Conformational adaptation in the E. coli sigma 32 protein in response to heat shock.

Abstract

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