ArticleBiophysical journal2010
Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 32 citations in OpenAlex.
- Reaction Coordinates Are Optimal Channels of Energy Flow.Annual review of physical chemistry · 2025Review
- Frequency-Selective Anharmonic Mode Analysis of Thermally Excited Vibrations in Proteins.Journal of chemical theory and computation · 2023Article
- Protein Dynamics to Define and Refine Disordered Protein Ensembles.The journal of physical chemistry. B · 2022Article
- Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.Acta crystallographica. Section F, Structural biology communications · 2019Review
- Traversing the folding pathway of proteins using temperature-aided cascade molecular dynamics with conformation-dependent charges.European biophysics journal : EBJ · 2016Article
- The anisotropic network model web server at 2015 (ANM 2.0).Bioinformatics (Oxford, England) · 2015Article
- On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins.Journal of chemical theory and computation · 2014Article
- Conformational dynamics of a ligand-free adenylate kinase.PloS one · 2013Article
- Molecular dynamics studies on the conformational transitions of adenylate kinase: a computational evidence for the conformational selection mechanism.BioMed research international · 2013Article
- Conformational Sampling of Maltose-transporter Components in Cartesian Collective Variables is Governed by the Low-frequency Normal Modes.The journal of physical chemistry letters · 2012Article
- Biomolecular dynamics: order-disorder transitions and energy landscapes.Reports on progress in physics. Physical Society (Great Britain) · 2012Article
- Towards the prediction of order parameters from molecular dynamics simulations in proteins.The Journal of chemical physics · 2012Article
- Structural distributions from single-molecule measurements as a tool for molecular mechanics.Chemical physics · 2012Article
- The dynamical mechanism of auto-inhibition of AMP-activated protein kinase.PLoS computational biology · 2011Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a novel sampling approach to explore large protein conformational transitions by determining unique substates from instantaneous normal modes calculated from an elastic network model, and applied to a progression of atomistic molecular dynamics snapshots. This unbiased sampling scheme allows us to direct the path sampling between the conformational end states over simulation timescales that are greatly reduced relative to the known experimental timescales. We use adenylate kinase as a test system to show that instantaneous normal modes can be used to identify substates that drive the structural fluctuations of adenylate kinase from its closed to open conformations, in which we observe 16 complete transitions in 4 mus of simulation time, reducing the timescale over conventional simulation timescales by two orders of magnitude. Analysis shows that the unbiased determination of substates is consistent with known pathways determined experimentally.
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