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369 records returned

Biochemical and Functional Properties of a Lectin Purified from Korean Large Black Soybeans - A Cultivar of Glycine Max.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, a 48-kDa lectin (KBL) was purified from Korean large black soybeans using liquid chromatography. The specific hemagglutinating activity of the KBL was 4096 titer/mg. EDTA-induced loss of hemagglutinating activity of KBL could be recovered by addition of Fe(3+) ions and some divalent cations as Ca(2+), Mn(2+), Fe(2+), Cu(2+), Zn(2+), and Pb(2+). Sugars such as D-(+)-galactose, D-(+)-raffinose, L-(+)-arabinose, alpha-D-(+)-melibiose, and alpha-lactose could inhibit the hemagglutinating activity of the lectin. Furthermore, the protein showed high thermal stability as well as stability over a wide range of pH va...
Source: Protein and Peptide Letters - September 1, 2009 Category: Biochemistry Authors: Fang EF, Wong JH, Lin P, Ng TB Tags: Protein Pept Lett Source Type: journals

Predicting Enzyme Subclasses by Using Support Vector Machine with Composite Vectors.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Based on enzyme sequence, using composite vectors with amino acid composition, low-frequency power spectral density, increment of diversity by combining a different form of pseudo amino acid composition to express the information of sequence, a support vector machine (SVM) for predicting enzyme subclasses is proposed. By the jackknife test, success rates of our algorithm are higher than other methods. PMID: 19645687 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - August 4, 2009 Category: Biochemistry Authors: Shi R, Hu X Tags: Protein Pept Lett Source Type: journals

Ribosome Display and Selection of Human Anti-placental Growth Factor scFv Derived from Ovarian Cancer Patients.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study highlights the ribosomal display technology for the selection of human antibody from patient-derived gene pools. PMID: 19645688 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - August 4, 2009 Category: Biochemistry Authors: Li F, Su P, Lin C, Li H, Cheng J Tags: Protein Pept Lett Source Type: journals

Furin Cleavage of Bacterial Expressed Glutathione-S-Transferase-Pro-Transforming Growth Factor beta1 Fusion Protein in vitro.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
To investigate the processing of transforming growth factor beta1 (TGFbeta1) pro-protein by furin protease we expressed a GST-pro-TGFbeta1 fusion protein in bacteria. Analysis of the furin digestion pattern revealed the liberation of 12.5 kDa TGFbeta1 monomers. There was no evidence for cleavage of an alternative furin site within the pro-protein. PMID: 19594430 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - July 15, 2009 Category: Biochemistry Authors: Kahle NA, Joffroy C, Popp SL, Knabbe C, Stope MB Tags: Protein Pept Lett Source Type: journals

Prediction of G-Protein-Coupled Receptor Classes in Low Homology Using Chou's Pseudo Amino Acid Composition with Approximate Entropy and Hydrophobicity Patterns.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We use approximate entropy and hydrophobicity patterns to predict G-protein-coupled receptors. Adaboost classifier is adopted as the prediction engine. A low homology dataset is used to validate the proposed method. Compared with the results reported, the successful rate is encouraging. The source code is written by Matlab. PMID: 19594431 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - July 15, 2009 Category: Biochemistry Authors: Gu Q, Ding YS, Zhang TL Tags: Protein Pept Lett Source Type: journals

Interaction of the Chaperone Calreticulin with Proteins and Peptides of Different Structural Classes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The interaction of calreticulin with native and denatured forms and polypeptides in proteolytic digests of proteins representing structural classes of all-alpha-helix (hemoglobin, serum albumin), all-beta-sheet (IgG) and alpha-helix + beta-sheets (lysozyme, ovalbumin) was investigated. The binding of calreticulin to denatured proteins was found to depend on conformation and structural class of the protein. No interaction was observed with the native proteins, whereas binding was seen for the denatured proteins, the order of interaction being lysozyme = IgG > ovalbumin >> hemoglobin = serum albumin. Moreover, t...
Source: Protein and Peptide Letters - July 15, 2009 Category: Biochemistry Authors: Duus K, Sandhu N, Jørgensen CS, Hansen PR, Steinø A, Thaysen-Andersen M, Højrup P, Houen G Tags: Protein Pept Lett Source Type: journals

Immunization with Peptide-Protein Conjugates: Impact on Benchmarking B-Cell Epitope Prediction for Vaccine Design.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Benchmarking B-cell epitope prediction for vaccine design is meaningful if based on empirical reference data pertaining to cross-reactivities of antipeptide antibodies with native protein antigens; yet it is complicated by such data acquired using antibodies raised against peptide-protein conjugates, as peptide-protein conjugation can differentially suppress antibody responses to peptide epitopes. PMID: 19594433 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - July 15, 2009 Category: Biochemistry Authors: Eugenio S, Caoili C Tags: Protein Pept Lett Source Type: journals

Production of Flavour Compounds from Fat During Cheese Ripening by Action of Lipases and Esterases.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The milk fat is an essential component for the development of correct flavour in cheese. The lipolysis and catabolism of fatty acids are two biochemical events very important on flavour development of some cheese varieties. The role and characteristics of various lipolytic agents during cheese ripening is reviewed and discused. PMID: 19508177 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Wolf IV, Meinardi CA, Zalazar CA Tags: Protein Pept Lett Source Type: journals

Distinction between Esterases and Lipases: Comparative Biochemical Properties of Sequence-related Carboxylesterases.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Carboxylesterases (Carboxyl ester hydrolase) include two groups of enzymes, namely non-specific esterases (EC 3.1.1.1) and lipases (EC 3.1.1.3) which have been early differentiated on the basis of their substrate specificity. Esterases hydrolyse solutions of water-soluble short acyl chain esters and are inactive against water-insoluble long chain triacylglycerols which, in turn, are specifically hydrolyzed by lipases. Based on the comparison of the primary structures, three families of sequence-related carboxylesterases, namely the lipoprotein lipase family (L-family), the hormone-sensitive lipase family (H-family) and...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Chahinian H, Sarda L Tags: Protein Pept Lett Source Type: journals

Use of Esterase Activities for the Detection of Chemical Neurotoxic Agents.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The quest for a quick and easy detection of the neurotoxin levels in the environment has fostered the search for systems alternative to currently employed analytical methods such as spectrophotometer, gas-liquid chromatography, thin-layer chromatography, and more recently mass spectrometry. These drawbacks lead to intense research efforts to develop biosensor devices for the determination of these compounds. In this review, we present an overview of the actual development of research in neurotoxin detection by using enzymatic biosensors based on esterase activity, in particular cholinesterases, and carboxylesterases. D...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Manco G, Nucci R, Febbraio F Tags: Protein Pept Lett Source Type: journals

Structure, Activities and Biomedical Applications of Human Butyrylcholinesterase.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Human butyrylcholinesterase (BuChE) is a serine enzyme present in most organs and plasma. No clear physiological function has yet been assigned to BuChE, but it is a pharmacologically and toxicologically important enzyme that plays a role in degradation of numerous ester-containing drugs and poisonous esters. Thus, BuChE-based bioscavengers are an alternative for prophylaxis and treatments of intoxications by these compounds. Also, BuChE has been integrated in biosensors for detection of organophosphorus compounds and other cholinesterase inhibitors. PMID: 19508180 [PubMed - as supplied by publisher] (Source: Prote...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Masson P, Carletti E, Nachon F Tags: Protein Pept Lett Source Type: journals

Human Carboxylesterases; an Update on CES1, CES2 and CES3.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Carboxylesterases belong to Phase I group of drug metabolizing enzymes. They hydrolyze a variety of drug esters, amides, carbamates and similar structures. There are five 'carboxylesterase' genes listed in the Human Genome Organization database. In this review, we will focus on the CES1, CES2 and CES3 genes and their protein products that have been partially characterized. Several variants of these three CESs result from alternate splicing, single nucleotide polymorphisms and multiple copy variants. The three CESs, are largely localized to tissues that are major sites of drug metabolism like the mucosa of the gastroint...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Sanghani SP, Sanghani PC, Schiel MA, Bosron WF Tags: Protein Pept Lett Source Type: journals

Conformational Stability of Esterase Enzymes from Different Sources.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In the last years we have performed a series of studies to characterize the conformational stability of three esterases from thermophilic and mesophilic sources: Aes esterase from Escherichia coli, EST2 from Alicyclobacillus acidocaldarius and AFEST from Archeoglobus fulgidus. These three esterases belong to the Hormone-sensitive lipase group of the superfamily of carboxylester hydrolases. The conformational stability of the three enzymes against temperature, urea and GuHCl has been determined by means of circular dichroism, fluorescence and differential scanning calorimetry measurements. Analysis of experimental data ...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Del Vecchio P, Graziano G, Barone G Tags: Protein Pept Lett Source Type: journals

Structural and Kinetic Overview of the Carboxylesterase EST2 from Alicyclobacillus acidocaldarius: A Comparison with the Other Members of the HSL Family.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Thermophilic and hyperthermophilic carboxylesterases (EC 3.1.1.1) are excellent model systems for studying structure function relationships as well as in vitro and in vivo evolution and possible biotechnological applications. In this paper we review the main aspect of one of most studied microbial representative of the hormone sensitive lipase family (HSL), namely carboxylesterase 2 (EST2) from Alicyclobacillus acidocaldarius. PMID: 19508183 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Mandrich L, Merone L, Manco G Tags: Protein Pept Lett Source Type: journals

Structure, Function and Applications of Carboxylesterases from Insects for Insecticide Resistance.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Carboxylesterases (EC 3.1.1.1) distribute broadly in insects, and play an important role in the metabolism with various functions. This paper reviews the insect carboxylesterases including the definitions and reaction mechanism, classification, structural context, functions especially on insecticide resistance, and its application. PMID: 19508184 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Yan S, Cui F, Qiao C Tags: Protein Pept Lett Source Type: journals

Cold-Adapted Esterases and Lipases: From Fundamentals to Application.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Micro-organisms that thrive at low temperatures produce cold-adapted enzymes which display high catalytic efficiency, generally associated with low thermal stability. In the recent past, researchers and industries have focused the attention on cold-adapted enzymes, whose peculiar properties make them particularly interesting either for investigating stability/flexibility relationships, or for their potential application in industrial processes. Among these enzymes, lipases and esterases, have potential utilisations in a broad range of biotechnological applications. In fact, these biocatalysts represent the most widely ...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Tutino ML, di Prisco G, Marino G, de Pascale D Tags: Protein Pept Lett Source Type: journals

Protein Engineering of Carboxyl Esterases by Rational Design and Directed Evolution.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In the past few years a considerable number of mutagenesis methods and high-throughput screening (HTS) systems have been developed and improved. In parallel computer programs or software packages for molecular modeling have be further investigated. Thus, the number of examples for successful directed evolution and rational design is increasing constantly. In this review the essential mutagenesis methods and HTS systems, especially for esterases, are described and various examples for the application of these protein engineering tools are provided. PMID: 19508186 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Schmidt M, Böttcher D, Bornscheuer UT Tags: Protein Pept Lett Source Type: journals

alpha/beta Hydrolase Fold; an Update.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The alpha/beta hydrolase superfamily has rapidly expanded in recent years and continues to do so at an expeditious pace. According to the ESTHER database (http://bioweb.ensam.inra.fr/ESTHER) 29000 papers have been published cataloguing 89 family groups, comprising a total of 15438 gene loci and 666 structures. This paper presents a snapshot of the current family taxonomy, catalytic chemistries, structural topologies and useful technologies emerging from the knowledge base at the current time. PMID: 19508187 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Carr PD, Ollis DL Tags: Protein Pept Lett Source Type: journals

Evaluation of Aflatoxin B1 - Acetylcholinesterase Dissociation Kinetic Using the Amperometric Biosensor Technology: Prospect for Toxicity Mechanism.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Aflatoxins are group of secondary metabolites from moulds. The main toxic effect of alfatoxins on body is based on metabolic activation on cytochrome P450 system. Recently, some studies appointed at anticholinergic properties of aflatoxins and inhibition of acetylcholinesterases (AChE) was described. Inhibition is reversible; however, some questions arose. Is the interaction firmly enough to prevent distribution of aflatoxins in body? Could be AChE considered as a scavenger of aflatoxins? Amperometric biosensor with immobilized acetylcholinesterase was used for evaluation of aflatoxin B1 (AFB1) - AChE complex spontaneo...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Pohanka M, Musilek K, Kuca K Tags: Protein Pept Lett Source Type: journals

Properties of a Kunitz-type trypsin inhibitor from Delonix regia seeds against digestive proteinases of Anagasta kuehniella (Z.) and Corcyra cephalonica (S.) (Lepidoptera: Pyralidae).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
DrTI was effective against trypsin-like enzymes from A. kuehniella and C. cephalonica, however an artificial diet was insufficient to affect the survival and body weight of either insect. The inhibitor stimulated chymotrypsin-like enzymes and probably induced the synthesis of enzymes insensitive to TLCK in neonate larvae. PMID: 19508189 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Macedo ML, Pando SC, Chevreuil LR, Marangoni S Tags: Protein Pept Lett Source Type: journals

A Designed beta-Hairpin Forming Peptide Undergoes a Consecutive Stepwise Process for Self-assembly into Nanofibrils.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We used a de novo designed, beta-hairpin forming T1 peptide as a model to investigate the kinetics of peptide fibrogenesis by a combination of light scattering (LS), circular dichroism (CD), fluorescence, and atomic force microscopy (AFM). The results demonstrate that the T1 fibrogenesis undergoes a consecutive stepwise process, with a high degree of cooperation, presenting sigmoidal time-courses of the peptide aggregation, the subsequent conformational conversion of the backbone, and the peptide sidechains' rearrangement. We suggest that the conformational conversion was initiated after the peptide aggregates reach a ...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Wang C, Sha Y Tags: Protein Pept Lett Source Type: journals

Efficient Expression of Aquaporin Z in Escherichia coli Cell-free System Using Different Fusion Vectors.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Aquaporin Z (AqpZ) is a typical orthodox aquaporin with 6 transmembrane domains and five connecting loops. In order to express this complex membrane protein efficiently, E. coli cell-free expression system was employed as an alternative to produce aquaporin Z. Using different fusion vectors containing AqpZ gene, the expression level of fusion proteins in cell-free system varied from 7.97 to 578.35 microg/ml, while 7.34 to 340.81 microg/ml for target protein (AqpZ). The free energy of mRNA secondary structure at translation initiation region (TIR) was predicted and demonstrated a positive relationship with the expressio...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Xu Z, Lian J, Cai J Tags: Protein Pept Lett Source Type: journals

Dynamic Kinetic Resolution of N-Benzoyl-DL-amino Acids via Peptide Bond Forming Reactions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Dynamic kinetic resolution (DKR) was demonstrated in the carbodiimide-mediated couplings of N-benzoyl-DL-amino acids with L-amino acid esters: the yields of the D-L-peptides significantly exceeded 50% in some cases. N-Benzoyl-DL-t-leucine afforded the D-L-peptide almost exclusively (up to 96% yield) in the reaction with methyl L-prolinate, which is the most efficient DKR obtained in the field of amino acids and derivatives. PMID: 19508192 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Miyazawa T, Hamada T Tags: Protein Pept Lett Source Type: journals

Identification of a Cell-Bound Extracellular Protease Overproduced by Sulfolobus Solfataricus in Peptide-Rich Media.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A new protease, named SsMTP was identified from the archeon Sulfolobus solfataricus. The enzyme is associated to the cell-membrane and over-produced in response to the peptide-enriched media. SsMTP has a molecular mass of 120 kDa showing optimal activity at pH 2.0 in the temperature range 70 - 90 degrees C, and a half-life of 20 days at 80 degrees C. Primary structure analysis revealed that SsMTP represents a novel type of multi-domain thermopsin-like protease containing the catalytic domain followed by two distinct domains, PKD and Y_Y_Y, which are usually involved in a range of protein-protein interactions among the ...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Cannio R, Catara G, Fiume I, Balestrieri M, Rossi M, Palmieri G Tags: Protein Pept Lett Source Type: journals

Exploring the Structural Stability of a Potential Antifungal Peptide Through Computational Analysis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We analyzed 27 antifungal peptides (AFPs) to understand their stability by various parameters like, stabilization centers, GROMOS, OPLS and FOLDEF force fields. Subsequently, we propose that AFP, NK-Lysin could be considered a potential candidate and also could act as a template for designing the therapeutic peptide drug against pathogenic fungi. PMID: 19508194 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Rajasekaran R, Rao S Tags: Protein Pept Lett Source Type: journals

TNF-alpha and Ghrelin: Opposite Effects on Immune System, Metabolism and Mental Health.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Tumor necrosis factor-alpha (TNF-alpha) is a glycoprotein hormone with important functions in inflammation and apoptosis. It plays a significant role as a pro-inflammatory cytokine in the defense against viral, bacterial and parasitic infections and autoimmune disorders. Furthermore, it influences energy homeostasis and has an anorexigenic effect on the hypothalamus. TNF-alpha has also been shown to be involved in the pathogenesis of psychiatric disorders such as depression or narcolepsy. Ghrelin is a peptide hormone which primarily regulates eating behavior through modulation of expression of orexigenic peptides in th...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Himmerich H, Sheldrick AJ Tags: Protein Pept Lett Source Type: journals

Synthesis of 4-Amino-thiazole Analogs of Fmoc-amino Acids and Thiazole Linked N-Orthogonally Protected Dipeptidomimetics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We report a one pot synthesis of Fmoc amino acid derived 4-amino-thiazole derivatives and thiazole linked N-orthogonally protected dipeptidomimetics by the condensation of N(alpha)-Fmoc alpha-halomethylketones with thiourea and Boc/Z-alpha-amino acid thioamides via modified Hantzch protocol. Side chain modified Fmoc amino acids containing 4-amino thiazole moiety have also been synthesized following the similar protocol. PMID: 19508196 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Narendra N, Vishwanatha TM, Sudarshan NS, Sureshbabu VV Tags: Protein Pept Lett Source Type: journals

Studies on an Antifungal Protein and a Chromatographically and Structurally Related Protein Isolated from the Culture Broth of Bacillus amyloliquefaciens.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
An antifungal protein with multiple stable biological activities unaffected by chemical modification of tyrosine and tryptophan, and a protein with N-terminal sequence and molecular mass resemblance but no identifiable activities were isolated from culture broth of Bacillus amyloliquefaciens. The findings are analogous to previous reports on thaumatin and thaumatin-like proteins. PMID: 19508197 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Wong JH, Ng TB Tags: Protein Pept Lett Source Type: journals

Evaluation of Protein Phosphorylation Site Predictors.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we selected six recently published methods (DISPHOS, NetPhosK, PPSP, KinasePhos, Scansite and PredPhospho) to evaluate their performance. First, we compiled three testing datasets containing experimentally verified phosphorylation sites for mammalian, Arabidopsis and rice proteins. Then, we present the prediction performance of the tested methods on these three independent datasets. Rather than quantitatively ranking the performance of these methods, we focused on providing an understanding of the overall performance of the predictors. Based on this evaluation, we found the following results: i) current phos...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Que S, Wang Y, Chen P, Tang Y, Zhang Z, He H Tags: Protein Pept Lett Source Type: journals

Solution Structure of a Photo-switchable Insect Kinin Thioxo-analog.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The photo-switchable insect kinin thioxo-analog Phe(1)-Tyr(2)-Psi[CS-N]-Pro(3)-Trp(4)-Gly(5)-NH(2) (Psi[CS-N](2)-Kinin) can change from ground state to photo-stationary state by following a pulse of UV radiation and its bioactivity increases simultaneously. To investigate the conformation-activity relationship, the solution structure of its ground state was determined by two-dimensional NMR spectroscopy. In contrast, the photo-stationary state could not be determined because of its relatively fast thermal reisomerization. The molecular dynamics-calculated structures based on NMR constraints demonstrate that the trans P...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Cong Z, Huang Y, Yang L, Ye D, Dong S Tags: Protein Pept Lett Source Type: journals

Salt-assisted Religation of Proteolyzed Glutathione-S-transferase Follows Hofmeister Series.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Proteases have been used not only for proteolysis but also in organic solvent-assisted religation processes. Here, we demonstrated the effect of salts on peptide bond resynthesis in Glutathione-S-transferase (GST) and have found it to be in the purview of the Hofmeister phenomena. Our results show that the efficiency and ease of religation increases with an increase in the surface charge densities of the cations used in the study. Thus, the yield of religated GST follows the order: Mg2(+)>Li(+)>Na(+)>K(+). Characteristics of the salt-religated GST were studied using size exclusion chromatography, C...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Kishan KV, Sharma A Tags: Protein Pept Lett Source Type: journals

Annotation of Non-synonymous single Polymorphisms in Human Liver Proteome by Mass Spectrometry.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A novel strategy to annotate nsSNP-peptides in human liver proteome based on LC-ESI-MS/MS and peptide database search was proposed. Totally 115 nsSNP-peptides in human liver proteins were annotated using our method. Among them, 42 peptides were found to be amino acid mutation, 73 peptides were wild type, 5 peptides were interpreted with both mutation and wild type. The function of nsSNP-peptide was predicted using SIFT algorithm, and 2 nsSNPs were predicted to be damaged for protein function. The results here show that the strategy is very effective for annotation of nsSNP at peptide level. PMID: 19508201 [PubMed -...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Chen M, Yang B, Ying W, He F, Qian X Tags: Protein Pept Lett Source Type: journals

Improve the Prediction of RNA-binding Residues Using Structural Neighbours.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The interactions between RNA-binding proteins (RBPs) with RNA play key roles in managing some of the cell's basic functions. The identification and prediction of RNA binding sites is important for understanding the RNA-binding mechanism. Computational approaches are being developed to predict RNA-binding residues based on the sequence- or structure-derived features. To achieve higher prediction accuracy, improvements on current prediction methods are necessary. We identified that the structural neighbors of RNA-binding and non-RNA-binding residues have different amino acid compositions. Combining this structure-derived...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Li Q, Cao Z, Liu H Tags: Protein Pept Lett Source Type: journals

Predicting Subcellular Localization of Gram-negative Bacterial Proteins by Linear Dimensionality Reduction Method.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
With the rapid increase of protein sequences in the post-genomic age, the need for an automated and accurate tool to predict protein subcellular localization becomes increasingly important. Many efforts have been tried. Most of them aim to find the optimal classification scheme and less of them take the simplifying the complexity of biological system into consideration. This work shows how to decrease the complexity of biological system with linear DR (Dimensionality Reduction) method by transforming the original high-dimensional feature vectors into the low-dimensional feature vectors. A powerful sequence encoding sch...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Wang T, Yang J Tags: Protein Pept Lett Source Type: journals

Arginyl Aminopeptidase-like 1 (RNPEPL1) is an Alternatively Processed Aminopeptidase with Specificity for Methionine, Glutamine, and Citrulline Residues.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A previously uncharacterized member of the M1 family of zinc metallopeptidases, arginyl aminopeptidase-like 1 (RNPEPL1; EC 3.4.11.1), was cloned and expressed, and the recombinant enzyme characterized. RNPEPL1 was a broad specificity aminopeptidase with preference for a P1 methionine, glutamine, or citrulline residue, and exhibited a broad pH preference, with maximal activity observed between pH 6.6 and 8.0. The enzyme was inhibited by calcium ions but unaffected by chloride ions, and was insensitive to specific inhibitors of the closely-related arginyl aminopeptidase, indicating similarity to leukotriene A(4) hydrolas...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Thompson MW, Beasley KA, Schmidt MD, Seipelt RL Tags: Protein Pept Lett Source Type: journals

Investigating the Effect of Temperature on Transient Partial Unfolding by Proteolysis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Protein inactivation frequently occurs through partially unfolded states under native conditions, and temperature is an important parameter that affects the susceptibility of proteins to inactivation. While the effect of temperature on global unfolding is well documented, however, experimental characterizations of the temperature effect on partial unfolding are rare. Proteolysis offers a valuable chance to investigate the temperature effect on partial unfolding. By investigating proteolysis kinetics, the energetics of the partially unfolded state responsible for proteolysis (the cleavable state) can be studied. E. coli...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Youn K, Park C Tags: Protein Pept Lett Source Type: journals

Effects of Peptidic Antagonists of Grb2-SH2 on Human Breast Cancer Cells.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The growth factor receptor-bound protein Src homology 2 (Grb2-SH2) plays an important role in the oncogenic Ras signaling pathway, which involves in cell proliferation and differentiation. Therefore, the antagonist of Grb2-SH2 has become a potential target for developing anticancer agents. Recently, we discovered a peptide 1 (Fmoc-Glu-Tyr-Aib-Asn-NH(2)) with high affinity for the Grb2-SH2 domain by using surface plasmon resonance (SPR)-biosensor technology. Herein, we report the further design of the lead peptide 1 by addition of an Arg-Gly-Asp sequence to 1 to enhance binding to Grb2-SH2 and inducing apoptosis in canc...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Chen CH, Chen MK, Jeng KC, Lung FD Tags: Protein Pept Lett Source Type: journals

Novel Antimicrobial Peptides Isolated from Skin Secretions of the Mexican Frog Hyla Eximia.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this work, we describe the original characterization of peptides and proteins present in the skin secretions of the Mexican amphibian Hyla eximia. To this purpose, a novel water/dark extraction method, as well as the classic electrical stimulation procedure, was applied in order to extract the skin secretion. Two novel antimicrobial peptides He-1 and He-2 were sequenced. In addition, a molecular mass fingerprint revealed more than one hundred different molecules. Eight peptides in homogeneous form were assayed against five species of bacteria. Thereafter, the peptide He-2 demonstrated high antiparasitic activity aga...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Villa-Hernández O, Hernández-Orihuela L, Del Carmen Rodríguez M, Zamudio-Zuñiga F, Castro-Franco R, Pando V, Batista CV Tags: Protein Pept Lett Source Type: journals

Quantitative Prediction of Critical Amino Acid Positions for Protein Folding.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The MIR algorithm provides an ab initio prediction of a protein's core residues. An improved version, the MIR2, is presented and validated on 3203 proteins from PDB. Structures are decomposed in Closed Loops, their limits constituting the observed core residues. They are predicted by MIR2 with an accuracy approaching 80%. PMID: 19508208 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Thireou T, Atlamazoglou V, Papandreou NA, Lonquety M, Chomilier J, Eliopoulos E Tags: Protein Pept Lett Source Type: journals

Stability, Subunit Interactions and Carbohydrate-Binding of the Seed Lectin from Pterocarpus Angolensis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
From 1 kg of defatted Pterocarpus angolensis (mukwa tree) seed meal, 21.6 grams of an alpha,D-mannose/glucose-specific lectin can be purified on mannose-Sepharose. Relative affinities for several (oligo)saccharides and glycoproteins were studied by haemagglutination-inhibition. Gel filtration shows that the lectin exists as a dimer above pH 5 and as a monomer below pH 3.5. This is confirmed by studies on the release of lectin subunits that were adsorbed from solution to lectin monomers immobilized onto Eupergit-c. From the gel filtration patterns it is calculated that a residue with pK(a) of about 4.4 is involved in di...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Echemendia-Blanco D, Van Driessche E, Ncube I, Read JS, Beeckmans S Tags: Protein Pept Lett Source Type: journals

Molecular Modeling of Human BAD, a Pro-apoptotic Bcl-2 Family Member, Integrating Glycolysis and Apoptosis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Comparison between the BAD complexes indicated that BAD all docks a hydrophobic surface of PKAc regardless of its phosphorylation. PKAc may prevent Bcl-xL from rebinding to BAD by phosphorylating human BAD at Ser118; whereas human BAD is phosphorylated on Ser75 in a BAD-Bcl-xL complex, resulting in the dissociation of BAD. PMID: 19508210 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Yang J Tags: Protein Pept Lett Source Type: journals

A Novel Approach to Predict Protein-Protein Interactions Related to Alzheimer's disease Based on Complex Network.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A protein domain interaction prediction program was complied using C(++) to predict whether a query protein could interact with other hub proteins. It is indicated that the proteins interacting with AATF (Apoptosis-Antagonizing Transcription Factor) possess a common conservative pattern: I-x(0,1)-E-x(2)-[A/E/N/T]-x-[E/K]. Our method is attempted to integrate the characteristics of protein interaction network with the simplest building blocks-conservative patterns. PMID: 19508211 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Jiang XF, Yang J Tags: Protein Pept Lett Source Type: journals

Analyses of the Proteomes of the Leaf, Hypocotyl, and Root of Young Soybean Seedlings.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The functions of organs in young soybean seedling were determined by means of proteomic analysis. Extracts from leaves, hypocotyls, and roots were separated by two-dimensional polyacrylamide gel electrophoresis, and the proteins were identified by mass spectrometry and protein sequencing. The identified proteins were categorized into various groups according to their function. The leaf was abundant in proteins associated with energy production (50.0%), the hypocotyl was rich in defense proteins (31.8%), and the root contained defense-related proteins (16.7%) and destination and storage proteins (26.7%). Stem 31-kDa gly...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Afroz A, Hashiguchi A, Khan R, Komatsu S Tags: Protein Pept Lett Source Type: journals

Isolation and Partial Characterization of a Novel Lipid Transfer Protein (LTP) and Antifungal Activity of Peptides from Chilli Pepper Seeds.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The aims of this study were to isolate and characterize peptides present in chilli pepper seeds and evaluate their antifungal activities. An isolated peptide closer to 9 kDa showed high sequence homology to the antimicrobial peptide lipid transfer protein. The peptide fraction containing the LTP inhibited the growth of the fungi, Fusarium oxysporum, Colletotrium lindemunthianum, the yeasts, Saccharomyces cerevisiae, Pichia membranifaciens, Candida tropicalis, Candida albicans, inhibited glucose-stimulated acidification of the medium by yeast cells of S. cerevisiae and caused several morphological changes in P. membrani...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Cruz LP, Ribeiro SF, Carvalho AO, Vasconcelos IM, Rodrigues R, Da Cunha M, Gomes VM Tags: Protein Pept Lett Source Type: journals

Molecular Dynamics of Some Pentapeptides Having a Strong Tendency to Helical Conformation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Some pentapeptides with higher alpha-helical tendency possess typical sequence pattern, such as "+ - + + - - +", "+ - - + - - +", "+ - + - - - +", and "- + + - - - +" ( "+" = D,N,E,Q,K,R,T,C, or H; "-" = L,I,V, or A), especially symmetrical motifs (a pair of reverse sequences beside palindromic segments), such as ALALA, QQAQE/EQAQQ, and REALE/ELAER, hint that the nascent peptide can fold a certain conformation in a two-way folding fashion. PMID: 19508214 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Huang ZR, Zhu TY, Wang TT, Wang XN, Yang J Tags: Protein Pept Lett Source Type: journals

The In situ Structural Characterization of the Influenza A Virus Matrix M1 Protein within a Virion.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The first attempt has been made to suggest a model of influenza A virus matrix M1 protein spatial structure and molecule orientation within a virion on the basis of tritium planigraphy data and theoretical prediction results. Limited in situ proteolysis of the intact virions with bromelain and surface plasmon resonance spectroscopy study of the M1 protein interaction with lipid coated surfaces were used for independent confirmation of the proposed model. PMID: 19508215 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Shishkov AV, Bogacheva EN, Dolgov AA, Chulichkov AL, Knyazev DG, Fedorova NV, Ksenofontov AL, Kordyukova LV, Lukashina EV, Mirsky VM, Baratova LA Tags: Protein Pept Lett Source Type: journals

Regulation of Endochondral Ossification by Osteogenic Growth Peptide C-terminal Pentapeptide [OGP(10-14)].Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In neonatal rat metatarsal organ culture, a bell-shaped dose-related curve in length of mineralized area, increases in the height of proliferative and hypertrophic zones, in the number of hypertrophic chondrocyte and in the amount of Runx2 mRNA, were revealed after treatment with OGP(10-14). We conclude that OGP(10-14) accelerates bone growth. PMID: 19508216 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Chen Z, Chang M, Peng Y, Zhao L, Zhan Y, Wang L, Wang R Tags: Protein Pept Lett Source Type: journals

Invertase from Hyper Producer Strain of Aspergillus niger: Physiochemical Properties, Thermodynamics and Active Site Residues Heat of Ionization.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Here we report for the first time heat of ionization of invertase (E.C.3.2.1.26) active site residues from hyper-producer strain of Aspergillus niger (34.1 U ml(-1)), along with its physiochemical properties, kinetics and thermodynamics of stability-function. The Invertase showed great potential for industry as being highly efficient (k(cat) = 24167 s(-1) at 65 degrees C, pH 5.0) and stable (half life= 12 h at 56 degrees C). PMID: 19508217 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Nadeem H, Rashid MH, Riaz M, Asma B, Javed MR, Perveen R Tags: Protein Pept Lett Source Type: journals

Insulin-binding Canavalin is Present in Canavalia ensiformis Seed Coat.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
An insulin-binding protein was isolated from Canavalia ensiformis seed coat, by using an insulin-Sepharose 4B affinity chromatography, and the protein was identified as canavalin (Canavalia 7S globulin) by mass spectrometry analysis. The major novelty of these data is the acidic nature of this globulin insulin-binding, in contrast to the basic Bg-like insulin-binding proteins so far reported in plants. PMID: 19508218 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters)
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Ribeiro ES, Uchôa AF, da Silva LG, Beghini DG, Ferreira AT, Perales J, Fernandes KV, Jacinto T, Xavier-Filho J, Oliveira AE Tags: Protein Pept Lett Source Type: journals

Overlapping Double Turn Conformations Adopted by Tetrapeptides Containing Non-coded alpha-Amino Isobutyric Acid (Aib) and Formation of Tape-like Structures Through Supramolecular Helix Mediated Self-assembly.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Single crystal X-ray diffraction studies and solvent dependent (1)H NMR titrations reveal that a set of four tetrapeptides with general formula Boc-Xx(1)-Aib(2)-Yy(3)-Zz(4)-OMe, where Xx, Yy and Zz are coded L-amino acids, adopt equivalent conformations that can be described as overlapping double turn conformations stabilized by two 4-->1 intramolecular hydrogen bonds between Yy(3)-NH and Boc C=O and Zz(4)-NH and Xx(1)C=O. In the crystalline state, the double turn structures are packed in head-to-tail fashion through intermolecular hydrogen bonds to create supramolecular helical structures. Field emission scanning e...
Source: Protein and Peptide Letters - June 28, 2009 Category: Biochemistry Authors: Kar S, Dutta A, Drew MG, Koley P, Pramanik A Tags: Protein Pept Lett Source Type: journals