E. coli, like other organisms, responds to heat shock by rapidly up-regulating several proteins, including chaperones. The heat-shock sigma factor, sigma 32 (sigma(32)), a transcription factor, plays a pivotal role in this response. The level of sigma(32) is normally kept low through a DnaK/J mediated degradation. Elevated temperature rapidly increases the sigma(32) level and initiates a heat-shock response. A plausible way for the up-regulation of free sigma(32) levels would be to destabilize the sigma(32):DnaK:DnaJ complex initiated via a conformational change in 03 2 structure at elevated temperatures. In this study, we have modeled the E. coli sigma(32) structure by homology modeling and conducted extensive molecular dynamics (MD) simulations at non-heat-shock (30 degrees C) and heat-shock (42 degrees C) temperatures. Substantial structural rearrangements at 42 degrees C were observed around the N-terminus (residues II-60, which cover the DnaJ binding region) and the region spanning residues 190-210 (covering the DnaK binding site, residues 198-201). At 42 degrees C, a large amount of helix melting and structural destabilization was observed around residues 11-60, while regions 91-101 and 216-221 of sigma(32) undergo conformational change, leading to formation of a lid-like structure over region 198-VLYL-201 resulting in reduced accessibility of the DnaK binding sites. These temperature induced melting and fluctuations observed around the DnaJ and/or DnaK binding regions suggest reduction of DnaK/DnaJ affinity for sigma(32) at 42 degrees C, which is further supported by our molecular docking analysis. Emission maxima of environment sensitive fluorescence probes inserted at several cysteine mutants of sigma(32) protein at 30 and 42 degrees C are also supportive of the structural changes observed in the molecular dynamics study.