Protein and Peptide Letters - Volume 14, Issue 7, 2007

This is the second and concluding part of the special issue of “Protein Peptide Letters” which presents some state-of-the art contributions in multi-dimensional research at the interface of Protein Peptide Informatics and Drug Designing. The first part focused at specific experimental and computational studies on Protein Kinases, GRPs, and peptide based vaccine designs and structuralbinding properties of several drug tar Read More

Among secondary structure elements, β-turns are ubiquitous and major feature of bioactive peptides. We analyzed 77 biologically active peptides with length varying from 9 to 20 residues. Out of 77 peptides, 58 peptides were found to contain at least one β-turn. Further, at the residue level, 34.9% of total peptide residues were found to be in β- turns, higher than the number of helical (32.3%) and β-sheet residues (6.9%). So, Read More

We report here an all-atom energy based Monte Carlo docking procedure tested on a dataset of 226 proteinligand complexes. Average root mean square deviation (RMSD) from crystal conformation was observed to be ∼ 0.53 Å. The correlation coefficient (r2) for the predicted binding free energies calculated using the docked structures against experimental binding affinities was 0.72. The docking protocol is web-enabled as Read More

Protein sequences vary in their length and are not readily amenable to conventional data mining techniques that need mapping in a fixed dimensional space. Thus, majority of the current methods for protein sequence classification are based on alignment of the query sequence either with a sequence or a profile of the sequence family. We present a method for mapping of protein sequences in a fixed dimensional desc Read More

Classification of newly determined protein structures is important in understanding their function and mechanism of action. Currently available methods employ a global structure alignment strategy and are computationally expensive. We propose a two-step methodology with a quick screen to significantly reduce the number of candidate structures followed by global structure alignment of the query structure with the reduce Read More

Transitions in amino-acid conformation angles tend to accompany various structural modifications in protein structures. Thus, to benefit the modeling of protein structures, the Conformation Angles DataBase (CADB-3.0) has been updated to visualize the conformational angles in varied regions (fully, generously, additionally and disallowed regions). In addition, options are provided to display the angles in the secondary st Read More

The Ramachandran plot displays the main chain conformation angles ( and Ψ) of the polypeptide chain of a protein molecule. The paper reports the updated version of the Ramachandran plot web server and has several improved options for displaying the conformation angles in various regions. In addition, options are provided to display the conformation angles in various secondary structural elements and regions within Read More

Using a data set of 454 crystal structures of peptides and 80 crystal structures of non-homologous proteins solved at ultra high resolution of 1.2 Å or better we have analyzed the occurrence of disallowed Ramachandran (, Ψ) angles. Out of 1492 and 13508 non-glycyl residues in peptides and proteins respectively 12 and 76 residues in the two datasets adopt clearly disallowed combinations of Ramachandran angles. These exa Read More

Lectins are carbohydrate binding proteins with important roles in many biological processes such as adhesion. Here we have identified 11 potential lectins from Mycobacterium tuberculosis H37Rv genome, using a comprehensive bioinformatics analysis, which will provide helpful clues in molecular mapping of pathogenesis and perhaps also serve as potential drug targets.

We have identified four repeats and five domains that are novel in proteins encoded by the Pyrobaculum aerophilum str. IM2 proteome using automated in silico methods. A “repeat” corresponds to a region comprising less than 55 amino acid residues that occurs more than once in the protein sequence and sometimes present in tandem. A “domain” corresponds to a conserved region comprising greater than 55 amino Read More

PrTX-I, a non-catalytic and myotoxic Lys49-PLA2 from Bothrops pirajai venom has been crystallized alone and in complex with bromophenacyl bromide (BPB), α-tocopherol and α-tocopherol acetate inhibitors. These crystals have shown to diffract X-rays between 2.34 and 1.65 Å resolution. All complexes crystals are isomorphous and belong to the space group P21 whereas native PrTX-I crystals belong to the P3121.

Temporin-1Vb, -1Oe, -1DRb, and -1TGb (10-8 - 10-6M) produced significant (p<0.05) and concentrationdependent stimulatory effects on insulin secretion from clonal rat BRIN-BD11 cells without increased release of lactate dehydrogenase. Temporin-1Va and temporin-1Vc (10-8 - 10-6M) also stimulated insulin-release but were cytotoxic at 10-6M. Temporin-1DRa was without effect. The temporins at 10-7 M had no effect on intr Read More

Leptin plays an important role in the regulation of food intake and thermogenesis, regulates long term energy balance and reproductive function and its concentrations are closely linked to body mass index. Leptin secretion is influenced by many factors and the age-related changes in different hormones might modify circulating leptin concentrations. Sex dimorphism in leptin concentrations has been clearly shown in pr Read More

We present the observation of separated protein bands after polyacrylamide (PAA) gel electrophoresis based on the staining-free detection of their ultra violet (UV)-induced fluorescence employing deep UV confocal fluorescence microscopy. Mixtures of the three biological compounds β-Galactosidase (from Escherichia coli), apo-Transferrin (bovine) and bovine serum albumin (BSA) have been separated and a staining fre Read More

Free radicals induce protein modifications, often associated to many biological phenomena. This mini-review overviews the approaches we have used to elucidate the radical-induced damages on sulfur-containing enzymes, such as ribonuclease and lysozyme, and the possible post-translational mechanism of the damage to another cell compartment, such as lipid domain.

The process of nucleocytoplasmic exchange of various macromolecules and metabolites between the nuclear and cytoplasmic compartment is crucial for cell function and survival. It is also closely involved with several pathogeneses including cancer and viral infections. Here, we will discuss the current understanding of the classical nuclear import pathway and the factors that are essential for this process.

Purified endoglucanase from C. biazotea mutant 51SMr was successfully immobilized on Eudragit L-100, with 75 % yield of immobilization. This method improved the kinetic and thermodynamic properties of the enzyme. Immobilization significantly decreased entropy and enthalpy of inactivation of biocatalyst and made it functionally and thermodynamically more stable and reusable compared to free one.