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STRUCTURAL, FUNCTIONAL AND EVOLUTIONARY ANALYSIS OF CHROMATE ION TRANSPORTER PROTEINS USING COMPUTATIONAL TOOLS AND TECHNIQUES

KrishiKosh

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Title STRUCTURAL, FUNCTIONAL AND EVOLUTIONARY ANALYSIS OF CHROMATE ION TRANSPORTER PROTEINS USING COMPUTATIONAL TOOLS AND TECHNIQUES
 
Creator Requab, Sayeda Tahera
 
Contributor Upadhyaya, Netaji
 
Subject LCHR, SCHR, phylogenetic analysis, chromate reductases, chromate ion transporter.
 
Description A transporter protein is a protein that serves the function of moving other materials within an organism. Transporter proteins are vital to the growth and life of all living things. Transporter proteins in biological membranes may be divided into channels and carriers. Channels function as selective pores that open in response to a chemical or electrophysiological stimulus, allowing movement of a solute down an electrochemical gradient.Active carrier proteins use an energy producing process to translocate a substrate against a concentration gradient. Secondary active transporters use the movement of a solute down a concentration gradient to drive the translocation of another substrate across a membrane. ATP-binding cassette (ABC) transporters couple hydrolysis of adenosine triphosphate (ATP) to the translocation of various substrates across cell membranes. ChrA is a membrane protein that confers resistance to the toxic ion chromate through the energy-dependent chromate efflux from the cytoplasm. In the protein databases, ChrA is a member of the chromate ion transporter (CHR) superfamily, composed of at least several dozens of members, distributed in the three domains of life. The aim of this work was to perform a phylogenetic analysis of the CHR superfamily. Chromate reduction is carried out by chromate reductases from diverse bacterial species generating Cr (III) that may be detoxified by other mechanisms. 358 numbers of chrA proteins were retrieved from NCBI protein database comprising different organisms (bacteria and fungus) out of which 237 are long chain chromate ion transporter (LCHR) ( 236-bacterial, 1-fungal) and rest 121 are short chain chromate ion transporter (SCHR) (all bacterial). The divergence studies among LCHR proteins and SCHR proteins were carried out. It was observed that in LCHR 237 proteins were grouped into 4 subgroups and in case of SCHR 121 proteins were grouped in to 6 subgroups. There were 25 conserved sites and 638 variable sites in LCHR proteins . There were no conserved sites but the variable sites were 293 in SCHR proteins. Secondary structure (Alpha helix, extended strand, random coil) were predicted of the both LCHR and SCHR proteins in %. The % of alpha helix and random coil of chromate ion transporter proteins were more than the extended strand in both LCHR & SCHR proteins. Functional domains were predicted of all LCHR proteins. LCHR proteins contained chromate transporter domains (IPR014047 & IPR003370) and other domain like IPR006187. Most of the LCHR proteins contained both chromate transporter domains IPR014047 and IPR003370. One LCHR protein of fungi that was Coprinopsis cinerea having amino acid length 546 and another LCHR protein of one organism that was Kyrpidia tusciae having amino acid length 252 contained only one chromate transporter domain IPR003370. But one LCHR protein of one organism that was Arthrobacter sp. having amino acid length 277 contained one chromate transporter domain IPR003370 and another claudin domain IPR006187. Functional domains were predicted of all SCHR proteins. SCHR proteins contained chromate transporter domain (IPR003370) and some other domains like IPR011006, IPR001789, IPR011991, IPR016032, IPR000792 and IPR024414. Most of the SCHR proteins contained chromate transporter domain IPR003370. One SCHR protein of one organism that was Roseburia hominis having amino acid length 129 contained uncharacterized domain IPR024414. But one SCHR protein of one organism that was Corynebacterium diphtheriae having amino acid length 199 contained five types of other domains IPR011006, IPR001789, IPR011991, IPR016032 and IPR000792. The 3D structure of the protein chrA of Burkholderia pseudomallei (AHK64337) was predicted using modeler by taking the suitable template of 2C5QA (Saccaromyces cerevisiae). The structural study implies that protein having more random coils, 6 alpha helixes, 6 beta sheets. The present study will help to understand the mechanism of chromate resistance of different micro-organisms.
 
Date 2017-01-19T16:17:27Z
2017-01-19T16:17:27Z
2014
 
Type Thesis
 
Identifier http://krishikosh.egranth.ac.in/handle/1/97183
 
Language en
 
Relation Th;4285
 
Format application/pdf