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

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 β2–β3, β3–β4 and β4–β5 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.

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► CRP belongs to cold shock domain protein family.
► Molecular docking-assisted for identification of potential ligands.
► CRP showed strong affinity for the nucleotide stretch consisting mainly of thymidine.
► The superimposition of CRP with 1MJC and 1CSP ranged in 0.69 and 1.43 RMSD values.
► Forms a clamp like structure which stabilizes (dT6) with energy value −694.24 kJ/mol.
► Residues The8, Asp28, Asp29, Leu 30, Phe31, etc. were important for ligand binding.