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Richard Pastor, Ph.D.

Publications


Principal Investigator thumbnail image

Richard Pastor
Senior Investigator

P: +1 301 435 2035
F: +1 301 480 6496
pastorr@nhlbi.nih.gov


Full Publications Listing

Bending free energy from simulation: correspondence of planar and inverse hexagonal lipid phases.
Sodt AJ, Pastor RW.
Biophys J. 2013 May 21;104(10):2202-11.
[Text Abstract on PubMed]

Theory of Polymer-Nanopore Interactions Refined Using Molecular Dynamics Simulations.
Balijepalli A, Robertson JW, Reiner JE, Kasianowicz JJ, Pastor RW.
J Am Chem Soc. 2013 Apr 16.
[Text Abstract on PubMed]

Assessing smectic liquid-crystal continuum models for elastic bilayer deformations.
Lee KI, Pastor RW, Andersen OS, Im W.
Chem Phys Lipids. 2013 Apr;169:19-26.
[Text Abstract on PubMed]

Prediction, refinement, and persistency of transmembrane helix dimers in lipid bilayers using implicit and explicit solvent/lipid representations: microsecond molecular dynamics simulations of ErbB1/B2 and EphA1.
Zhang L, Sodt AJ, Venable RM, Pastor RW, Buck M.
Proteins. 2013 Mar;81(3):365-76.
[Text Abstract on PubMed]

The tension of a curved surface from simulation.
Sodt AJ, Pastor RW.
J Chem Phys. 2012 Dec 21;137(23):234101.
[Text Abstract on PubMed]

Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers.
Kim T, Lee KI, Morris P, Pastor RW, Andersen OS, Im W.
Biophys. J. 2012 Apr 4;102(7):1551-60.
[Text Abstract on PubMed]

Structure and elasticity of lipid membranes with genistein and daidzein bioflavinoids using X-ray scattering and MD simulations.
Raghunathan M, Zubovski Y, Venable RM, Pastor RW, Nagle JF, Tristram-Nagle S.
J Phys Chem B. 2012 Apr 5;116(13):3918-27.
[Text Abstract on PubMed]

Depth of a-synuclein in a bilayer determined by fluorescence, neutron reflectometry, and computation.
Pfefferkorn CM, Heinrich F, Sodt AJ, Maltsev AS, Pastor RW, Lee JC.
Biophys. J. 2012 Feb 8;102(3):613-21.
[Text Abstract on PubMed]

Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores.
Lee KI, Jo S, Rui H, Egwolf B, Roux B, Pastor RW, Im W.
J Comput Chem. 2012 Jan 30;33(3):331-9.
[Text Abstract on PubMed]

Evidence for a fence that impedes the diffusion of phosphatidylinositol 4,5-bisphosphate out of the forming phagosomes of macrophages.
Golebiewska U, Kay JG, Masters T, Grinstein S, Im W, Pastor RW, Scarlata S, McLaughlin S.
Mol. Biol. Cell. 2011 Sep;22(18):3498-507.
[Text Abstract on PubMed]

Coarse-grained model for PEGylated lipids: effect of PEGylation on the size and shape of self-assembled structures.
Lee H, Pastor RW.
J Phys Chem B. 2011 Jun 23;115(24):7830-7.
[Text Abstract on PubMed]

Brownian dynamics simulations of ion transport through the VDAC.
Lee KI, Rui H, Pastor RW, Im W.
Biophys J. 2011 Feb 2;100(3):611-9.
[Text Abstract on PubMed]

Molecular dynamics studies of ion permeation in VDAC.
Rui H, Lee KI, Pastor RW, Im W.
Biophys J. 2011 Feb 2;100(3):602-10.
[Text Abstract on PubMed]

Development of the CHARMM Force Field for Lipids.
Pastor RW, Mackerell AD Jr.
J Phys Chem Lett. 2011 01 ;2(13):1526-1532.
[Text Abstract on PubMed]

Single molecule diffusion of membrane-bound proteins: window into lipid contacts and bilayer dynamics.
Knight JD, Lerner MG, Marcano-Velázquez JG, Pastor RW, Falke JJ.
Biophys J. 2010 Nov 3;99(9):2879-87.
[Text Abstract on PubMed]

Comparing simulated and experimental translation and rotation constants: range of validity for viscosity scaling.
Venable RM, Hatcher E, Guvench O, Mackerell AD Jr, Pastor RW.
J Phys Chem B. 2010 Oct 7;114(39):12501-7.
[Text Abstract on PubMed]

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types.
Klauda JB, Venable RM, Freites JA, O'Connor JW, Tobias DJ, Mondragon-Ramirez C, Vorobyov I, MacKerell, Pastor RW.
J Phys Chem B. 2010 Jun 17;114(23):7830-43.
[Text Abstract on PubMed]

Molecular dynamics studies of the conformation of sorbitol.
Lerbret A, Mason PE, Venable RM, Cesàro A, Saboungi ML, Pastor RW, Brady JW.
Carbohydr. Res. 2009 Nov 2;344(16):2229-35.
[Text Abstract on PubMed]

A coarse-grained model for polyethylene oxide and polyethylene glycol: conformation and hydrodynamics.
Lee H, de Vries AH, Marrink SJ, Pastor RW.
J Phys Chem B. 2009 Oct 8;113(40):13186-94.
[Text Abstract on PubMed]

CHARMM: the biomolecular simulation program.
Brooks BR, Brooks, Mackerell, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M.
J Comput Chem. 2009 Jul 30;30(10):1545-614.
[Text Abstract on PubMed]

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses.
Guvench O, Hatcher ER, Venable RM, Pastor RW, Mackerell AD.
J Chem Theory Comput. 2009 Aug 20;5(9):2353-2370.
[Text Abstract on PubMed]

Molecular dynamics simulations of PIP2 and PIP3 in lipid bilayers: determination of ring orientation, and the effects of surface roughness on a Poisson-Boltzmann description.
Li Z, Venable RM, Rogers LA, Murray D, Pastor RW.
Biophys. J. 2009 Jul 8;97(1):155-63.
[Text Abstract on PubMed]

Comparison of the extended isotropic periodic sum and particle mesh Ewald methods for simulations of lipid bilayers and monolayers.
Venable RM, Chen LE, Pastor RW.
J Phys Chem B. 2009 Apr 30;113(17):5855-62.
[Text Abstract on PubMed]

Additive empirical force field for hexopyranose monosaccharides.
Guvench O, Greene SN, Kamath G, Brady JW, Venable RM, Pastor RW, Mackerell.
J Comput Chem. 2008 Nov 30;29(15):2543-64.
[Text Abstract on PubMed]

Structure and dynamics of helix-0 of the N-BAR domain in lipid micelles and bilayers.
Löw C, Weininger U, Lee H, Schweimer K, Neundorf I, Beck-Sickinger AG, Pastor RW, Balbach J.
Biophys. J. 2008 Nov 1;95(9):4315-23.
[Text Abstract on PubMed]

Pathways and populations: stereoelectronic insights into the exocyclic torsion of 5-(hydroxymethyl)tetrahydropyran.
Woodcock HL, Brooks BR, Pastor RW.
J. Am. Chem. Soc. 2008 May 21;130(20):6345-7.
[Text Abstract on PubMed]

Collective and noncollective models of NMR relaxation in lipid vesicles and multilayers.
Klauda JB, Eldho NV, Gawrisch K, Brooks BR, Pastor RW.
J Phys Chem B. 2008 May 15;112(19):5924-9.
[Text Abstract on PubMed]

Langevin network model of myosin.
Miller BT, Zheng W, Venable RM, Pastor RW, Brooks BR.
J Phys Chem B. 2008 May 15;112(19):6274-81.
[Text Abstract on PubMed]

Rotation of lipids in membranes: molecular dynamics simulation, 31P spin-lattice relaxation, and rigid-body dynamics.
Klauda JB, Roberts MF, Redfield AG, Brooks BR, Pastor RW.
Biophys. J. 2008 Apr 15;94(8):3074-83.
[Text Abstract on PubMed]

Molecular dynamics studies of polyethylene oxide and polyethylene glycol: hydrodynamic radius and shape anisotropy.
Lee H, Venable RM, Mackerell AD Jr, Pastor RW.
Biophys J. 2008 Aug ;95(4):1590-9.
[Text Abstract on PubMed]

Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-ethoxy tetrahydropyran.
Woodcock HL, Moran D, Pastor RW, MacKerell, Brooks BR.
Biophys. J. 2007 Jul 1;93(1):1-10.
[Text Abstract on PubMed]

Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method.
Klauda JB, Wu X, Pastor RW, Brooks BR.
J Phys Chem B. 2007 May 3;111(17):4393-400.
[Text Abstract on PubMed]

Dynamical motions of lipids and a finite size effect in simulations of bilayers.
Klauda JB, Brooks BR, Pastor RW.
J Chem Phys. 2006 Oct 14;125(14):144710.
[Text Abstract on PubMed]

Simulation-based methods for interpreting x-ray data from lipid bilayers.
Klauda JB, Kucerka N, Brooks BR, Pastor RW, Nagle JF.
Biophys. J. 2006 Apr 15;90(8):2796-807.
[Text Abstract on PubMed]

Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme.
Buck M, Bouguet-Bonnet S, Pastor RW, MacKerell.
Biophys. J. 2006 Feb 15;90(4):L36-8.
[Text Abstract on PubMed]

Molecular dynamics simulations of the influenza hemagglutinin fusion peptide in micelles and bilayers: conformational analysis of peptide and lipids.
Lagüe P, Roux B, Pastor RW.
J. Mol. Biol. 2005 Dec 16;354(5):1129-41.
[Text Abstract on PubMed]

A molecular dynamics study of the response of lipid bilayers and monolayers to trehalose.
Skibinsky A, Venable RM, Pastor RW.
Biophys. J. 2005 Dec;89(6):4111-21.
[Text Abstract on PubMed]

Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis.
Klauda JB, Pastor RW, Brooks BR.
J Phys Chem B. 2005 Aug 25;109(33):15684-6.
[Text Abstract on PubMed]

An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer.
Klauda JB, Brooks BR, MacKerell, Venable RM, Pastor RW.
J Phys Chem B. 2005 Mar 24;109(11):5300-11.
[Text Abstract on PubMed]

Discriminating the helical forms of peptides by NMR and molecular dynamics simulation.
Freedberg DI, Venable RM, Rossi A, Bull TE, Pastor RW.
J. Am. Chem. Soc. 2004 Aug 25;126(33):10478-84.
[Text Abstract on PubMed]

Application of NMR, molecular simulation, and hydrodynamics to conformational analysis of trisaccharides.
Dixon AM, Venable R, Widmalm G, Bull TE, Pastor RW.
Biopolymers. 2003 Aug;69(4):448-60.
[Text Abstract on PubMed]

Sample size considerations for establishing clinical bioequivalence of allergen formulations.
Rabin RL, Slater JE, Lachenbruch P, Pastor RW.
Arb Paul Ehrlich Inst Bundesamt Sera Impfstoffe Frankf A M. 2003(94):24-33.
[Text Abstract on PubMed]

Micelle-bound conformation of a hairpin-forming peptide: combined NMR and molecular dynamics study.
Dixon AM, Venable RM, Pastor RW, Bull TE.
Biopolymers. 2002 Nov 15;65(4):284-98.
[Text Abstract on PubMed]

Lipid bilayers, NMR relaxation, and computer simulations.
Pastor RW, Venable RM, Feller SE.
Acc. Chem. Res. 2002 Jun;35(6):438-46.
[Text Abstract on PubMed]

Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions.
Dolan EA, Venable RM, Pastor RW, Brooks BR.
Biophys. J. 2002 May;82(5):2317-25.
[Text Abstract on PubMed]

ICAM-1 enhances MHC-peptide activation of CD8(+) T cells without an organized immunological synapse.
Goldstein JS, Chen T, Gubina E, Pastor RW, Kozlowski S.
Eur. J. Immunol. 2000 Nov;30(11):3266-70.
[Text Abstract on PubMed]

The determination of equivalent doses of standardized allergen vaccines.
Slater JE, Pastor RW.
J. Allergy Clin. Immunol. 2000 Mar;105(3):468-74.
[Text Abstract on PubMed]

The stability of house dust mite allergens in glycerinated extracts.
Soldatova LN, Paupore EJ, Burk SH, Pastor RW, Slater JE.
J. Allergy Clin. Immunol. 2000 Mar;105(3):482-8.
[Text Abstract on PubMed]

Statistical considerations in the establishment of release criteria for allergen vaccines in the USA.
Slater JE, Gam AA, Solanki MD, Burk SH, May FM, Pastor RW.
Arb Paul Ehrlich Inst Bundesamt Sera Impfstoffe Frankf A M. 1999(93):47-55; discussion 56.
[Text Abstract on PubMed]

Solution structure and dynamics of linked cell attachment modules of mouse fibronectin containing the RGD and synergy regions: comparison with the human fibronectin crystal structure.
Copié V, Tomita Y, Akiyama SK, Aota S, Yamada KM, Venable RM, Pastor RW, Krueger S, Torchia DA.
J. Mol. Biol. 1998 Apr 3;277(3):663-82.
[Text Abstract on PubMed]

Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies.
Feller SE, Yin D, Pastor RW, MacKerell.
Biophys. J. 1997 Nov;73(5):2269-79.
[Text Abstract on PubMed]

Length scales of lipid dynamics and molecular dynamics.
Feller SE, Pastor RW.
Pac Symp Biocomput. 1997:142-50.
[Text Abstract on PubMed]

On simulating lipid bilayers with an applied surface tension: periodic boundary conditions and undulations.
Feller SE, Pastor RW.
Biophys. J. 1996 Sep;71(3):1350-5.
[Text Abstract on PubMed]

A method for characterizing transition concertedness from polymer dynamics computer simulations.
Brown ML, Venable RM, Pastor RW.
Biopolymers. 1995 Jan;35(1):31-46.
[Text Abstract on PubMed]

Molecular dynamics simulations of a lipid bilayer and of hexadecane: an investigation of membrane fluidity.
Venable RM, Zhang Y, Hardy BJ, Pastor RW.
Science. 1993 Oct 8;262(5131):223-6.
[Text Abstract on PubMed]

Conformational states of a TT mismatch from molecular dynamics simulation of duplex d (CGCGATTCGCG).
Venable RM, Widmalm G, Brooks BR, Egan W, Pastor RW.
Biopolymers. 1992 Jul;32(7):783-94.
[Text Abstract on PubMed]

Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible.
Barbato G, Ikura M, Kay LE, Pastor RW, Bax A.
Biochemistry. 1992 Jun 16;31(23):5269-78.
[Text Abstract on PubMed]

Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide.
Loncharich RJ, Brooks BR, Pastor RW.
Biopolymers. 1992 May;32(5):523-35.
[Text Abstract on PubMed]

Mean field stochastic boundary molecular dynamics simulation of a phospholipid in a membrane.
De Loof H, Harvey SC, Segrest JP, Pastor RW.
Biochemistry. 1991 Feb 26;30(8):2099-113.
[Text Abstract on PubMed]

Model for the structure of the lipid bilayer.
Pastor RW, Venable RM, Karplus M.
Proc. Natl. Acad. Sci. U.S.A. 1991 Feb 1;88(3):892-6.
[Text Abstract on PubMed]

Synexin: molecular mechanism of calcium-dependent membrane fusion and voltage-dependent calcium-channel activity. Evidence in support of the "hydrophobic bridge hypothesis" for exocytotic membrane fusion.
Pollard HB, Rojas E, Pastor RW, Rojas EM, Guy HR, Burns AL.
Ann. N. Y. Acad. Sci. 1991;635:328-51.
[Text Abstract on PubMed]

Theoretically determined three-dimensional structures for amphipathic segments of the HIV-1 gp41 envelope protein.
Venable RM, Pastor RW, Brooks BR, Carson FW.
AIDS Res. Hum. Retroviruses. 1989 Feb;5(1):7-22.
[Text Abstract on PubMed]

Frictional models for stochastic simulations of proteins.
Venable RM, Pastor RW.
Biopolymers. 1988 Jun;27(6):1001-14.
[Text Abstract on PubMed]

Theoretically determined three-dimensional structure for the repeating tetrapeptide unit of the circumsporozoite coat protein of the malaria parasite Plasmodium falciparum.
Brooks BR, Pastor RW, Carson FW.
Proc. Natl. Acad. Sci. U.S.A. 1987 Jul;84(13):4470-4.
[Text Abstract on PubMed]

Local sequence patterns of hydrophobicity and solvent accessibility in soluble globular proteins.
Lipman DJ, Pastor RW, Lee B.
Biopolymers. 1987 Jan;26(1):17-26.
[Text Abstract on PubMed]

A recognition site on synthetic helical oligonucleotides for monoclonal anti-native DNA autoantibody.
Stollar BD, Zon G, Pastor RW.
Proc. Natl. Acad. Sci. U.S.A. 1986 Jun;83(12):4469-73.
[Text Abstract on PubMed]

Resonance raman studies of macrocyclic complexes. 1. Structural and electronic effects in synthetic metal(II) porphyrin analogues.
Woodruff WH, Pastor RW, Dabrowiak JC.
J. Am. Chem. Soc. 1976 Dec 8;98(25):7999-8006.
[Text Abstract on PubMed]

Resonance raman studies of macrocyclic complexes. 2. Antiresonance and selective intensity enhancement in synthetic metal(II) porphyrin analogues.
Nafie LA, Pastor RW, Dabrowiak JC, Woodruff WH.
J. Am. Chem. Soc. 1976 Dec 8;98(25):8007-14.
[Text Abstract on PubMed]

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