ArticleProceedings of the National Academy of Sciences of the United States of America2010
Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Computational analysis of deleterious single nucleotide polymorphisms in catechol O-Methyltransferase conferring risk to post-traumatic stress disorder.Journal of psychiatric research · 2021Article
- How Useful can the Voigt Profile be in Protein Folding Processes?The protein journal · 2021Article
- Membrane potential and dynamics in a ternary lipid mixture: insights from molecular dynamics simulations.Physical chemistry chemical physics : PCCP · 2018Article
- From a Highly Disordered to a Metastable State: Uncovering Insights of α-Synuclein.ACS chemical neuroscience · 2018Article
- A pathway for protective quenching in antenna proteins of Photosystem II.Scientific reports · 2017Article
- Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- My 65 years in protein chemistry.Quarterly reviews of biophysics · 2015Review
- Local vs global motions in protein folding.Journal of chemical theory and computation · 2013Article
- Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70.PLoS computational biology · 2013Article
- 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
- Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion.Proteins · 2012Article
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5 authors.
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Abstract
Structural fluctuations of a protein are essential for the function of native proteins and for protein folding. To understand how the main chain in the native state of a protein fluctuates on different time scales, we examined the rotational correlation functions (RCFs), C(t), of the backbone N-H bonds and of the dihedral angles γ built on four consecutive C(α) atoms. Using molecular dynamics simulations of a model α/β protein (VA3) in its native state, we demonstrate that these RCFs decay as stretched exponentials, ln[C(t)] ≈ D(α)t(α) with a constant D(α) and an exponent α (0 < α < 0.35) varying with the free-energy profiles (FEPs) along the amino acid sequence. The probability distributions of the fluctuations of the main chain computed at short time scale (1 ps) were identical to those computed at large time scale (1 ns) if the time is rescaled by a factor depending on α < 1. This self-similar property and the nonexponential decays (α ≠ 1) of the RCFs are described by a rotational diffusion equation with a time-dependent diffusion coefficient D(t) = αD(α)t(α-1). The present findings agree with observations of subdiffusion (α < 1) of fluorescent probes within a protein molecule. The subdiffusion of (15)N-H bonds did not affect the value of the order parameter S(2) extracted from the NMR relaxation data by assuming normal diffusion (α = 1) of (15)N-H bonds on a nanosecond time scale. However, we found that the RCF does not converge to S(2) on the nanosecond time scale for residues with multiple-minima FEPs.
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