Dataset Information

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.

ABSTRACT: The AMOEBA polarizable atomic multipole force field for nucleic acids is presented. Valence and electrostatic parameters were determined from high-level quantum mechanical data, including structures, conformational energy, and electrostatic potentials, of nucleotide model compounds. Previously derived parameters for the phosphate group and nucleobases were incorporated. A total of over 35 ?s of condensed-phase molecular dynamics simulations of DNA and RNA molecules in aqueous solution and crystal lattice were performed to validate and refine the force field. The solution and/or crystal structures of DNA B-form duplexes, RNA duplexes, and hairpins were captured with an average root-mean-squared deviation from NMR structures below or around 2.0 Å. Structural details, such as base pairing and stacking, sugar puckering, backbone and ?-torsion angles, groove geometries, and crystal packing interfaces, agreed well with NMR and/or X-ray. The interconversion between A- and B-form DNAs was observed in ethanol-water mixtures at 328 K. Crystal lattices of B- and Z-form DNA and A-form RNA were examined with simulations. For the RNA tetraloop, single strand tetramers, and HIV TAR with 29 residues, the simulated conformational states, 3 J-coupling, nuclear Overhauser effect, and residual dipolar coupling data were compared with NMR results. Starting from a totally unstacked/unfolding state, the rCAAU tetranucleotide was folded into A-form-like structures during ?1 ?s molecular dynamics simulations.

SUBMITTER: Zhang C

PROVIDER: S-EPMC5893433 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.

Zhang Changsheng C Lu Chao C Jing Zhifeng Z Wu Chuanjie C Piquemal Jean-Philip JP Ponder Jay W JW Ren Pengyu P

Journal of chemical theory and computation 20180306 4

The AMOEBA polarizable atomic multipole force field for nucleic acids is presented. Valence and electrostatic parameters were determined from high-level quantum mechanical data, including structures, conformational energy, and electrostatic potentials, of nucleotide model compounds. Previously derived parameters for the phosphate group and nucleobases were incorporated. A total of over 35 μs of condensed-phase molecular dynamics simulations of DNA and RNA molecules in aqueous solution and crysta ...[more]

PMID: 29438622

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Project description:Modeling the change in the electrostatics of organic molecules upon moving from vacuum into solvent, due to polarization, has long been an interesting problem. In vacuum, experimental values for the dipole moments and polarizabilities of small, rigid molecules are known to high accuracy; however, it has generally been difficult to determine these quantities for a polar molecule in water. A theoretical approach introduced by Onsager [J. Am. Chem. Soc. 58, 1486 (1936)] used vacuum properties of small molecules, including polarizability, dipole moment, and size, to predict experimentally known permittivities of neat liquids via the Poisson equation. Since this important advance in understanding the condensed phase, a large number of computational methods have been developed to study solutes embedded in a continuum via numerical solutions to the Poisson-Boltzmann equation. Only recently have the classical force fields used for studying biomolecules begun to include explicit polarization in their functional forms. Here the authors describe the theory underlying a newly developed polarizable multipole Poisson-Boltzmann (PMPB) continuum electrostatics model, which builds on the atomic multipole optimized energetics for biomolecular applications (AMOEBA) force field. As an application of the PMPB methodology, results are presented for several small folded proteins studied by molecular dynamics in explicit water as well as embedded in the PMPB continuum. The dipole moment of each protein increased on average by a factor of 1.27 in explicit AMOEBA water and 1.26 in continuum solvent. The essentially identical electrostatic response in both models suggests that PMPB electrostatics offers an efficient alternative to sampling explicit solvent molecules for a variety of interesting applications, including binding energies, conformational analysis, and pK(a) prediction. Introduction of 150 mM salt lowered the electrostatic solvation energy between 2 and 13 kcalmole, depending on the formal charge of the protein, but had only a small influence on dipole moments.

Dataset Information

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.

Publications

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.

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