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 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.

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, 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 feature with evolutionary (PSSM) and other structural information (secondary structure and solvent accessibility) significantly improves the predictions over existing methods. Using a multiple linear regression approach and 6-fold cross validation, our best model can achieve an overall correct rate of 87.8% and MCC of 0.47, with a specificity of 93.4%, correctly predict 52.4% of the RNA-binding residues for a dataset containing 107 non-homologous RNA-binding proteins. Compared with existing methods, including the amino acid compositions of structure neighbors lead to clearly improvement. A web server was developed for predicting RNA binding residues in a protein sequence (or structure), which is available at http://jeele.go.3322.org/RNA/.

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 stimuli between infected and non infected plants were tested.

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 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. membranifaciens.

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 glycoprotein, 20 kDa chaperonin, 50S ribosomal protein, and trypsin inhibitor were common to all three tissues. The sequence information obtained from the soybean proteome should be helpful in predicting the functions of unknown proteins.

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 virtual library screening. The putative binding mode for the antagonists served as the templates for pharmacophore modeling and a virtually generated library have been screened for novel A2AAR antagonist development.

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 spontaneous dissociation, where AFB1 acts as an inhibitor. Displacement of solution with substrate and AFB1 by the intact one enabled estimation of dissociation kinetics. The dissociation rate constant kdis was found 0.0047 ± 0.0005 s-1. The half time (t1/2) of complex dissociation was 146 s. The achieved data appoint at fact that AChE could allow to distribute aflatoxins in body instead acting as a scavenger. Analytical impact of study is discussed, too.

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-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 Pro conformer is the predominant conformation for the ground state in aqueous solution, which was also confirmed by the very weak signal of the cis Pro conformer in the spectroscopy. The aromatic side chains of residues 2 and 4 form an electrostatic interaction rather than 1 and 4. The results explain the low bioactivity before UV irradiation, and indicate the importance of the 1-4 electrostatic interaction for the activity of insect kinins.

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 studied compounds, confirming the applicability of the used spectral method for structural determination. The influence of the protonation on the IR-spectroscopic patterns of the both amino acids is discussed.

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 building blocks-conservative patterns.

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.

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.