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Picosecond fluctuating protein energy landscape mapped by pressure–temperature molecular dynamics simulation

Meinhold, Lars and Smith, Jeremy C. and Kitao, Akio and Zewail, Ahmed H. (2007) Picosecond fluctuating protein energy landscape mapped by pressure–temperature molecular dynamics simulation. Proceedings of the National Academy of Sciences of the United States of America, 104 (44). pp. 17261-17265. ISSN 0027-8424. PMCID PMC2077243. https://resolver.caltech.edu/CaltechAUTHORS:MEIpnas07

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Abstract

Microscopic statistical pressure fluctuations can, in principle, lead to corresponding fluctuations in the shape of a protein energy landscape. To examine this, nanosecond molecular dynamics simulations of lysozyme are performed covering a range of temperatures and pressures. The well known dynamical transition with temperature is found to be pressure-independent, indicating that the effective energy barriers separating conformational substates are not significantly influenced by pressure. In contrast, vibrations within substates stiffen with pressure, due to increased curvature of the local harmonic potential in which the atoms vibrate. The application of pressure is also shown to selectively increase the damping of the anharmonic, low-frequency collective modes in the protein, leaving the more local modes relatively unaffected. The critical damping frequency, i.e., the frequency at which energy is most efficiently dissipated, increases linearly with pressure. The results suggest that an invariant description of protein energy landscapes should be subsumed by a fluctuating picture and that this may have repercussions in, for example, mechanisms of energy dissipation accompanying functional, structural, and chemical relaxation.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://www.pnas.org/content/104/44/17261.longPublisherArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2077243/PubMed CentralArticle
Additional Information:© 2007 the National Academy of Sciences. Contributed by Ahmed H. Zewail, August 30, 2007 (sent for review June 28, 2007). Published online on October 23, 2007, 10.1073/pnas.0708199104. This work was supported by the Physical Biology Center for Ultrafast Science and Technology. L.M. acknowledges support from a Deutsche Physikalische Gesellschaft/Deutsche Forschungsgemeinschaft fellowship to visit Japan before joining the group at The California Institute of Technology. Author contributions: L.M., J.C.S., A.K., and A.H.Z. performed research; and L.M., J.C.S., A.K., and A.H.Z. wrote the paper. The authors declare no conflict of interest.
Funders:
Funding AgencyGrant Number
Deutsche Physikalische GesellschaftUNSPECIFIED
Deutsche Forschungsgemeinschaft (DFG)UNSPECIFIED
Subject Keywords:critical damping; dynamical transition; energy dissipation; harmonic-anharmonic motions
Issue or Number:44
PubMed Central ID:PMC2077243
Record Number:CaltechAUTHORS:MEIpnas07
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:MEIpnas07
Alternative URL:http://dx.doi.org/10.1073/pnas.0708199104
Official Citation:Lars Meinhold, Jeremy C. Smith, Akio Kitao, and Ahmed H. Zewail Picosecond fluctuating protein energy landscape mapped by pressure–temperature molecular dynamics simulation PNAS 2007 104 (44) 17261-17265; published ahead of print October 23, 2007, doi:10.1073/pnas.0708199104
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:10476
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:09 May 2008
Last Modified:03 Oct 2019 00:09

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