in biomolecular multidimensional NMR offers increased acquisition speed and resolution and, if appropriate conditions are met, an increase in sensitivity. Sparse sampling of indirectly detected time domains combined with the direct truly multidimensional Fourier transform has elicited particular attention because of the ability to generate a final spectrum amenable to traditional analysis techniques. A number of sparse sampling schemes have been described including radial sampling, random sampling, concentric sampling and variations thereof. A fundamental feature of these sampling schemes is that the resulting time domain data array is not amenable to traditional Fourier transform based processing and phasing correction techniq... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5411995 Tue, 15 Nov 2011 05:00:00 +0100 5411995 http://www.medworm.com/index.php?rid=5411996&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22076570%26dopt%3DAbstract Authors: Tomlinson JH, Williamson MP Abstract Temperature coefficients have been measured for backbone amide (1)H and (15)N nuclei in the B1 domain of protein G (GB1), using temperatures in the range 283-313 K, and pH values from 2.0 to 9.0. Many nuclei display pH-dependent coefficients, which were fitted to one or two pK(a) values. (1)H coefficients showed the expected behaviour, in that hydrogen-bonded amides have less negative values, but for those amides involved in strong hydrogen bonds in regular secondary structure there is a negative correlation between strength of hydrogen bond and size of temperature coefficient. The best correlation to temperature coefficient is with secondary shift, indicative of a very approximately uniform thermal expansion. The largest pH-dependent ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5411996 Fri, 11 Nov 2011 05:00:00 +0100 5411996 http://www.medworm.com/index.php?rid=5376733&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22038647%26dopt%3DAbstract Authors: Yu W, Lee W, Lee W, Kim S, Chang I Abstract Unravelling the complex correlation between chemical shifts of (13) C (α), (13) C (β), (13) C', (1) H (α), (15) N, (1) H ( N ) atoms in amino acids of proteins from NMR experiment and local structural environments of amino acids facilitates the assignment of secondary structures of proteins. This is an important impetus for both determining the three-dimensional structure and understanding the biological function of proteins. The previous empirical correlation scores which relate chemical shifts of (13) C (α), (13) C (β), (13) C', (1) H ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5376733 Sun, 30 Oct 2011 04:00:00 +0100 5376733 http://www.medworm.com/index.php?rid=5376732&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22038648%26dopt%3DAbstract Authors: Gal M, Edmonds KA, Milbradt AG, Takeuchi K, Wagner G Abstract Experiments detecting low gyromagnetic nuclei have recently been proposed to utilize the relatively slow relaxation properties of these nuclei in comparison to (1)H. Here we present a new type of (15)N direct-detection experiment. Like the previously proposed CaN experiment (Takeuchi et al. in J Biomol NMR 47:271-282, 2010), the hCaN experiment described here sequentially connects amide (15)N resonances, but utilizes the initial high polarization and the faster recovery of the (1)H nucleus to shorten the recycling delay. This allows recording 2D (15)N-detected NMR experiments on proteins within a few hours, while still obtaining superior resolution for (13)C and (15)N, establishing sequential assignments through... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5376732 Sun, 30 Oct 2011 04:00:00 +0100 5376732 http://www.medworm.com/index.php?rid=5376731&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22038649%26dopt%3DAbstract Authors: Thakur CS, Dayie TK Abstract Selective isotopic labeling provides an unparalleled window within which to study the structure and dynamics of RNAs by high resolution NMR spectroscopy. Unlike commonly used carbon sources, the asymmetry of (13)C-labeled pyruvate provides selective labeling in both the ribose and base moieties of nucleotides using E. coli variants, that until now were not feasible. Here we show that an E. coli mutant strain that lacks succinate and malate dehydrogenases (DL323) and grown on [3-(13)C]-pyruvate affords ribonucleotides with site specific labeling at C5' (~95%) and C1' (~42%) and minimal enrichment elsewhere in the ribose ring. Enrichment is also achieved at purine C2 and C8 (~95%) and pyrimidine C5 (~100%) positions with minimal labeling at pyrim... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5376731 Sun, 30 Oct 2011 04:00:00 +0100 5376731 http://www.medworm.com/index.php?rid=5376734&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22038621%26dopt%3DAbstract Authors: Lalli D, Schanda P, Chowdhury A, Retel J, Hiller M, Higman VA, Handel L, Agarwal V, Reif B, van Rossum B, Akbey U, Oschkinat H Abstract Well-resolved (2)H-(13)C correlation spectra, reminiscent of (1)H-(13)C correlations, are obtained for perdeuterated ubiquitin and for perdeuterated outer-membrane protein G (OmpG) from E. coli by exploiting the favorable lifetime of (2)H double-quantum (DQ) states. Sufficient signal-to-noise was achieved due to the short deuterium T (1), allowing for high repetition rates and enabling 3D experiments with a (2)H-(13)C transfer step in a reasonable time. Well-resolved 3D (2)H(DQ)-(13)C-(13)C correlations of ubiquitin and OmpG were recorded within 3.5 days each. An essentially complete assignment of (2)H(DQα) shifts and of a subs... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5376734 Tue, 25 Oct 2011 04:00:00 +0100 5376734 http://www.medworm.com/index.php?rid=5376735&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22008951%26dopt%3DAbstract We report enhanced sensitivity NMR measurements of intrinsically disordered proteins in the presence of paramagnetic relaxation enhancement (PRE) agents such as Ni(2+)-chelated DO2A. In proton-detected (1)H-(15)N SOFAST-HMQC and carbon-detected (H-flip)(13)CO-(15)N experiments, faster longitudinal relaxation enables the usage of even shorter interscan delays. This results in higher NMR signal intensities per units of experimental time, without adverse line broadening effects. At 40 mmol·L(-1) of the PRE agent, we obtain a 1.7- to 1.9-fold larger signal to noise (S/N) for the respective 2D NMR experiments. High solvent accessibility of intrinsically disordered protein (IDP) residues renders this class of proteins particularly amenable to the outlined approach. PMID: 22008951 [PubMed -... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5376735 Wed, 19 Oct 2011 04:00:00 +0100 5376735 http://www.medworm.com/index.php?rid=5309175&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21984356%26dopt%3DAbstract We present results from a study aimed at identifying the exchanging sites and level of exchange and at testing a strategy for minimizing (1)H contamination during wheat germ cell-free translation of proteins produced from deuterated amino acids by adding known inhibitors of transaminases (1 mM aminooxyacetic acid) and glutamate synthetase (0.1 mM L: -methionine sulfoximine). By using a wheat germ cell-free expression system, we produced [U-(2)H, (15)N]-chlorella ubiquitin without and with added inhibitors, and [U-(15)N]-chlorella ubiquitin as a reference to determine the extent of deuterium incorporation. We also prepared a sample of [U-(13)C, (15)N]-chlorella ubiquitin, for use in assigning the sites of exchange. The added inhibitors did not reduce the protein yield and were successful ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5309175 Sat, 08 Oct 2011 04:00:00 +0100 5309175 http://www.medworm.com/index.php?rid=5294018&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21976256%26dopt%3DAbstract Authors: Mote KR, Gopinath T, Traaseth NJ, Kitchen J, Gor'kov PL, Brey WW, Veglia G Abstract Oriented solid-state NMR is the most direct methodology to obtain the orientation of membrane proteins with respect to the lipid bilayer. The method consists of measuring (1)H-(15)N dipolar couplings (DC) and (15)N anisotropic chemical shifts (CSA) for membrane proteins that are uniformly aligned with respect to the membrane bilayer. A significant advantage of this approach is that tilt and azimuthal (rotational) angles of the protein domains can be directly derived from analytical expression of DC and CSA values, or, alternatively, obtained by refining protein structures using these values as harmonic restraints in simulated annealing calculations. The Achilles' heel of this approach is th... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5294018 Fri, 07 Oct 2011 04:00:00 +0100 5294018 http://www.medworm.com/index.php?rid=5294020&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21964698%26dopt%3DAbstract Authors: Gossert AD, Hinniger A, Gutmann S, Jahnke W, Strauss A, Fernández C Abstract An easy to use and robust approach for amino acid type selective isotope labeling in insect cells is presented. It relies on inexpensive commercial media and can be implemented in laboratories without sophisticated infrastructure. In contrast to previous protocols, where either high protein amounts or high incorporation ratios were obtained, here we achieve both at the same time. By supplementing media with a well considered amount of yeast extract, similar protein amounts as with full media are obtained, without compromising on isotope incorporation. In single and dual amino acid labeling experiments incorporation ratios are consistently ≥90% for all amino acids tested. This enables NMR studie... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5294020 Sun, 02 Oct 2011 04:00:00 +0100 5294020 http://www.medworm.com/index.php?rid=5294019&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21964699%26dopt%3DAbstract Authors: Fliniaux O, Gaillard G, Lion A, Cailleu D, Mesnard F, Betsou F Abstract A blood pre-centrifugation delay of 24 h at room temperature influenced the proton NMR spectroscopic profiles of human serum. A blood pre-centrifugation delay of 24 h at 4°C did not influence the spectroscopic profile as compared with 4 h delays at either room temperature or 4°C. Five or ten serum freeze-thaw cycles also influenced the proton NMR spectroscopic profiles. Certain common in vitro preanalytical variations occurring in biobanks may impact the metabolic profile of human serum. PMID: 21964699 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5294019 Sun, 02 Oct 2011 04:00:00 +0100 5294019 http://www.medworm.com/index.php?rid=5272792&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21953355%26dopt%3DAbstract Authors: Stevens TJ, Fogh RH, Boucher W, Higman VA, Eisenmenger F, Bardiaux B, van Rossum BJ, Oschkinat H, Laue ED Abstract Solid-state magic-angle-spinning (MAS) NMR of proteins has undergone many rapid methodological developments in recent years, enabling detailed studies of protein structure, function and dynamics. Software development, however, has not kept pace with these advances and data analysis is mostly performed using tools developed for solution NMR which do not directly address solid-state specific issues. Here we present additions to the CcpNmr Analysis software package which enable easier identification of spinning side bands, straightforward analysis of double quantum spectra, automatic consideration of non-uniform labelling schemes, as well as extension of other ex... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5272792 Wed, 28 Sep 2011 04:00:00 +0100 5272792 http://www.medworm.com/index.php?rid=5272793&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21947871%26dopt%3DAbstract Authors: Krähenbühl B, Hiller S, Wider G Abstract A four-dimensional (4D) APSY (automated projection spectroscopy)-HBCB(CG)CDHD experiment is presented. This 4D experiment correlates aromatic with aliphatic carbon and proton resonances from the same amino acid side chain of proteins in aqueous solution. It thus allows unambiguous sequence-specific assignment of aromatic amino acid ring signals based on backbone assignments. Compared to conventional 2D approaches, the inclusion of evolution periods on (1)H(β) and (13)C(δ) efficiently removes overlaps, and provides two additional frequencies for consequent automated or manual matching. The experiment was successfully applied to three proteins with molecular weights from 6 to 13 kDa. For the complementation of the assignment of t... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5272793 Tue, 27 Sep 2011 04:00:00 +0100 5272793 http://www.medworm.com/index.php?rid=5272794&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21947838%26dopt%3DAbstract Authors: Huang W, Varani G, Drobny GP Abstract Formation of the complex between human immunodeficiency virus type-1 Tat protein and the transactivation response region (TAR) RNA is vital for transcriptional elongation, yet the structure of the Tat-TAR complex remains to be established. The NMR structures of free TAR, and TAR bound to Tat-derived peptides have been obtained by solution NMR, but only a small number of intermolecular NOEs could be identified unambiguously, preventing the determination of a complete structure. Here we show that a combination of multiple solid state NMR REDOR experiments can be used to obtain multiple distance constraints from (15)N to (13)C spins within the backbone and side chain guanidinium groups of arginine in a Tat-derived peptide, using (19)F spi... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5272794 Sun, 25 Sep 2011 04:00:00 +0100 5272794 http://www.medworm.com/index.php?rid=5272795&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21947837%26dopt%3DAbstract Authors: Miyanoiri Y, Takeda M, Jee J, Ono AM, Okuma K, Terauchi T, Kainosho M Abstract Tryptophan (Trp) residues are frequently found in the hydrophobic cores of proteins, and therefore, their side-chain conformations, especially the precise locations of the bulky indole rings, are critical for determining structures by NMR. However, when analyzing [U-(13)C,(15)N]-proteins, the observation and assignment of the ring signals are often hampered by excessive overlaps and tight spin couplings. These difficulties have been greatly alleviated by using stereo-array isotope labeled (SAIL) proteins, which are composed of isotope-labeled amino acids optimized for unambiguous side-chain NMR assignment, exclusively through the (13)C-(13)C and (13)C-(1)H spin coupling networks (Kainosho et al.... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5272795 Fri, 23 Sep 2011 04:00:00 +0100 5272795 http://www.medworm.com/index.php?rid=5272796&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21938394%26dopt%3DAbstract Authors: Tang M, Sperling LJ, Berthold DA, Schwieters CD, Nesbitt AE, Nieuwkoop AJ, Gennis RB, Rienstra CM Abstract X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 Å crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yi... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5272796 Thu, 22 Sep 2011 04:00:00 +0100 5272796 http://www.medworm.com/index.php?rid=5240695&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21927934%26dopt%3DAbstract Authors: Saio T, Ogura K, Shimizu K, Yokochi M, Burke TR, Inagaki F Abstract A nuclear magnetic resonance-based ligand screening strategy utilizing a paramagnetic lanthanide probe is presented. By fixing a paramagnetic lanthanide ion to a target protein, a pseudo-contact shift (PCS) and a paramagnetic relaxation enhancement (PRE) can be observed for both the target protein and its bound ligand. Based on PRE and PCS information, the bound ligand is then screened from the compound library and the structure of the ligand-protein complex is determined. PRE is an isotropic paramagnetic effect observed within 30 Å from the lanthanide ion, and is utilized for the ligand screening in the present study. PCS is an anisotropic paramagnetic effect providing long-range (~40 Å) distance and ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5240695 Sat, 17 Sep 2011 04:00:00 +0100 5240695 http://www.medworm.com/index.php?rid=5240694&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21927935%26dopt%3DAbstract Authors: Su XC, Loh CT, Qi R, Otting G PMID: 21927935 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5240694 Sat, 17 Sep 2011 04:00:00 +0100 5240694 http://www.medworm.com/index.php?rid=5225677&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21922277%26dopt%3DAbstract We describe here two advances in the characterization of phosphoesters in saccharides: (1) the use of (1)H-(31)P GHMBC to determine the site-specific identity of phosphoester moieties in heterogeneous mixtures and (2) the use of Unsymmetrical/Generalized Indirect Covariance (U/GIC) to calculate a carbon-phosphorus 2D spectrum. The sensitivity of the (1)H-(31)P GHMBC is far greater than the "standard" (1)H-(31)P GHSQC and allows long-range (3-5)J(HP) couplings to be readily detected. This is the first example to be reported of using U/GIC to calculate a carbon-phosphorus spectrum. The U/GIC processing affords, in many cases, a fivefold to tenfold or greater increase in signal-to-noise ratios in the calculated spectrum. When coupled with the high sensitivity of (1)H-(31)P HMBC, U/GIC process... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5225677 Fri, 16 Sep 2011 04:00:00 +0100 5225677 http://www.medworm.com/index.php?rid=5225681&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21918814%26dopt%3DAbstract Authors: Gill ML, Palmer AG Abstract Multiplet-filtered and gradient-selected heteronuclear zero-quantum coherence (gsHZQC) TROSY experiments are described for measuring (1)H-(13)C correlations for (13)CH(3) methyl groups in proteins. These experiments provide improved suppression of undesirable, broad outer components of the heteronuclear zero-quantum multiplet in medium-sized proteins, or in flexible sites of larger proteins, compared to previously described HZQC sequences (Tugarinov et al. in J Am Chem Soc 126:4921-4925, 2004; Ollerenshaw et al. in J Biomol NMR 33:25-41, 2005). Hahn-echo versions of the gsHZQC experiment also are described for measuring zero- and double-quantum transverse relaxation rate constants for identification of chemical exchange broadening. Application o... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5225681 Thu, 15 Sep 2011 04:00:00 +0100 5225681 http://www.medworm.com/index.php?rid=5225688&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21915680%26dopt%3DAbstract Authors: Rasia RM, Lescop E, Palatnik JF, Boisbouvier J, Brutscher B Abstract It has been demonstrated that protein folds can be determined using appropriate computational protocols with NMR chemical shifts as the sole source of experimental restraints. While such approaches are very promising they still suffer from low convergence resulting in long computation times to achieve accurate results. Here we present a suite of time- and sensitivity optimized NMR experiments for rapid measurement of up to six RDCs per residue. Including such an RDC data set, measured in less than 24 h on a single aligned protein sample, greatly improves convergence of the Rosetta-NMR protocol, allowing for overnight fold calculation of small proteins. We demonstrate the performance of our fast fold calc... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5225688 Wed, 14 Sep 2011 04:00:00 +0100 5225688 http://www.medworm.com/index.php?rid=5225695&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21912982%26dopt%3DAbstract Authors: Baturin SJ, Okon M, McIntosh LP Abstract We have developed NMR spectroscopic methods to investigate the tyrosines within Bacillus circulans xylanase (BcX). Four slowly exchanging buried tyrosine hydroxyl protons with chemical shifts between 7.5 and 12.5 ppm were found using a long-range (13)C-HSQC experiment that exploits the (3)J(CH) coupling between the ring (1)H(η) and (13)C(ε) nuclei. The NMR signals from these protons were assigned via (13)C-tyrosine selective labelling and a suite of scalar and (13)C,(15)N-filtered/edited NOE correlation spectra. Of the fifteen tyrosines in BcX, only the buried Tyr79 and Tyr105 showed four distinct, rather than two averaged, signals from ring (13)C-(1)H pairs, indicative of slow flipping on the chemical shift timescale. Ring flipp... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5225695 Tue, 13 Sep 2011 04:00:00 +0100 5225695 http://www.medworm.com/index.php?rid=5215583&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21892794%26dopt%3DAbstract Authors: Peters F, Maestre-Martinez M, Leonov A, Kovačič L, Becker S, Boelens R, Griesinger C Abstract Here we present Cys-Ph-TAHA, a new nonadentate lanthanide tag for the paramagnetic labelling of proteins. The tag can be easily synthesized and is stereochemically homogenous over a wide range of temperatures, yielding NMR spectra with a single set of peaks. Bound to ubiquitin, it induced large residual dipolar couplings and pseudocontact shifts that could be measured easily and agreed very well with the protein structure. We show that Cys-Ph-TAHA can be used to label large proteins that are biochemically challenging such as the Lac repressor in a 90 kDa ternary complex with DNA and inducer. PMID: 21892794 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5215583 Sun, 04 Sep 2011 04:00:00 +0100 5215583 http://www.medworm.com/index.php?rid=5171131&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21866436%26dopt%3DAbstract Authors: Tang S, Case DA Abstract Individual peptide groups in proteins must exhibit some variation in the chemical shift anisotropy (CSA) of their constituent atoms, but not much is known about the extent or origins of this dispersion. Direct spectroscopic measurement of CSA remains technically challenging, and theoretical methods can help to overcome these limitations by estimating shielding tensors for arbitrary structures. Here we use an automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach to compute (15)N, (13)C' and (1)H chemical shift tensors for human ubiquitin and the GB1 and GB3 fragments of staphylococcal protein G. The average and range of variation of the anisotropies is in good agreement with experimental estimates from solid-state NMR, an... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5171131 Thu, 25 Aug 2011 23:00:00 +0100 5171131 http://www.medworm.com/index.php?rid=5171134&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21858640%26dopt%3DAbstract Authors: Schmid N, Allison JR, Dolenc J, Eichenberger AP, Kunz AP, van Gunsteren WF Abstract For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, (3) J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure ref... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5171134 Fri, 19 Aug 2011 23:00:00 +0100 5171134 http://www.medworm.com/index.php?rid=5171138&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21847629%26dopt%3DAbstract Authors: Marius Clore G Abstract While an extensive body of knowledge has accumulated on the structures of transcription factors, DNA and their complexes from both NMR and crystallography, much less is known at a molecular level regarding the mechanisms whereby transcription factors locate their specific DNA target site within an overwhelming sea of non-specific DNA sites. Indirect kinetic data suggested that three processes are involved in the search procedure: jumping by dissociation of the protein from the DNA followed by re-association at another site, direct transfer from one DNA molecule or segment to another, and one-dimensional sliding. In this brief perspective I summarize recent NMR developments from our laboratory that have permitted direct characterization of the specie... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5171138 Tue, 16 Aug 2011 23:00:00 +0100 5171138 http://www.medworm.com/index.php?rid=5138772&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21826518%26dopt%3DAbstract Authors: Nadaud PS, Sengupta I, Helmus JJ, Jaroniec CP Magic-angle spinning solid-state NMR measurements of (15)N longitudinal paramagnetic relaxation enhancements (PREs) in (13)C,(15)N-labeled proteins modified with Cu(2+)-chelating tags can yield multiple long-range electron-nucleus distance restraints up to ~20 Å (Nadaud et al. in J Am Chem Soc 131:8108-8120, 2009). Using the EDTA-Cu(2+) K28C mutant of B1 immunoglobulin binding domain of protein G (GB1) as a model, we investigate the effects on such measurements of intermolecular electron-nucleus couplings and intrinsic metal binding sites, both of which may potentially complicate the interpretation of PRE data in terms of the intramolecular protein fold. To quantitatively assess the influence of intermolecular (15)N-Cu(2+) interac... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5138772 Mon, 08 Aug 2011 23:00:00 +0100 5138772 http://www.medworm.com/index.php?rid=5138745&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21826519%26dopt%3DAbstract Authors: Linden AH, Franks WT, Akbey U, Lange S, van Rossum BJ, Oschkinat H X-ray crystallography using synchrotron radiation and the technique of dynamic nuclear polarization (DNP) in nuclear magnetic resonance (NMR) require samples to be kept at temperatures below 100 K. Protein dynamics are poorly understood below the freezing point of water and down to liquid nitrogen temperatures. Therefore, we investigate the α-spectrin SH3 domain by magic angle spinning (MAS) solid state NMR (ssNMR) at various temperatures while cooling slowly. Cooling down to 95 K, the NMR-signals of SH3 first broaden and at lower temperatures they separate into several peaks. The coalescence temperature differs depending on the individual residue. The broadening is shown to be inhomogeneous by hole-burning ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5138745 Mon, 08 Aug 2011 23:00:00 +0100 5138745 http://www.medworm.com/index.php?rid=5138732&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21826520%26dopt%3DAbstract Authors: Dasgupta S, Hu X, Keizers PH, Liu WM, Luchinat C, Nagulapalli M, Overhand M, Parigi G, Sgheri L, Ubbink M Calmodulin is a two-domain protein which in solution can adopt a variety of conformations upon reorientation of its domains. The maximum occurrence (MO) of a set of calmodulin conformations that are representative of the overall conformational space possibly sampled by the protein, has been calculated from the paramagnetism-based restraints. These restraints were measured after inclusion of a lanthanide binding tag in the C-terminal domain to supplement the data obtained by substitution of three paramagnetic lanthanide ions to the calcium ion in the second calcium binding loop of the N-terminal domain. The analysis shows that the availability of paramagnetic restraints ari... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5138732 Mon, 08 Aug 2011 23:00:00 +0100 5138732 http://www.medworm.com/index.php?rid=5138796&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21822966%26dopt%3DAbstract Authors: Linser R Proteins with excessive deuteration give access to proton detected solid-state NMR spectra of extraordinary resolution and sensitivity. The high spectral quality achieved after partial proton back-exchange has been shown to start a new era for backbone assignment, protein structure elucidation, characterization of protein dynamics, and access to protein parts undergoing motion. The large absence of protons at non-exchangeable sites, however, poses a serious hurdle for characterization of side chains, which play an important role especially for structural understanding of the protein core and the investigation of protein-protein and protein-ligand interactions, e.g. This has caused the perdeuteration approach to almost exclusively be amenable to backbone characterizati... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5138796 Sat, 06 Aug 2011 23:00:00 +0100 5138796 http://www.medworm.com/index.php?rid=5088479&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21786031%26dopt%3DAbstract Authors: Jia X, Yagi H, Su XC, Stanton-Cook M, Huber T, Otting G Paramagnetic relaxation enhancements from unpaired electrons observed in nuclear magnetic resonance (NMR) spectra present powerful long-range distance restraints. The most frequently used paramagnetic tags, however, are tethered to the protein via disulfide bonds, requiring proteins with single cysteine residues for covalent attachment. Here we present a straightforward strategy to tag proteins site-specifically with paramagnetic lanthanides without a tether and independent of cysteine residues. It relies on preferential binding of the complex between three dipicolinic acid molecules (DPA) and a lanthanide ion (Ln(3+)), [Ln(DPA)(3)](3-), to a pair of positively charged amino acids whose charges are not compensated by nega... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5088479 Sun, 31 Jul 2011 23:00:00 +0100 5088479 http://www.medworm.com/index.php?rid=5088477&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21809183%26dopt%3DAbstract Authors: Lauzon CB, van Zijl P, Stivers JT Chemical Exchange Saturation Transfer (CEST) is an MRI approach that can indirectly detect exchange broadened protons that are invisible in traditional NMR spectra. We modified the CEST pulse sequence for use on high-resolution spectrometers and developed a quantitative approach for measuring exchange rates based upon CEST spectra. This new methodology was applied to the rapidly exchanging Hδ1 and Hε2 protons of His57 in the catalytic triad of bovine chymotrypsinogen-A (bCT-A). CEST enabled observation of Hε2 at neutral pH values, and also allowed measurement of solvent exchange rates for His57-Hδ1 and His57-Hε2 across a wide pH range (3-10). Hδ1 exchange was only dependent upon the charge state of the His57 (k (ex,Im+) = 470 s(-1), k... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5088477 Sun, 31 Jul 2011 23:00:00 +0100 5088477 http://www.medworm.com/index.php?rid=5088478&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21805376%26dopt%3DAbstract We describe the procedures and protocols devised, and discuss possibilities and limitations of the assignment of this largest protein assigned today by solid-state NMR, and for which no solution-state NMR shifts were available. A comparison of the NMR chemical shifts with crystallographic data reveals that regions with high crystallographic B-factors are particularly difficult to assign. While the secondary structure elements derived from the chemical shift data correspond mainly to those present in the X-ray crystal structure, we detect an additional helical element and structural variability in the protein crystal, most probably originating from the different molecules in the asymmetric unit, with the observation of doubled resonances in several parts, including entire stretches, of the ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5088478 Sat, 30 Jul 2011 23:00:00 +0100 5088478 http://www.medworm.com/index.php?rid=5038789&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21748265%26dopt%3DAbstract Authors: Nucci NV, Marques BS, Bédard S, Dogan J, Gledhill JM, Moorman VR, Peterson RW, Valentine KG, Wand AL, Wand AJ Comprehensive application of solution NMR spectroscopy to studies of macromolecules remains fundamentally limited by the molecular rotational correlation time. For proteins, molecules larger than 30 kDa require complex experimental methods, such as TROSY in conjunction with isotopic labeling schemes that are often expensive and generally reduce the potential information available. We have developed the reverse micelle encapsulation strategy as an alternative approach. Encapsulation of proteins within the protective nano-scale water pool of a reverse micelle dissolved in ultra-low viscosity nonpolar solvents overcomes the slow tumbling problem presented by large prote... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5038789 Mon, 11 Jul 2011 23:00:00 +0100 5038789 http://www.medworm.com/index.php?rid=5038788&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21748266%26dopt%3DAbstract Authors: Sahakyan AB, Vranken WF, Cavalli A, Vendruscolo M Protein methyl groups have recently been the subject of much attention in NMR spectroscopy because of the opportunities that they provide to obtain information about the structure and dynamics of proteins and protein complexes. With the advent of selective labeling schemes, methyl groups are particularly interesting in the context of chemical shift based protein structure determination, an approach that to date has exploited primarily the mapping between protein structures and backbone chemical shifts. In order to extend the scope of chemical shifts for structure determination, we present here the CH3Shift method of performing structure-based predictions of methyl chemical shifts. The terms considered in the predictions take ac... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5038788 Mon, 11 Jul 2011 23:00:00 +0100 5038788 http://www.medworm.com/index.php?rid=5038790&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21732209%26dopt%3DAbstract Authors: Chen J, Wang J NMR structural determination of large multi-domain proteins is a challenging task due to significant spectral overlap with a particular difficulty in unambiguous identification of domain-domain interactions. Segmental labeling is a NMR strategy that allows for isotopically labeling one domain and leaves the other domain unlabeled. This significantly simplifies spectral overlaps and allows for quick identification of domain-domain interaction. Here, a novel segmental labeling strategy is presented for detection of inter-domain NOEs. To identify domain-domain interactions in human apolipoprotein E (apoE), a multi-domain, 299-residues α-helical protein, on-column expressed protein ligation was utilized to generate a segmental-labeled apoE samples in which the N-te... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=5038790 Tue, 05 Jul 2011 23:00:00 +0100 5038790 http://www.medworm.com/index.php?rid=4994553&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21710190%26dopt%3DAbstract We describe a general computational approach to site-specific resonance assignments in multidimensional NMR studies of uniformly (15)N,(13)C-labeled biopolymers, based on a simple Monte Carlo/simulated annealing (MCSA) algorithm contained in the program MCASSIGN2. Input to MCASSIGN2 includes lists of multidimensional signals in the NMR spectra with their possible residue-type assignments (which need not be unique), the biopolymer sequence, and a table that describes the connections that relate one signal list to another. As output, MCASSIGN2 produces a high-scoring sequential assignment of the multidimensional signals, using a score function that rewards good connections (i.e., agreement between relevant sets of chemical shifts in different signal lists) and penalizes bad connections, unas... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4994553 Mon, 27 Jun 2011 23:00:00 +0100 4994553 http://www.medworm.com/index.php?rid=4994554&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21706248%26dopt%3DAbstract Authors: Zeng J, Zhou P, Donald BR One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called NASCA: (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4994554 Fri, 24 Jun 2011 23:00:00 +0100 4994554 http://www.medworm.com/index.php?rid=4994555&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21698488%26dopt%3DAbstract This report describes a novel method for overexpression of (13)C-labeled oligosaccharides using genetically engineered Saccharomyces cerevisiae cells, in which a homogeneous high-mannose-type oligosaccharide accumulates because of deletions of genes encoding three enzymes involved in the processing pathway of asparagine-linked oligosaccharides in the Golgi complex. Using uniformly (13)C-labeled glucose as the sole carbon source in the culture medium of these engineered yeast cells, high yields of the isotopically labeled Man(8)GlcNAc(2) oligosaccharide could be successfully harvested from glycoprotein extracts of the cells. Furthermore, (13)C labeling at selected positions of the sugar residues in the oligosaccharide could be achieved using a site-specific (13)C-enriched glucose as the met... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4994555 Wed, 22 Jun 2011 23:00:00 +0100 4994555 http://www.medworm.com/index.php?rid=4994556&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21688157%26dopt%3DAbstract Authors: Catoire LJ, Damian M, Baaden M, Guittet E, Banères JL The mechanism of signal transduction mediated by G protein-coupled receptors is a subject of intense research in pharmacological and structural biology. Ligand association to the receptor constitutes a critical event in the activation process. Solution-state NMR can be amenable to high-resolution structure determination of agonist molecules in their receptor-bound state by detecting dipolar interactions in a transferred mode, even with equilibrium dissociation constants below the micromolar range. This is possible in the case of an inherent ultra-fast diffusive association of charged ligands onto a highly charged extracellular surface, and by slowing down the (1)H-(1)H cross-relaxation by perdeuterating the receptor. Here,... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4994556 Sat, 18 Jun 2011 23:00:00 +0100 4994556 http://www.medworm.com/index.php?rid=4945798&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21681650%26dopt%3DAbstract Authors: Hansen AL, Kay LE A new pulse sequence is presented for the measurement of relaxation dispersion profiles quantifying millisecond time-scale exchange dynamics of side-chain carbonyl groups in uniformly (13)C labeled proteins. The methodology has been tested using the 87-residue colicin E7 immunity protein, Im7, which is known to fold via a partially structured low populated intermediate that interconverts with the folded, ground state on the millisecond time-scale. Comparison of exchange parameters extracted for this folding 'reaction' using the present methodology with those obtained from more 'traditional' (15)N and backbone carbonyl probes establishes the utility of the approach. The extracted excited state side-chain carbonyl chemical shifts indicate that the Asx/Glx side-... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4945798 Fri, 17 Jun 2011 23:00:00 +0100 4945798 http://www.medworm.com/index.php?rid=4945801&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21667298%26dopt%3DAbstract We present results on 13 synthetic and experimental datasets from 8 different structures, including two homodimers. Using just two alignment media, EPAR achieves an average assignment accuracy greater than 80%. With three media, the average accuracy is higher than 94%. The algorithm also outputs a prediction of the assignment accuracy, which has a correlation of 0.77 to the true accuracy. This prediction score can be used to establish the needed confidence in assignment accuracy. PMID: 21667298 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4945801 Sat, 11 Jun 2011 23:00:00 +0100 4945801 http://www.medworm.com/index.php?rid=4945800&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21667299%26dopt%3DAbstract Authors: Sastry M, Xu L, Georgiev IS, Bewley CA, Nabel GJ, Kwong PD NMR spectroscopic characterization of the structure or the dynamics of proteins generally requires the production of samples isotopically enriched in (15)N, (13)C, or (2)H. The bacterial expression systems currently in use to obtain isotopic enrichment, however, cannot produce a number of eukaryotic proteins, especially those that require post-translational modifications such as N-linked glycosylation for proper folding or activity. Here, we report the use of an adenovirus vector-based mammalian expression system to produce isotopically enriched (15)N or (15)N/(13)C samples of an outer domain variant of the HIV-1 gp120 envelope glycoprotein with 15 sites of N-linked glycosylation. Yields for the (15)N- and (15)N/(13)C-... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4945800 Sat, 11 Jun 2011 23:00:00 +0100 4945800 http://www.medworm.com/index.php?rid=4945799&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21674236%26dopt%3DAbstract Authors: Herbst C, Herbst J, Leppert J, Ohlenschläger O, Görlach M, Ramachandran R An approach for conveniently implementing low-power CN ( n ) (ν) and RN ( n ) (ν) symmetry-based band-selective mixing sequences for generating homo- and heteronuclear chemical shift correlation NMR spectra of low γ nuclei in biological solids is demonstrated. Efficient magnetisation transfer characteristics are achieved by selecting appropriate symmetries requiring the application of basic RF elements of relatively long duration and numerically tailoring the RF field modulation profile of the basic element. The efficacy of the approach is experimentally shown by the acquisition of (15)N-(13)C dipolar and (13)C-(13)C scalar and dipolar coupling mediated chemical shift correlation spectra at represen... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4945799 Fri, 10 Jun 2011 23:00:00 +0100 4945799 http://www.medworm.com/index.php?rid=4897183&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21638015%26dopt%3DAbstract Authors: Vögeli B Highly precise and accurate measurements of very small NMR cross-correlated relaxation rates, namely those between protein H (i) (N) -N(i) and C (i-1) (α) -C(i-1)' dipoles, are demonstrated with an error of 0.03 s(-1) for GB3. Because the projection angles between the two dipole vectors are very close to the magic angle the rates range only from -0.2 to +0.2 s(-1). Small changes of the average vector orientations have a dramatic impact on the relative values. The rates suggest deviation from idealized peptide plane geometry caused by twists around the C'-N bonds and/or pyramidalization of the nitrogen atoms. A clear alternating pattern along the sequence is observed in β strands 1, 3 and 4 of GB3, where the side chains of almost all residues with large positive r... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4897183 Thu, 02 Jun 2011 23:00:00 +0100 4897183 http://www.medworm.com/index.php?rid=4897189&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21626212%26dopt%3DAbstract Authors: Borkar A, Kumar D, Hosur RV Development of efficient strategies and automation represent important milestones of progress in rapid structure determination efforts in proteomics research. In this context, we present here an efficient algorithm named as AUTOBA (Automatic Backbone Assignment) designed to automate the assignment protocol based on HN(C)N suite of experiments. Depending upon the spectral dispersion, the user can record 2D or 3D versions of the experiments for assignment. The algorithm uses as inputs: (i) protein primary sequence and (ii) peak-lists from user defined HN(C)N suite of experiments. In the end, one gets H(N), (15)N, C(α) and C' assignments (in common BMRB format) for the individual residues along the polypeptide chain. The success of the algorithm has b... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4897189 Sat, 28 May 2011 23:00:00 +0100 4897189 http://www.medworm.com/index.php?rid=4897187&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21626213%26dopt%3DAbstract Authors: Schmitz C, Bonvin AM In order to enhance the structure determination process of macromolecular assemblies by NMR, we have implemented long-range pseudocontact shift (PCS) restraints into the data-driven protein docking package HADDOCK. We demonstrate the efficiency of the method on a synthetic, yet realistic case based on the lanthanide-labeled N-terminal ε domain of the E. coli DNA polymerase III (ε186) in complex with the HOT domain. Docking from the bound form of the two partners is swiftly executed (interface RMSDs < 1 Å) even with addition of very large amount of noise, while the conformational changes of the free form still present some challenges (interface RMSDs in a 3.1-3.9 Å range for the ten lowest energy complexes). Finally, using exclusively PCS as expe... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4897187 Sat, 28 May 2011 23:00:00 +0100 4897187 http://www.medworm.com/index.php?rid=4897186&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21626214%26dopt%3DAbstract Authors: Amero C, Asunción Durá M, Noirclerc-Savoye M, Perollier A, Gallet B, Plevin MJ, Vernet T, Franzetti B, Boisbouvier J Obtaining sequence-specific assignments remains a major bottleneck in solution NMR investigations of supramolecular structure, dynamics and interactions. Here we demonstrate that resonance assignment of methyl probes in high molecular weight protein assemblies can be efficiently achieved by combining fast NMR experiments, residue-type-specific isotope-labeling and automated site-directed mutagenesis. The utility of this general and straightforward strategy is demonstrated through the characterization of intermolecular interactions involving a 468-kDa multimeric aminopeptidase, PhTET2. PMID: 21626214 [PubMed - as supplied by publisher] (Source: Journal of B... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4897186 Sat, 28 May 2011 23:00:00 +0100 4897186 http://www.medworm.com/index.php?rid=4897185&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21626215%26dopt%3DAbstract Authors: Schuyler AD, Maciejewski MW, Arthanari H, Hoch JC The full resolution afforded by high-field magnets is rarely realized in the indirect dimensions of multidimensional NMR experiments because of the time cost of uniformly sampling to long evolution times. Emerging methods utilizing nonuniform sampling (NUS) enable high resolution along indirect dimensions by sampling long evolution times without sampling at every multiple of the Nyquist sampling interval. While the earliest NUS approaches matched the decay of sampling density to the decay of the signal envelope, recent approaches based on coupled evolution times attempt to optimize sampling by choosing projection angles that increase the likelihood of resolving closely-spaced resonances. These approaches employ knowledge about ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4897185 Sat, 28 May 2011 23:00:00 +0100 4897185 http://www.medworm.com/index.php?rid=4897184&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21626216%26dopt%3DAbstract Authors: Sugase K We developed a new method to elucidate the binding kinetics k(on) and k(off), and the dissociation constant K(D) (=k(off)/k(on)), of protein-protein interactions without observable bound resonances of the protein of interest due to high molecular weight in a complex with a large target protein. In our method, k(on) and k(off) rates are calculated from the analysis of longitudinal relaxation rates of free resonances measured for multiple samples containing different concentration ratios of (15)N-labeled protein and substoichiometric amounts of the target protein. The method is applicable to interactions that cannot be analyzed by relaxation dispersion spectroscopy due to slow interactions on millisecond to second timescale and/or minimal conformational (chemical shift)... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4897184 Fri, 27 May 2011 23:00:00 +0100 4897184 http://www.medworm.com/index.php?rid=4897190&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21618018%26dopt%3DAbstract Authors: Bieri M, d'Auvergne EJ, Gooley PR Investigation of protein dynamics on the ps-ns and μs-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was developed for fast and simple model-free analysis and is fully integrated into the software package relax. It is written in Python and uses wxPython to build the graphical user interface (GUI) for maximum performance and multi-platform use. This software allows the analysis of NMR relaxation data wit... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4897190 Thu, 26 May 2011 23:00:00 +0100 4897190 http://www.medworm.com/index.php?rid=4897191&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21611840%26dopt%3DAbstract Authors: Juranić N, Nemutlu E, Zhang S, Dzeja P, Terzic A, Macura S Intramolecular correlations among the (18)O-labels of metabolic oligophosphates, mapped by J-decoupled (31)P NMR 2D chemical shift correlation spectroscopy, impart stringent constraints to the (18)O-isotope distributions over the whole oligophosphate moiety. The multiple deduced correlations of isotopic labels enable determination of site-specific fractional isotope enrichments and unravel the isotopologue statistics. This approach ensures accurate determination of (18)O-labeling rates of phosphometabolites, critical in biochemical energy conversion and metabolic flux transmission. The biological usefulness of the J-decoupled (31)P NMR 2D chemical shift correlation maps was validated on adenosine tri-phosphate fractio... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4897191 Tue, 24 May 2011 23:00:00 +0100 4897191 http://www.medworm.com/index.php?rid=4897192&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21604143%26dopt%3DAbstract In this study, we use random coil peptides containing glutamine instead of glycine to determine the random coil chemical shifts and the neighbor correction factors. The resulting correction factors correlate to changes in the populations of the major wells in the Ramachandran plot, which demonstrates that changes in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict (13)C chemical shifts of intrinsically disordered proteins compared to existing datasets, and may thus improve the identification of small populations of transient structure in disordered proteins. PMID: 21604143 [PubMed - as supplied by publisher] (Source: Journal of Bimo... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4897192 Sat, 21 May 2011 23:00:00 +0100 4897192 http://www.medworm.com/index.php?rid=4897193&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21603954%26dopt%3DAbstract We present new NMR methods to measure slow translational diffusion coefficients of biomolecules. Like the heteronuclear stimulated echo experiment (XSTE), these new methods rely on the storage of information about spatial localization during the diffusion delay as longitudinal polarization of nuclei with long T(1) such as nitrogen-15. The new BEST-XSTE sequence combines features of Band-selective Excitation Short-Transient (BEST) and XSTE methods. By avoiding the saturation of all protons except those of amide groups, one can increase the sensitivity by 45% in small proteins. The new experiment which combines band-Selective Optimized Flip-Angle Short-Transient with XSTE (SOFAST-XSTE) offers an alternative when very short recovery delays are desired. A modification of the HSQC-edited versio... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4897193 Fri, 20 May 2011 23:00:00 +0100 4897193 http://www.medworm.com/index.php?rid=4797705&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21503632%26dopt%3DAbstract Authors: Johnson E NMR order parameters are calculated from molecular dynamics computer simulations of ubiquitin and the apo (Ca(2+)-free) state of calbindin D(9k). Calculations are performed in an expanding reference frame so as to discriminate between the effects of short- and long-range motions. This approach reveals that the dominant contributions to the order parameters are short-range. Longer-range contributions are limited to specific sites, many of which have been recognized in previous studies of correlated motions. These sites are identified on the basis of an effective reorientational number, n ( eff ). Not only does this parameter identify sites of short- and long-range motion, it also provides a way of evaluating the separability condition that is key to the Lipari-Szabo m... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4797705 Sat, 30 Apr 2011 23:00:00 +0100 4797705 http://www.medworm.com/index.php?rid=4797704&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21519904%26dopt%3DAbstract Authors: Roldan JL, Blackledge M, van Nuland NA, Azuaga AI CD2 associated protein (CD2AP) is an adaptor protein that plays an important role in cell to cell union needed for the kidney function. It contains three N-terminal SH3 domains that are able to interact among others with CD2, ALIX, c-Cbl and Ubiquitin. To understand the role of the individual SH3 domains of this adaptor protein we have performed a complete structural, thermodynamic and dynamic characterization of the separate domains using NMR and DSC. The energetic contributions to the stability and the backbone dynamics have been related to the structural features of each domain using the structure-based FoldX algorithm. We have found that the N-terminal SH3 domain of both adaptor proteins CD2AP and CIN85 are the most stable ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4797704 Mon, 25 Apr 2011 23:00:00 +0100 4797704 http://www.medworm.com/index.php?rid=4690920&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21461951%26dopt%3DAbstract In this study, metabolic changes in three NCL mouse models were examined looking for pathways correlated with neurodegeneration. Two mouse models; motor neuron degeneration (mnd) mouse and a variant model of late infantile NCL, termed the neuronal ceroid lipofuscinosis (nclf) mouse were investigated experimentally. Both models exhibit a characteristic accumulation of autofluorescent lipopigment in neuronal and non neuronal cells. The NMR profiles derived from extracts of the cortex and cerebellum from mnd and nclf mice were distinguished according to disease/wildtype status. In particular, a perturbation in glutamine and glutamate metabolism, and a decrease in γ-amino butyric acid (GABA) in the cerebellum and cortices of mnd (adolescent mice) and nclf mice relative to wildtype at all ages... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4690920 Sat, 02 Apr 2011 23:00:00 +0100 4690920 http://www.medworm.com/index.php?rid=4690922&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21448734%26dopt%3DAbstract Authors: Ikeya T, Jee JG, Shigemitsu Y, Hamatsu J, Mishima M, Ito Y, Kainosho M, Güntert P A fully automated method is presented for determining NMR solution structures of proteins using exclusively NOESY spectra as input, obviating the need to measure any spectra only for obtaining resonance assignments but devoid of structural information. Applied to two small proteins, the approach yielded structures that coincided closely with conventionally determined structures. PMID: 21448734 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4690922 Tue, 29 Mar 2011 23:00:00 +0100 4690922 http://www.medworm.com/index.php?rid=4690921&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21448735%26dopt%3DAbstract Authors: Han B, Liu Y, Ginzinger SW, Wishart DS A new computer program, called SHIFTX2, is described which is capable of rapidly and accurately calculating diamagnetic (1)H, (13)C and (15)N chemical shifts from protein coordinate data. Compared to its predecessor (SHIFTX) and to other existing protein chemical shift prediction programs, SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3× smaller) than the next best performing program. It also provides significantly more coverage (up to 10% more), is significantly faster (up to 8.5×) and capable of calculating a wider variety of backbone and side chain chemical shifts (up to 6×) than many other shift predictors. In particular, SHIFTX2 is able to attain correlation c... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4690921 Tue, 29 Mar 2011 23:00:00 +0100 4690921 http://www.medworm.com/index.php?rid=4690923&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21445678%26dopt%3DAbstract Authors: Weingarth M, Masuda Y, Takegoshi K, Bodenhausen G, Tekely P Sensitive 2D solid-state (13)C-(13)C correlation spectra of amyloid β fibrils have been recorded at very fast spinning frequencies and very high magnetic fields. It is demonstrated that PARIS-xy recoupling using moderate rf amplitudes can provide structural information by promoting efficient magnetization transfer even under such challenging experimental conditions. Furthermore, it has been shown both experimentally and by numerical simulations that the method is not very sensitive to dipolar truncation effects and can reveal direct transfer across distances of about 3.5-4Å. PMID: 21445678 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4690923 Mon, 28 Mar 2011 23:00:00 +0100 4690923 http://www.medworm.com/index.php?rid=4632918&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21431831%26dopt%3DAbstract Authors: García VP Carbohydrates influence many essential biological events such as apoptosis, differentiation, tumor metastasis, cancer, neurobiology, immunology, development, host-pathogen interactions, diabetes, signal transduction, protein folding, and many other contexts. We now report on the structure determination of pregnane glycosides isolated from the aerial parts of Ceropegia fusca Bolle (Asclepiadaceae). The observation of cicatrizant, vulnerary and cytostatic activities in some humans and animals of Ceropegia fusca Bolle, a species endemic to the Canary Islands, encouraged us to begin a pharmacological study to determine their exact therapeutic properties. High resolution (1)H-NMR spectra of pregnane glycosides very often display well-resolved signals that can be used as ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4632918 Thu, 24 Mar 2011 00:00:00 +0100 4632918 http://www.medworm.com/index.php?rid=4632921&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21424579%26dopt%3DAbstract Authors: Nováček J, Zawadzka-Kazimierczuk A, Papoušková V, Zídek L, Sanderová H, Krásný L, Koźmiński W, Sklenář V Two novel 5D NMR experiments (CACONCACO, NCOCANCO) for backbone assignment of disordered proteins are presented. The pulse sequences exploit relaxation properties of the unstructured proteins and combine the advantages of (13)C-direct detection, non-uniform sampling, and longitudinal relaxation optimization to maximize the achievable resolution and minimize the experimental time. The pulse sequences were successfully tested on the sample of partially disordered delta subunit from RNA polymerase from Bacillus subtilis. The unstructured part of this 20 kDa protein consists of 81 amino acids with frequent sequential repeats. A collection of 0.0003% of the data nee... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4632921 Sun, 20 Mar 2011 00:00:00 +0100 4632921 http://www.medworm.com/index.php?rid=4632925&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21424227%26dopt%3DAbstract Authors: Bouvignies G, Vallurupalli P, Cordes MH, Hansen DF, Kay LE A method based on the Carr-Purcell-Meiboom-Gill relaxation dispersion experiment is presented for measuring the temperature coefficients of amide proton chemical shifts of low populated 'invisible' protein states that exchange with a 'visible' ground state on the millisecond time-scale. The utility of the approach is demonstrated with an application to an I58D mutant of the Pfl6 Cro protein that undergoes exchange between the native, folded state and a cold denatured, unfolded conformational ensemble that is populated at a level of 6% at 2.5°C. A wide distribution of amide temperature coefficients is measured for the unfolded state. The distribution is centered about -5.6 ppb/K, consistent with an absence of intra-mo... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4632925 Fri, 18 Mar 2011 00:00:00 +0100 4632925 http://www.medworm.com/index.php?rid=4632928&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21416162%26dopt%3DAbstract Authors: Vugmeyster L, Ostrovsky D Temperature-dependence of protein dynamics can provide information on details of the free energy landscape by probing the characteristics of the potential responsible for the fluctuations. We have investigated the temperature-dependence of picosecond to nanosecond backbone dynamics at carbonyl carbon sites in chicken villin headpiece subdomain protein using a combination of three NMR relaxation rates: (13)C' longitudinal rate, and two cross-correlated rates involving dipolar and chemical shift anisotropy (CSA) relaxation mechanisms, (13)C'/(13)C'-(13)C(α) CSA/dipolar and (13)C'/(13)C'-(15)N CSA/dipolar. Order parameters have been extracted using the Lipari-Szabo model-free approach assuming a separation of the time scales of internal and molecular mo... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4632928 Thu, 17 Mar 2011 00:00:00 +0100 4632928 http://www.medworm.com/index.php?rid=4632930&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21409563%26dopt%3DAbstract Authors: Nowling RJ, Vyas J, Weatherby G, Fenwick MW, Ellis HJ, Gryk MR NMR spectroscopists are hindered by the lack of standardization for spectral data among the file formats for various NMR data processing tools. This lack of standardization is cumbersome as researchers must perform their own file conversion in order to switch between processing tools and also restricts the combination of tools employed if no conversion option is available. The CONNJUR Spectrum Translator introduces a new, extensible architecture for spectrum translation and introduces two key algorithmic improvements. This first is translation of NMR spectral data (time and frequency domain) to a single in-memory data model to allow addition of new file formats with two converter modules, a reader and a writer, ins... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4632930 Wed, 16 Mar 2011 00:00:00 +0100 4632930 http://www.medworm.com/index.php?rid=4570921&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21380855%26dopt%3DAbstract In this study we examine different sample limited conditions and compare the detection sensitivity of the micro-coil with a standard 5 mm NMR probe. Sample concentration is evaluated as a means to leverage the greatly improved mass sensitivity of the micro-coil probes. With very small sample volumes, the sensitivity of the micro-coil probe does indeed provide a significant advantage over the standard probe. Concentrating the samples does improve the signal detection, but the benefits do not follow the expected linear increase and are both matrix and metabolite specific. Absolute quantitation will be affected by concentration, but an analysis of relative concentrations is still possible. The choice of the micro-coil probe over a standard tube based probe will depend upon a number of factor... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4570921 Sun, 06 Mar 2011 00:00:00 +0100 4570921 http://www.medworm.com/index.php?rid=4570920&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21380856%26dopt%3DAbstract In this study, we use multidimensional (1)H-(13)C nuclear magnetic resonance (NMR) spectroscopy and multiple reaction mode mass spectrometry (MRM-MS) to measure the kinetics of de novo glutamate biosynthesis via AST, ALT, and GA in intact cells and RBC lysates. We show that up to 89% of the erythrocyte glutamate pool can be derived from ALT and that ALT-derived glutamate is subsequently used for glutathione synthesis. PMID: 21380856 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4570920 Sun, 06 Mar 2011 00:00:00 +0100 4570920 http://www.medworm.com/index.php?rid=4570922&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21380509%26dopt%3DAbstract Authors: Bernini P, Bertini I, Luchinat C, Nincheri P, Staderini S, Turano P (1)H NMR metabolic profiling of urine, serum and plasma has been used to monitor the impact of the pre-analytical steps on the sample quality and stability in order to propose standard operating procedures (SOPs) for deposition in biobanks. We analyzed the quality of serum and plasma samples as a function of the elapsed time (t = 0-4 h) between blood collection and processing and of the time from processing to freezing (up to 24 h). The stability of the urine metabolic profile over time (up to 24 h) at various storage temperatures was monitored as a function of the different pre-analytical treatments like pre-storage centrifugation, filtration, and addition of the bacteriostatic preservative sodium azide.... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4570922 Sat, 05 Mar 2011 00:00:00 +0100 4570922 http://www.medworm.com/index.php?rid=4570925&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21373839%26dopt%3DAbstract Authors: Hu K, Westler WM, Markley JL Chemical shift assignment is the first step toward the structure elucidation of natural products and other chemical compounds. We propose here the use of 2D concurrent HMQC-COSY as an experiment for rapid chemical shift assignment of small molecules. This experiment provides well-dispersed (1)H-(13)C peak patterns that are distinctive for different functional groups plus (1)H-(1)H COSY connectivities that serve to identify adjacent groups. The COSY diagonal peaks, which are phased to be absorptive, resemble (1)H-(13)C HMQC cross peaks. We demonstrate the applicability of this experiment for rapidly and unambiguously establishing correlations between different functional groups through the analysis of the spectrum of a metabolite (jasmonic acid) dis... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4570925 Fri, 04 Mar 2011 00:00:00 +0100 4570925 http://www.medworm.com/index.php?rid=4570924&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21373840%26dopt%3DAbstract In this study, it is demonstrated that two of the 48 standard media components, choline and histidine are depleted at a faster rate than many other nutrients. Augmenting the starting media with extra choline and histidine improves the long-term liver slice viability as measured by higher tissues levels of lactate dehydrogenase (LDH), glutathione and ATP, as well as lower LDH levels in the media at time points out to 94 h after initiation of incubation. In both models, media components and cellular metabolites are measured over time and correlated with currently accepted endpoint measures. PMID: 21373840 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4570924 Fri, 04 Mar 2011 00:00:00 +0100 4570924 http://www.medworm.com/index.php?rid=4570923&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21373841%26dopt%3DAbstract Authors: Weljie AM, Bondareva A, Zang P, Jirik FR Hypoxia can promote invasive behavior in cancer cells and alters the response to therapeutic intervention as a result of changes in the expression many genes, including genes involved in intermediary metabolism. Although metabolomics technologies are capable of simultaneously measuring a wide range of metabolites in an untargeted manner, these methods have been relatively under utilized in the study of cancer cell responses to hypoxia. Thus, (1)H NMR metabolomics was used to examine the effects of hypoxia in the MDA-MB-231 human breast cancer cell line, both in vitro and in vivo. Cell cultures were compared with respect to their metabolic responses during growth under either hypoxic (1% O(2)) or normoxic conditions. Orthogonal partial l... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4570923 Fri, 04 Mar 2011 00:00:00 +0100 4570923 http://www.medworm.com/index.php?rid=4570928&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21360154%26dopt%3DAbstract Authors: Gifford JL, Ishida H, Vogel HJ Here we present a novel NMR method for the structure determination of calcium-calmodulin (Ca(2+)-CaM)-peptide complexes from a limited set of experimental restraints. A comparison of solved CaM-peptide structures reveals invariability in CaM's backbone conformation and a structural plasticity in CaM's domain orientation enabled by a flexible linker. Knowing this, the collection and analysis of an extensive set of NOESY spectra is redundant. Although RDCs can define CaM domain orientation in the complex, they lack the translational information required to position the domains on the bound peptide and highlight the necessity of intermolecular NOEs. Here we employ a specific isotope labeling strategy in which the role of methionine in CaM-peptide in... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4570928 Tue, 01 Mar 2011 00:00:00 +0100 4570928 http://www.medworm.com/index.php?rid=4570927&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21360155%26dopt%3DAbstract In this study, all vitamin C sources were removed after weaning from the diet of Gulo-/- mice (n = 7) and wild type controls (n = 7) for 12 weeks before collection of serum. A replicate study was performed with similar parameters but animals were harvested pre-symptomatically after 2-3 weeks. The serum concentration of 50 metabolites was determined by quantitative profiling of 1D proton NMR spectra. Multivariate statistical models were used to describe metabolic changes as compared to control animals; replicate study animals were used for external validation of the resulting models. The results of the study highlight the metabolites and pathways known to require ascorbate for proper flux. PMID: 21360155 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4570927 Tue, 01 Mar 2011 00:00:00 +0100 4570927 http://www.medworm.com/index.php?rid=4570926&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21360156%26dopt%3DAbstract Authors: Mercier P, Lewis MJ, Chang D, Baker D, Wishart DS Nuclear magnetic resonance (NMR) and Mass Spectroscopy (MS) are the two most common spectroscopic analytical techniques employed in metabolomics. The large spectral datasets generated by NMR and MS are often analyzed using data reduction techniques like Principal Component Analysis (PCA). Although rapid, these methods are susceptible to solvent and matrix effects, high rates of false positives, lack of reproducibility and limited data transferability from one platform to the next. Given these limitations, a growing trend in both NMR and MS-based metabolomics is towards targeted profiling or "quantitative" metabolomics, wherein compounds are identified and quantified via spectral fitting prior to any statistical analysis. Despi... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4570926 Tue, 01 Mar 2011 00:00:00 +0100 4570926 http://www.medworm.com/index.php?rid=4570931&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21350847%26dopt%3DAbstract Authors: Fan TW, Lane AN An important goal of metabolomics is to characterize the changes in metabolic networks in cells or various tissues of an organism in response to external perturbations or pathologies. The profiling of metabolites and their steady state concentrations does not directly provide information regarding the architecture and fluxes through metabolic networks. This requires tracer approaches. NMR is especially powerful as it can be used not only to identify and quantify metabolites in an unfractionated mixture such as biofluids or crude cell/tissue extracts, but also determine the positional isotopomer distributions of metabolites derived from a precursor enriched in stable isotopes such as (13)C and (15)N via metabolic transformations. In this article we demonstrate t... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4570931 Sat, 26 Feb 2011 00:00:00 +0100 4570931 http://www.medworm.com/index.php?rid=4570930&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21359513%26dopt%3DAbstract Authors: Ali K, Maltese F, Toepfer R, Choi YH, Verpoorte R (1)H NMR (nuclear magnetic resonance spectroscopy) has been used for metabolomic analysis of 'Riesling' and 'Mueller-Thurgau' white wines from the German Palatinate region. Diverse two-dimensional NMR techniques have been applied for the identification of metabolites, including phenolics. It is shown that sensory analysis correlates with NMR-based metabolic profiles of wine. (1)H NMR data in combination with multivariate data analysis methods, like principal component analysis (PCA), partial least squares projections to latent structures (PLS), and bidirectional orthogonal projections to latent structures (O2PLS) analysis, were employed in an attempt to identify the metabolites responsible for the taste of wine, using a non-tar... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4570930 Sat, 26 Feb 2011 00:00:00 +0100 4570930 http://www.medworm.com/index.php?rid=4570929&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21359514%26dopt%3DAbstract Authors: Xu Q, Vu H, Liu L, Wang TC, Schaefer WH Mitochondrial toxicity has been a serious concern, not only in preclinical drug development but also in clinical trials. In mitochondria, there are several distinct metabolic processes including fatty acid β-oxidation, the tricarboxylic acid (TCA) cycle, and oxidative phosphorylation (OXPHOS), and each process contains discrete but often intimately linked steps. Interruption in any one of those steps can cause mitochondrial dysfunction. Detection of inhibition to OXPHOS can be complicated in vivo because intermediate endogenous metabolites can be recycled in situ or circulated systemically for metabolism in other organs or tissues. Commonly used assays for evaluating mitochondrial function are often applied to ex vivo or in vitro sample... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4570929 Sat, 26 Feb 2011 00:00:00 +0100 4570929 http://www.medworm.com/index.php?rid=4570932&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21350846%26dopt%3DAbstract In this study, we examined the biological variation in (1)H NMR-based metabolic profiling of two model systems, the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Using relative standard deviations (RSD) as a measure of variability, our results reveal that both model systems have significant amounts of biological variation. The C. elegans metabolome possesses greater metabolic variance with average RSD values of 29 and 39%, depending on the food source that was used. The S. cerevisiae exometabolome RSD values ranged from 8% to 12% for the four strains examined. We also determined whether biological variation occurs between pairs of phenotypically identical yeast strains. Multivariate statistical analysis allowed us to discriminate between pair members based on thei... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4570932 Fri, 25 Feb 2011 00:00:00 +0100 4570932 http://www.medworm.com/index.php?rid=4517032&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21340669%26dopt%3DAbstract Authors: Sykes BD PMID: 21340669 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4517032 Wed, 23 Feb 2011 00:00:00 +0100 4517032 http://www.medworm.com/index.php?rid=4517034&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21336865%26dopt%3DAbstract Authors: Chen J, Li Q, Liu CC, Zhou P, Bu G, Wang J PMID: 21336865 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4517034 Sat, 19 Feb 2011 00:00:00 +0100 4517034 http://www.medworm.com/index.php?rid=4517033&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21336866%26dopt%3DAbstract Authors: Su XC, Otting G PMID: 21336866 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4517033 Sat, 19 Feb 2011 00:00:00 +0100 4517033 http://www.medworm.com/index.php?rid=4517035&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21318579%26dopt%3DAbstract Authors: Su XC, Loh CT, Qi R, Otting G Selectively isotope labelled protein samples can be prepared in vivo or in vitro from selectively labelled amino acids but, in many cases, metabolic conversions between different amino acids result in isotope scrambling. The best results are obtained by cell-free protein synthesis, where metabolic enzymes are generally less active, but isotope scrambling can never be suppressed completely. We show that reduction of E. coli S30 extracts with NaBH(4) presents a simple and inexpensive way to achieve cleaner selective isotope labelling in cell-free protein synthesis reactions. The purpose of the NaBH(4) is to inactivate all pyridoxal-phosphate (PLP) dependent enzymes by irreversible reduction of the Schiff bases formed between PLP and lysine side chai... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4517035 Sat, 12 Feb 2011 00:00:00 +0100 4517035 http://www.medworm.com/index.php?rid=4459272&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21305337%26dopt%3DAbstract Authors: Cai L, Kosov DS, Fushman D We performed density functional calculations of backbone (15)N shielding tensors in the regions of beta-sheet and turns of protein G. The calculations were carried out for all twenty-four beta-sheet residues and eight beta-turn residues in the protein GB3 and the results were compared with the available experimental data from solid-state and solution NMR measurements. Together with the alpha-helix data, our calculations cover 39 out of the 55 residues (or 71%) in GB3. The applicability of several computational models developed previously (Cai et al. in J Biomol NMR 45:245-253, 2009) to compute (15)N shielding tensors of alpha-helical residues is assessed. We show that the proposed quantum chemical computational model is capable of predicting isotropi... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4459272 Wed, 09 Feb 2011 00:00:00 +0100 4459272 http://www.medworm.com/index.php?rid=4459274&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21286785%26dopt%3DAbstract Authors: Plevin MJ, Hamelin O, Boisbouvier J, Gans P A new method for stereospecific assignment of prochiral methyl groups in proteins is presented in which protein samples are produced using U-[(13)C]glucose and subsaturating amounts of 2-[(13)C]methyl-acetolactate. The resulting non-uniform labeling pattern allows proR and proS methyl groups to be easily distinguished by their different phases in a constant-time two-dimensional (1)H-(13)C correlation spectra. Protein samples are conveniently prepared using the same media composition as the main uniformly-labeled sample and contain higher levels of isotope-enrichment than fractional labeling approaches. This new strategy thus represents an economically-attractive, robust alternative for obtaining isotopically-encoded stereospecific NM... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4459274 Tue, 01 Feb 2011 00:00:00 +0100 4459274 http://www.medworm.com/index.php?rid=4459277&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21279668%26dopt%3DAbstract Authors: Mao L, Inoue K, Tao Y, Montelione GT, McDermott AE, Inouye M Using the single-protein-production (SPP) system, a protein of interest can be exclusively produced in high yield from its ACA-less gene in Escherichia coli expressing MazF, an ACA-specific mRNA interferase. It is thus feasible to study a membrane protein by solid-state NMR (SSNMR) directly in natural membrane fractions. In developing isotope-enrichment methods, we observed that (13)C was also incorporated into phospholipids, generating spurious signals in SSNMR spectra. Notable, with the SPP system a protein can be produced in total absence of cell growth caused by antibiotics. Here, we demonstrate that cerulenin, an inhibitor of phospholipid biosynthesis, can suppress isotope incorporation in the lipids without aff... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4459277 Sun, 30 Jan 2011 00:00:00 +0100 4459277 http://www.medworm.com/index.php?rid=4459278&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21271275%26dopt%3DAbstract Authors: Gruene T, Cho MK, Karyagina I, Kim HY, Grosse C, Giller K, Zweckstetter M, Becker S Long-range structural information derived from paramagnetic relaxation enhancement observed in the presence of a paramagnetic nitroxide radical is highly useful for structural characterization of globular, modular and intrinsically disordered proteins, as well as protein-protein and protein-DNA complexes. Here we characterized the conformation of a spin-label attached to the homodimeric protein CylR2 using a combination of X-ray crystallography, electron paramagnetic resonance (EPR) and NMR spectroscopy. Close agreement was found between the conformation of the spin label observed in the crystal structure with interspin distances measured by EPR and signal broadening in NMR spectra, suggesting ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4459278 Fri, 28 Jan 2011 00:00:00 +0100 4459278 http://www.medworm.com/index.php?rid=4459279&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21259120%26dopt%3DAbstract Authors: Mäntylahti S, Hellman M, Permi P Extensive resonance overlap exacerbates assignment of intrinsically disordered proteins (IDPs). This issue can be circumvented by utilizing (15)N, (13)C' and (1)H(N) spins, where the chemical shift dispersion is mainly dictated by the characteristics of consecutive amino acid residues. Especially (15)N and (13)C' spins offer superior chemical shift dispersion in comparison to (13)C(α) and (13)C(β) spins. However, HN-detected experiments suffer from exchange broadening of amide proton signals on IDPs especially under alkali conditions. To that end, we propose here two novel HA-detected experiments, (HCA)CON(CA)H and (HCA)NCO(CA)H and a new assignment protocol based on panoply of unidirectional HA-detected experiments that enable robust backbo... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4459279 Tue, 25 Jan 2011 00:00:00 +0100 4459279 http://www.medworm.com/index.php?rid=4391275&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21253842%26dopt%3DAbstract Authors: Etzkorn M, Böckmann A, Baldus M It is shown that real-time 2D solid-state NMR can be used to obtain kinetic and structural information about the process of protein aggregation. In addition to the incorporation of kinetic information involving intermediate states, this approach can offer atom-specific resolution for all detectable species. The analysis was carried out using experimental data obtained during aggregation of the 10.4 kDa Crh protein, which has been shown to involve a partially unfolded intermediate state prior to aggregation. Based on a single real-time 2D (13)C-(13)C transition spectrum, kinetic information about the refolding and aggregation step could be extracted. In addition, structural rearrangements associated with refolding are estimated and several diff... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4391275 Fri, 21 Jan 2011 00:00:00 +0100 4391275 http://www.medworm.com/index.php?rid=4391276&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21246256%26dopt%3DAbstract We report on successful implementation and optimization of isotope labeling protocols, previously used for soluble secreted proteins, to produce homogeneous samples of a eukaryotic seven-transmembrane helical protein, rhodopsin from Leptosphaeria maculans. Even in shake-flask cultures, yields exceeded 5 mg of purified uniformly (13)C,(15)N-labeled protein per liter of culture. The protein was stable (at least several weeks at 5°C) and functionally active upon reconstitution into lipid membranes at high protein-to-lipid ratio required for solid-state NMR. The samples gave high-resolution (13)C and (15)N solid-state magic angle spinning NMR spectra, amenable to a detailed structural analysis. We believe that similar protocols can be adopted for challenging mammalian targets, which often re... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4391276 Wed, 19 Jan 2011 00:00:00 +0100 4391276 http://www.medworm.com/index.php?rid=4391277&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21234644%26dopt%3DAbstract We report random coil chemical shifts and sequence correction factors determined for a GGXGG peptide series following the approach of Schwarzinger et al. (J Am Chem Soc 123(13):2970-2978, 2001). The chemical shifts are determined at neutral pH in order to match the conditions of most studies of intrinsically disordered proteins. Temperature has a non-negligible effect on the (13)C random coil chemical shifts, so temperature coefficients are reported for the random coil chemical shifts to allow extrapolation to other temperatures. The pH dependence of the histidine random coil chemical shifts is investigated in a titration series, which allows the accurate random coil chemical shifts to be obtained at any pH. By correcting the random coil chemical shifts for the effects of temperature and p... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4391277 Sat, 15 Jan 2011 00:00:00 +0100 4391277 http://www.medworm.com/index.php?rid=4304737&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21190061%26dopt%3DAbstract Authors: Wüthrich K PMID: 21190061 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4304737 Thu, 30 Dec 2010 00:00:00 +0100 4304737 http://www.medworm.com/index.php?rid=4304736&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21190062%26dopt%3DAbstract Authors: Bagai I, Ragsdale SW, Zuiderweg ER The solution NMR resonance assignment of the protein backbone is most commonly carried out using triple resonance experiments that involve (15)N and (1)HN resonances. The assignment becomes problematic when there is resonance overlap of (15)N-(1)HN cross peaks. For such residues, one cannot unambiguously link the "left" side of the NH root to the "right" side, and the residues associated with such overlapping HN resonances remain often unassigned. Here we present a solution to this problem: a hybrid (4d,3d) reduced-dimensionality HN(CO)CA(CON)CA sequence. In this experiment, the Ca(i) resonance is modulated with the frequency of the Ca(i-1) resonance, which helps in resolving the ambiguity involved in connecting the Ca(i) and Ca(i-1) resonanc... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4304736 Thu, 30 Dec 2010 00:00:00 +0100 4304736 http://www.medworm.com/index.php?rid=4304735&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21190063%26dopt%3DAbstract Authors: Favier A, Brutscher B Experimental sensitivity remains a major drawback for the application of NMR spectroscopy to fragile and low concentrated biomolecular samples. Here we describe an efficient polarization enhancement mechanism in longitudinal-relaxation enhanced fast-pulsing triple-resonance experiments. By recovering undetectable (1)H polarization originating from longitudinal relaxation during the pulse sequence, the steady-state (15)N polarization becomes enhanced by up to a factor of ~5 with respect to thermal equilibrium yielding significant sensitivity improvements compared to conventional schemes. The benefits of BEST-TROSY experiments at high magnetic field strength are illustrated for various protein applications, but they will be equally useful for other protonat... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4304735 Thu, 30 Dec 2010 00:00:00 +0100 4304735 http://www.medworm.com/index.php?rid=4304734&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21191805%26dopt%3DAbstract Authors: Wang X, Tash B, Flanagan JM, Tian F Experimental residual dipolar couplings (RDCs) in combination with structural models have the potential for accelerating the protein backbone resonance assignment process because RDCs can be measured accurately and interpreted quantitatively. However, this application has been limited due to the need for very high-resolution structural templates. Here, we introduce a new approach to resonance assignment based on optimal agreement between the experimental and calculated RDCs from a structural template that contains all assignable residues. To overcome the inherent computational complexity of such a global search, we have adopted an efficient two-stage search algorithm and included connectivity data from conventional assignment experiments. In... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4304734 Thu, 30 Dec 2010 00:00:00 +0100 4304734 http://www.medworm.com/index.php?rid=4304738&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21188472%26dopt%3DAbstract Authors: Refaei MA, Combs A, Kojetin DJ, Cavanagh J, Caperelli C, Rance M, Sapitro J, Tsang P NMR spectroscopy has distinct advantages for providing insight into protein structures, but faces significant resolution challenges as protein size increases. To alleviate such resonance overlap issues, the ability to produce segmentally labeled proteins is beneficial. Here we show that the S. aureus transpeptidase sortase A can be used to catalyze the ligation of two separately expressed domains of the same protein, MecA (B. subtilis). The yield of purified, segmentally labeled MecA protein conjugate is ~40%. The resultant HSQC spectrum obtained from this domain-labeled conjugate demonstrates successful application of sortase A for segmental labeling of multi-domain proteins for solution NMR ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4304738 Wed, 29 Dec 2010 00:00:00 +0100 4304738 http://www.medworm.com/index.php?rid=4304739&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21184138%26dopt%3DAbstract Authors: Higman VA, Boyd J, Smith LJ, Redfield C RDCs for the 14 kDa protein hen egg-white lysozyme (HEWL) have been measured in eight different alignment media. The elongated shape and strongly positively charged surface of HEWL appear to limit the protein to four main alignment orientations. Furthermore, low levels of alignment and the protein's interaction with some alignment media increases the experimental error. Together with heterogeneity across the alignment media arising from constraints on temperature, pH and ionic strength for some alignment media, these data are suitable for structure refinement, but not the extraction of dynamic parameters. For an analysis of protein dynamics the data must be obtained with very low errors in at least three or five independent alignment me... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4304739 Fri, 24 Dec 2010 00:00:00 +0100 4304739 http://www.medworm.com/index.php?rid=4304740&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21170670%26dopt%3DAbstract We present a computational method for finding optimal labeling patterns for the backbone assignment of membrane proteins and other large proteins that cannot be assigned by conventional strategies. Following the approach of Kainosho and Tsuji (Biochemistry 21:6273-6279 (1982)), types of amino acids are labeled with (13)C or/and (15)N such that cross peaks between (13)CO(i - 1) and (15)NH(i) result only for pairs of sequentially adjacent amino acids of which the first is labeled with (13)C and the second with (15)N. In this way, unambiguous sequence-specific assignments can be obtained for unique pairs of amino acids that occur exactly once in the sequence of the protein. To be practical, it is crucial to limit the number of differently labeled protein samples that have to be prepared while... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4304740 Sat, 18 Dec 2010 00:00:00 +0100 4304740 http://www.medworm.com/index.php?rid=4269626&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21161328%26dopt%3DAbstract Authors: Lemak A, Gutmanas A, Chitayat S, Karra M, Farès C, Sunnerhagen M, Arrowsmith CH The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution - especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampli... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4269626 Tue, 14 Dec 2010 00:00:00 +0100 4269626 http://www.medworm.com/index.php?rid=4269627&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21153044%26dopt%3DAbstract Authors: Krishnarjuna B, Jaipuria G, Thakur A, D'Silva P, Atreya HS Sequence specific resonance assignment constitutes an important step towards high-resolution structure determination of proteins by NMR and is aided by selective identification and assignment of amino acid types. The traditional approach to selective labeling yields only the chemical shifts of the particular amino acid being selected and does not help in establishing a link between adjacent residues along the polypeptide chain, which is important for sequential assignments. An alternative approach is the method of amino acid selective 'unlabeling' or reverse labeling, which involves selective unlabeling of specific amino acid types against a uniformly (13)C/(15)N labeled background. Based on this method, we present a n... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4269627 Thu, 09 Dec 2010 00:00:00 +0100 4269627 http://www.medworm.com/index.php?rid=4213909&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21110064%26dopt%3DAbstract Authors: Takeuchi K, Gal M, Takahashi H, Shimada I, Wagner G Described here is a set of three-dimensional (3D) NMR experiments that rely on CACA-TOCSY magnetization transfer via the weak [Formula: see text] coupling. These pulse sequences, which resemble recently described (13)C detected CACA-TOCSY (Takeuchi et al. 2010) experiments, are recorded in (1)H(2)O, and use (1)H excitation and detection. These experiments require alternate (13)C-(12)C labeling together with perdeuteration, which allows utilizing the small [Formula: see text] scalar coupling that is otherwise masked by the stronger (1)J(CC) couplings in uniformly (13)C labeled samples. These new experiments provide a unique assignment ladder-mark that yields bidirectional supra-sequential information and can readily straddle p... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4213909 Fri, 26 Nov 2010 00:00:00 +0100 4213909 http://www.medworm.com/index.php?rid=4146213&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21057854%26dopt%3DAbstract Authors: Thakur CS, Sama JN, Jackson ME, Chen B, Dayie TK Escherichia coli (E. coli) is an ideal organism to tailor-make labeled nucleotides for biophysical studies of RNA. Recently, we showed that adding labeled formate enhanced the isotopic enrichment at protonated carbon sites in nucleotides. In this paper, we show that growth of a mutant E. coli strain DL323 (lacking succinate and malate dehydrogenases) on (13)C-2-glycerol and (13)C-1,3-glycerol enables selective labeling at many useful sites for RNA NMR spectroscopy. For DL323 E. coli grown in (13)C-2-glycerol without labeled formate, all the ribose carbon atoms are labeled except the C3' and C5' carbon positions. Consequently the C1', C2' and C4' positions remain singlet. In addition, only the pyrimidine base C6 atoms are substan... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4146213 Sat, 06 Nov 2010 00:00:00 +0100 4146213 http://www.medworm.com/index.php?rid=4146214&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21052777%26dopt%3DAbstract Authors: Yokoyama J, Matsuda T, Koshiba S, Kigawa T Improvement of the cell-free protein synthesis system (CF) over the past decade have made it one of the most powerful protein production methods. The CF approach is especially useful for stable-isotope (SI) labeling of proteins for NMR analysis. However, it is less popular than expected, partly because the SI-labeled amino acids used for SI labeling by the CF are too expensive. In the present study, we developed a simple and inexpensive method for producing an SI-labeled protein using Escherichia coli cell extract-based CF. This method takes advantage of endogenous metabolic conversions to generate SI-labeled asparagine, glutamine, cysteine, and tryptophan, which are much more expensive than the other 16 kinds of SI-labeled amino acid... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4146214 Thu, 04 Nov 2010 00:00:00 +0100 4146214 http://www.medworm.com/index.php?rid=4134911&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21049303%26dopt%3DAbstract Authors: Volkov AN, Ubbink M, van Nuland NA Many biomolecular interactions proceed via a short-lived encounter state, consisting of multiple, lowly-populated species invisible to most experimental techniques. Recent development of paramagnetic relaxation enhancement (PRE) nuclear magnetic resonance (NMR) spectroscopy has allowed to directly visualize such transient intermediates in a number of protein-protein and protein-DNA complexes. Here we present an analysis of the recently published PRE NMR data for a protein complex of yeast cytochrome c (Cc) and cytochrome c peroxidase (CcP). First, we describe a simple, general method to map out the spatial and temporal distributions of binding geometries constituting the Cc-CcP encounter state. We show that the spatiotemporal mapping provides... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4134911 Thu, 04 Nov 2010 00:00:00 +0100 4134911 http://www.medworm.com/index.php?rid=4106983&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20960033%26dopt%3DAbstract We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that backbone amides in the microcrystalline α-spectrin SH3 domain exchange rather slowly with the solvent (with exchange rates negligible within the individual (15)N-T (1) timescales). We observed chemical exchange for 6 residues with HDX exchange rates in the range from 0.2 to 5 s(-1). Backbone amide (15)N longitudinal relaxation times that we determined previously are not significantly affected for most residues, yielding no systematic artifacts upon quantification of backbone dynamics (Chevelkov et al. 2008b). Significant exc... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4106983 Tue, 19 Oct 2010 23:00:00 +0100 4106983 http://www.medworm.com/index.php?rid=4075127&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20949307%26dopt%3DAbstract Authors: Ruschak AM, Velyvis A, Kay LE A straightforward approach for the production of highly deuterated proteins labeled with (13)C and (1)H at Ile-γ2 methyl positions is described. The utility of the methodology is illustrated with an application involving the half proteasome (360 kDa). High quality 2D Ile (13)C(γ2),(1)H(γ2) HMQC data sets, exploiting the methyl-TROSY principle, are recorded with excellent sensitivity and resolution, that compare favorably with Ile (13)C(δ1),(1)H(δ1) spectra. This labeling scheme adds to a growing list of different approaches that are significantly impacting the utility of solution NMR spectroscopy in studies of supra-molecular systems. PMID: 20949307 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4075127 Wed, 13 Oct 2010 23:00:00 +0100 4075127 http://www.medworm.com/index.php?rid=4060481&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20931264%26dopt%3DAbstract We present a methodology for automating protein resonance assignments of MAS SSNMR spectral data and its application to experimental peak lists of the β1 immunoglobulin binding domain of protein G (GB1) derived from a uniformly (13)C- and (15)N-labeled sample. This application to the 56 amino acid GB1 produced an overall 84.1% assignment of the N, CO, CA, and CB resonances with no errors using peak lists from NCACX 3D, CANcoCA 3D, and CANCOCX 4D experiments. This proof of concept demonstrates the tractability of this problem. PMID: 20931264 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4060481 Thu, 07 Oct 2010 23:00:00 +0100 4060481 http://www.medworm.com/index.php?rid=4039862&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20924647%26dopt%3DAbstract Authors: Nausner M, Goger M, Bendet-Taicher E, Schlagnitweit J, Jerschow A, Müller N We have assessed the potential of an alternative probe tuning strategy based on the spin-noise response for application in common high-resolution multi-dimensional biomolecular NMR experiments with water signal suppression on aqueous and salty samples. The method requires the adjustment of the optimal tuning condition, which may be offset by several 100 kHz from the conventional tuning settings using the noise response of the water protons as an indicator. Although the radio frequency-pulse durations are typically longer under such conditions, signal-to-noise gains of up to 22% were achieved. At salt concentrations up to 100 mM a substantial sensitivity gain was observed. PMID: 20924647 [PubMed ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4039862 Tue, 05 Oct 2010 23:00:00 +0100 4039862 http://www.medworm.com/index.php?rid=4039863&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20890634%26dopt%3DAbstract Authors: Motáčková V, Nováček J, Zawadzka-Kazimierczuk A, Kazimierczuk K, Zídek L, Sanderová H, Krásný L, Koźmiński W, Sklenář V A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly repetitive sequence is presented. The protocol is based on three resolution-enhanced NMR experiments: 5D HN(CA)CONH provides sequential connectivity, 5D HabCabCONH is utilized to identify amino acid types, and 5D HC(CC-TOCSY)CONH is used to assign the side-chain resonances. The improved resolution was achieved by a combination of high dimensionality and long evolution times, allowed by non-uniform sampling in the indirect dimensions. Random distribution of the data points and Sparse Multidimensional Fourier Transform processing were used. Succe... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=4039863 Fri, 01 Oct 2010 23:00:00 +0100 4039863 http://www.medworm.com/index.php?rid=3981366&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20844927%26dopt%3DAbstract Authors: Hayashi K, Kojima C The E. coli protein expression system is one of the most useful methods employed for NMR sample preparation. However, the production of some recombinant proteins in E. coli is often hampered by difficulties such as low expression level and low solubility. To address these problems, a modified cold-shock expression system containing a glutathione S-transferase (GST) tag, the pCold-GST system, was investigated. The pCold-GST system successfully expressed 9 out of 10 proteins that otherwise could not be expressed using a conventional E. coli expression system. Here, we applied the pCold-GST system to 84 proteins and 78 proteins were successfully expressed in the soluble fraction. Three other cold-shock expression systems containing a maltose binding protein ta... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3981366 Wed, 15 Sep 2010 23:00:00 +0100 3981366 http://www.medworm.com/index.php?rid=3970067&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20838855%26dopt%3DAbstract Authors: Jaipuria G, Thakur A, D'Silva P, Atreya HS Three-dimensional (3D) structure determination of proteins is benefitted by long-range distance constraints comprising the methyl groups, which constitute the hydrophobic core of proteins. However, in methyl groups (of Ala, Ile, Leu, Met, Thr and Val) there is a significant overlap of (13)C and (1)H chemical shifts. Such overlap can be resolved using the recently proposed (3,2)D HCCH-COSY, a G-matrix Fourier transform (GFT) NMR based experiment, which facilitates editing of methyl groups into distinct spectral regions by combining their (13)C chemical shifts with that of the neighboring, directly attached, (13)C nucleus. Using this principle, we present three GFT experiments: (a) (4,3)D NOESY-HCCH, (b) (4,3)D (1)H-TOCSY-HCCH and (c) (... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3970067 Mon, 13 Sep 2010 23:00:00 +0100 3970067 http://www.medworm.com/index.php?rid=3938707&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20803233%26dopt%3DAbstract Authors: Tang M, Comellas G, Mueller LJ, Rienstra CM High resolution (13)C-detected solid-state NMR spectra of the deuterated beta-1 immunoglobulin binding domain of the protein G (GB1) have been collected to show that all (15)N, (13)C', (13)Calpha and (13)Cbeta sites are resolved in (13)C-(13)C and (15)N-(13)C spectra, with significant improvement in T (2) relaxation times and resolution at high magnetic field (750 MHz). The comparison of echo T (2) values between deuterated and protonated GB1 at various spinning rates and under different decoupling schemes indicates that (13)Calpha T (2)' times increase by almost a factor of two upon deuteration at all spinning rates and under moderate decoupling strength, and thus the deuteration enables application of scalar-based correlation exper... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3938707 Sat, 28 Aug 2010 23:00:00 +0100 3938707 http://www.medworm.com/index.php?rid=3899717&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20734112%26dopt%3DAbstract In this study, reasonable signal to noise can be achieved between 60-76% (19)F enrichment, without any detectable perturbations from labeling. PMID: 20734112 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3899717 Mon, 23 Aug 2010 23:00:00 +0100 3899717 http://www.medworm.com/index.php?rid=3899716&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20734113%26dopt%3DAbstract Authors: Butterfoss GL, Derose EF, Gabel SA, Perera L, Krahn JM, Mueller GA, Zheng X, London RE Methionine residues fulfill a broad range of roles in protein function related to conformational plasticity, ligand binding, and sensing/mediating the effects of oxidative stress. A high degree of internal mobility, intrinsic detection sensitivity of the methyl group, and low copy number have made methionine labeling a popular approach for NMR investigation of selectively labeled protein macromolecules. However, selective labeling approaches are subject to more limited information content. In order to optimize the information available from such studies, we have performed DFT calculations on model systems to evaluate the conformational dependence of (3) J (CSCC), (3) J (CSCH), and the isotro... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3899716 Mon, 23 Aug 2010 23:00:00 +0100 3899716 http://www.medworm.com/index.php?rid=3850835&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20694505%26dopt%3DAbstract We present a simple method, ARTSY, for extracting (1)J(NH) couplings and (1)H-(15)N RDCs from an interleaved set of two-dimensional (1)H-(15)N TROSY-HSQC spectra, based on the principle of quantitative J correlation. The primary advantage of the ARTSY method over other methods is the ability to measure couplings without scaling peak positions or altering the narrow line widths characteristic of TROSY spectra. Accuracy of the method is demonstrated for the model system GB3. Application to the catalytic core domain of HIV integrase, a 36 kDa homodimer with unfavorable spectral characteristics, demonstrates its practical utility. Precision of the RDC measurement is limited by the signal-to-noise ratio, S/N, achievable in the 2D TROSY-HSQC spectrum, and is approximately given by 30/(S/N) Hz. ... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3850835 Fri, 06 Aug 2010 23:00:00 +0100 3850835 http://www.medworm.com/index.php?rid=3823417&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20683638%26dopt%3DAbstract This study suggests that uniformly (15)N,(13)C-labeled recombinant proteins may be produced in cultured mammalian cells starting from a mixture of labeled essential amino acids, glucose, and glutamate. PMID: 20683638 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3823417 Tue, 03 Aug 2010 23:00:00 +0100 3823417 http://www.medworm.com/index.php?rid=3823419&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20680401%26dopt%3DAbstract We present a suite of software for the complete and easy deposition of NMR data to the PDB and BMRB. This suite uses the CCPN framework and introduces a freely downloadable, graphical desktop application called CcpNmr Entry Completion Interface (ECI) for the secure editing of experimental information and associated datasets through the lifetime of an NMR project. CCPN projects can be created within the CcpNmr Analysis software or by importing existing NMR data files using the CcpNmr FormatConverter. After further data entry and checking with the ECI, the project can then be rapidly deposited to the PDBe using AutoDep, or exported as a complete deposition NMR-STAR file. In full CCPN projects created with ECI, it is straightforward to select chemical shift lists, restraint data sets, structu... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3823419 Mon, 02 Aug 2010 23:00:00 +0100 3823419 http://www.medworm.com/index.php?rid=3823418&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20680402%26dopt%3DAbstract Authors: Baskaran K, Brunner K, Munte CE, Kalbitzer HR Applying the chemical shift prediction programs SHIFTX and SHIFTS to a data base of protein structures with known chemical shifts we show that the averaged chemical shifts predicted from the structural ensembles explain better the experimental data than the lowest energy structures. This is in agreement with the fact that proteins in solution occur in multiple conformational states in fast exchange on the chemical shift time scale. However, in contrast to the real conditions in solution at ambient temperatures, the standard NMR structural calculation methods as well chemical shift prediction methods are optimized to predict the lowest energy ground state structure that is only weakly populated at physiological temperatures. An anal... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3823418 Sat, 31 Jul 2010 23:00:00 +0100 3823418 http://www.medworm.com/index.php?rid=3823420&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20665069%26dopt%3DAbstract Authors: Pacheco V, Ma P, Thielmann Y, Hartmann R, Weiergräber OH, Mohrlüder J, Willbold D Gamma-aminobutyric acid type A receptor-associated protein (GABARAP) belongs to a family of small ubiquitin-like adaptor proteins implicated in intracellular vesicle trafficking and autophagy. We have used diffusion-ordered nuclear magnetic resonance spectroscopy to study the temperature and concentration dependence of the diffusion properties of GABARAP. Our data suggest the presence of distinct conformational states and provide support for self-association of GABARAP molecules. Assuming a monomer-dimer equilibrium, a temperature-dependent dissociation constant could be derived. Based on a temperature series of (1)H(15)N heteronuclear single quantum coherence nuclear magnetic resonance spe... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3823420 Tue, 27 Jul 2010 23:00:00 +0100 3823420 http://www.medworm.com/index.php?rid=3776684&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20644980%26dopt%3DAbstract Authors: Vila JA, Serrano P, Wüthrich K, Scheraga HA To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of (13)C(alpha) chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue alpha/beta protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed (13)C(alpha) chemical shifts. A new ensemble of 20 conformers representing the NMR structure of the NAB, which was calculated with an input containing backbon... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3776684 Mon, 19 Jul 2010 23:00:00 +0100 3776684 http://www.medworm.com/index.php?rid=3776683&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20644981%26dopt%3DAbstract Authors: Umemoto R, Nishida N, Ogino S, Shimada I PMID: 20644981 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3776683 Mon, 19 Jul 2010 23:00:00 +0100 3776683 http://www.medworm.com/index.php?rid=3776685&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20628786%26dopt%3DAbstract We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and (13)C(beta) chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and (13)C(beta) atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for delta(15)N, delta(13)C', delta(13)C(alpha), delta(13)C(beta), delta(1)H(alpha) and delta... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3776685 Tue, 13 Jul 2010 23:00:00 +0100 3776685 http://www.medworm.com/index.php?rid=3724768&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20596883%26dopt%3DAbstract Authors: Todokoro Y, Kobayashi M, Sato T, Kawakami T, Yumen I, Aimoto S, Fujiwara T, Akutsu H The subunit c-ring of H(+)-ATP synthase (F(o) c-ring) plays an essential role in the proton translocation across a membrane driven by the electrochemical potential. To understand its structure and function, we have carried out solid-state NMR analysis under magic-angle sample spinning. The uniformly [(13)C, (15)N]-labeled F(o) c from E. coli (EF(o) c) was reconstituted into lipid membranes as oligomers. Its high resolution two- and three-dimensional spectra were obtained, and the (13)C and (15)N signals were assigned. The obtained chemical shifts suggested that EF(o) c takes on a hairpin-type helix-loop-helix structure in membranes as in an organic solution. The results on the magnetization tr... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3724768 Thu, 01 Jul 2010 23:00:00 +0100 3724768 http://www.medworm.com/index.php?rid=3700341&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20574814%26dopt%3DAbstract Authors: Ogura K, Kumeta H, Inagaki F We developed an NMR pulse sequence, 3D HCA(N)CO, to correlate the chemical shifts of protein backbone (1)Halpha and (13)Calpha to those of (13)C' in the preceding residue. By applying (2)H decoupling, the experiment was accomplished with high sensitivity comparable to that of HCA(CO)N. When combined with HCACO, HCAN and HCA(CO)N, the HCA(N)CO sequence allows the sequential assignment using backbone (13)C' and amide (15)N chemical shifts without resort to backbone amide protons. This assignment strategy was demonstrated for (13)C/(15)N-labeled GB1 dissolved in (2)H(2)O. The quality of the GB1 structure determined in (2)H(2)O was similar to that determined in H(2)O in spite of significantly smaller number of NOE correlations. Thus this strategy enabl... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3700341 Wed, 23 Jun 2010 23:00:00 +0100 3700341 http://www.medworm.com/index.php?rid=3672723&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20556482%26dopt%3DAbstract Authors: Takeuchi K, Heffron G, Sun ZY, Frueh DP, Wagner G Heteronuclear direct-detection experiments, which utilize the slower relaxation properties of low gamma nuclei, such as (13)C have recently been proposed for sequence-specific assignment and structural analyses of large, unstructured, and/or paramagnetic proteins. Here we present two novel (15)N direct-detection experiments. The CAN experiment sequentially connects amide (15)N resonances using (13)C(alpha) chemical shift matching, and the CON experiment connects the preceding (13)C' nuclei. When starting from the same carbon polarization, the intensities of nitrogen signals detected in the CAN or CON experiments would be expected four times lower than those of carbon resonances observed in the corresponding (13)C-detecting expe... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3672723 Wed, 16 Jun 2010 23:00:00 +0100 3672723 http://www.medworm.com/index.php?rid=3672724&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20549304%26dopt%3DAbstract Authors: Tolbert BS, Miyazaki Y, Barton S, Kinde B, Starck P, Singh R, Bax A, Case DA, Summers MF Ribonucleic acid structure determination by NMR spectroscopy relies primarily on local structural restraints provided by (1)H- (1)H NOEs and J-couplings. When employed loosely, these restraints are broadly compatible with A- and B-like helical geometries and give rise to calculated structures that are highly sensitive to the force fields employed during refinement. A survey of recently reported NMR structures reveals significant variations in helical parameters, particularly the major groove width. Although helical parameters observed in high-resolution X-ray crystal structures of isolated A-form RNA helices are sensitive to crystal packing effects, variations among the published X-ray str... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3672724 Mon, 14 Jun 2010 23:00:00 +0100 3672724 http://www.medworm.com/index.php?rid=3672725&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20544375%26dopt%3DAbstract We present here a set of (13)C-direct detected NMR experiments to facilitate the resonance assignment of RNA oligonucleotides. Three experiments have been developed: (1) the (H)CC-TOCSY-experiment utilizing a virtual decoupling scheme to assign the intraresidual ribose (13)C-spins, (2) the (H)CPC-experiment that correlates each phosphorus with the C4' nuclei of adjacent nucleotides via J(C,P) couplings and (3) the (H)CPC-CCH-TOCSY-experiment that correlates the phosphorus nuclei with the respective C1',H1' ribose signals. The experiments were applied to two RNA hairpin structures. The current set of (13)C-direct detected experiments allows direct and unambiguous assignment of the majority of the hetero nuclei and the identification of the individual ribose moieties following their sequenti... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3672725 Thu, 10 Jun 2010 23:00:00 +0100 3672725 http://www.medworm.com/index.php?rid=3653124&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20532590%26dopt%3DAbstract Authors: Nunez M, Guittet E, Pompon D, van Heijenoort C, Truan G PMID: 20532590 [PubMed - as supplied by publisher] (Source: Journal of Bimolecular NMR) Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3653124 Mon, 07 Jun 2010 23:00:00 +0100 3653124 http://www.medworm.com/index.php?rid=3633380&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20524044%26dopt%3DAbstract Authors: Dolenc J, Missimer JH, Steinmetz MO, van Gunsteren WF The C-terminal trigger sequence is essential in the coiled-coil formation of GCN4-p1; its conformational properties are thus of importance for understanding this process at the atomic level. A solution NMR model structure of a peptide, GCN4p16-31, encompassing the GCN4-p1 trigger sequence was proposed a few years ago. Derived using a standard single-structure refinement protocol based on 172 nuclear Overhauser effect (NOE) distance restraints, 14 hydrogen-bond and 11 varphi torsional-angle restraints, the resulting set of 20 NMR model structures exhibits regular alpha-helical structure. However, the set slightly violates some measured NOE bounds and does not reproduce all 15 measured (3)J(H(N)-H(Calpha))-coupling constants,... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3633380 Thu, 03 Jun 2010 23:00:00 +0100 3633380 http://www.medworm.com/index.php?rid=3578386&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20474086%26dopt%3DAbstract Authors: Säwén E, Huttunen E, Zhang X, Yang Z, Widmalm G The use of lactic acid bacteria in fermentation of milk results in favorable physical and rheological properties due to in situ exopolysaccharide (EPS) production. The EPS from S. thermophilus ST1 produces highly viscous aqueous solutions and its structure has been investigated by NMR spectroscopy. Notably, all aspects of the elucidation of its primary structure including component analysis and absolute configuration of the constituent monosaccharides were carried out by NMR spectroscopy. An array of techniques was utilized including, inter alia, PANSY and NOESY-HSQC TILT experiments. The EPS is composed of hexasaccharide repeating units with the following structure: --> 3)[alpha-D-Glcp-(1 --> 4)]-beta-D-Galp-(1 --&gt... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3578386 Thu, 20 May 2010 08:51:05 +0100 3578386 http://www.medworm.com/index.php?rid=3564066&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20461447%26dopt%3DAbstract Authors: Denisov AY, Kloser E, Gray DG, Mittermaier AK Cellulose nanocrystals (CNCs) form liquid crystals in aqueous solution that confer alignment to macromolecules and permit the measurement of residual dipolar couplings. CNCs possess many attractive features as an alignment medium. They are inexpensive, non-toxic, chemically inert, and robust to denaturants and temperature. Despite these advantages, CNCs are seldom employed as an alignment medium and the range of their applicability has not yet been explored. We have re-examined the use of CNCs in biomolecular NMR by analyzing the effects concentration, ionic strength, and temperature on molecular alignment. Stable alignment was obtained over wide ranges of temperature (10-70 degrees C) and pH (2.5-8.0), which makes CNCs potentially... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3564066 Tue, 11 May 2010 23:00:00 +0100 3564066 http://www.medworm.com/index.php?rid=3553938&cid=s_34011_61_f&fid=34011&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20454834%26dopt%3DAbstract We describe a novel pulse sequence, MQ-HNCO-TROSY, for the measurement of scalar and residual dipolar couplings between amide proton and nitrogen in larger proteins. The experiment utilizes the whole 2T(N) polarization transfer delay for labeling of (15)N chemical shift in a constant time manner, which efficiently doubles the attainable resolution in (15)N dimension with respect to the conventional HNCO-TROSY experiment. In addition, the accordion principle is employed for measuring (J + D)(NH)s, and the multiplet components are selected with the generalized version of the TROSY scheme introduced by Nietlispach (J Biomol NMR 31:161-166, 2005). Therefore, cross peak overlap is diminished while the time period during which the (15)N spin is susceptible to fast transverse relaxation associate... Journal of Bimolecular NMR journals http://www.medworm.com/rss/comments.php?id=3553938 Fri, 07 May 2010 23:00:00 +0100 3553938