Protein and Peptide Letters - Volume 17, Issue 3, 2010

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 Read More

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 RNAbinding mechanism. Computational approaches are being developed to predict RNA-binding residues based on the sequence- or structure-derived features. To achieve higher prediction accuracy, improvemen Read More

Using Phaseoleae defensins available in databases, a putative defensin gene was isolated in cowpea (Vigna unguiculata (L.) Walp.) and cloned from genomic cowpea DNA. The putative mature defensin sequence displays the characteristic defensins residues arrangement, secondary and tertiary structures were predicted and splicing analysis was performed. Using RT-PCR, defensin expression and differences in response to biotic Read More

Bryothamnion seaforthii lectin (BSL) induced reversible concentration-related relaxation of endothelized aorta, maximal at 30μg/ml (IC50= 4.8 ± 0.6μg/ml). This effect was inhibited by L-NAME and reversed by mucin, probably via interaction with a specific lectin-binding site on the endothelium activating nitric oxide synthase.

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 me Read More

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 Read More

A2A adenosine receptor (A2AAR) antagonists are considered to be useful in cancer immunotherapy and vaccines and as potential drugs for the treatment of Parkinson's disease. To better understand the chemical features responsible for the recognition mechanism and the receptor-ligand interaction, we performed the molecular docking study using selective A2AAR antagonists and combined with a pharmacophore based v Read More

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 aflatoxi Read More

The photo-switchable insect kinin thioxo-analog Phe1-Tyr2-ψ[CS-N]-Pro3-Trp4-Gly5-NH2 (ψ[CS-N]2-Kinin) can change from ground state to photo-stationary state by following a pulse of UV irradiation 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-stati Read More

Spectral investigation including IR-characteristic bands assignment of the amino acids zwitterions L-Valine (LVal) and L-Proline (L-Pro) was carried out by linear-dichroic infrared (IR-LD) spectroscopy of oriented solid sample as a nematic liquid crystal suspension. The obtained experimental IR-LD results (transition moment directions) were compared with known crystal X-ray data for molecules orientation in the unit cells of the stu Read More

Human cystathionine β-synthase (CBS) is a pyridoxal 5'-phosphate (PLP) dependent hemoprotein, which catalyzes the condensation of serine and homocysteine. Our mutagenesis studies suggest that Arg-266 is important to sense structural changes in heme-binding site, and that Gln-222 as well as Tyr-223 are involved in interactions with substrates.

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 Read More

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-wa Read More

An endonuclease from Xanthomonas oryzae pathovar oryzae KACC 10331, XorKI, was heterologously produced in Escherichia coli by applying the stationary state induction method. The yield was 5.4 mg of XorKI per liter of LB medium. XorKI existed in multiple oligomeric forms as evidenced by gel filtration chromatography. The specific activity of purified XorKI was 323000 units per mg.

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.

In the presence of ginkgolides A and B a recombinant human prion protein (90-231) is more susceptible to proteolysis, which is characteristic for the non-infective form of prion proteins and more thermostable than in the absence of ginkgolides. Probably, ginkgolides exert a neuroprotective effect through a rearrangement of the prion structure.

The search for potential inhibitors that target so far unexplored bacterial enzyme mono-N-succinyl-L,Ldiaminopimelic acid desuccinylase (DapE) has stimulated a development of methodology for quick and efficient preparation of mono-N-acylated 2,6-diaminopimelic acid (DAP) derivatives bearing the different carboxyl groups or lipophilic moieties on their amino group.