ArticleBiophysical journal2007
Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
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- Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor.Journal of molecular modeling · 2016Article
- Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.The Journal of membrane biology · 2015Review
- Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence.PloS one · 2015Article
- Integrating protein structural dynamics and evolutionary analysis with Bio3D.BMC bioinformatics · 2014Article
- Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.PLoS computational biology · 2014Article
- PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment.Journal of molecular biology · 2013Article
- Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics.PLoS computational biology · 2013Article
- FlexE: Using elastic network models to compare models of protein structure.Journal of chemical theory and computation · 2012Article
- Elastic Network Models are Robust to Variations in Formalism.Journal of chemical theory and computation · 2012Article
- Are different stoichiometries feasible for complexes between lymphotoxin-alpha and tumor necrosis factor receptor 1?BMC structural biology · 2012Article
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- Normal mode analysis with molecular geometry restraints: bridging molecular mechanics and elastic models.Archives of biochemistry and biophysics · 2011Article
- Interaction energy based protein structure networks.Biophysical journal · 2010Article
- Characterizing protein energy landscape by self-learning multiscale simulations: application to a designed β-hairpin.Biophysical journal · 2010Article
- Sequence composition and environment effects on residue fluctuations in protein structures.The Journal of chemical physics · 2010Article
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2 authors.
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Abstract
Coarse-graining of protein interactions provides a means of simulating large biological systems. Here, a coarse-graining method, REACH, is introduced, in which the force constants of a residue-scale elastic network model are calculated from the variance-covariance matrix obtained from atomistic molecular dynamics (MD) simulation. In test calculations, the C(alpha)-atoms variance-covariance matrices are calculated from the ensembles of 1-ns atomistic MD trajectories in monomeric and dimeric myoglobin, and used to derive coarse-grained force constants for the local and nonbonded interactions. Construction of analytical model functions of the distance-dependence of the interresidue force constants allows rapid calculation of the REACH normal modes. The model force constants from monomeric and dimeric myoglobin are found to be similar in magnitude to each other. The MD intra- and intermolecular mean-square fluctuations and the vibrational density of states are well reproduced by the residue-scale REACH normal modes without requiring rescaling of the force constant parameters. The temperature-dependence of the myoglobin REACH force constants reveals that the dynamical transition in protein internal fluctuations arises principally from softening of the elasticity in the nonlocal interactions. The REACH method is found to be a reliable way of determining spatiotemporal protein motion without the need for expensive computations of long atomistic MD simulations.
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