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The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins

Content Provider	PubMed Central
Author	Shi, Yue Xia, Zhen Zhang, Jiajing Best, Robert Wu, Chuanjie Ponder, Jay W. Ren, Pengyu
Abstract	Development of the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes permanent electrostatic multipole moments through the quadrupole at each atom, and explicitly treats polarization effects in various chemical and physical environments. The atomic multipole electrostatic parameters for each amino acid residue type are derived from high-level gas phase quantum mechanical calculations via a consistent and extensible protocol. Molecular polarizability is modeled via a Thole-style damped interactive induction model based upon distributed atomic polarizabilities. Inter- and intramolecular polarization is treated in a consistent fashion via the Thole model. The intramolecular polarization model ensures transferability of electrostatic parameters among different conformations, as demonstrated by the agreement between QM and AMOEBA electrostatic potentials, and dipole moments of dipeptides. The backbone and side chain torsional parameters were determined by comparing to gas-phase QM (RI-TRIM MP2/CBS) conformational energies of dipeptides and to statistical distributions from the Protein Data Bank. Molecular dynamics simulations are reported for short peptides in explicit water to examine their conformational properties in solution. Overall the calculated conformational free energies and J-coupling constants are consistent with PDB statistics and experimental NMR results, respectively. In addition, the experimental crystal structures of a number of proteins are well maintained during molecular dynamics (MD) simulation. While further calculations are necessary to fully validate the force field, initial results suggest the AMOEBA polarizable multipole force field is able to describe the structure and energetics of peptides and proteins, in both gas-phase and solution environments.
Related Links	http://dx.doi.org/10.1021/ct4003702
Ending Page	4063
Page Count	18
Starting Page	4046
File Format	PDF
ISSN	15499618
e-ISSN	15499626
Journal	Journal of chemical theory and computation
Issue Number	9
Volume Number	9
Language	English
Publisher Date	2013-09-10
Access Restriction	Open
Subject Keyword	Physical and Theoretical Chemistry Computer Science Applications Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Physical and Theoretical Chemistry Computer Science Applications

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