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

Fiorin G, Marinelli F, Faraldo-Gómez JD.

J Comput Chem. 2019 Oct 11. doi: 10.1002/jcc.26075. [Epub ahead of print]


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

Li M, Wang Y, Banerjee R, Marinelli F, Silberberg S, Faraldo-Gómez JD, Hattori M, Swartz KJ.

Elife. 2019 Jun 24;8. pii: e47060. doi: 10.7554/eLife.47060.


Membrane physiologists of all kinds meet at Woods Hole.

Robertson JL, Faraldo-Gómez JD.

J Gen Physiol. 2019 Mar 4;151(3):273. doi: 10.1085/jgp.201912340. Epub 2019 Feb 22. No abstract available.


TRPV1 pore turret dictates distinct DkTx and capsaicin gating.

Geron M, Kumar R, Zhou W, Faraldo-Gómez JD, Vásquez V, Priel A.

Proc Natl Acad Sci U S A. 2018 Dec 11;115(50):E11837-E11846. doi: 10.1073/pnas.1809662115. Epub 2018 Nov 21.


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

Hustedt EJ, Marinelli F, Stein RA, Faraldo-Gómez JD, Mchaourab HS.

Biophys J. 2018 Oct 2;115(7):1200-1216. doi: 10.1016/j.bpj.2018.08.008. Epub 2018 Aug 16.


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

Ficici E, Zhou W, Castellano S, Faraldo-Gómez JD.

Proc Natl Acad Sci U S A. 2018 Jul 3;115(27):E6172-E6181. doi: 10.1073/pnas.1802080115. Epub 2018 Jun 18.


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

Srivastava AP, Luo M, Zhou W, Symersky J, Bai D, Chambers MG, Faraldo-Gómez JD, Liao M, Mueller DM.

Science. 2018 May 11;360(6389). pii: eaas9699. doi: 10.1126/science.aas9699. Epub 2018 Apr 12.


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

Anselmi C, Davies KM, Faraldo-Gómez JD.

J Gen Physiol. 2018 May 7;150(5):763-770. doi: 10.1085/jgp.201812033. Epub 2018 Apr 11.


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

Zhou W, Faraldo-Gómez JD.

Biochim Biophys Acta Bioenerg. 2018 Sep;1859(9):789-796. doi: 10.1016/j.bbabio.2018.03.019. Epub 2018 Apr 7.


The prokaryotic Na+/Ca2+ exchanger NCX_Mj transports Na+ and Ca2+ in a 3:1 stoichiometry.

Shlosman I, Marinelli F, Faraldo-Gómez JD, Mindell JA.

J Gen Physiol. 2018 Jan 2;150(1):51-65. doi: 10.1085/jgp.201711897. Epub 2017 Dec 13.


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

Ficici E, Faraldo-Gómez JD, Jennings ML, Forrest LR.

J Gen Physiol. 2017 Dec 4;149(12):1149-1164. doi: 10.1085/jgp.201711836. Epub 2017 Nov 22.


Atomistic simulations indicate the c-subunit ring of the F1Fo ATP synthase is not the mitochondrial permeability transition pore.

Zhou W, Marinelli F, Nief C, Faraldo-Gómez JD.

Elife. 2017 Feb 10;6. pii: e23781. doi: 10.7554/eLife.23781.


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

Leone V, Faraldo-Gómez JD.

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


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

Zhou W, Leone V, Krah A, Faraldo-Gómez JD.

J Phys Chem B. 2017 Apr 20;121(15):3297-3307. doi: 10.1021/acs.jpcb.6b08051. Epub 2016 Oct 24.


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

Liao J, Marinelli F, Lee C, Huang Y, Faraldo-Gómez JD, Jiang Y.

Nat Struct Mol Biol. 2016 Jun;23(6):590-599. doi: 10.1038/nsmb.3230. Epub 2016 May 16.


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

Bae C, Anselmi C, Kalia J, Jara-Oseguera A, Schwieters CD, Krepkiy D, Won Lee C, Kim EH, Kim JI, Faraldo-Gómez JD, Swartz KJ.

Elife. 2016 Feb 10;5. pii: e11273. doi: 10.7554/eLife.11273.


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

Branduardi D, Marinelli F, Faraldo-Gómez JD.

J Comput Chem. 2016 Mar 5;37(6):575-86. doi: 10.1002/jcc.23991. Epub 2015 Jul 7.


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

Marinelli F, Faraldo-Gómez JD.

Biophys J. 2015 Jun 16;108(12):2779-82. doi: 10.1016/j.bpj.2015.05.024.


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

Leone V, Pogoryelov D, Meier T, Faraldo-Gómez JD.

Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):E1057-66. doi: 10.1073/pnas.1421202112. Epub 2015 Feb 23.


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

Marinelli F, Almagor L, Hiller R, Giladi M, Khananshvili D, Faraldo-Gómez JD.

Proc Natl Acad Sci U S A. 2014 Dec 16;111(50):E5354-62. doi: 10.1073/pnas.1415751111. Epub 2014 Dec 2.


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

Matthies D, Zhou W, Klyszejko AL, Anselmi C, Yildiz Ö, Brandt K, Müller V, Faraldo-Gómez JD, Meier T.

Nat Commun. 2014 Nov 10;5:5286. doi: 10.1038/ncomms6286.


Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB.

Eicher T, Seeger MA, Anselmi C, Zhou W, Brandstätter L, Verrey F, Diederichs K, Faraldo-Gómez JD, Pos KM.

Elife. 2014 Sep 19;3. doi: 10.7554/eLife.03145.


Channeling your inner energy.

Faraldo-Gómez JD.

Nat Struct Mol Biol. 2014 Jul;21(7):575-7. doi: 10.1038/nsmb.2854. No abstract available.


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

Dutagaci B, Becker-Baldus J, Faraldo-Gómez JD, Glaubitz C.

Biochim Biophys Acta. 2014 Oct;1838(10):2511-9. doi: 10.1016/j.bbamem.2014.05.024. Epub 2014 May 29.


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

Branduardi D, Faraldo-Gómez JD.

J Chem Theory Comput. 2013 Sep 10;9(9):4140-4154.


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

Corbi-Verge C, Marinelli F, Zafra-Ruano A, Ruiz-Sanz J, Luque I, Faraldo-Gómez JD.

Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):E3372-80. doi: 10.1073/pnas.1303966110. Epub 2013 Aug 19.


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

Schulz S, Iglesias-Cans M, Krah A, Yildiz O, Leone V, Matthies D, Cook GM, Faraldo-Gómez JD, Meier T.

PLoS Biol. 2013;11(6):e1001596. doi: 10.1371/journal.pbio.1001596. Epub 2013 Jun 25.


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

Garzón D, Anselmi C, Bond PJ, Faraldo-Gómez JD.

J Biol Chem. 2013 Jul 5;288(27):19528-36. doi: 10.1074/jbc.M113.470179. Epub 2013 May 15.


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.

Mayer F, Leone V, Langer JD, Faraldo-Gómez JD, Müller V.

J Biol Chem. 2012 Nov 16;287(47):39327-37. doi: 10.1074/jbc.M112.411223. Epub 2012 Sep 24.


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

Davies KM, Anselmi C, Wittig I, Faraldo-Gómez JD, Kühlbrandt W.

Proc Natl Acad Sci U S A. 2012 Aug 21;109(34):13602-7. doi: 10.1073/pnas.1204593109. Epub 2012 Aug 3.


Engineering rotor ring stoichiometries in the ATP synthase.

Pogoryelov D, Klyszejko AL, Krasnoselska GO, Heller EM, Leone V, Langer JD, Vonck J, Müller DJ, Faraldo-Gómez JD, Meier T.

Proc Natl Acad Sci U S A. 2012 Jun 19;109(25):E1599-608. doi: 10.1073/pnas.1120027109. Epub 2012 May 24.


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

Symersky J, Pagadala V, Osowski D, Krah A, Meier T, Faraldo-Gómez JD, Mueller DM.

Nat Struct Mol Biol. 2012 Apr 15;19(5):485-91, S1. doi: 10.1038/nsmb.2284.


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

Schlegel K, Leone V, Faraldo-Gómez JD, Müller V.

Proc Natl Acad Sci U S A. 2012 Jan 17;109(3):947-52. doi: 10.1073/pnas.1115796109. Epub 2012 Jan 4.


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

Marinelli F, Kuhlmann SI, Grell E, Kunte HJ, Ziegler C, Faraldo-Gómez JD.

Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):E1285-92. doi: 10.1073/pnas.1112534108. Epub 2011 Nov 14.


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

Sanderson JP, Waldburger-Hauri K, Garzón D, Matulis G, Mansour S, Pumphrey NJ, Lissin N, Villiger PM, Jakobsen B, Faraldo-Gómez JD, Gadola SD.

Eur J Immunol. 2012 Jan;42(1):248-55. doi: 10.1002/eji.201141956. Epub 2011 Nov 28.


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

Bond PJ, Faraldo-Gómez JD.

J Biol Chem. 2011 Jul 22;286(29):25872-81. doi: 10.1074/jbc.M111.223321. Epub 2011 May 21.


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

Staritzbichler R, Anselmi C, Forrest LR, Faraldo-Gómez JD.

J Chem Theory Comput. 2011 Apr 12;7(4):1167-1176.


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

Faraldo-Gómez JD, Forrest LR.

Curr Opin Struct Biol. 2011 Apr;21(2):173-9. doi: 10.1016/ Epub 2011 Feb 16. Review.


The 2.5 Å structure of CD1c in complex with a mycobacterial lipid reveals an open groove ideally suited for diverse antigen presentation.

Scharf L, Li NS, Hawk AJ, Garzón D, Zhang T, Fox LM, Kazen AR, Shah S, Haddadian EJ, Gumperz JE, Saghatelian A, Faraldo-Gómez JD, Meredith SC, Piccirilli JA, Adams EJ.

Immunity. 2010 Dec 14;33(6):853-62. doi: 10.1016/j.immuni.2010.11.026.


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

Pogoryelov D, Krah A, Langer JD, Yildiz Ö, Faraldo-Gómez JD, Meier T.

Nat Chem Biol. 2010 Dec;6(12):891-9. doi: 10.1038/nchembio.457. Epub 2010 Oct 24.


On the question of hydronium binding to ATP-synthase membrane rotors.

Leone V, Krah A, Faraldo-Gómez JD.

Biophys J. 2010 Oct 6;99(7):L53-5. doi: 10.1016/j.bpj.2010.07.046.


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

Anselmi C, Grininger M, Gipson P, Faraldo-Gómez JD.

J Am Chem Soc. 2010 Sep 8;132(35):12357-64. doi: 10.1021/ja103354w.


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

Krah A, Pogoryelov D, Langer JD, Bond PJ, Meier T, Faraldo-Gómez JD.

Biochim Biophys Acta. 2010 Jun-Jul;1797(6-7):763-72. doi: 10.1016/j.bbabio.2010.04.014. Epub 2010 Apr 21.


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

Krah A, Pogoryelov D, Meier T, Faraldo-Gómez JD.

J Mol Biol. 2010 Jan 8;395(1):20-7. doi: 10.1016/j.jmb.2009.10.059. Epub 2009 Oct 31.


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

Garzón D, Bond PJ, Faraldo-Gómez JD.

Mol Immunol. 2009 Dec;47(2-3):253-60. doi: 10.1016/j.molimm.2009.09.029. Epub 2009 Oct 13.


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

Pogoryelov D, Yildiz O, Faraldo-Gómez JD, Meier T.

Nat Struct Mol Biol. 2009 Oct;16(10):1068-73. doi: 10.1038/nsmb.1678. Epub 2009 Sep 27.


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

Meier T, Krah A, Bond PJ, Pogoryelov D, Diederichs K, Faraldo-Gómez JD.

J Mol Biol. 2009 Aug 14;391(2):498-507. doi: 10.1016/j.jmb.2009.05.082. Epub 2009 Jun 3.


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

Engh AM, Faraldo-Gómez JD, Maduke M.

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


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

Engh AM, Faraldo-Gómez JD, Maduke M.

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


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

Faraldo-Gómez JD, Roux B.

Proc Natl Acad Sci U S A. 2007 Aug 21;104(34):13643-8. Epub 2007 Aug 15.

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