Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 110, Issue 47, Pages 18916-18921Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1313202110
Keywords
orientation quaternion; bias-exchange umbrella sampling; conformational free energy
Categories
Funding
- Extreme Science and Engineering Discovery Environment [MCA06N060]
- Taub cluster of the Computational Science and Engineering Program at the University of Illinois at Urbana-Champaign
- National Institutes of Health [U54-GM087519, R01-GM086749, P41-GM104601]
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During their transport cycle, ATP-binding cassette (ABC) transporters undergo large-scale conformational changes between inward-and outward-facing states. Using an approach based on designing system-specific reaction coordinates and using nonequilibrium work relations, we have performed extensive all-atom molecular dynamics simulations in the presence of explicit membrane/ solvent to sample a large number of mechanistically distinct pathways for the conformational transition of MsbA, a bacterial ABC exporter whose structure has been solved in multiple functional states. The computational approach developed here is based on (i) extensive exploration of system-specific biasing protocols (e. g., using collective variables designed based on available lowresolution crystal structures) and (ii) using nonequilibrium work relations for comparing the relevance of the transition pathways. The most relevant transition pathway identified using this approach involves several distinct stages reflecting the complex nature of the structural changes associated with the function of the protein. The opening of the cytoplasmic gate during the outwardto inward-facing transition of apo MsbA is found to be disfavored when the periplasmic gate is open and facilitated by a twisting motion of the nucleotide-binding domains that involves a dramatic change in their relative orientation. These results highlight the cooperativity between the transmembrane and the nucleotidebinding domains in the conformational transition of ABC exporters. The approach introduced here provides a framework to study large-scale conformational changes of other membrane transporters whose computational investigation at an atomic resolution may not be currently feasible using conventional methods.
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