ArticleBiophysical journal2011
Simulations of the alternating access mechanism of the sodium symporter Mhp1.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 65 citations in OpenAlex.
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- Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling.Journal of chemical theory and computation · 2023Article
- Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling.bioRxiv : the preprint server for biology · 2023Article
- Weighted ensemble: Recent mathematical developments.The Journal of chemical physics · 2023Article
- Integrated AlphaFold2 and DEER investigation of the conformational dynamics of a pH-dependent APC antiporter.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Heteromeric Solute Carriers: Function, Structure, Pathology and Pharmacology.Advances in experimental medicine and biology · 2021Review
- A kinetic mechanism for enhanced selectivity of membrane transport.PLoS computational biology · 2020Article
- Locking Two Rigid-body Bundles in an Outward-Facing Conformation: The Ion-coupling Mechanism in a LeuT-fold Transporter.Scientific reports · 2019Article
- Statistical Uncertainty Analysis for Small-Sample, High Log-Variance Data: Cautions for Bootstrapping and Bayesian Bootstrapping.Journal of chemical theory and computation · 2019Article
- Computational Estimation of Microsecond to Second Atomistic Folding Times.Journal of the American Chemical Society · 2019Article
- Recent developments in nucleobase cation symporter-1 (NCS1) family transport proteins from bacteria, archaea, fungi and plants.Journal of biosciences · 2018Review
- Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways.Biophysical journal · 2018Article
- Substrate Specificity of the FurE Transporter Is Determined by Cytoplasmic Terminal Domain Interactions.Genetics · 2017Article
- Topological Dissection of the Membrane Transport Protein Mhp1 Derived from Cysteine Accessibility and Mass Spectrometry.Analytical chemistry · 2017Article
- Weighted Ensemble Simulation: Review of Methodology, Applications, and Software.Annual review of biophysics · 2017Review
- Path-sampling strategies for simulating rare events in biomolecular systems.Current opinion in structural biology · 2017Review
- Article
- Simulating the Function of the MjNhaP1 Transporter.The journal of physical chemistry. B · 2016Article
- Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein-Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide.The journal of physical chemistry letters · 2016Article
- Allantoin transport protein, PucI, from Bacillus subtilis: evolutionary relationships, amplified expression, activity and specificity.Microbiology (Reading, England) · 2016Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Sodium coupled cotransporters of the five-helix inverted repeat (5HIR) superfamily use an alternating access mechanism to transport a myriad of small molecules across the cell membrane. One of the primary steps in this mechanism is the conformational transition from a state poised to bind extracellular substrates to a state that is competent to deliver substrate to the cytoplasm. Here, we construct a coarse-grained model of the 5HIR benzylhydantoin transporter Mhp1 that incorporates experimental structures of the outward- and inward-open states to investigate the mechanism of this conformational change. Using the weighted ensemble path-sampling method, we rigorously sample the outward- to inward-facing transition path ensemble. The transition path ensemble reveals a heterogeneous set of pathways connecting the two states and identifies two modes of transport: one consistent with a strict alternating access mechanism and another where decoupling of the inner and outer gates causes the transient formation of a continuous permeation pathway through the transporter. We also show that the conformational switch between the outward- and inward-open states results from rigid body motions of the hash motif relative to the substrate bundle, supporting the rocking bundle hypothesis. Finally, our methodology provides the groundwork for more chemically detailed investigations of the alternating mechanism.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.