Protein and Peptide Letters - Volume 14, Issue 6, 2007

Protein and Peptide Informatics offers enormous applications in deciphering of the molecular basis of diseases and in the discovery, design and delivery of biologically active and medicinally effective molecules. The past few decades have witnessed new horizons of research and a paradigm shift in drug designing strategies and technology development with promising achievements to leap ahead in the post-genomic era. This Read More

Phosphorylation by protein kinases is a very common and crucial process in many signal transduction pathways in eukaryotes. This review describes comparative protein kinase analysis of two apicomplexa Plasmodium falciparum (3D7 strain) and Plasmodium yoelii yoelii (17XNL strain) which are causative agents of malaria in human and African rat respectively. Sensitive bioinformatics techniques enable identification of Read More

The catalytic regions of Protein Kinases are known to have similarity in primary chains. However, it is not known whether there is a signature profile specific to a particular catalytic region? Whether the signature profile, if any, is unique to a protein kinases family in a particular species or in a group of species? We have attempted analyzing some of these aspects by statistical data mining using an authentic and exhaustive data Read More

P. falciparum encodes PfEMP-1 which is important in pathogenicity and virulence. We have analyzed the structure of the Duffy binding like (DBLα) domain of var genes and predicted the antigenic sites and T and B cell epitopes which present a highly variable picture with major implications in immune interactions and vaccine design.

Immunoinformatics provides tools for reverse vaccinology and encompasses development of knowledge bases and algorithms for prediction of epitopes. AgAbDb, a database archiving molecular interactions of antigen-antibody cocrystal structures, has been developed (http://202.41.70.51:8080/agabdb2/). Analyses of antibody-binding sites on proteins helped to fine-tune the parameters for prediction of Read More

Design and synthesis of peptide vaccines is of significant pharmaceutical importance. A knowledge based statistical model is fitted here for prediction of binding of an antigenic site of a protein or a B-cell epitope on a CDR (complementarity determining region) of an immunoglobulin. Linear analogues of the 3D structure of the epitopes are computed using this model. Extension for prediction of peptide epitopes from t Read More

Virus neutralizing MAb binding and T helper cell stimulating peptide epitopes from structural and nonstructural proteins of Japanese encephalitis virus were delineated. It was observed that priming by T helper peptides potentiated neutralizing antibody response against JE virus. Immunization with chimeric T helper - B cell peptides could thus protect mice from lethal challenge with JE virus.

Major Histocompatibility Complex (MHC) molecules are cell surface glycoproteins that are central to the process of immunity. MHC Class I and II molecules differ in their peptide binding specificity. In this study we have analyzed a non redundant set of MHC binding peptides derived from MHCPEP database, in terms of tripeptides and their positional preference. Results indicate that certain tripeptides have a preference to Read More

A key step in rational vaccine development is to understand how antigens are recognized by their receptors. Several crystal structures of MHC/HLA molecules are now available. We report a structural bioinformatics study of peptide- HLA complexes to derive features that generate recognition specificity, useful for guiding the design process.

We report here the 2.5Å structure of HIV-1 protease tethered-dimer ritonavir complex. The inhibitor bound in the active site has different conformations in the two orientations. There is only one hydrogen bond between the inhibitor and the enzyme. The conserved flap-water is not found in the present complex.

In the search for selectivity, the aspartic proteases are known to be a very difficult case because the enzymes of this family are not only sequentially but structurally also very similar. To gain insight into the selectivity and specificity of the aspartic proteases family we characterized the binding sites of four malarial aspartic protease (plasmepsin I, plasmepsin II, plasmepsin IV, P. vivax plasmepsin) and two human aspartic Read More

Glutathione S-transferase (GST) proteins play vital role in living organism that includes detoxification of exogenous and endogenous chemicals, survivability during stress condition. This paper describes a method developed for predicting GST proteins. We have used a dataset of 107 GST and 107 non-GST proteins for training and the performance of the method was evaluated with five-fold cross-validation technique. First a SV Read More

It is important to understand the conformational biases that are present in unfolded states to understand protein folding. In this context, it is surprising that even a short tripeptide like AFA samples folded/ordered conformation as demonstrated recently by NMR experiments of the peptide in aqueous solution at 280 K. In this paper, we present molecular dynamics simulation of the peptide in explicit water using OPLS-AA/L al Read More

Gastrin-releasing peptide (GRP) is a member of bombesin-like peptides and bombesin and neuromedin B are other members of this family. They act on receptors that belong to the GPCR superfamily and exert important physiological functions upon binding to their receptors. The biologically active C-terminal decapeptide of GRP (GRP10) was studied in explicit DMPC bilayers using molecular dynamics simulations. In the initial c Read More

The small Tims are chaperones that facilitate insertion of hydrophobic precursors into the inner mitochondrial membrane. We purified Tim12 and found it forms dimers that bind to Tim9. In this interaction, Tim12 undergoes structural changes that may be important for transport of its substrates in the mitochondrial carrier import pathway.

A dataset of experimentally characterized, human Golgi GlyTs with type II membrane topology was created. Based on the experimentally observed acceptor substrate preferences, the GlyTs were classified into five functional categories: biosynthesis of blood group antigens, glycolipids, N-glycans, O-glycans and glycosaminoglycans. The cytoplasmic, transmembrane and stem (CTS) regions were predicted and their length Read More

CD20, a B-cell-specific protein, is a primary target for immunotherapy of B-cell lymphomas. We used a mimotopes of CD20 to construct vaccines for B-cell-related disorders. The immunogenicity of the vaccines was tested in BALB/c mice. Results of this study suggest that the mimotope may be a useful tool for the construction of a functional vaccine to treat B cell-related disorders.

Pigment epithelium-derived factor (PEDF) is a potent inhibitor of angiogenesis, suggesting that loss of this factor may be involved in angiogenic eye disease. Here, we show that PEDF inhibits angiotensin II-induced smooth muscle cell proliferation through its anti-oxidative properties. Our present study suggests that PEDF may play a protective role against atherosclerosis.

S14G-humanin (S14G-HN) is one of the latest of a new family of neuropeptides with protective action against Alzheimer's disease insults. The structure of S14G-HN was studied with both spectroscopic techniques and molecular dynamics simulation. Secondary structure predictions and modeling of backbone conformation were carried out. Side chain reconstruction, homology modeling and molecular dynamics (MD) sim Read More