Bioactive brominated metabolites from the red sea sponge pseudoceratina arabica
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Jihan M. Badr, Lamiaa A. Shaala, Mohamed I. Abou-Shoer, Mona K. Tawfik, and Abdel-Azim M. HabibWeb Release Date: Fri, 4 Jul 2008 00:00:00 EDT (Note) DOI: 10.1021/np8002113 (Source: Journal of Natural Products)
Source: Journal of Natural Products - July 4, 2008 Category: Biochemistry Source Type: journals
Improved procedure for direct coupling of carbohydrates to proteins via reductive amination
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Jeffrey C. Gildersleeve, Oyindasola Oyelaran, John T. Simpson, and Benjamin AllredWeb Release Date: Thu, 3 Jul 2008 00:00:00 EDT (Technical Note) DOI: 10.1021/bc800153t (Source: Bioconjugate Chemistry)
Source: Bioconjugate Chemistry - July 4, 2008 Category: Biochemistry Source Type: journals
Triplex profiling of functionally distinct chaperones (erp29/pdi/bip) reveals marked heterogeneity of the endoplasmic reticulum proteome in cancer
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Steven D. Shnyder, Jonathan E. Mangum, and Michael J. HubbardWeb Release Date: Fri, 4 Jul 2008 00:00:00 EDT (Article) DOI: 10.1021/pr800126n (Source: Journal of Proteome Research)
Source: Journal of Proteome Research - July 4, 2008 Category: Biochemistry Source Type: journals
Sesquiterpenes and aliphatic diketones from cultures of the basidiomycete conocybe siliginea
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Zhong-Yu Zhou, Jian-Guo Tang, Fei Wang, Ze-Jun Dong, and Ji-Kai LiuWeb Release Date: Fri, 4 Jul 2008 00:00:00 EDT (Article) DOI: 10.1021/np8002657 (Source: Journal of Natural Products)
Source: Journal of Natural Products - July 4, 2008 Category: Biochemistry Source Type: journals
Kinetic studies and bioactivity of potential manzamine prodrugs
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Abbas Gholipour Shilabin, Noer Kasanah, Babu L. Tekwani, and Mark T. HamannWeb Release Date: Fri, 4 Jul 2008 00:00:00 EDT (Article) DOI: 10.1021/np800163u (Source: Journal of Natural Products)
Source: Journal of Natural Products - July 4, 2008 Category: Biochemistry Source Type: journals
Paw paw and cancer: annonaceous acetogenins from discovery to commercial products
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Jerry L. McLaughlinWeb Release Date: Fri, 4 Jul 2008 00:00:00 EDT (Review) DOI: 10.1021/np800191t (Source: Journal of Natural Products)
Source: Journal of Natural Products - July 4, 2008 Category: Biochemistry Source Type: journals
Product notes
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New Products (Source: Journal of Proteome Research)
Source: Journal of Proteome Research - July 3, 2008 Category: Biochemistry Source Type: journals
Government and society: is your protein on the hit parade?
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During election years, we often hear too much about the leading candidates and too little about the rest of the pack. (Source: Journal of Proteome Research)
Source: Journal of Proteome Research - July 3, 2008 Category: Biochemistry Source Type: journals
Proteomics project
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First draft of the human ductal salivary proteome (Source: Journal of Proteome Research)
Source: Journal of Proteome Research - July 3, 2008 Category: Biochemistry Source Type: journals
Research profile: the effect of ozone on rice seedlings
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Ground-level ozone is a pollutant that can cause lung irritation, chest pain, and other symptoms in humans. (Source: Journal of Proteome Research)
Source: Journal of Proteome Research - July 3, 2008 Category: Biochemistry Source Type: journals
Research profile: enrichment of plasma membrane proteins from pluripotent cells
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Recently, much media attention has been focused on the possibility that human embryonic stem cells (hESCs) could be used to treat various illnesses. (Source: Journal of Proteome Research)
Source: Journal of Proteome Research - July 3, 2008 Category: Biochemistry Source Type: journals
Toolbox
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Census for quantitation | TIQAM | Metabolomics analyses with AI-Binning | DBMLoc (Source: Journal of Proteome Research)
Source: Journal of Proteome Research - July 3, 2008 Category: Biochemistry Source Type: journals
Currents
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: High-throughput method for mammalian protein function | The effect of antimitotic chemotherapy drugs on mitotic proteins | Proteome map of Arabidopsis thaliana | Figuring out in vivo protein–protein interactions | How ibuprofen may protect against Alzheimer’s disease | Identifying wheat allergens (Source: Journal of Proteome Research)
Source: Journal of Proteome Research - July 3, 2008 Category: Biochemistry Source Type: journals
Editorial
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GlycoScience Ireland Initiative (Source: Journal of Proteome Research)
Source: Journal of Proteome Research - July 3, 2008 Category: Biochemistry Source Type: journals
Solid phase synthesis of a glycopeptide analogue using the acid sensitive 4-methoxybenzhydryl bromide resin.
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A convenient solid phase synthesis of a Thrombin Receptor Glycopeptide Mimetic analogue namely, 1-O-Methyl-2-N-{1'-(argininocarbonyl)-4'-[(4''-fluoro)-benzylamido]-cyclohexane}-glucosamine using Fmoc/tBu methodology and the 4-Methoxybenzhydryl bromide resin is described. The synthesized analogue was purified by Reverse Phase High Performance Liquid Chromatography (RP-HPLC) and was identified by Electron Spray Ionization-Mass Spectrometry (ESI-MS) and Nuclear Magnetic Resonance (NMR). The synthetic protocol introduced for the first time successfully the acid sensitive 4-Methoxybenzhydryl bromide resin as a scaffold for ...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Tselios T, Kelaidonis K, Resvani A, Prousalis K, Matsoukas J, Tsegenidis T Tags: Protein Pept Lett Source Type: journals
Determination of some kinetic and characteristic properties of glutathione s-transferase from bovine erythrocytes.
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Determination of some kinetic and characteristic properties of glutathione S-transferase from bovine erythrocytes.
Protein Pept Lett. 2008;15(1):6-12
Authors: Güvercin S, Erat M, Sakiroğlu H
Glutathione S-transferase was purified from bovine erythrocytes and some kinetic and characteristic properties of the enzyme were investigated. The purification procedure was composed of preparation of homogenate and Glutathione-Agarose affinity chromatography. Thanks to the procedure, the enzyme was purified 6,800 fold with 97% yield and a specific activity of 136 EU/mg proteins. On sodium dodecyl sulfate polyac...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Güvercin S, Erat M, Sakiroğlu H Tags: Protein Pept Lett Source Type: journals
Dna cleavage study using copper (ii)-glyaibhis: a tripeptide complex based on atcun peptide motifs.
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DNA cleavage study using copper (II)-GlyAibHis: a tripeptide complex based on ATCUN peptide motifs.
Protein Pept Lett. 2008;15(1):13-9
Authors: Singh RK, Sharma NK, Prasad R, Singh UP
Development of new chemical nucleases is a matter of great interest because of their extensive use in biotechnology and as therapeutic agents. The ATCUN (amino terminal Cu(II) and Ni(II) binding) is a peptide motif that occurs naturally in the serum albumins. The similar peptide motif (GlyAibHis) having unnatural amino acid Aib (alpha-aminoisobutyric acid) was synthesized and its Cu(II) complex was characterized by ESI-MS and spec...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Singh RK, Sharma NK, Prasad R, Singh UP Tags: Protein Pept Lett Source Type: journals
Oxidative stress induced functional and structural modifications of high molecular mass goat brain cystatin.
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Cystatins are thiol proteinase inhibitors ubiquitously present in mammalian body. In brain, they prevent unwanted proteolysis and are involved in several neurodegenerative diseases. In the present study, it has been demonstrated that photoactivated riboflavin and H2O2 induced modifications of high molecular mass goat brain cystatin (HM-GBC) leads to its inactivation and degradation. It was found that the damage with both the oxidants occurred mainly because of the hydroxyl radicals. It has been also proposed that susceptibility of HM-GBC to oxidation by reactive oxygen species generated in vivo arise from oxidative mod...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Sumbul S, Bano B Tags: Protein Pept Lett Source Type: journals
Molecular modeling of two cyp2c19 snps and its implications for personalized drug design.
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Molecular modeling of two CYP2C19 SNPs and its implications for personalized drug design.
Protein Pept Lett. 2008;15(1):27-32
Authors: Wang JF, Wei DQ, Chen C, Li Y, Chou KC
CYP2C19 is an important member of the cytochrome P-450 enzyme superfamily and plays a significant role in the drug metabolism. In order to gain insights for developing personalized drugs, the structure-activity relationships of two SNPs, W120R and I331V, with the ligands of CEC, Fluvoxamine, Lescol and Ticlopidine were investigated through the structure-activity relationship approach. By means of a series of docking studies, the binding poc...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Wang JF, Wei DQ, Chen C, Li Y, Chou KC Tags: Protein Pept Lett Source Type: journals
Coilcheck: an interactive server for the analysis of interface regions in coiled coils.
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COILCHECK: an interactive server for the analysis of interface regions in coiled coils.
Protein Pept Lett. 2008;15(1):33-8
Authors: Alva V, Syamala Devi DP, Sowdhamini R
Coiled coils are important structural modules and domains of protein-protein interactions. Further, they provide the required framework to proteins, like kinesins, myosins and SNAREs, which are either structural or involved in transport of biomolecules. We provide an interactive webserver to measure the strength of interactions between two helices involved in coiled coils. Interactions are measured using non-bonded and electrostatic interaction...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Alva V, Syamala Devi DP, Sowdhamini R Tags: Protein Pept Lett Source Type: journals
Effect of ca2+ on beta-propeller phytases.
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Effect of Ca2+ on beta-propeller phytases.
Protein Pept Lett. 2008;15(1):39-42
Authors: Fu S, Sun J, Qian L
Beta-propeller phytases (BPPs) are a special class of enzyme that are mainly isolated from Bacillus and are widely used in animal nutrition, human health and environmental protection. BPPs class exhibits both unique Ca2+-dependent catalytic property and highly strict substrate specificity for the calcium-phytate complex. This review describes the effect of Ca2+ on the catalytic activity, thermal stability, and structural conformation of BPPs.
PMID: 18221011 [PubMed - indexed for MEDLINE] (Source: Prot...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Fu S, Sun J, Qian L Tags: Protein Pept Lett Source Type: journals
Detection of a gamma-carboxy-glutamate as novel post-translational modification of human transthyretin.
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During analysis of the proteome in the cerebrospinal fluid (CSF) of the Caucasian form of moyamoya disease (MMD), a novel post-translational modification of human transthyretin was observed. Two-dimensional electrophoresis and subsequent peptide sequencing with ESI-MS/MS were performed to discover the gamma-carboxylation of the Glu-42 (Gla-42).
PMID: 18221012 [PubMed - indexed for MEDLINE] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Rüggeberg S, Horn P, Li X, Vajkoczy P, Franz T Tags: Protein Pept Lett Source Type: journals
The heavy-light chain loop of human cathepsin-l modulates its activity and stability.
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The heavy-light chain loop of human cathepsin-L modulates its activity and stability.
Protein Pept Lett. 2008;15(1):47-53
Authors: Fairhead M, van der Walle CF
Differences evident in the sequence alignment of human cathepsin-L with shrimp cathepsin-L and silicatein-alpha suggest the indirect involvement of the heavy to light chain loop (E 286 to E 289) in the function of these enzymes. Deletion of the loop and adjacent residues S 290 to N 293, decreased specific protease activity by 81% and 63%, respectively; complete substitution for the corresponding silicatein-alpha loop decreased activity by 35%. In all cas...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Fairhead M, van der Walle CF Tags: Protein Pept Lett Source Type: journals
The hypervariable d3 domain of salmonella flagellin is an autonomous folding unit.
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The hypervariable D3 domain of Salmonella flagellin is an autonomous folding unit.
Protein Pept Lett. 2008;15(1):54-7
Authors: Sebestyén A, Muskotál A, Végh BM, Vonderviszt F
The hypervariable D3 domain of Salmonella flagellin, composed of the 190-285 segment, is the major determinant of flagellar antigenicity. D3 was cloned and overexpressed in E. coli. Although previous studies concluded that D3 is stabilized by interactions with the D2 domain, our calorimetric experiments have revealed that isolated D3 has a stable tertiary structure which is highly resistant against proteolytic digestion. Rep...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Sebestyén A, Muskotál A, Végh BM, Vonderviszt F Tags: Protein Pept Lett Source Type: journals
S-adenosylmethionine inhibits ubiquitin-proteasome system in vitro and on rat vascular smooth muscle cells.
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S-adenosylmethionine is a metabolite regulating many biological processes; S-adenosylmethionine effect on ubiquitin-proteasome system (UPS) has not been studied yet. We investigated S-adenosylmethionine effects on UPS activity both in vitro, by inhibitor screening assay, and in rat vascular smooth muscle cells, by Western Blot of proteasomal targets. We found that S-adenosylmethionine inhibited UPS activity.
PMID: 18221015 [PubMed - indexed for MEDLINE] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: D'Anselmi F, Cucina A, Cavallaro G, Bizzarri M, Cavallaro RA, Fuso A, Cavallaro A, Scarpa S Tags: Protein Pept Lett Source Type: journals
Secondary structure of the mirp1 (kcne2) potassium channel ancillary subunit.
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Secondary structure of the MiRP1 (KCNE2) potassium channel ancillary subunit.
Protein Pept Lett. 2008;15(1):63-75
Authors: Abbott GW, Ramesh B, Srai SK
MiRP1 (encoded by the KCNE2 gene) is one of a family of five single transmembrane domain voltage-gated potassium (Kv) channel ancillary subunits currently under intense scrutiny to establish their position in channel complexes and elucidate alpha subunit contact points, but its structure is unknown. MiRP1 mutations are associated with inherited and acquired cardiac arrhythmia. Here, synthetic peptides corresponding to human MiRP1 (full-length and separate domain...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Abbott GW, Ramesh B, Srai SK Tags: Protein Pept Lett Source Type: journals
The interaction between two arabidopsis polyadenylation factor subunits involves an evolutionarily-conserved motif and has implications for the assembly and function of the polyadenylation complex.
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The interaction between two Arabidopsis polyadenylation factor subunits involves an evolutionarily-conserved motif and has implications for the assembly and function of the polyadenylation complex.
Protein Pept Lett. 2008;15(1):76-88
Authors: Addepalli B, Hunt AG
The polyadenylation factor subunit "Factor Interacting with Poly(A) polymerase" (Fip1) is an important bridging subunit in the eukaryotic polyadenylation complex. To better understand the functioning of Fip1 in Arabidopsis, a random combinatorial screen for peptides that interact with a conserved plant-specific domain in the protein was conducted. A se...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Addepalli B, Hunt AG Tags: Protein Pept Lett Source Type: journals
Processing of dna replication and repair intermediates by the concerted action of recq helicases and rad2 structure-specific nucleases.
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Processing of DNA replication and repair intermediates by the concerted action of RecQ helicases and Rad2 structure-specific nucleases.
Protein Pept Lett. 2008;15(1):89-102
Authors: Sharma S, Sommers JA, Brosh RM
Processing of DNA replication and repair intermediates is a critical aspect of genome stability maintenance. The coordinated action of RecQ-like helicases with structure-specific nucleases such as Flap Endonuclease 1 plays an important role in the processing of certain DNA structures associated with the replication fork, DNA repair, or telomeres. We will summarize our current understanding of how and i...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Sharma S, Sommers JA, Brosh RM Tags: Protein Pept Lett Source Type: journals
Interaction of calreticulin with amyloid beta peptide 1-42.
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The interaction of calreticulin with amyloid beta (Abeta) was investigated using solid phase and solution binding assays. Calreticulin bound Abeta 1-42 in a time and concentration dependent fashion. The binding was optimal at pH 5 and was stimulated by Ca2+ and inhibited by Zn2+ at pH 7. Interaction took place through the hydrophobic C-terminus of Abeta 1-42 and the polypeptide binding site of calreticulin. The results are discussed in the light of a reported role of calreticulin as a cell surface scavenger receptor.
PMID: 18221019 [PubMed - indexed for MEDLINE] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Duus K, Hansen PR, Houen G Tags: Protein Pept Lett Source Type: journals
Structural and functional diversity of nudix fold.
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Structural and functional diversity of Nudix fold.
Protein Pept Lett. 2008;15(1):108-12
Authors: Lin J, Tian B, Hua Y
Nudix hydrolases catalyze the hydrolysis of nucleoside diphosphates linked to other moieties X, and contain the sequence motif or Nudix box, GX5EX7REUXEEXGU. The mechanisms of Nudix hydrolases are highly diverse in the position on the substrate. In this paper, we examined the sequences and structures of the MutT/Nudix superfamily. And two recent developed methods were employed for data analyses of the superfamily. One is QH method evaluating the similarities among structures for structural phylo...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Lin J, Tian B, Hua Y Tags: Protein Pept Lett Source Type: journals
Crystallization and preliminary x-ray analysis of fluorescent protein mbanana.
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Crystallization and preliminary X-ray analysis of fluorescent protein mBanana.
Protein Pept Lett. 2008;15(1):113-4
Authors: Zhou Y, Wu Y, Song J, Ding Y, Hu X, Zhang Z
mBanana is a novel monomeric red fluorescent protein mutant. It was cloned and expressed in Escherichia coli with 10 histidine residues at its N-terminal. After cleavage of the His tag by TEV protease, the mBanana was further purified and crystallized by the hanging-drop vapor-diffusion technique. The crystals can diffract to 2.0A resolution and one set of completed data was collected. It showed that the orthorhombic mBanana crystal was in space ...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Zhou Y, Wu Y, Song J, Ding Y, Hu X, Zhang Z Tags: Protein Pept Lett Source Type: journals
Purification, crystallization and preliminary x-ray studies of axcesd required for efficient cellulose biosynthesis in acetobacter xylinum.
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Purification, crystallization and preliminary X-ray studies of AxCesD required for efficient cellulose biosynthesis in Acetobacter xylinum.
Protein Pept Lett. 2008;15(1):115-7
Authors: Hu S, Gao Y, Tajima K, Yao M, Yoda T, Shimura D, Satoh Y, Kawano S, Tanaka I, Munekata M
AxCesD protein required for bacterial cellulose biosynthesis in Acetobacter xylinum was overexpressed in E. coli, purified and crystallized. Single crystals of SeMet-substituted AxCesD were obtained by the sitting-drop vapor-diffusion method. The crystal belongs to the primitive trigonal space group P3 2, with unit-cell parameters a = b = 77....
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Hu S, Gao Y, Tajima K, Yao M, Yoda T, Shimura D, Satoh Y, Kawano S, Tanaka I, Munekata M Tags: Protein Pept Lett Source Type: journals
Editorial. bace or beta-secretase -a target for drug discovery for treatment of alzheimer's disease.
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Editorial. BACE or beta-secretase -a target for drug discovery for treatment of Alzheimer's disease.
Protein Pept Lett. 2008;15(2):118
Authors: Dunn BM
PMID: 18289103 [PubMed - indexed for MEDLINE] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Dunn BM Tags: Protein Pept Lett Source Type: journals
Large-scale purification of human bace expressed in mammalian cells and removal of the prosegment with hiv-1 protease to improve crystal diffraction.
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Large-scale purification of human BACE expressed in mammalian cells and removal of the prosegment with HIV-1 protease to improve crystal diffraction.
Protein Pept Lett. 2008;15(2):119-30
Authors: Emmons TL, Shuck ME, Babcock MS, Holloway JS, Leone JW, Durbin JD, Paddock DJ, Prince DB, Heinrikson RL, Fischer HD, Bienkowski MJ, Benson TE, Tomasselli AG
BACE, or beta-secretase, is an attractive target in the treatment of Alzheimer's Disease because of its involvement in the generation of amyloid beta peptides. BACE is a type I transmembrane aspartyl protease composed of pre-, pro-, catalytic, transmembrane and cyt...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Emmons TL, Shuck ME, Babcock MS, Holloway JS, Leone JW, Durbin JD, Paddock DJ, Prince DB, Heinrikson RL, Fischer HD, Bienkowski MJ, Benson TE, Tomasselli AG Tags: Protein Pept Lett Source Type: journals
High yield expression of human bace constructs in eschericia coli for refolding, purification, and high resolution diffracting crystal forms.
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High yield expression of human BACE constructs in Eschericia coli for refolding, purification, and high resolution diffracting crystal forms.
Protein Pept Lett. 2008;15(2):131-43
Authors: Tomasselli AG, Paddock DJ, Emmons TL, Mildner AM, Leone JW, Lull JM, Cialdella JI, Prince DB, Fischer HD, Heinrikson RL, Benson TE
BACE (beta-site APP cleaving enzyme) or beta-secretase, the enzyme responsible for processing APP to give the N-terminal portion of the Abeta peptide, is a membrane bound aspartyl protease consisting of an ectodomain catalytic unit, a C-terminal transmembrane segment and a cytoplasmic domain. Three...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Tomasselli AG, Paddock DJ, Emmons TL, Mildner AM, Leone JW, Lull JM, Cialdella JI, Prince DB, Fischer HD, Heinrikson RL, Benson TE Tags: Protein Pept Lett Source Type: journals
Prediction of mutations in h3n2 hemagglutinins of influenza a virus from north america based on different datasets.
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Prediction of mutations in H3N2 hemagglutinins of influenza A virus from North America based on different datasets.
Protein Pept Lett. 2008;15(2):144-52
Authors: Wu G, Yan S
With rapid increase in influenza A virus database, an important issue is whether the predictions are similar based on different datasets. Here we stratify 482 H3N2 hemagglutinins from influenza A virus in North America to different datasets. The predictions are made using logistic regression. The results show that the different datasets have significant impact on the predictions.
PMID: 18289106 [PubMed - indexed for MEDLINE] (Source: Pr...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Wu G, Yan S Tags: Protein Pept Lett Source Type: journals
Construction, purification and characterization of untagged human liver alanine-glyoxylate aminotransferase expressed in escherichia coli.
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We report for the first time the expression of untagged AGT together with a new rapid protocol for its purification. In addition, the kinetic parameters for the forward and reverse transamination catalyzed by untagged AGT as well as the spectroscopic features, the K(D(PLP)), the pH and thermal stability of the enzyme in the holo- and apo-form have been determined. This investigation will be the starting point for a detailed understanding of the contributions of the N- and C-termini on the dimerization and folding of AGT, and on its import into the peroxisome. This is prerequisite to understand how pathological mutations af...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Cellini B, Montioli R, Bianconi S, López-Alonso JP, Voltattorni CB Tags: Protein Pept Lett Source Type: journals
Conformational analysis corresponding to intra-chain disulfide bridged peptides in proteins of known three-dimensional structure.
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We have carried out a systematic analysis in order to evaluate whether Intra-Chain Disulfide Bridged Peptides (ICDBPs) observed in proteins of known three-dimensional structure adopt structurally similar conformations as they may correspond to structural/functional motifs. 406 representative ICDBPs comprising between 3 to 17 amino acid residues could be classified according to peptide sequence length and main-chain secondary structure conformation into 146 classes. ICDBPs comprising 6 amino acid residues are maximally represented in the Protein Data Bank. They also represent the maximum number of main-chain secondary s...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Sridhar S, Guruprasad K Tags: Protein Pept Lett Source Type: journals
Influence of the n- and c-terminal regions of leu-lys rich antimicrobial peptide on antimicrobial activity.
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In this study, P11, K(3)K(4)L(5)L(6)-deleted peptide, acted independent on the ionic environment. Furthermore, P11 causes significant morphological alterations of the fungal surfaces as shown by scanning electron microscopy.
PMID: 18289109 [PubMed - indexed for MEDLINE] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Park HK, Lim HT, Chae BJ, Hahm KS, Park Y Tags: Protein Pept Lett Source Type: journals
In silico modulation of hmgn-1 binding to histones and gene expression by interplay of phosphorylation and o-glcnac modification.
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In silico modulation of HMGN-1 binding to histones and gene expression by interplay of phosphorylation and O-GlcNAc modification.
Protein Pept Lett. 2008;15(2):193-9
Authors: Ahmad I, Khan TS, Hoessli DC, Walker-Nasir E, Kaleem A, Shakoori AR, Nasir-ud-Din
Utilizing different computational methods; phosphorylation, O-GlcNAc modification and Yin Yang sites are predicted in HMGN-1. Prediction results suggest that interplay of phosphorylation and O-GlcNAc modification regulates binding and removal of HMGN-1 with the nucleosome and its translocation from nucleus to cytoplasm and back to nucleus, consequently modul...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Ahmad I, Khan TS, Hoessli DC, Walker-Nasir E, Kaleem A, Shakoori AR, Nasir-ud-Din Tags: Protein Pept Lett Source Type: journals
Redox state of cytochrome c regulates cellular ros and caspase cascade in permeablized cell model.
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Redox state of cytochrome c regulates cellular ROS and caspase cascade in permeablized cell model.
Protein Pept Lett. 2008;15(2):200-5
Authors: Li M, Wang AJ, Xu JX
In a permeablized cell system, oxidized cyt c is able to induce caspase cascade whereas reduced cyt c cannot. In in vitro experiments, oxidized cyt c can promote H(2)O(2) generation. It is suggested that the redox state of cyt c might regulate the initiation of apoptosis via regulation of cellular ROS level.
PMID: 18289111 [PubMed - indexed for MEDLINE] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Li M, Wang AJ, Xu JX Tags: Protein Pept Lett Source Type: journals
Sonication induced intermediate in prion protein conversion.
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We have observed that hamster prion protein (PrP(C)) undergoes conformational changes on exposure to heat or sonication. If a sonication induced new conformer is seeded with a small amount of its abnormal pathogenic isoform (PrP(Sc)) it undergoes a significant conversion to a proteinase-resistant isoform. This suggests the presence of a third stable PrP conformer, which may be intermediate in the conversion of PrP(C) to PrP(Sc).
PMID: 18289112 [PubMed - indexed for MEDLINE] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Zukas AA, Bruederle CE, Carter JM Tags: Protein Pept Lett Source Type: journals
Binding of tris to bacillus licheniformis alpha-amylase can affect its starch hydrolysis activity.
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Binding of Tris to Bacillus licheniformis alpha-amylase can affect its starch hydrolysis activity.
Protein Pept Lett. 2008;15(2):212-4
Authors: Ghalanbor Z, Ghaemi N, Marashi SA, Amanlou M, Habibi-Rezaei M, Khajeh K, Ranjbar B
Bacillus licheniformis alpha-amylase (BLA) is routinely used as a model thermostable amylase in biochemical studies. Its starch hydrolysis activity has recently been studied in Tris buffer. Here, we address the question that whether the application of Tris buffer may influence the results of BLA activity analyses. Based on the inhibition studies and docking simulations, we suggest that Tr...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Ghalanbor Z, Ghaemi N, Marashi SA, Amanlou M, Habibi-Rezaei M, Khajeh K, Ranjbar B Tags: Protein Pept Lett Source Type: journals
Biophysical characterization of fibroblast growth factor homologous factor-1b (fhf-1b): sodium dodecyl sulfate promotes two state folding.
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Biophysical characterization of fibroblast growth factor homologous factor-1b (FHF-1b): sodium dodecyl sulfate promotes two state folding.
Protein Pept Lett. 2008;15(2):215-8
Authors: Dubey VK, Singh BK, Sarkar N, Pande M, Jagannadham MV
The current article describes the biophysical characterization and folding studies of fibroblast growth factor homologous factor-1b (FHF-1b) in comparison with acidic fibroblast growth factor (FGF-1). Our data indicates that FHF-1 is significantly more stable than FGF-1. The folding mechanism of these two proteins seems to be different although they share high degree of sequenc...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Dubey VK, Singh BK, Sarkar N, Pande M, Jagannadham MV Tags: Protein Pept Lett Source Type: journals
Preparation of a tat-related transporter peptide for carrying the adenovirus vector into cells.
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Preparation of a Tat-related transporter peptide for carrying the adenovirus vector into cells.
Protein Pept Lett. 2008;15(2):219-22
Authors: Kida S, Eto Y, Maeda M, Yoshioka Y, Nakagawa S, Hojo K, Tsuda Y, Mayumia T, Kawasaki K
We synthesized a Tat-related peptide acetyl-Gly-Arg-Lys-Lys-Arg-Arg-Gln-Arg-Arg-Arg-Pro-Pro-Gln-Gly-Cys amide, Ac-Tat(48-60)-Gly-Cys-NH(2), having high intracellular permeability, and conjugated this peptide to adenovirus vector to enhance gene transfer efficiency of adenovirus vector into cells. The peptide was prepared by the solid-phase peptide synthesis method and a bifunctional cro...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Kida S, Eto Y, Maeda M, Yoshioka Y, Nakagawa S, Hojo K, Tsuda Y, Mayumia T, Kawasaki K Tags: Protein Pept Lett Source Type: journals
Empirical parameters for estimating protein-protein binding energies: number of short- and long-distance atom-atom contacts.
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The number of atom-atom contacts in long distance can fit to the experimental binding energies in a dataset containing 151 experimental data with the correlation coefficient about 0.68. Based on this factor, a set of distance-dependent empirical potentials for various types of short-distance (2.4 A-5 A) contacts was obtained by guided fitting, i.e. a set of two parameters fitting. Incorporation of these short-distance potentials improved the correlation coefficients to 0.881.
PMID: 18289116 [PubMed - indexed for MEDLINE] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Li YC, Zeng ZH Tags: Protein Pept Lett Source Type: journals
Crystallization and preliminary x-ray analysis of anti-obesity peptide hormone oxyntomodulin.
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Oxyntomodulin is a proglucagon-derived gut hormone that reduces food intake and body weight, thus represents a potential therapy for obesity. We synthesized and crystallized oxyntomodulin. The crystal diffracts x-ray to 2.4 A resolution and belongs to space group P2(1)3 with unit-cell parameters a=b=c= 48.44 A, alpha=beta=gamma=90 degrees . Preliminary analysis indicates a trimer packing in one asymmetric unit.
PMID: 18289117 [PubMed - indexed for MEDLINE] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Li P, Rogers T, Smiley D, Dimarchi RD, Zhang F Tags: Protein Pept Lett Source Type: journals
Crystallization and preliminary x-ray studies of ton_0559, a putative member of the haloacid dehalogenase (had) superfamily from thermococcus onnurineus na1.
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Crystallization and preliminary X-ray studies of TON_0559, a putative member of the haloacid dehalogenase (HAD) superfamily from Thermococcus onnurineus NA1.
Protein Pept Lett. 2008;15(2):235-7
Authors: Nguyen CM, Lee HS, Cho Y, Lee JH, Ha SC, Hwang HY, Kim KK
To elucidate the molecular basis underlying their broad substrate specificity and reaction mechanism of the enzymes belonging to the haloacid dehalogenase (HAD) superfamily, TON_0559, a putative HAD subfamily protein from a hyperthermophilic archaeon Thermococcus onnurineus NA1, was expressed, purified and crystallized. X-ray diffraction data were collect...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Nguyen CM, Lee HS, Cho Y, Lee JH, Ha SC, Hwang HY, Kim KK Tags: Protein Pept Lett Source Type: journals
Host defense peptides and the new line of defence against multiresistant infections.
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Increasing antibiotic resistance has led to an urgent need for new therapeutic approaches. Host defense peptides are known to be antimicrobial and have revealed broad immunomodulatory functions for both innate and adaptive immunity. This review will focus on the role of host defense peptides in infection and immune response and discuss its potential and limitations as a future therapeutical agent.
PMID: 18336350 [PubMed - in process] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Hirsch T, Jacobsen F, Steinau HU, Steinstraesser L Tags: Protein Pept Lett Source Type: journals
Conformational studies suggest that the double stranded beta helix scaffold provides an optimal balance between protein stability and function.
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In this study, Bacillus subtilis quercetinase was used as a model system to understand the conformational determinants of functional diversity within the cupin fold. Controlled proteolysis experiments revealed that this enzyme is active, thermo-stable and maintains its quaternary arrangement even after substantial (ca 33 %) cleavage of the protein. The results presented in this manuscript thus show that the DSBH scaffold offers a novel balance between protein stability and function by locating the active site and substrate recognition features in the most stable region of the protein.
PMID: 18336351 [PubMed - in proces...
Source: Protein and Peptide Letters - July 3, 2008 Category: Biochemistry Authors: Rajavel M, Kulkarni NN, Gopal B Tags: Protein Pept Lett Source Type: journals
