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Computational Molecular Bioscience 2011年第1期1卷 1-6页

作者： angshuman bagchi 不详

A new class of enzyme was established that hydrolyze the ester bond between D-Tyr bound onto its cognate t-RNA. The enzyme is called D-Tyr-tRNA deacylase. The three dimensional structure of the D-Tyr-tRNA deacylase from industrially important microorganism Bacillus lichenformis DSM13 was predicted by comparative modeling approach. Since the protein acts as a dimer a dimeric model of the enzyme was constructed. The interactions responsible for dimerization were also predicted. With the help of docking and molecular dynamics simulations the favourable binding mode of the enzyme was predicted. The probable biochemical mechanism of the hydrolysis process was elucidated. This study provides a rational framework to interpret the molecular mechanistic details of the removal of toxic D-Tyr-tRNA from the cells of industrially important microorganism Bacillus lichenformis DSM13 using the enzyme D-Tyr-tRNA deacylase.

关键词： Molecular Modeling Molecular Docking Molecular Dynamics Industrially Important Microorganism Ester Hydrolysis D-Tyr-tRNA Deacylase

A Brief Overview of a Few Popular and Important Protein Databases

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维普期刊数据库

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Computational Molecular Bioscience 2012年第4期2卷 115-120页

作者： angshuman bagchi Department of Biochemistry and Biophysics University of Kalyani Kalyani India

Database is a repository of information. In today’s world there are different types of databases available. In this present review the focus is on a few popular and most widely used biological databases that store protein sequence and structure information. The databases that are of utmost importance to do basic biological research work are PDB, SCOP, CATH and UniProt/SwissProt and GenBank. These databases have different utilities & they play important roles in different fields of biology and bioinformatics. PDB provides the structural information of proteins, protein-complexes and proteins complexed with other macromolecules. SCOP & CATH store various annotations of protein sequences and structures. UniProt is a central repository of protein sequences & functions created by joining the information contained in SwissProt, TrEMBL.

关键词： Database SCOP CATH UniProt PDB

Structural analyses of the interactions of SoxY and SoxZ from thermo-neutrophilic Hydrogenobacter thermophilus

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维普期刊数据库

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Journal of Biophysical Chemistry 2011年第4期2卷 408-413页

作者： angshuman bagchi Tapash Chandra Ghosh 不详

Microbial redox reactions of inorganic sulfur compounds are one of the important reactions responsible for the recycling of this element to maintain the environmental sulfur balance. These reactions are carried out by phylogenetically diverse set of microorganisms. The sulfur oxidizing gene cluster (sox) of thermo-neutrophilic bacterium Hydrogenobacter thermophilus consists of soxYZAXB. The bacterium shows optimal thiosulfate oxidation activity at 60°C. There are practically no reports regarding the structural biology of the sulfur oxidation proc- ess in this organism. In the present context, we employed homology modeling to construct the three dimensional structures of SoxY and SoxZ from Hydrogenobacter thermophilus. With the help of docking simulations we have identified the amino acid residues of these proteins in- volved in the interactions. The thermodynamics of the protein-protein interactions have also been analyzed. The probable biochemical mechanism of the binding of thiosulfate has been elucidated. Our study provides a rational framework to understand the molecular mechanism of the sulfur oxidation biochemistry.

关键词： Molecular Modeling Sox Operon Molecular Docking Thermodynamics

A Review on Phylogenetic Analysis: A Journey through Modern Era

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维普期刊数据库

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Computational Molecular Bioscience 2014年第3期4卷 39-45页

作者： Sourav Singha Roy Rakhi Dasgupta angshuman bagchi Department of Biochemistry and Biophysics University of Kalyani Kalyani India

Phylogenetic analysis may be considered to be a highly reliable and important bioinformatics tool. The importance of phylogenetic analysis lies in its simple manifestation and easy handling of data. The simple tree representation of the evolution makes the phylogenetic analysis easier to comprehend and represent as well. The varied applications of phylogenetics in different fields of biology make this analysis an absolute necessity. The different aspects of phylogenetic analysis have been described in a comprehensive manner. This review may be useful to those who would like to have a firsthand knowledge of phylogenetics.

关键词： Phyllogeny Tree Structure Evolutionary Time Evolution of Function