Analysis of Protein Dynamics Simulations by a Stochastic Point Process Approach
(2013) In Journal of Chemical Theory and Computation 9(6). p.2838-2848- Abstract
- MD simulations can now explore the complex dynamics of proteins and their associated solvent in atomic detail on a millisecond time scale. Among the phenomena that thereby become amenable to detailed study are intermittent conformational transitions where the protein accesses transient high-energy states' that often play key roles in biology. Here, we present a coherent theoretical framework, based on the stochastic theory of stationary point processes, that allows the essential dynamical characteristics of such processes to be efficiently extracted from the MD trajectory without assuming Poisson statistics. Since the complete information content of a point process is contained in the sequence of residence or interevent times, the... (More)
- MD simulations can now explore the complex dynamics of proteins and their associated solvent in atomic detail on a millisecond time scale. Among the phenomena that thereby become amenable to detailed study are intermittent conformational transitions where the protein accesses transient high-energy states' that often play key roles in biology. Here, we present a coherent theoretical framework, based on the stochastic theory of stationary point processes, that allows the essential dynamical characteristics of such processes to be efficiently extracted from the MD trajectory without assuming Poisson statistics. Since the complete information content of a point process is contained in the sequence of residence or interevent times, the experimentally relevant survival correlation function can be computed several orders of magnitude more efficiently than with the conventional, approach, involving averaging over initial times. We also present a detailed analysis of the statistical and binning errors, of particular importance when MD results are compared with experiment. As an illustration of the general theoretical framework,, we use a 1 ms MD trajectory of the protein BPTI to analyze the exchange, kinetics of an internal water molecule and the dynamics of the rare conformational fluctuations that govern the rate of this exchange process. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/3983211
- author
- Halle, Bertil LU and Persson, Filip LU
- organization
- publishing date
- 2013
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Journal of Chemical Theory and Computation
- volume
- 9
- issue
- 6
- pages
- 2838 - 2848
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- wos:000320484500028
- scopus:84878900779
- pmid:26583872
- ISSN
- 1549-9618
- DOI
- 10.1021/ct400161u
- language
- English
- LU publication?
- yes
- id
- b6ac463b-d678-49d9-af1c-96667924353e (old id 3983211)
- date added to LUP
- 2016-04-01 10:17:14
- date last changed
- 2022-01-25 21:45:00
@article{b6ac463b-d678-49d9-af1c-96667924353e,
abstract = {{MD simulations can now explore the complex dynamics of proteins and their associated solvent in atomic detail on a millisecond time scale. Among the phenomena that thereby become amenable to detailed study are intermittent conformational transitions where the protein accesses transient high-energy states' that often play key roles in biology. Here, we present a coherent theoretical framework, based on the stochastic theory of stationary point processes, that allows the essential dynamical characteristics of such processes to be efficiently extracted from the MD trajectory without assuming Poisson statistics. Since the complete information content of a point process is contained in the sequence of residence or interevent times, the experimentally relevant survival correlation function can be computed several orders of magnitude more efficiently than with the conventional, approach, involving averaging over initial times. We also present a detailed analysis of the statistical and binning errors, of particular importance when MD results are compared with experiment. As an illustration of the general theoretical framework,, we use a 1 ms MD trajectory of the protein BPTI to analyze the exchange, kinetics of an internal water molecule and the dynamics of the rare conformational fluctuations that govern the rate of this exchange process.}},
author = {{Halle, Bertil and Persson, Filip}},
issn = {{1549-9618}},
language = {{eng}},
number = {{6}},
pages = {{2838--2848}},
publisher = {{The American Chemical Society (ACS)}},
series = {{Journal of Chemical Theory and Computation}},
title = {{Analysis of Protein Dynamics Simulations by a Stochastic Point Process Approach}},
url = {{http://dx.doi.org/10.1021/ct400161u}},
doi = {{10.1021/ct400161u}},
volume = {{9}},
year = {{2013}},
}