An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer

Klauda, Jeffery B.; Brooks, Bernard R.; MacKerell, Alexander D.; Venable, Richard M.; Pastor, Richard W.

doi:10.1021/jp0468096

Cited by 307 publications

(508 citation statements)

References 51 publications

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“…Isothermal compressibilities were calculated from (3) according to Klauda et al,62 where V is the volume, 〈δV 2 〉 is the volume fluctuation, and k B is Boltzmann's constant. The slope of the mean squared displacement versus time was used to determine the self-diffusivity for the periodic boundary condition, D PBC .…”

Section: Methodsmentioning

confidence: 99%

Polarizable Empirical Force Field for the Primary and Secondary Alcohol Series Based on the Classical Drude Model

Anisimov

Vorobyov

Roux

et al. 2007

J. Chem. Theory Comput.

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138

248

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A polarizable empirical force field based on the classical Drude oscillator has been developed for the aliphatic alcohol series. The model is optimized with emphasis on condensed-phase properties and is validated against a variety of experimental data. Transferability of the developed parameters is emphasized by the use of a single electrostatic model for the hydroxyl group throughout the alcohol series. Aliphatic moiety parameters were transferred from the polarizable alkane parameter set, with only the Lennard-Jones parameters on the carbon in methanol optimized. The developed model yields good agreement with pure solvent properties with the exception of the heats of vaporization of 1-propanol and 1-butanol, which are underestimated by approximately 6%; special LJ parameters for the oxygen in these two molecules that correct for this limitation are presented. Accurate treatment of the free energies of aqueous solvation required the use of atom-type specific O alcohol -O water LJ interaction terms, with specific terms used for the primary and secondary alcohols. With respect to gas phase properties the polarizable model overestimates experimental dipole moments and quantum mechanical interaction energies with water by approximately 10 and 8 %, respectively, a significant improvement over 44 and 46 % overestimations of the corresponding properties in the CHARMM22 fixed-charge additive model. Comparison of structural properties of the polarizable and additive models for the pure solvents and in aqueous solution shows significant differences indicating atomic details of intermolecular interactions to be sensitive to the applied force field. The polarizable model predicts pure solvent and aqueous phase dipole moment distributions for ethanol centered at 2.4 and 2.7 D, respectively, a significant increase over the gas phase value of 1.8 D, whereas in a solvent of lower polarity, benzene, a value of 1.9 is obtained. The ability of the polarizable model to yield changes in dipole moment as well as the reproduction of a range of condensed phase properties indicates its utility in the study of the properties of alcohols in a variety of condensed phase environments as well as representing an important step in the development of a comprehensive force field for biological molecules.

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Section: Methodsmentioning

confidence: 99%

Polarizable Empirical Force Field for the Primary and Secondary Alcohol Series Based on the Classical Drude Model

Anisimov

Vorobyov

Roux

et al. 2007

J. Chem. Theory Comput.

Self Cite

138

248

View full text Add to dashboard Cite

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“…34 The position and velocity scaling appropriate for the zero-tension algorithm was applied to the center-of-geometry positions of the molecules. For the allatom DPPC trajectories, we used three 50 ns segments from Klauda et al, 35,36 and the simulation protocol is described therein.…”

Section: A Simulation Protocolmentioning

confidence: 99%

An implicit solvent coarse-grained lipid model with correct stress profile

Sodt

Head‐Gordon

2010

The Journal of Chemical Physics

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We develop a coarse-grained parametrization strategy for lipid membranes that we illustrate for a dipalmitoylphosphatidylcholine bilayer. Our coarse-graining approach eliminates the high cost of explicit solvent but maintains more lipid interaction sites. We use a broad attractive tail-tail potential and extract realistic bonded potentials of mean force from all-atom simulations, resulting in a model with a sharp gel to fluid transition, a correct bending modulus, and overall very reasonable dynamics when compared with experiment. We also determine a quantitative stress profile and correct breakdown of contributions from lipid components when compared with detailed all-atom simulation benchmarks, which has been difficult to achieve for implicit membrane models. Such a coarse-grained lipid model will be necessary for efficiently simulating complex constructs of the membrane, such as protein assembly and lipid raft formation, within these nonaqueous chemical environments.

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“…The CHARMM version 27 force field was used to represent the protein 68 with parameters appropriate for retinal 69 , while the recently refined CHARMM saturated chain 70 , polyunsaturated chain 71 , and cholesterol 72 parameters were used to describe the lipids. Construction and equilibration were performed using CHARMM27 68,73 , while production calculations were performed using Blue Matter 74 , a molecular dynamics package specially written to take advantage of the Blue Gene/L hardware 74 .…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Dynamic Structure of Retinylidene Ligand of Rhodopsin Probed by Molecular Simulations

Lau

Grossfield

Feller

et al. 2007

Journal of Molecular Biology

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SummaryRhodopsin is currently the only available atomic-resolution template for understanding biological functions of the G protein-coupled receptor (GPCR) family. The structural basis for the phenomenal dark state stability of 11-cis-retinal bound to rhodopsin and its ultrafast photoreaction are active topics of research. In particular, the β-ionone ring of the retinylidene inverse agonist is crucial for the activation mechanism. We analyzed a total of 23 independent, 100-ns all-atom molecular dynamics simulations for rhodopsin embedded in a lipid bilayer in the microcanonical (N,V,E) ensemble. Analysis of intramolecular fluctuations predicts hydrogen-out-of-plane (HOOP) wagging modes of retinal consistent with those found in Raman vibrational spectroscopy. We show that sampling and ergodicity of the ensemble of simulations are crucial for determining the distribution of conformers of retinal bound to rhodopsin. The polyene chain is rigidly locked into a single, twisted conformation, consistent with the function of retinal as an inverse agonist in the dark state. Most surprisingly, the β-ionone ring is mobile within its binding pocket; interactions are nonspecific and the cavity is sufficiently large to enable structural heterogeneity. We find that retinal occupies two distinct conformations in the dark state, contrary to most previous assumptions. The β-ionone ring can rotate relative to the polyene chain, thereby populating both positively and negatively twisted 6-s-cis enantiomers. This result, while unexpected, strongly agrees with experimental solid-state 2 H NMR spectra. Correlation analysis identifies the residues most critical to controlling mobility of retinal; we find that Trp 265 moves away from the ionone ring prior to any conformational transition. Our findings reinforce how Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. HHS Public Access Graphical AbstractCover. Structure of retinal ligand of G protein-coupled receptor rhodopsin in the inverse agonist form as obtained from molecular simulations.

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An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer

Cited by 307 publications

References 51 publications

Polarizable Empirical Force Field for the Primary and Secondary Alcohol Series Based on the Classical Drude Model

Polarizable Empirical Force Field for the Primary and Secondary Alcohol Series Based on the Classical Drude Model

An implicit solvent coarse-grained lipid model with correct stress profile

Dynamic Structure of Retinylidene Ligand of Rhodopsin Probed by Molecular Simulations

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