(672d) Docking Refinement and Molecular Dynamics Studies Elucidating the Molecular Mechanism of Attractant Signaling to Dhma By E. coli Tsr (Faculty Candidate)
AIChE Annual Meeting
Friday, November 20, 2020 - 8:45am to 9:00am
In this study, we show an application of an in-house docking-refinement1 protocol to reveal a structural mechanism by which the Escherichia coli (E. coli) Tsr chemoreceptor distinguishes between the (R)- and (S) enantiomers of DHMA2, metabolites of norepinephrine, a hormone that is released in high quantities in the gastrointestinal tract. We used the docking-refinement protocol, MD simulations, free energy calculations, and structural analyses to elucidate their binding and to predict which enantiomer induces a stronger signal upon binding to Tsr. The initial docking-refinement studies suggested a difference in Tsr-DHMA interaction and orientation between the two enantiomers. Starting with the binding modes derived from the docking-refinement, we used five 100 ns MD simulations per system to investigate the stability of the putative poses and their effect on Tsr. The MD simulations coupled with principal component analysis (PCA) and dynamic cross correlation (DCC) analysis predicted the piston-like motion by an Î±-helix of Tsr to be of higher magnitude for (R)- than (S)-DHMA due to differences in specific interactions of the ligands with residues in the binding pocket. This prediction justified the effort to experimentally separate the commercially available racemic mixture of (R)-DHMA and (S)-DHMA into the pure enantiomers, which could then be tested for their activity independently. The predicted difference in signaling response between the enantiomers was validated through tests of chemotaxis in vivo, showing that the computationally revealed difference between (R)- and (S)-DHMA binding corresponds to different behavioral responses in E. coli. Our study shows that the use of docking-refinement to generate near-optimal initial modes as initial structures for MD simulations can be used to avoid longer simulations3, with the conclusions of the simulation studies confirmed by experiments2.
- Orr AA, Jayaraman A, Tamamis P. Molecular Modeling of Chemoreceptor:Ligand Interactions. Methods Mol Biol. 2018;1729:353-372.
- Orr AA, Yang J, Sule N, Chawla R, Hull KG, Zhu M, Romo D, Lele PP, Jayaraman A, Manson MD, Tamamis P. Molecular Mechanism for Attractant Signaling to DHMA by E. coli Tsr. Biophys J. 2020;118(2):492-504.
- Podgorny AR, Ray JCJ. Tasting the Terroir with Tsr. Biophys J. 2020;118(2):279-280.