Jose D Faraldo-Gómez

Jose D Faraldo-Gómez

UNVERIFIED PROFILE

Are you Jose D Faraldo-Gómez?   Register this Author

Register author
Jose D Faraldo-Gómez

Jose D Faraldo-Gómez

Publications by authors named "Jose D Faraldo-Gómez"

Are you Jose D Faraldo-Gómez?   Register this Author

63Publications

652Reads

42Profile Views

Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics.

J Comput Chem 2020 Feb 11;41(5):449-459. Epub 2019 Oct 11.

Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland, 20814.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/jcc.26075DOI Listing
February 2020

DHHC20 Palmitoyl-Transferase Reshapes the Membrane to Foster Catalysis.

Biophys J 2020 Feb 14;118(4):980-988. Epub 2019 Nov 14.

Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bpj.2019.11.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7036711PMC
February 2020

Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles.

Biophys J 2020 Feb 15. Epub 2020 Feb 15.

Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bpj.2020.02.005DOI Listing
February 2020

Large-scale state-dependent membrane remodeling by a transporter protein.

Elife 2019 12 19;8. Epub 2019 Dec 19.

Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.50576DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6957315PMC
December 2019

Molecular mechanisms of human P2X3 receptor channel activation and modulation by divalent cation bound ATP.

Elife 2019 06 24;8. Epub 2019 Jun 24.

Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.47060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6590987PMC
June 2019

Membrane physiologists of all kinds meet at Woods Hole.

J Gen Physiol 2019 03 22;151(3):273. Epub 2019 Feb 22.

Theoretical Molecular Biophysics Laboratory, National Heart, Lung & Blood Institute, National Institutes of Health, Bethesda, MD

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1085/jgp.201912340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400522PMC
March 2019

TRPV1 pore turret dictates distinct DkTx and capsaicin gating.

Proc Natl Acad Sci U S A 2018 12 21;115(50):E11837-E11846. Epub 2018 Nov 21.

The Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Karem, 9112102 Jerusalem, Israel;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1809662115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294906PMC
December 2018

Confidence Analysis of DEER Data and Its Structural Interpretation with Ensemble-Biased Metadynamics.

Biophys J 2018 10 16;115(7):1200-1216. Epub 2018 Aug 16.

Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S00063495183093
Publisher Site
http://dx.doi.org/10.1016/j.bpj.2018.08.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6170522PMC
October 2018

Membrane plasticity facilitates recognition of the inhibitor oligomycin by the mitochondrial ATP synthase rotor.

Biochim Biophys Acta Bioenerg 2018 09 7;1859(9):789-796. Epub 2018 Apr 7.

Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Room 5N307A, Bethesda, MD 20892, United States. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbabio.2018.03.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6176861PMC
September 2018

Broadly conserved Na-binding site in the N-lobe of prokaryotic multidrug MATE transporters.

Proc Natl Acad Sci U S A 2018 07 18;115(27):E6172-E6181. Epub 2018 Jun 18.

Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1802080115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6142261PMC
July 2018

Mitochondrial ATP synthase dimers spontaneously associate due to a long-range membrane-induced force

J Gen Physiol 2018 05 11;150(5):763-770. Epub 2018 Apr 11.

Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1085/jgp.201812033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5940253PMC
May 2018

High-resolution cryo-EM analysis of the yeast ATP synthase in a lipid membrane.

Science 2018 05 12;360(6389). Epub 2018 Apr 12.

Department of Biological Chemistry and Molecular Biology, Chicago Medical School, Rosalind Franklin University, 3333 Green Bay Road, North Chicago, IL 60064, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.aas9699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5948177PMC
May 2018

The prokaryotic Na/Ca exchanger NCX_Mj transports Na and Ca in a 3:1 stoichiometry.

J Gen Physiol 2018 01 13;150(1):51-65. Epub 2017 Dec 13.

Membrane Transport Biophysics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD

View Article

Download full-text PDF

Source
http://www.jgp.org/lookup/doi/10.1085/jgp.201711897
Publisher Site
http://dx.doi.org/10.1085/jgp.201711897DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749117PMC
January 2018

Asymmetry of inverted-topology repeats in the AE1 anion exchanger suggests an elevator-like mechanism.

J Gen Physiol 2017 Dec 22;149(12):1149-1164. Epub 2017 Nov 22.

Computational Structural Biology Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1085/jgp.201711836DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5715908PMC
December 2017

Predicted Structures of the Proton-Bound Membrane-Embedded Rotor Rings of the Saccharomyces cerevisiae and Escherichia coli ATP Synthases.

J Phys Chem B 2017 04 24;121(15):3297-3307. Epub 2016 Oct 24.

Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jpcb.6b08051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5593136PMC
April 2017

Atomistic simulations indicate the c-subunit ring of the FF ATP synthase is not the mitochondrial permeability transition pore.

Elife 2017 02 10;6. Epub 2017 Feb 10.

Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.23781DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5323039PMC
February 2017

Structure and mechanism of the ATP synthase membrane motor inferred from quantitative integrative modeling.

J Gen Physiol 2016 12 7;148(6):441-457. Epub 2016 Nov 7.

Theoretical Molecular Biophysics Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1085/jgp.201611679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5129741PMC
December 2016

Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger.

Nat Struct Mol Biol 2016 06 16;23(6):590-599. Epub 2016 May 16.

Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nsmb.3230DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918766PMC
June 2016

Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg(2+) through the SOMA string method.

J Comput Chem 2016 Mar 7;37(6):575-86. Epub 2015 Jul 7.

Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, Frankfurt-am-Main, DE 60438, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/jcc.23991DOI Listing
March 2016

Structural insights into the mechanism of activation of the TRPV1 channel by a membrane-bound tarantula toxin.

Elife 2016 Feb 10;5. Epub 2016 Feb 10.

Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.11273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4764579PMC
February 2016

Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions.

Biophys J 2015 Jun;108(12):2779-82

Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bpj.2015.05.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4472218PMC
June 2015

On the principle of ion selectivity in Na+/H+-coupled membrane proteins: experimental and theoretical studies of an ATP synthase rotor.

Proc Natl Acad Sci U S A 2015 Mar 23;112(10):E1057-66. Epub 2015 Feb 23.

Theoretical Molecular Biophysics Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892; Theoretical Molecular Biophysics Group and

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1421202112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364180PMC
March 2015

Sodium recognition by the Na+/Ca2+ exchanger in the outward-facing conformation.

Proc Natl Acad Sci U S A 2014 Dec 2;111(50):E5354-62. Epub 2014 Dec 2.

Theoretical Molecular Biophysics Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892; and

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1415751111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273333PMC
December 2014

High-resolution structure and mechanism of an F/V-hybrid rotor ring in a Na⁺-coupled ATP synthase.

Nat Commun 2014 Nov 10;5:5286. Epub 2014 Nov 10.

1] Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany [2] Cluster of Excellence Macromolecular Complexes, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms6286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228694PMC
November 2014

Ceramide-lipid interactions studied by MD simulations and solid-state NMR.

Biochim Biophys Acta 2014 Oct 29;1838(10):2511-9. Epub 2014 May 29.

Institute of Biophysical Chemistry, J.W. Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbamem.2014.05.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137758PMC
October 2014

Channeling your inner energy.

Nat Struct Mol Biol 2014 Jul;21(7):575-7

Theoretical Molecular Biophysics Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nsmb.2854DOI Listing
July 2014

A new type of Na(+)-driven ATP synthase membrane rotor with a two-carboxylate ion-coupling motif.

PLoS Biol 2013 25;11(6):e1001596. Epub 2013 Jun 25.

Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pbio.1001596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692424PMC
January 2014

Two-state dynamics of the SH3-SH2 tandem of Abl kinase and the allosteric role of the N-cap.

Proc Natl Acad Sci U S A 2013 Sep 19;110(36):E3372-80. Epub 2013 Aug 19.

Department of Physical Chemistry and Institute of Biotechnology, University of Granada, 18071 Granada, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1303966110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767523PMC
September 2013

String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems.

J Chem Theory Comput 2013 Sep;9(9):4140-4154

Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, DE-60438, Frankfurt-am-Main, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ct400469wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981481PMC
September 2013

Dynamics of the antigen-binding grooves in CD1 proteins: reversible hydrophobic collapse in the lipid-free state.

J Biol Chem 2013 Jul 15;288(27):19528-36. Epub 2013 May 15.

Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Max von Laue Strasse 3, 60438 Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/jbc.M113.470179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707654PMC
July 2013

A c subunit with four transmembrane helices and one ion (Na+)-binding site in an archaeal ATP synthase: implications for c ring function and structure.

J Biol Chem 2012 Nov 24;287(47):39327-37. Epub 2012 Sep 24.

Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/jbc.M112.411223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3501044PMC
November 2012

Structure of the yeast F1Fo-ATP synthase dimer and its role in shaping the mitochondrial cristae.

Proc Natl Acad Sci U S A 2012 Aug 3;109(34):13602-7. Epub 2012 Aug 3.

Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1204593109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427116PMC
August 2012

Engineering rotor ring stoichiometries in the ATP synthase.

Proc Natl Acad Sci U S A 2012 Jun 24;109(25):E1599-608. Epub 2012 May 24.

Department of Structural Biology, Max-Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1120027109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3382517PMC
June 2012

Structure of the c(10) ring of the yeast mitochondrial ATP synthase in the open conformation.

Nat Struct Mol Biol 2012 Apr 15;19(5):485-91, S1. Epub 2012 Apr 15.

Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, Chicago, Illinois, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nsmb.2284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3343227PMC
April 2012

Natural variations at position 93 of the invariant Vα24-Jα18 α chain of human iNKT-cell TCRs strongly impact on CD1d binding.

Eur J Immunol 2012 Jan 28;42(1):248-55. Epub 2011 Nov 28.

Academic Unit of Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/eji.201141956DOI Listing
January 2012

Promiscuous archaeal ATP synthase concurrently coupled to Na+ and H+ translocation.

Proc Natl Acad Sci U S A 2012 Jan 4;109(3):947-52. Epub 2012 Jan 4.

Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1115796109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3271924PMC
January 2012

Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins.

Proc Natl Acad Sci U S A 2011 Dec 14;108(49):E1285-92. Epub 2011 Nov 14.

Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://www.pnas.org/cgi/doi/10.1073/pnas.1112534108
Publisher Site
http://dx.doi.org/10.1073/pnas.1112534108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3241785PMC
December 2011

Molecular mechanism of selective recruitment of Syk kinases by the membrane antigen-receptor complex.

J Biol Chem 2011 Jul 21;286(29):25872-81. Epub 2011 May 21.

Max Planck Institute of Biophysics and the Cluster of Excellence Macromolecular Complexes, 60438 Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/jbc.M111.223321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3138262PMC
July 2011

Modeling and simulation of ion-coupled and ATP-driven membrane proteins.

Curr Opin Struct Biol 2011 Apr 16;21(2):173-9. Epub 2011 Feb 16.

Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Max-von-Laue-Str 3, 60438 Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.sbi.2011.01.013DOI Listing
April 2011

GRIFFIN: A versatile methodology for optimization of protein-lipid interfaces for membrane protein simulations.

J Chem Theory Comput 2011 Apr;7(4):1167-1176

Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/abs/10.1021/ct100576m
Publisher Site
http://dx.doi.org/10.1021/ct100576mDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3972769PMC
April 2011

Structural and energetic basis for H+ versus Na+ binding selectivity in ATP synthase Fo rotors.

Biochim Biophys Acta 2010 Jun-Jul;1797(6-7):763-72. Epub 2010 Apr 21.

Theoretical Molecular Biophysics Group, Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbabio.2010.04.014DOI Listing
January 2011

Microscopic rotary mechanism of ion translocation in the F(o) complex of ATP synthases.

Nat Chem Biol 2010 Dec 24;6(12):891-9. Epub 2010 Oct 24.

Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nchembio.457DOI Listing
December 2010

Mechanism of substrate shuttling by the acyl-carrier protein within the fatty acid mega-synthase.

J Am Chem Soc 2010 Sep;132(35):12357-64

Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ja103354wDOI Listing
September 2010

On the structure of the proton-binding site in the F(o) rotor of chloroplast ATP synthases.

J Mol Biol 2010 Jan 31;395(1):20-7. Epub 2009 Oct 31.

Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmb.2009.10.059DOI Listing
January 2010

Predicted structural basis for CD1c presentation of mycobacterial branched polyketides and long lipopeptide antigens.

Mol Immunol 2009 Dec 13;47(2-3):253-60. Epub 2009 Oct 13.

Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molimm.2009.09.029DOI Listing
December 2009

High-resolution structure of the rotor ring of a proton-dependent ATP synthase.

Nat Struct Mol Biol 2009 Oct 27;16(10):1068-73. Epub 2009 Sep 27.

Department of Structural Biology, Max-Planck Institute of Biophysics, Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nsmb.1678DOI Listing
October 2009

Complete ion-coordination structure in the rotor ring of Na+-dependent F-ATP synthases.

J Mol Biol 2009 Aug 3;391(2):498-507. Epub 2009 Jun 3.

Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmb.2009.05.082DOI Listing
August 2009

The mechanism of fast-gate opening in ClC-0.

J Gen Physiol 2007 Oct 10;130(4):335-49. Epub 2007 Sep 10.

Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.

View Article

Download full-text PDF

Source
http://www.jgp.org/lookup/doi/10.1085/jgp.200709759
Publisher Site
http://dx.doi.org/10.1085/jgp.200709759DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2151655PMC
October 2007

The role of a conserved lysine in chloride- and voltage-dependent ClC-0 fast gating.

J Gen Physiol 2007 Oct 10;130(4):351-63. Epub 2007 Sep 10.

Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.

View Article

Download full-text PDF

Source
http://www.jgp.org/lookup/doi/10.1085/jgp.200709760
Publisher Site
http://dx.doi.org/10.1085/jgp.200709760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2151651PMC
October 2007

On the importance of a funneled energy landscape for the assembly and regulation of multidomain Src tyrosine kinases.

Proc Natl Acad Sci U S A 2007 Aug 15;104(34):13643-8. Epub 2007 Aug 15.

Center for Integrative Science, University of Chicago, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0704041104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1959435PMC
August 2007

Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: assessing entropic and environmental effects.

J Comput Chem 2007 Jul;28(10):1634-47

Department of Pediatrics, Institute for Molecularc Pediatric Sciences, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/jcc.20652DOI Listing
July 2007

Mechanism of intracellular block of the KcsA K+ channel by tetrabutylammonium: insights from X-ray crystallography, electrophysiology and replica-exchange molecular dynamics simulations.

J Mol Biol 2007 Jan 29;365(3):649-62. Epub 2006 Sep 29.

Institute for Molecular Pediatric Sciences and Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Sciences, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmb.2006.09.069DOI Listing
January 2007

Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol.

J Lipid Res 2006 Dec 21;47(12):2614-30. Epub 2006 Sep 21.

Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA.

View Article

Download full-text PDF

Source
http://www.jlr.org/lookup/doi/10.1194/jlr.M600232-JLR200
Publisher Site
http://dx.doi.org/10.1194/jlr.M600232-JLR200DOI Listing
December 2006

Membrane protein dynamics and detergent interactions within a crystal: a simulation study of OmpA.

Proc Natl Acad Sci U S A 2006 Jun 9;103(25):9518-23. Epub 2006 Jun 9.

Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0600398103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1480439PMC
June 2006

Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.

Proteins 2004 Dec;57(4):783-91

Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10021, USA.

View Article

Download full-text PDF

Source
http://doi.wiley.com/10.1002/prot.20257
Publisher Site
http://dx.doi.org/10.1002/prot.20257DOI Listing
December 2004

Electrostatics of ion stabilization in a ClC chloride channel homologue from Escherichia coli.

J Mol Biol 2004 Jun;339(4):981-1000

Department of Biochemistry, Weill Medical College of Cornell University, Whitney Building, 1300 York Avenue, New York, NY 10021, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmb.2004.04.023DOI Listing
June 2004

Molecular dynamics simulations of the bacterial outer membrane protein FhuA: a comparative study of the ferrichrome-free and bound states.

Biophys J 2003 Sep;85(3):1406-20

Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1303317PMC
http://dx.doi.org/10.1016/S0006-3495(03)74573-1DOI Listing
September 2003

Acquisition of siderophores in gram-negative bacteria.

Nat Rev Mol Cell Biol 2003 Feb;4(2):105-16

Department of Biochemistry, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nrm1015DOI Listing
February 2003

OmpA: a pore or not a pore? Simulation and modeling studies.

Biophys J 2002 Aug;83(2):763-75

Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1302185PMC
http://dx.doi.org/10.1016/S0006-3495(02)75207-7DOI Listing
August 2002

Setting up and optimization of membrane protein simulations.

Eur Biophys J 2002 Jun 19;31(3):217-27. Epub 2002 Feb 19.

Laboratory of Molecular Biophysics, Department of Biochemistry, The Rex Richards Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/s00249-002-0207-5
Publisher Site
http://dx.doi.org/10.1007/s00249-002-0207-5DOI Listing
June 2002