ArticleBiophysical journal2013
Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase.
Article in Biophysical journal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Adaptive Normal Mode Sampling (aMDeNM) Enhances Exploration of Protein Conformational Space and Reveals the Functional Role of Frequency Coupling.Journal of chemical theory and computation · 2026Article
- Generation of Pathway Signatures by Combining Normal Modes with Weighted Ensemble Simulations.bioRxiv : the preprint server for biology · 2026Article
- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- Dissecting Large-Scale Structural Transitions in Membrane Transporters Using Advanced Simulation Technologies.The journal of physical chemistry. B · 2025Review
- An accelerated molecular dynamics study for investigating protein pathways using the bond-boost hyperdynamics method.Protein science : a publication of the Protein Society · 2025Article
- Extended Sampling of Macromolecular Conformations from Uniformly Distributed Points on Multidimensional Normal Mode Hyperspheres.Journal of chemical theory and computation · 2024Article
- HIV-1-envelope trimer transitions from prefusion-closed to CD4-bound-open conformations through an occluded-intermediate state.Computational and structural biotechnology journal · 2024Article
- Exploring Protein Conformational Changes Using a Large-Scale Biophysical Sampling Augmented Deep Learning Strategy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Predicting protein conformational motions using energetic frustration analysis and AlphaFold2.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- HIV-1-envelope trimer transitions from prefusion-closed to CD4-bound-open conformations through an occluded-intermediate state.bioRxiv : the preprint server for biology · 2024Article
- MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search.Journal of chemical information and modeling · 2024Article
- MinActionPath2: path generation between different conformations of large macromolecular assemblies by action minimization.Nucleic acids research · 2024Article
- Scalable computation of anisotropic vibrations for large macromolecular assemblies.Nature communications · 2024Article
- Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing.International journal of molecular sciences · 2023Article
- Small GTPase Ran: Depicting the nucleotide-specific conformational landscape of the functionally important C-terminus.Frontiers in molecular biosciences · 2023Article
- Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods.Frontiers in molecular biosciences · 2022Article
- Protein conformational transitions explored by a morphing approach based on normal mode analysis in internal coordinates.PloS one · 2021Article
- An Information-Theory-Based Approach for Optimal Model Reduction of Biomolecules.Journal of chemical theory and computation · 2020Article
- Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods.Current opinion in structural biology · 2020Review
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Abstract
Efficient and accurate mapping of transition pathways is a challenging problem in allosteric proteins. We propose here a to our knowledge new methodology called collective molecular dynamics (coMD). coMD takes advantage of the collective modes of motions encoded by the fold, simultaneously evaluating the interactions and energetics via a full-atomic MD simulation protocol. The basic approach is to deform the structure collectively along the modes predicted by the anisotropic network model, upon selecting them via a Monte Carlo/Metropolis algorithm from among the complete pool of all accessible modes. Application to adenylate kinase, an allosteric enzyme composed of three domains, CORE, LID, and NMP, shows that both open-to-closed and closed-to-open transitions are readily sampled by coMD, with large-scale motions of the LID dominating. An energy-barrier crossing occurs during the NMP movements. The energy barrier originates from a switch between the salt bridges K136-D118 at the LID-CORE interface and K57-E170 and D33-R156 at the CORE-NMP and LID-NMP interfaces, respectively. Despite its simplicity and computing efficiency, coMD yields ensembles of transition pathways in close accord with detailed full atomic simulations, lending support to its utility as a multiscale hybrid method for efficiently exploring the allosteric transitions of multidomain or multimeric proteins.
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