NDLI: Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins.

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Liquid-structure forces and electrostatic modulation of biomolecular interactions in solution.

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Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.

Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins.

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Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Rojas, Ana V. Liwo, Adam Scheraga, Harold A.
Description	Author Affiliation: Rojas AV ( Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.)
Abstract	The implementation of molecular dynamics with the united-residue (UNRES) force field is extended to treat multichain proteins. Constant temperature was maintained in the simulations with Berendsen or Langevin thermostats. The method was tested on three alpha-helical proteins (1G6U and GCN4-p1, each with two chains, and 1C94, with four chains). Simulations were carried out for both the isolated single chains and the multichain complexes. The proteins were folded by starting from the extended conformation with random initial velocities and with the chains parallel to each other. No symmetry constraints or structure information were included for the single chains or the multichain complexes. In the case of single-chain simulations, a high percentage of the trajectories (100% for 1G6U, 90% for GCN4-p1, and 80% for 1C94) converged to nativelike structures (assumed as the experimental structure of a monomer in the multichain complex), showing that, for the proteins studied in this work with the UNRES force field, the interactions between chains are not critical for stabilization of the individual chains. In the case of multichain simulations, the native structures of the 1G6U and GCN4-p1 complexes, but not that of 1C94, are predicted successfully. The association of the subunits does not follow a unique mechanism; the monomers were observed to fold both before and simultaneously with their association.
ISSN	15206106
e-ISSN	15205207
Journal	The Journal of Physical Chemistry B
Issue Number	1
Volume Number	111
Language	English
Publisher	American Chemical Society (United States)
Publisher Date	2007-01-11
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Proteins Chemistry Biophysics Chemistry, Physical Computer Simulation Dimerization Leucine Macromolecular Substances Models, Molecular Models, Statistical Molecular Conformation Protein Conformation Protein Structure, Secondary Protein Structure, Tertiary Temperature Time Factors Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Physical chemistry
Content Type	Text
Resource Type	Article
Subject	Surfaces, Coatings and Films Materials Chemistry Medicine Physical and Theoretical Chemistry

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