ArticleProteins2012
Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion.
Article in Proteins, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- Difference contact maps: From what to why in the analysis of the conformational flexibility of proteins.PloS one · 2020Article
- Relative Contributions of Solubility and Mobility to the Stability of Amorphous Solid Dispersions of Poorly Soluble Drugs: A Molecular Dynamics Simulation Study.Pharmaceutics · 2018Article
- Allosteric Dynamic Control of Binding.Biophysical journal · 2015Article
- Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions.The Journal of chemical physics · 2013Article
- Dynamic fluctuations provide the basis of a conformational switch mechanism in apo cyclic AMP receptor protein.PLoS computational biology · 2013Article
- Elastic Network Models are Robust to Variations in Formalism.Journal of chemical theory and computation · 2012Article
- Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Recent studies suggest that protein motions observed in molecular simulations are related to biochemical activities, although the computed time scales do not necessarily match those of the experimentally observed processes. The molecular origin of this conflicting observation is explored here for a test protein, cyanovirin-N (CV-N), through a series of molecular dynamics simulations that span a time range of three orders of magnitude up to 0.4 μs. Strikingly, increasing the simulation time leads to an approximately uniform amplification of the motional sizes, while maintaining the same conformational mechanics. Residue fluctuations exhibit amplitudes of 1-2 Å in the nanosecond simulations, whereas their average sizes increase by a factor of 4-5 in the microsecond regime. The mean-square displacements averaged over all residues (y) exhibit a power law dependence of the form y ∝ x(0.26) on the simulation time (x). Essential dynamics analysis of the trajectories, on the other hand, demonstrates that CV-N has robust preferences to undergo specific types of motions that already can be detected at short simulation times, provided that multiple runs are performed and carefully analyzed.
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Registered trials
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