Identifying the protein folding nucleus using molecular dynamics

Nikolay V. Dokholyan; Sergey V. Buldyrev; H. Eugene Stanley; Eugene I. Shakhnovich

doi:10.1006/jmbi.1999.3534

Identifying the protein folding nucleus using molecular dynamics

Nikolay V. Dokholyan, Sergey V. Buldyrev, H. Eugene Stanley, Eugene I. Shakhnovich

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131 Scopus citations

Abstract

Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their appearance determines folding cooperativity and drives the model protein into its folded conformation. Amino acid residues participating in those contacts may serve as 'accelerator pedals' used by molecular evolution to control protein folding rate. (C) 2000 Academic Press.

Original language	English (US)
Pages (from-to)	1183-1188
Number of pages	6
Journal	Journal of Molecular Biology
Volume	296
Issue number	5
DOIs	https://doi.org/10.1006/jmbi.1999.3534
State	Published - Mar 10 2000

All Science Journal Classification (ASJC) codes

Structural Biology
Molecular Biology

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10.1006/jmbi.1999.3534

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abstract = "Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their appearance determines folding cooperativity and drives the model protein into its folded conformation. Amino acid residues participating in those contacts may serve as 'accelerator pedals' used by molecular evolution to control protein folding rate. (C) 2000 Academic Press.",

author = "Dokholyan, {Nikolay V.} and Buldyrev, {Sergey V.} and Stanley, {H. Eugene} and Shakhnovich, {Eugene I.}",

note = "Funding Information: We thank R. S. Dokholyan for careful reading of the manuscript. N.V.D. is supported by NIH NRSA molecular biophysics predoctoral traineeship (GM08291-09) and by NIH postdoctoral fellowship (GM20251-01). E.I.S. is supported by NIH grant RO1-52126. The Center for Polymer Studies acknowledges the support of the NSF.",

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doi = "10.1006/jmbi.1999.3534",

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AU - Dokholyan, Nikolay V.

AU - Buldyrev, Sergey V.

AU - Stanley, H. Eugene

AU - Shakhnovich, Eugene I.

N1 - Funding Information: We thank R. S. Dokholyan for careful reading of the manuscript. N.V.D. is supported by NIH NRSA molecular biophysics predoctoral traineeship (GM08291-09) and by NIH postdoctoral fellowship (GM20251-01). E.I.S. is supported by NIH grant RO1-52126. The Center for Polymer Studies acknowledges the support of the NSF.

PY - 2000/3/10

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AB - Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their appearance determines folding cooperativity and drives the model protein into its folded conformation. Amino acid residues participating in those contacts may serve as 'accelerator pedals' used by molecular evolution to control protein folding rate. (C) 2000 Academic Press.

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Identifying the protein folding nucleus using molecular dynamics

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