ArticleProceedings of the National Academy of Sciences of the United States of America2013
Mechanistic picture for conformational transition of a membrane transporter at atomic resolution.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
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Who cites it
81 citing papers in PubMed.
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- Comparative Study of the Bending Free Energies of C- and G-Based DNA: A-, B-, and Z-DNA and Associated Mismatched Trinucleotide Repeats.Journal of chemical information and modeling · 2025Article
- Structural dynamics of sphingosine kinase 1 regulation and inhibition.Research square · 2025Article
- Dissecting Large-Scale Structural Transitions in Membrane Transporters Using Advanced Simulation Technologies.The journal of physical chemistry. B · 2025Review
- Conformational free energy landscape of a glutamate transporter and microscopic details of its transport mechanism.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Membrane-dependent dynamics and dual translocation mechanisms of ABCB4: Insights from molecular dynamics simulations.Computational and structural biotechnology journal · 2025Article
- Mechanical stress and anionic lipids synergistically stabilize an atypical structure of the angiotensin II type 1 receptor (AT1).PLoS computational biology · 2024Article
- Deciphering the Interdomain Coupling in a Gram-Negative Bacterial Membrane Insertase.The journal of physical chemistry. B · 2024Article
- Identification of new correctors for traffic-defective ABCB4 variants by a high-content screening approach.Communications biology · 2024Article
- GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models.The journal of physical chemistry. B · 2024Article
21 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
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 low-resolution 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 outward- to 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 nucleotide-binding 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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