ArticleJournal of molecular biology2010
Probing the periplasmic-open state of lactose permease in response to sugar binding and proton translocation.
Article in Journal of molecular biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Self-Guided Molecular Simulation Methods.International journal of molecular sciences · 2025Review
- Recent Developments in Amber Biomolecular Simulations.Journal of chemical information and modeling · 2025Article
- Reformulation of the self-guided molecular simulation method.The Journal of chemical physics · 2020Article
- Structural and Functional Adaptability of Sucrose and Lactose Permeases fromBiochemistry · 2020Article
- Current Advances in Studying Clinically Relevant Transporters of the Solute Carrier (SLC) Family by Connecting Computational Modeling and Data Science.Computational and structural biotechnology journal · 2019Review
- Uptake dynamics in the Lactose permease (LacY) membrane protein transporter.Scientific reports · 2018Article
- Self-guided Langevin dynamics via generalized Langevin equation.Journal of computational chemistry · 2016Article
- CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.Journal of chemical theory and computation · 2016Article
- How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets?Journal of chemical theory and computation · 2015Article
- Computational characterization of structural dynamics underlying function in active membrane transporters.Current opinion in structural biology · 2015Review
- CHARMM-GUI Membrane Builder toward realistic biological membrane simulations.Journal of computational chemistry · 2014Article
- Flexible gates generate occluded intermediates in the transport cycle of LacY.Journal of molecular biology · 2014Article
- Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps.Journal of structural biology · 2013Article
- Use of molecular modelling to probe the mechanism of the nucleoside transporter NupG.Molecular membrane biology · 2013Article
- Understanding the basis of a class of paradoxical mutations in AraC through simulations.Proteins · 2013Article
- Proton-coupled dynamics in lactose permease.Structure (London, England : 1993) · 2012Article
- Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling.The Journal of chemical physics · 2012Article
- Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics.Advances in chemical physics · 2012Article
- Force-momentum-based self-guided Langevin dynamics: a rapid sampling method that approaches the canonical ensemble.The Journal of chemical physics · 2011Article
- Lactose permease and the alternating access mechanism.Biochemistry · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Based on the crystal structure of lactose permease (LacY) open to the cytoplasm, a hybrid molecular simulation approach with self-guided Langevin dynamics is used to describe conformational changes that lead to a periplasmic-open state. This hybrid approach consists of implicit (IM) and explicit (EX) membrane simulations and requires self-guided Langevin dynamics to enhance protein motions during the IM simulations. The pore radius of the lumen increases by 3.5 Å on the periplasmic side and decreases by 2.5 Å on the cytoplasmic side (relative to the crystal structure), suggesting a lumen that is fully open to the periplasm to allow for extracellular sugar transport and closed to the cytoplasm. Based on our simulations, the mechanism that triggers this conformational change to the periplasmic-open state is the protonation of Glu269 and binding of the disaccharide. Then, helix packing is destabilized by breaking of several side chains involved in hydrogen bonding (Asn245, Ser41, Glu374, Lys42, and Gln242). For the periplasmic-open conformations obtained from our simulations, helix-helix distances agree well with experimental measurements using double electron-electron resonance, fluorescence resonance energy transfer, and varying sized cross-linkers. The periplasmic-open conformations are also in compliance with various substrate accessibility/reactivity measurements that indicate an opening of the protein lumen on the periplasmic side on sugar binding. The comparison with these measurements suggests a possible incomplete closure of the cytoplasmic half in our simulations. However, the closure is sufficient to prevent the disaccharide from transporting to the cytoplasm, which is in accordance with the well-established alternating access model. Ser53, Gln60, and Phe354 are determined to be important in sugar transport during the periplasmic-open stage of the sugar transport cycle and the sugar is found to undergo an orientational change in order to escape the protein lumen.
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