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Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model.

De Vos O, Venable RM, Van Hecke T, Hummer G, Pastor RW, Ghysels A.

J Chem Theory Comput. 2018 Jul 10;14(7):3811-3824. doi: 10.1021/acs.jctc.8b00115. Epub 2018 Jun 28.


Parameterization of the CHARMM All-Atom Force Field for Ether Lipids and Model Linear Ethers.

Leonard AN, Pastor RW, Klauda JB.

J Phys Chem B. 2018 Jul 5;122(26):6744-6754. doi: 10.1021/acs.jpcb.8b02743. Epub 2018 Jun 21.


Molecular dynamics simulations of lipid nanodiscs.

Pourmousa M, Pastor RW.

Biochim Biophys Acta Biomembr. 2018 May 3. pii: S0005-2736(18)30133-0. doi: 10.1016/j.bbamem.2018.04.015. [Epub ahead of print]


Tertiary structure of apolipoprotein A-I in nascent high-density lipoproteins.

Pourmousa M, Song HD, He Y, Heinecke JW, Segrest JP, Pastor RW.

Proc Natl Acad Sci U S A. 2018 May 15;115(20):5163-5168. doi: 10.1073/pnas.1721181115. Epub 2018 Apr 30.


Structural properties of apolipoprotein A-I mimetic peptides that promote ABCA1-dependent cholesterol efflux.

Islam RM, Pourmousa M, Sviridov D, Gordon SM, Neufeld EB, Freeman LA, Perrin BS Jr, Pastor RW, Remaley AT.

Sci Rep. 2018 Feb 13;8(1):2956. doi: 10.1038/s41598-018-20965-2.


Graph-Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions.

Han K, Venable RM, Bryant AM, Legacy CJ, Shen R, Li H, Roux B, Gericke A, Pastor RW.

J Phys Chem B. 2018 Feb 1;122(4):1484-1494. doi: 10.1021/acs.jpcb.7b10730. Epub 2018 Jan 22.


Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations.

Leonard AN, Simmonett AC, Pickard FC 4th, Huang J, Venable RM, Klauda JB, Brooks BR, Pastor RW.

J Chem Theory Comput. 2018 Feb 13;14(2):948-958. doi: 10.1021/acs.jctc.7b00948. Epub 2018 Jan 9.


Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes.

Beaven AH, Sodt AJ, Pastor RW, Koeppe RE 2nd, Andersen OS, Im W.

J Chem Theory Comput. 2017 Oct 10;13(10):5054-5064. doi: 10.1021/acs.jctc.7b00400. Epub 2017 Sep 22.


Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes.

Ghysels A, Venable RM, Pastor RW, Hummer G.

J Chem Theory Comput. 2017 Jun 13;13(6):2962-2976. doi: 10.1021/acs.jctc.7b00039. Epub 2017 May 19.


Gramicidin A Channel Formation Induces Local Lipid Redistribution II: A 3D Continuum Elastic Model.

Sodt AJ, Beaven AH, Andersen OS, Im W, Pastor RW.

Biophys J. 2017 Mar 28;112(6):1198-1213. doi: 10.1016/j.bpj.2017.01.035.


Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation.

Beaven AH, Maer AM, Sodt AJ, Rui H, Pastor RW, Andersen OS, Im W.

Biophys J. 2017 Mar 28;112(6):1185-1197. doi: 10.1016/j.bpj.2017.01.028.


Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions.

Venable RM, Ingólfsson HI, Lerner MG, Perrin BS Jr, Camley BA, Marrink SJ, Brown FLH, Pastor RW.

J Phys Chem B. 2017 Apr 20;121(15):3443-3457. doi: 10.1021/acs.jpcb.6b09111. Epub 2017 Jan 6.


Identification of a novel lipid binding motif in apolipoprotein B by the analysis of hydrophobic cluster domains.

Gordon SM, Pourmousa M, Sampson M, Sviridov D, Islam R, Perrin BS Jr, Kemeh G, Pastor RW, Remaley AT.

Biochim Biophys Acta Biomembr. 2017 Feb;1859(2):135-145. doi: 10.1016/j.bbamem.2016.10.019. Epub 2016 Nov 1.


Nonadditive Compositional Curvature Energetics of Lipid Bilayers.

Sodt AJ, Venable RM, Lyman E, Pastor RW.

Phys Rev Lett. 2016 Sep 23;117(13):138104. Epub 2016 Sep 23.


Simulations of Membrane-Disrupting Peptides II: AMP Piscidin 1 Favors Surface Defects over Pores.

Perrin BS Jr, Fu R, Cotten ML, Pastor RW.

Biophys J. 2016 Sep 20;111(6):1258-1266. doi: 10.1016/j.bpj.2016.08.015.


Simulations of Membrane-Disrupting Peptides I: Alamethicin Pore Stability and Spontaneous Insertion.

Perrin BS Jr, Pastor RW.

Biophys J. 2016 Sep 20;111(6):1248-1257. doi: 10.1016/j.bpj.2016.08.014.


Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes.

Camley BA, Lerner MG, Pastor RW, Brown FL.

J Chem Phys. 2015 Dec 28;143(24):243113. doi: 10.1063/1.4932980.


Hexagonal Substructure and Hydrogen Bonding in Liquid-Ordered Phases Containing Palmitoyl Sphingomyelin.

Sodt AJ, Pastor RW, Lyman E.

Biophys J. 2015 Sep 1;109(5):948-55. doi: 10.1016/j.bpj.2015.07.036.


Mechanical properties of lipid bilayers from molecular dynamics simulation.

Venable RM, Brown FLH, Pastor RW.

Chem Phys Lipids. 2015 Nov;192:60-74. doi: 10.1016/j.chemphyslip.2015.07.014. Epub 2015 Jul 31. Review.


The Curvature Induction of Surface-Bound Antimicrobial Peptides Piscidin 1 and Piscidin 3 Varies with Lipid Chain Length.

Perrin BS Jr, Sodt AJ, Cotten ML, Pastor RW.

J Membr Biol. 2015 Jun;248(3):455-67. doi: 10.1007/s00232-014-9733-1. Epub 2014 Oct 8.


Determination of biomembrane bending moduli in fully atomistic simulations.

Levine ZA, Venable RM, Watson MC, Lerner MG, Shea JE, Pastor RW, Brown FL.

J Am Chem Soc. 2014 Oct 1;136(39):13582-5. doi: 10.1021/ja507910r. Epub 2014 Sep 16.


CHARMM all-atom additive force field for sphingomyelin: elucidation of hydrogen bonding and of positive curvature.

Venable RM, Sodt AJ, Rogaski B, Rui H, Hatcher E, MacKerell AD Jr, Pastor RW, Klauda JB.

Biophys J. 2014 Jul 1;107(1):134-45. doi: 10.1016/j.bpj.2014.05.034.


Molecular modeling of lipid membrane curvature induction by a peptide: more than simply shape.

Sodt AJ, Pastor RW.

Biophys J. 2014 May 6;106(9):1958-69. doi: 10.1016/j.bpj.2014.02.037.


High-resolution structures and orientations of antimicrobial peptides piscidin 1 and piscidin 3 in fluid bilayers reveal tilting, kinking, and bilayer immersion.

Perrin BS Jr, Tian Y, Fu R, Grant CV, Chekmenev EY, Wieczorek WE, Dao AE, Hayden RM, Burzynski CM, Venable RM, Sharma M, Opella SJ, Pastor RW, Cotten ML.

J Am Chem Soc. 2014 Mar 5;136(9):3491-504. doi: 10.1021/ja411119m. Epub 2014 Jan 22.


The molecular structure of the liquid-ordered phase of lipid bilayers.

Sodt AJ, Sandar ML, Gawrisch K, Pastor RW, Lyman E.

J Am Chem Soc. 2014 Jan 15;136(2):725-32. doi: 10.1021/ja4105667. Epub 2014 Jan 3.


Simulations of anionic lipid membranes: development of interaction-specific ion parameters and validation using NMR data.

Venable RM, Luo Y, Gawrisch K, Roux B, Pastor RW.

J Phys Chem B. 2013 Sep 5;117(35):10183-92. doi: 10.1021/jp401512z. Epub 2013 Aug 22.


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. doi: 10.1016/j.bpj.2013.03.048.


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 May 8;135(18):7064-72. doi: 10.1021/ja4026193. Epub 2013 Apr 30.


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. doi: 10.1016/j.chemphyslip.2013.01.005. Epub 2013 Jan 21.


The tension of a curved surface from simulation.

Sodt AJ, Pastor RW.

J Chem Phys. 2012 Dec 21;137(23):234101. doi: 10.1063/1.4769880.


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. doi: 10.1016/j.bpj.2012.03.014. Epub 2012 Apr 3.


Depth of α-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. doi: 10.1016/j.bpj.2011.12.051. Epub 2012 Feb 7.


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. doi: 10.1021/jp211904j. Epub 2012 Feb 29.


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. doi: 10.1002/jcc.21952. Epub 2011 Nov 21.


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. doi: 10.1091/mbc.E11-02-0114. Epub 2011 Jul 27.


Development of the CHARMM Force Field for Lipids.

Pastor RW, Mackerell AD Jr.

J Phys Chem Lett. 2011;2(13):1526-1532.


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. doi: 10.1021/jp2020148. Epub 2011 May 27.


Brownian dynamics simulations of ion transport through the VDAC.

Lee KI, Rui H, Pastor RW, Im W.

Biophys J. 2011 Feb 2;100(3):611-619. doi: 10.1016/j.bpj.2010.12.3708.


Molecular dynamics studies of ion permeation in VDAC.

Rui H, Lee KI, Pastor RW, Im W.

Biophys J. 2011 Feb 2;100(3):602-610. doi: 10.1016/j.bpj.2010.12.3711.


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. doi: 10.1016/j.bpj.2010.08.046.


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. doi: 10.1021/jp105549s.


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 AD Jr, Pastor RW.

J Phys Chem B. 2010 Jun 17;114(23):7830-43. doi: 10.1021/jp101759q.


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.


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. doi: 10.1021/jp9058966.


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. doi: 10.1016/j.carres.2009.08.003. Epub 2009 Aug 8.


CHARMM: the biomolecular simulation program.

Brooks BR, Brooks CL 3rd, Mackerell AD Jr, 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. doi: 10.1002/jcc.21287. Review.


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. doi: 10.1021/jp900843x.

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