ArticleBiophysical journal2010
Evaluating elastic network models of crystalline biological molecules with temperature factors, correlated motions, and diffuse x-ray scattering.
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 23 papers.
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Who cites it
23 citing papers in PubMed.
- Machine learning in molecular biophysics: Protein allostery, multi-level free energy simulations, and lipid phase transitions.Biophysics reviews · 2025Review
- Why are large conformational changes well described by harmonic normal modes?Biophysical journal · 2021Article
- Correlated Motions in Structural Biology.Biochemistry · 2021Review
- Diffuse X-ray scattering from correlated motions in a protein crystal.Nature communications · 2020Article
- Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein.Structural dynamics (Melville, N.Y.) · 2019Article
- Analyzing Fluctuation Properties in Protein Elastic Networks with Sequence-Specific and Distance-Dependent Interactions.Biomolecules · 2019Article
- Article
- Bringing diffuse X-ray scattering into focus.Current opinion in structural biology · 2018Review
- Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering.IUCrJ · 2018Article
- Interactions that know no boundaries.IUCrJ · 2018Article
- X-ray Scattering Studies of Protein Structural Dynamics.Chemical reviews · 2017Review
- Measuring and modeling diffuse scattering in protein X-ray crystallography.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Acoustic vibrations contribute to the diffuse scatter produced by ribosome crystals.Acta crystallographica. Section D, Biological crystallography · 2015Article
- Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles.Acta crystallographica. Section D, Biological crystallography · 2015Article
- Comparison of the Internal Dynamics of Metalloproteases Provides New Insights on Their Function and Evolution.PloS one · 2015Article
- WEBnm@ v2.0: Web server and services for comparing protein flexibility.BMC bioinformatics · 2014Article
- Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Diffuse X-ray scattering to model protein motions.Structure (London, England : 1993) · 2014Article
- Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics.PLoS computational biology · 2013Article
- Elastic Network Models are Robust to Variations in Formalism.Journal of chemical theory and computation · 2012Article
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3 authors.
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Abstract
In this study, the variance-covariance matrix of protein motions is used to compare several elastic network models within the theoretical framework of x-ray scattering from crystals. A set of 33 ultra-high resolution structures is used to characterize the average scaling behavior of the vibrational density of states and make comparisons between experimental and theoretical temperature factors. Detailed investigations of the vibrational density of states, correlations, and predicted diffuse x-ray scatter are carried out for crystalline Staphylococcal nuclease; correlations and diffuse x-ray scatter are also compared to predictions from the translation, libration, screw model and a liquid-like dynamics model. We show that elastic network models developed to best predict temperature factors without regard for the crystal environment have relatively strong long-range interactions that yield very short-ranged atom-atom correlations. Further, we find that the low-frequency modes dominate the variance-covariance matrix only for those models with a physically reasonable vibrational density of states, and the fraction of modes required to converge the correlations is higher than that typically used for elastic network model studies. The practical implications are explored using computed diffuse x-ray scatter, which can be measured experimentally.
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