New-generation amber united-atom force field.

New-generation amber united-atom force field. Research Abstract Details 

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New-generation amber united-atom force field. Abstract Text:

Lijiang Yang,Chun-Hu Tan,Meng-Juei Hsieh,Junmei Wang,Yong Duan,Piotr Cieplak,James Caldwell,Peter A Kollman,Ray Luo,

We have developed a new-generation Amber united-atom force field for simulations involving highly demanding conformational sampling such as protein folding and protein-protein binding. In the new united-atom force field, all hydrogens on aliphatic carbons in all amino acids are united with carbons except those on Calpha. Our choice of explicit representation of all protein backbone atoms aims at minimizing perturbation to protein backbone conformational distributions and to simplify development of backbone torsion terms. Tests with dipeptides and solvated proteins show that our goal is achieved quite successfully. The new united-atom force field uses the same new RESP charging scheme based on B3LYP/cc-pVTZ//HF/6-31g** quantum mechanical calculations in the PCM continuum solvent as that in the Duan et al. force field. van der Waals parameters are empirically refitted starting from published values with respect to experimental solvation free energies of amino acid side-chain analogues. The suitability of mixing new point charges and van der Waals parameters with existing Amber covalent terms is tested on alanine dipeptide and is found to be reasonable. Parameters for all new torsion terms are refitted based on the new point charges and the van der Waals parameters. Molecular dynamics simulations of three small globular proteins in the explicit TIP3P solvent are performed to test the overall stability and accuracy of the new united-atom force field. Good agreements between the united-atom force field and the Duan et al. all-atom force field for both backbone and side-chain conformations are observed. In addition, the per-step efficiency of the new united-atom force field is demonstrated for simulations in the implicit generalized Born solvent. A speedup around two is observed over the Duan et al. all-atom force field for the three tested small proteins. Finally, the efficiency gain of the new united-atom force field in conformational sampling is further demonstrated with a well-known toy protein folding system, an 18 residue polyalanine in distance-dependent dielectric. The new united-atom force field is at least a factor of 200 more efficient than the Duan et al. all-atom force field for ab initio folding of the tested peptide.

New-generation amber united-atom force field. Publishing Authors By Initials

L Yang,CH Tan,MJ Hsieh,J Wang,Y Duan,P Cieplak,J Caldwell,PA Kollman,R Luo,

For similar proteins research abstracts see: proteins research

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New-generation amber united-atom force field. Journal Published:

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

Journal: The journal of physical chemistry. B

VOLUME: 110

Page Numbers: 13166-76

Journal Abbreviation:

ISSN: 1520-6106

DAY: 6

MONTH: Jul

YEAR: 2006

New-generation amber united-atom force field. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 101157530

New-generation amber united-atom force field. Keywords Mesh Terms:

KEYWORDS: Proteins

MESH TERMS: chemistry

Chemical & Substance for Abstract: New-generation amber united-atom force field. Information

Substance Name: Proteins

Registry Number: 0

Grant and Affiliation Information for New-generation amber united-atom force field.

AFFILIATION: Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA.

Country: United States

AGENCY: United States NIGMS

GRANT: GM069620

ACRONYM: GM

MEDLINETA: J Phys Chem B

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