ArticleJournal of computational chemistry2014
Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers.
Article in Journal of computational chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 41 citations in OpenAlex.
- STIM1 transmembrane helix dimerization captured by AI-guided transition path sampling.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Spontaneous Dimerization and Distinct Packing Modes of Transmembrane Domains in Receptor Tyrosine Kinases.Biochemistry · 2024Article
- Spontaneous Dimerization and Distinct Packing Modes of Transmembrane Domains in Receptor Tyrosine Kinases.bioRxiv : the preprint server for biology · 2024Article
- Enzyme-substrate hybrid β-sheet controls geometry and water access to the γ-secretase active site.Communications biology · 2023Article
- Molecular mechanism of CD44 homodimerization modulated by palmitoylation and membrane environments.Biophysical journal · 2022Article
- A Free-Energy Landscape Analysis of Calmodulin Obtained from an NMR Data-Utilized Multi-Scale Divide-and-Conquer Molecular Dynamics Simulation.Life (Basel, Switzerland) · 2021Article
- The energetics of protein-lipid interactions as viewed by molecular simulations.Biochemical Society transactions · 2020Review
- Accelerating Membrane Simulations with Hydrogen Mass Repartitioning.Journal of chemical theory and computation · 2019Article
- Effect of Membrane Composition on Receptor Association: Implications of Cancer Lipidomics on ErbB Receptors.The Journal of membrane biology · 2018Review
- Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association.Journal of chemical theory and computation · 2018Article
- Conformational Heterogeneity of the HIV Envelope Glycan Shield.Scientific reports · 2017Article
- Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.Biochimica et biophysica acta · 2016Review
- Computational Studies of Molecular Permeation through Connexin26 Channels.Biophysical journal · 2016Article
- Article
- Dimerization of the EphA1 receptor tyrosine kinase transmembrane domain: Insights into the mechanism of receptor activation.Biochemistry · 2014Article
- Theory of Adaptive Optimization for Umbrella Sampling.Journal of chemical theory and computation · 2014Article
- Cholesterol modulates the dimer interface of the β₂-adrenergic receptor via cholesterol occupancy sites.Biophysical journal · 2014Article
- Primary and secondary dimer interfaces of the fibroblast growth factor receptor 3 transmembrane domain: characterization via multiscale molecular dynamics simulations.Biochemistry · 2014Article
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Structural information of a transmembrane (TM) helix dimer is useful in understanding molecular mechanisms of important biological phenomena such as signal transduction across the cell membrane. Here, we describe an umbrella sampling (US) scheme for predicting the structure of a TM helix dimer in implicit membrane using the interhelical crossing angle and the TM-TM relative rotation angles as the reaction coordinates. This scheme conducts an efficient conformational search on TM-TM contact interfaces, and its robustness is tested by predicting the structures of glycophorin A (GpA) and receptor tyrosine kinase EphA1 (EphA1) TM dimers. The nuclear magnetic resonance (NMR) structures of both proteins correspond to the global free-energy minimum states in their free-energy landscapes. In addition, using the landscape of GpA as a reference, we also examine the protocols of temperature replica-exchange molecular dynamics (REMD) simulations for structure prediction of TM helix dimers in implicit membrane. A wide temperature range in REMD simulations, for example, 250-1000 K, is required to efficiently obtain a free-energy landscape consistent with the US simulations. The interhelical crossing angle and the TM-TM relative rotation angles can be used as reaction coordinates in multidimensional US and be good measures for conformational sampling of REMD simulations.
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