ArticleMethods in molecular biology (Clifton, N.J.)2021
Continuous Constant pH Molecular Dynamics Simulations of Transmembrane Proteins.
Article in Methods in molecular biology (Clifton, N.J.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Interior pH-sensing residue of human voltage-gated proton channel HBiophysical journal · 2024Article
- Energy coupling and stoichiometry of ZneLife · 2023Article
- Comparative Performance of High-Throughput Methods for Protein pJournal of chemical information and modeling · 2023Article
- PKAD-2: New entries and expansion of functionalities of the database of experimentally measured pKa's of proteins.Journal of computational biophysics and chemistry · 2023Article
- Galvani Offset Potential and Constant-pH Simulations of Membrane Proteins.The journal of physical chemistry. B · 2022Article
- A Guide to the Continuous Constant pH Molecular Dynamics Methods in Amber and CHARMM [Article v1.0].Living journal of computational molecular science · 2022Article
- Article
- Protein pACS omega · 2021Article
- How μ-opioid receptor recognizes fentanyl.Nature communications · 2021Article
- HowbioRxiv : the preprint server for biology · 2020Article
- How mu-Opioid Receptor Recognizes Fentanyl.Research square · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Many membrane channels, transporters, and receptors utilize a pH gradient or proton coupling to drive functionally relevant conformational transitions. Conventional molecular dynamics simulations employ fixed protonation states, thus neglecting the coupling between protonation and conformational equilibria. Here we describe the membrane-enabled hybrid-solvent continuous constant pH molecular dynamics method for capturing atomic details of proton-coupled conformational dynamics of transmembrane proteins. Example protocols from our recent application studies of proton channels and ion/substrate transporters are discussed.
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