Protein and Peptide Letters - Volume 20, Issue 10, 2013

Knowledge of structural classes is applied in numerous important predictive tasks that address structural and functional features of proteins, although the prediction accuracy of the protein structural classes is not high. In this study, 45 different features were rationally designed to model the differences between protein structural classes, among which, 30 of them reflect the combined protein sequence information. In ter Read More

Protein insertion sequences and their biological role in many organisms have been largely unknown. Here we study proteomes of 12 organisms of diverse genomes for insertion length and amino acid preferences. A total of 871 common proteins were catalogued amongst the 12 organisms for structure based sequence alignment. This underscores the key observations: (i) AT-richness seems to have no implication on the averag Read More

Kallikrein-related peptidases (KLKs) are trypsin-like and chymotrypsin-like serine proteases which are expressed in several tissues. Their activity is tightly controlled by inhibitors including members of the serine protease Kazal-type (SPINK) family. These enzymes are promising targets for the treatment of skin desquamation, inflammation and cancer. Spink3 or caltrin I is expressed in mouse pancreas and males accessory glan Read More

Classifying sequences is one of the central problems in computational biosciences. Several tools have been released to map an unknown molecular entity to one of the known classes using solely its sequence data. However, all of the existing tools are problem-specific and restricted to an alphabet constrained by relevant biological structure. Here, we introduce TRAINER, a new online tool designed to serve as a generic seq Read More

In this study, the problem of predicting interspecies transmission of avian influenza viruses (AIVs) was investigated with machine learning methods. We identified 87 signature positions in AIV protein sequences with information entropy method and encoded these positions with five amino acid factor scores (AAFactors) concentrated from 491 physicochemical and biochemical properties of amino acids. We constructed four pred Read More

We have developed a microwave (MW)-assisted peptide synthesis using Fmoc-amino acid nanoparticles in water previously. It is an organic solvent-free, environmentally friendly method for peptide synthesis. In this study, we have investigated the racemization of cysteine during an aqueous based coupling reaction with MW irradiation. Under our MW-assisted protocol using WSCI and DMTMM, the coupling reaction can be perf Read More

Thrombin, a highly specific protease of blood coagulation, has two exosites that modulate its specificity. We designed two sets of synthetic substrate FRET peptides with 25- or 11- amino acids (aa) each, based on the PAR 1 sequence, to characterize the effect of exosite 1 engagement on substrate catalysis and preference. The 25-aa set encompassed a sequence binding to exosite 1, and structural modeling showed that b Read More

Epstein-Barr virus (EBV) is a human oncogenic herpesvirus associating with several malignant diseases. Latent membrane protein 2 (LMP2) of EBV is considered to be an ideal candidate for immunotherapy or prophylactic EBV vaccine. We designed a LMP2 multiepitope containing T and B-cell epitope-rich peptides and constructed a recombinant plasmid containing mammalian codonoptimization EBV LMP2 multiepitope (pcDNA Read More

Ozone stress induces leaf injuries and yield losses in soybean. To identify the proteins associated with the stress response, ozone tolerant and sensitive cultivars were analyzed by 2D-PAGE. After 11 days of ozone stress unifoliate leaves of tolerant soybean cv. Enrei developed 15% and sensitive cv. Nakasennari developed 52% leaf injury symptoms. Analysis of proteins in the unifoliate leaves identified six proteins in toler Read More

The marine ecosystem is able to provide enormous biomolecule diversity that could be used for treatment of various diseases. In this highly competitive environment, organisms need chemical barriers to reduce or avoid microorganism contamination. Among the molecules that protect these animals the antimicrobial peptides (AMPs) are included. In the present study, crude extracts of coral coral specimens Carijoa riisei, Read More

A 64-kDa hemagglutinin from a Phaseolus vulgaris cultivar, the northeast red bean, was purified by a protocol composed of three chromatographic steps involving affinity chromatography on Affi-gel blue gel, cation exchange chromatography on SP-Sepharose and FPLC-gel filtration on Superdex 75. The purified hemagglutinin appeared as a single 32-kDa band in SDS-PAGE indicating its dimeric nature. The N-terminal amino acid s Read More

Hyriopsis cumingii (Lea, Unionidae), a freshwater bivalve species widely distributed in China and commercially exploited for freshwater pearl production, was chosen as the reference model to investigate the protein signature in the organic scaffold matching calcium carbonate crystallization mode. This study takes advantage of different calcium carbonate habits production by the organism: aragonite in shell an Read More

New methods for reliable quantitative analysis of biological network data are in high demand in today’s bioinformatics and systems biology. Here we demonstrate the applicability of the co-citation, developed earlier for the analysis of scientific literature for finding functionally similar nodes in protein-protein interaction networks in several model organisms. We prove the power of our approach in a novel way: the predicted clos Read More