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  Conformational dynamics of cytochrome c: Correlation to hydrogen exchange

García, A. E., & Hummer, G. (1999). Conformational dynamics of cytochrome c: Correlation to hydrogen exchange. Proteins: Structure, Function, and Genetics, 36(2), 175-191. doi:10.1002/(SICI)1097-0134(19990801)36:2<175:AID-PROT4>3.0.CO;2-R.

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García, Angel E.1, Author
Hummer, Gerhard1, Author                 
1Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA, ou_persistent22              


Free keywords: hydration dynamics, molecular dynamics, nonlinear dynamics, protein hydration, strange dynamics
 Abstract: We study the dynamical fluctuations of horse heart cytochrome c by molecular dynamics (MD) simulations in aqueous solution, at four temperatures: 300 K, 360 K, 430 K, and 550 K. Each simulation covers a production time of at least 1.5 nanoseconds (ns). The conformational dynamics of the system is analyzed in terms of collective motions that involve the whole protein, and local motions that involve the formation and breaking of intramolecular hydrogen bonds. The character of the MD trajectories can be described within the framework of rugged energy landscape dynamics. The MD trajectories sample multiple conformational minima, with basins in protein conformational space being sampled for a few hundred picoseconds. The trajectories of the system in configurational space can be described in terms of diffusion of a particle in real space with a waiting time distribution due to partial trapping in shallow minima. As a consequence of the hierarchical nature of the dynamics, the mean square displacement autocorrelation function, 〈|}x(t) − x(0){|2〉, exhibits a power law dependence on time, with an exponent of around 0.5 for times shorter than 100 ps, and an exponent of 1.75 for longer times. This power law behavior indicates that the system exhibits suppressed diffusion (sub-diffusion) in sampling of configurational space at time scales shorter than 100 ps, and enhanced (super-diffusion) at longer time scales. The multi-basin feature of the trajectories is present at all temperatures simulated. Structural changes associated with inter-basin displacements correspond to collective motions of the Ω loops and coiled regions and relative motions of the α-helices as rigid bodies. Similar motions may be involved in experimentally observed amide hydrogen exchange. However, some groups showing large correlated motions do not expose the amino hydrogens to the solvent. We show that large fluctuations are not necessarily correlated to hydrogen exchange. For example, regions of the proteins forming α helices and turns show significant fluctuations, but as rigid bodies, and the hydrogen bonds involved in the formation of these structures do not break in proportion to these fluctuations. Proteins 1999;36:175–191. Published 1999 Wiley‒Liss, Inc.


Language(s): eng - English
 Dates: 1998-12-011999-03-261999-08-01
 Publication Status: Published in print
 Pages: 17
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1002/(SICI)1097-0134(19990801)36:2<175::AID-PROT4>3.0.CO;2-R
BibTex Citekey: garcia_conformational_1999
 Degree: -



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Title: Proteins: Structure, Function, and Genetics
  Other : Proteins: Struct., Funct., Genet.
Source Genre: Journal
Publ. Info: New York, NY : John Wiley & Sons
Pages: - Volume / Issue: 36 (2) Sequence Number: - Start / End Page: 175 - 191 Identifier: ISSN: 0887-3585
CoNE: https://pure.mpg.de/cone/journals/resource/954925553393