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Title: The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time

Here, internal motions of proteins are essential to their function. The time dependence of protein structural fluctuations is highly complex, manifesting subdiffusive, non-exponential behavior with effective relaxation times existing over many decades in time, from ps up to ~10 2s (refs 1-4). Here, using molecular dynamics simulations, we show that, on timescales from 10 –12 to 10 –5s, motions in single proteins are self-similar, non-equilibrium and exhibit ageing. The characteristic relaxation time for a distance fluctuation, such as inter-domain motion, is observation-time-dependent, increasing in a simple, power-law fashion, arising from the fractal nature of the topology and geometry of the energy landscape explored. Diffusion over the energy landscape follows a non-ergodic continuous time random walk. Comparison with single-molecule experiments suggests that the non-equilibrium self-similar dynamical behavior persists up to timescales approaching the in vivo lifespan of individual protein molecules.
Authors:
 [1] ;  [2] ;  [3] ;  [4] ;  [3] ;  [1]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  2. Shanghai Jiao Tong Univ., Shanghai (China)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  4. Rhein-Main Univ. of Applied Sciences, Weisbaden (Germany)
Publication Date:
Grant/Contract Number:
AC05-00OR22725
Type:
Accepted Manuscript
Journal Name:
Nature Physics
Additional Journal Information:
Journal Volume: 12; Journal Issue: 2; Journal ID: ISSN 1745-2473
Publisher:
Nature Publishing Group (NPG)
Research Org:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1327648

Hu, Xiaohu, Hong, Liang, Smith, Micholas Dean, Neusius, Thomas, Cheng, Xiaolin, and Smith, Jeremy C. The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time. United States: N. p., Web. doi:10.1038/nphys3553.
Hu, Xiaohu, Hong, Liang, Smith, Micholas Dean, Neusius, Thomas, Cheng, Xiaolin, & Smith, Jeremy C. The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time. United States. doi:10.1038/nphys3553.
Hu, Xiaohu, Hong, Liang, Smith, Micholas Dean, Neusius, Thomas, Cheng, Xiaolin, and Smith, Jeremy C. 2015. "The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time". United States. doi:10.1038/nphys3553. https://www.osti.gov/servlets/purl/1327648.
@article{osti_1327648,
title = {The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time},
author = {Hu, Xiaohu and Hong, Liang and Smith, Micholas Dean and Neusius, Thomas and Cheng, Xiaolin and Smith, Jeremy C.},
abstractNote = {Here, internal motions of proteins are essential to their function. The time dependence of protein structural fluctuations is highly complex, manifesting subdiffusive, non-exponential behavior with effective relaxation times existing over many decades in time, from ps up to ~102s (refs 1-4). Here, using molecular dynamics simulations, we show that, on timescales from 10–12 to 10–5s, motions in single proteins are self-similar, non-equilibrium and exhibit ageing. The characteristic relaxation time for a distance fluctuation, such as inter-domain motion, is observation-time-dependent, increasing in a simple, power-law fashion, arising from the fractal nature of the topology and geometry of the energy landscape explored. Diffusion over the energy landscape follows a non-ergodic continuous time random walk. Comparison with single-molecule experiments suggests that the non-equilibrium self-similar dynamical behavior persists up to timescales approaching the in vivo lifespan of individual protein molecules.},
doi = {10.1038/nphys3553},
journal = {Nature Physics},
number = 2,
volume = 12,
place = {United States},
year = {2015},
month = {11}
}