Abstract
The heat shock response mechanism is a very vital biochemical process and is mainly controlled by σ32 protein. The function of σ32 is temperature dependent and at lower temperatures σ32 is inactivated by its interactions with DnaK. This interaction is completely abolished above 42°C till date no molecular details of the interactions are available. In the present scenario, an attempt has been made to analyze first the predicted structure of σ32 obtained by comparative modeling techniques and then to study the interactions between σ32 and DnaK. From this molecular modeling study we could specifically identify the binding sites of the interactions of σ32 with DnaK which will enlighten the mechanism of regulation of its activity and stability by DnaK. Our study provides the idea for future mutational experiments in order to find out the possible roles of the amino acids of region2 and region3 of σ32 in stability as well as in binding with DnaK.
Highlights
The proper conformation of proteins and cellular survival is challenged by stress conditions like extreme heat which results in a massive aggregation of proteins inside both eukaryotic and prokaryotic cells
We report a three dimensional model of σ32 built by homology modeling
The amino acid sequence of σ32 protein from E. coli K-12 was collected from Uniprot
Summary
The proper conformation of proteins and cellular survival is challenged by stress conditions like extreme heat which results in a massive aggregation of proteins inside both eukaryotic and prokaryotic cells. Under non-stress conditions, σ32 is neutralized by an interaction with DnaK and DnaJ proteins Accumulation of unfolded proteins upon heat stress conditions titrates away the DnaK system, leaving behind free σ32, which associates with RNA polymerase and in turn initiates transcription of heat shock genes. In order to build σ32 –DnaK complex, the modeled structure of σ32 was docked with the crystal structure of DnaK protein (PDB Code: 1DKX) using the program GRAMM [17]. The model of σ32 –DnaK protein complex was protonated at pH 7.5 using Accelrys Discovery Studio 2.5 and subjected to 2000 cycles of energy minimization using CHARMM force fields with steepest descent (SD) algorithm until the structure of the σ32 – DnaK protein complex reached the final energy derivative of 0.001 kcal / mole. DnaK is colored in cyan and σ32 in red; (C) Superimposition of the backbone atoms of the binding interface of DnaK docked σ32 at 32 ̊C (red) and 43 ̊C (cyan)
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