Conformational Adaptation in the E. coli Sigma 32 Protein in Response to Heat Shock
IR@IICB: CSIR-Indian Institute of Chemical Biology, Kolkata
View Archive Info| Field | Value | |
| Title |
Conformational Adaptation in the E. coli Sigma 32 Protein in
Response to Heat Shock
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| Creator |
Chakraborty, Abhijit
Mukherjee, Srijata Chattopadhyay, Ruchira Roy, Siddhartha Chakrabarti, Saikat |
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| Subject |
Structural Biology & Bioinformatics
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| Description |
E. coli, like other organisms, responds to heat shock by
rapidly up-regulating several proteins, including chaperones. The heatshock sigma factor, sigma 32 (σ32), a transcription factor, plays a pivotal role in this response. The level of σ32 is normally kept low through a DnaK/J mediated degradation. Elevated temperature rapidly
increases the σ32 level and initiates a heat-shock response. A plausible way for the up-regulation of free σ32 levels would be to destabilize the σ32:DnaK:DnaJ complex initiated via a conformational change in σ32 structure at elevated temperatures. In this study, we have modeled the
E. coli σ32 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 σ32 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 σ32 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 σ32 protein at 30 and 42 °C are also supportive of the structural changes observed in the molecular dynamics study.
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| Publisher |
American Chemical Society
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| Date |
2014
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| Type |
Article
PeerReviewed |
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| Format |
application/pdf
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| Identifier |
http://www.eprints.iicb.res.in/2178/1/JOURNAL_OF_PHYSICAL_CHEMISTRY_B__V_118(_18)_4793%2D4802;2014[103].pdf
Chakraborty, Abhijit and Mukherjee, Srijata and Chattopadhyay, Ruchira and Roy, Siddhartha and Chakrabarti, Saikat (2014) Conformational Adaptation in the E. coli Sigma 32 Protein in Response to Heat Shock. The Journal of Physical Chemistry B, 118 (18). pp. 4793-4802. |
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| Relation |
http://dx.doi.org/10.1021/jp501272n
http://www.eprints.iicb.res.in/2178/ |
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