Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations.

Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations. Research Abstract Details 

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Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations. Abstract Text:

David A C Beck,George W N White,Valerie Daggett,

Two independent replica-exchange molecular dynamics (REMD) simulations with an explicit water model were performed of the Trp-cage mini-protein. In the first REMD simulation, the replicas started from the native conformation, while in the second they started from a nonnative conformation. Initially, the first simulation yielded results qualitatively similar to those of two previously published REMD simulations: the protein appeared to be over-stabilized, with the predicted melting temperature 50-150K higher than the experimental value of 315K. However, as the first REMD simulation progressed, the protein unfolded at all temperatures. In our second REMD simulation, which starts from a nonnative conformation, there was no evidence of significant folding. Transitions from the unfolded to the folded state did not occur on the timescale of these simulations, despite the expected improvement in sampling of REMD over conventional molecular dynamics (MD) simulations. The combined 1.42 micros of simulation time was insufficient for REMD simulations with different starting structures to converge. Conventional MD simulations at a range of temperatures were also performed. In contrast to REMD, the conventional MD simulations provide an estimate of Tm in good agreement with experiment. Furthermore, the conventional MD is a fraction of the cost of REMD and continuous, realistic pathways of the unfolding process at atomic resolution are obtained.

Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations. Publishing Authors By Initials

DA Beck,GW White,V Daggett,

For similar water research abstracts see: water research

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Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations. Journal Published:

PUBLICATION TYPE: Journal Article

Journal: Journal of structural biology

VOLUME: 157

Page Numbers: 514-23

Journal Abbreviation: J. Struct. Biol.

ISSN: 1047-8477

DAY: 11

MONTH: 10

YEAR: 2006

Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 9011206

Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations. Keywords Mesh Terms:

KEYWORDS: Water

MESH TERMS: chemistry

Chemical & Substance for Abstract: Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations. Information

Substance Name: Water

Registry Number: 7732-18-5

Grant and Affiliation Information for Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations.

AFFILIATION: Biomolecular Structure and Design Program, University of Washington, Seattle, WA 98195, USA.

Country: United States

AGENCY: United States NIGMS

GRANT: R01 GM050789-12

ACRONYM: GM

MEDLINETA: J Struct Biol

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