ArticleBiophysical journal2010
Anharmonic normal mode analysis of elastic network model improves the modeling of atomic fluctuations in protein crystal structures.
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 12 papers.
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12 citing papers in PubMed.
- Asymmetric Dynamics Between the Protomers of the σ2 Receptor Homodimer.Journal of chemical information and modeling · 2025Article
- Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes.Proteins · 2025Article
- Deciphering conformational dynamics in AFM data using fast nonlinear NMA and FFT-based search with AFMFit.Communications biology · 2025Article
- Why are large conformational changes well described by harmonic normal modes?Biophysical journal · 2021Article
- Normal mode analysis calculation for a full-atom model with a smaller number of degrees of freedom for huge protein molecules.Biophysics and physicobiology · 2019Article
- Elastic network models capture the motions apparent within ensembles of RNA structures.RNA (New York, N.Y.) · 2014Article
- Sequence-based Gaussian network model for protein dynamics.Bioinformatics (Oxford, England) · 2014Article
- PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment.Journal of molecular biology · 2013Article
- Structural intermediates in a model of the substrate translocation path of the bacterial glutamate transporter homologue GltPh.The journal of physical chemistry. B · 2012Article
- Probing molecular mechanisms of the Hsp90 chaperone: biophysical modeling identifies key regulators of functional dynamics.PloS one · 2012Article
- Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles.European biophysics journal : EBJ · 2011Review
- Normal mode analysis with molecular geometry restraints: bridging molecular mechanics and elastic models.Archives of biochemistry and biophysics · 2011Article
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Abstract
Protein conformational dynamics, despite its significant anharmonicity, has been widely explored by normal mode analysis (NMA) based on atomic or coarse-grained potential functions. To account for the anharmonic aspects of protein dynamics, this study proposes, and has performed, an anharmonic NMA (ANMA) based on the C(alpha)-only elastic network models, which assume elastic interactions between pairs of residues whose C(alpha) atoms or heavy atoms are within a cutoff distance. The key step of ANMA is to sample an anharmonic potential function along the directions of eigenvectors of the lowest normal modes to determine the mean-squared fluctuations along these directions. ANMA was evaluated based on the modeling of anisotropic displacement parameters (ADPs) from a list of 83 high-resolution protein crystal structures. Significant improvement was found in the modeling of ADPs by ANMA compared with standard NMA. Further improvement in the modeling of ADPs is attained if the interactions between a protein and its crystalline environment are taken into account. In addition, this study has determined the optimal cutoff distances for ADP modeling based on elastic network models, and these agree well with the peaks of the statistical distributions of distances between C(alpha) atoms or heavy atoms derived from a large set of protein crystal structures.
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