Computational studies on HdeA and its pH‐Dependent Activation

Abstract

HdeA is a chaperone protein found in pathogenic gram‐negative bacteria such as Escherichia coli that forms homodimers, provides bacterial stress response and acid resistance. HdeA is inactive in its dimeric form and becomes activated in low pH environments such as the mammalian stomach. In low pH environments, it binds to other periplasmic proteins protecting them from aggregation and denaturation. Computational biophysical methods such as constant pH molecular dynamics (cpHMD) in explicit solvent have been utilized to couple protein dynamics and protonation states in order to reveal a plausible unfolding mechanism for HdeA. Our computational studies are providing insight into the unfolding mechanisms for HdeA. CpHMD was used to measure the 16 pKa values of the acidic GLU and ASP residues. Solvent Accessible Surface Area (SASA) analysis has shown that pH 7.0 has the highest amount of buried area while pH 2.0 has the least amount of buried area. This is in agreement with experimental findings which show that at pH 7.0 HdeA remains a well‐folded homodimer, while at pH 2.0 HdeA unfolds into monomers (Garrison and Crowhurst, 2013). Interestingly, analysis of individual residue fluctuations has shown that some dimer interface core residues fluctuate more when HdeA is in its active state while other core residues become more static at lower pHs. Both monomer and dimer simulations show that residue GlN4 gets protected at low pH consistent with deuterium exchange experiments. These findings are creating a complex but detailed view of HdeA's transition from its inactive dimeric state to active monomeric state.Support or Funding Information8TL4GM118977‐02NIH BUILD PODERThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.