Prediction of ligand binding site by insilico approach in cold resistant protein isolated from cold resistant mutant of Pseudomonas fluorescen

Amit, Kumar and Mahejibin, Khan (2012) Prediction of ligand binding site by insilico approach in cold resistant protein isolated from cold resistant mutant of Pseudomonas fluorescen. Journal of Molecular Graphics and Modelling, 38. pp. 101-111.

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Abstract

Cold shock proteins perform vital functions, such as mRNA masking, coupling of transcription to translation and developmental timing and regulation, which aids in survival of microbes in cold stress. Pseudomonas fluorescens is an ecologically important bacterium which helps in plant growth promotion. Since the cold tolerant mutant of the bacterium is able to grow at the temperature ranges from 30 to 4◦C, it is of interest to study the process of its survival in the extreme temperatures. Therefore, this study is focused on the three dimensional structure and molecular modeling of cold resistant protein (CRP) from P. fluorescens to predict its molecular mechanism. Investigating the structure of CRP confirmed the presence of a conserved domain characteristic of the cold shock domain (CSD) family and a single nucleotide binding domain. When 3D structure of CRP was compared with the existing cold shock proteins, major deviations were found in the loop regions connecting the �2–�3, �3–�4 and �4–�5 sheets. Docking studies showed that CRP forms a significant clamp like structure at the substrate binding cleft which stabilizes the ligand. Therefore, it can be concluded that CRP has a strong affinity for the poly thymidine (poly T) stretch and can be considered a candidate for transcription regulation.

Item Type:	Article
Uncontrolled Keywords:	Cold shock domain Cold resistant protein Molecular modeling Transcription regulation Pseudomonas fluorescens
Subjects:	500 Natural Sciences and Mathematics > 07 Life Sciences > 04 Microbiology > 02 Bacteriology
Divisions:	Food Microbiology
Depositing User:	Food Sci. & Technol. Information Services
Date Deposited:	23 Sep 2016 10:03
Last Modified:	23 Sep 2016 10:03
URI:	http://ir.cftri.res.in/id/eprint/12317

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