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José D. Faraldo-Gómez, Ph.D.


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José D. Faraldo-Gómez

P: +1 301 496 4854

Full Publications Listing

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.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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 Jun;11(6):e1001596.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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 May;19(5):485-91, S1.
[Text Abstract on PubMed]

Structure of the mitochondrial ATP synthase and its role in shaping mitochondria cristae.
Davies KM, Daum B, Kühlbrandt W, Anselmi C, Faraldo-Gómez J.
Microsc Microanal. 2012 Jul ;18 Suppl 2:56-7.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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 01 ;1797(6-7):763-72.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: assessing entropic and environmental effects.
Faraldo-Gómez JD, Roux B.
J Comput Chem. 2007 Jul 30;28(10):1634-47.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

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.
[Text Abstract on PubMed]

Mechanism of intracellular block of the KcsA K+ channel by tetrabutylammonium: insights from X-ray crystallography, electrophysiology and replica-exchange molecular dynamics simulations.
Faraldo-Gómez JD, Kutluay E, Jogini V, Zhao Y, Heginbotham L, Roux B.
J Mol Biol. 2007 Jan 19;365(3):649-62.
[Text Abstract on PubMed]

Membrane protein dynamics and detergent interactions within a crystal: a simulation study of OmpA.
Bond PJ, Faraldo-Gómez JD, Deol SS, Sansom MS.
Proc Natl Acad Sci U S A. 2006 Jun 20;103(25):9518-23.
[Text Abstract on PubMed]

Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol.
Murcia M, Faráldo-Gómez JD, Maxfield FR, Roux B.
J Lipid Res. 2006 Dec ;47(12):2614-30.
[Text Abstract on PubMed]

Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.
Faraldo-Gómez JD, Forrest LR, Baaden M, Bond PJ, Domene C, Patargias G, Cuthbertson J, Sansom MS.
Proteins. 2004 Dec 1;57(4):783-91.
[Text Abstract on PubMed]

Electrostatics of ion stabilization in a ClC chloride channel homologue from Escherichia coli.
Faraldo-Gómez JD, Roux B.
J Mol Biol. 2004 Jun 11;339(4):981-1000.
[Text Abstract on PubMed]

Molecular dynamics simulations of the bacterial outer membrane protein FhuA: a comparative study of the ferrichrome-free and bound states.
Faraldo-Gómez JD, Smith GR, Sansom MS.
Biophys J. 2003 Sep ;85(3):1406-20.
[Text Abstract on PubMed]

Molecular dynamics simulations on the first two helices of Vpu from HIV-1.
Sramala I, Lemaitre V, Faraldo-Gómez JD, Vincent S, Watts A, Fischer WB.
Biophys J. 2003 May ;84(5):3276-84.
[Text Abstract on PubMed]

Acquisition of siderophores in gram-negative bacteria.
Faraldo-Gómez JD, Sansom MS.
Nat Rev Mol Cell Biol. 2003 Feb ;4(2):105-16.
[Text Abstract on PubMed]

OmpA: a pore or not a pore? Simulation and modeling studies.
Bond PJ, Faraldo-Gómez JD, Sansom MS.
Biophys J. 2002 Aug ;83(2):763-75.
[Text Abstract on PubMed]

Setting up and optimization of membrane protein simulations.
Faraldo-Gómez JD, Smith GR, Sansom MS.
Eur Biophys J. 2002 Jun ;31(3):217-27.
[Text Abstract on PubMed]

Water in ion channels and pores--simulation studies.
Sansom MS, Bond P, Beckstein O, Biggin PC, Faraldo-Gómez J, Law RJ, Patargias G, Tieleman DP.
Novartis Found Symp. 2002 01 ;245:66-78; discussion 79-83, 165-8.
[Text Abstract on PubMed]