Activation mechanism of a signaling protein at atomic resolution from advanced computations.

Activation mechanism of a signaling protein at atomic resolution from advanced computations. Research Abstract Details 

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Activation mechanism of a signaling protein at atomic resolution from advanced computations. Abstract Text:

Liang Ma,Qiang Cui,

Advanced computational techniques including transition path sampling and free energy calculations are combined synergistically to reveal the activation mechanism at unprecedented resolution for a small signaling protein, chemotaxis protein Y. In the conventional "Y-T coupling" model for response regulators, phosphorylation induces the displacement of the conserved Thr87 residue through hydrogen-bond formation, which in turn makes it sterically possible for Tyr106 to isomerize from a solvent exposed configuration to a buried rotameric state. More than 160 unbiased activation trajectories show, however, that the rotation of Tyr106 does not rely on the displacement of Thr87 per se. Free energy calculations reveal that the Tyr106 rotation is a low-barrier process in the absence of the Thr87-phosphate hydrogen bond, although the rotation is stabilized by the formation of this interaction. The simulations also find that structural change in the beta4-alpha4 loop does not gate the Tyr106 rotation as suggested previously; rather, the rotation of Tyr106 stabilizes the activated configuration of this loop. The computational strategy used and mechanistic insights obtained have an impact on the study of signaling proteins and allosteric systems in general.

Activation mechanism of a signaling protein at atomic resolution from advanced computations. Publishing Authors By Initials

L Ma,Q Cui,

For similar natural sciences: physics: thermodynamics research abstracts see: natural sciences: physics: thermodynamics research

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Activation mechanism of a signaling protein at atomic resolution from advanced computations. Journal Published:

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: Journal of the American Chemical Society

VOLUME: 129

Page Numbers: 10261-8

Journal Abbreviation: J. Am. Chem. Soc.

ISSN: 0002-7863

DAY: 26

MONTH: 07

YEAR: 2007

Activation mechanism of a signaling protein at atomic resolution from advanced computations. Information

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LANGUAGE: eng

NlmUniqueID: 7503056

Activation mechanism of a signaling protein at atomic resolution from advanced computations. Keywords Mesh Terms:

KEYWORDS: Thermodynamics

MESH TERMS: chemistry

Chemical & Substance for Abstract: Activation mechanism of a signaling protein at atomic resolution from advanced computations. Information

Substance Name: methyl-accepting chemotaxis proteins

Registry Number: 0

Grant and Affiliation Information for Activation mechanism of a signaling protein at atomic resolution from advanced computations.

AFFILIATION: Graduate program in Biophysics and Department of Chemistry and Theoretical Chemical Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA.

Country: United States

AGENCY: United States NIGMS

GRANT: R01-GM071428-02

ACRONYM: GM

MEDLINETA: J Am Chem Soc

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