Research Articles
[*] denotes corresponding (co)authorship


48. Zhou W, Marinelli F, *Faraldo-Gómez JD (2017). Atomistic simulations indicate the c-subunit ring of the F1Fo ATP synthase is not the mitochondrial permeability transition pore. eLife 6:e23781 Link

47. Zhou W, Leone V, Krah A, *Faraldo-Gómez JD (2017). Predicted structures of the proton-bound membrane-rmbedded rotor rings of the Saccharomyces cerevisiaei and Escherichia coli ATP synthases. J Phys Chem B 121:3297-3307 (Klaus Schulten Memorial Issue) Link


46. Leone V, *Faraldo-Gómez JD (2016). Structure and mechanism of the ATP synthase membrane motor inferred from quantitative integrative modeling. J Gen Physiol 148:441-457 Link

45. Liao J, Marinelli F, Lee C, Huang Y, *Faraldo-Gómez JD, Jiang Y (2016). Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger. Nature Struct Mol Biol 23:590-599 Link

44. Branduardi D, Marinelli F, *Faraldo-Gómez JD (2016). Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg(2+) through the SOMA string method. J Comput Chem 37:575-586 Link

43. Bae C, Anselmi C, Kalia J, Jara-Osegura A, Schwieters CD, Krepkiy D, Lee CW, Kim EH, Kim JI, *Faraldo-Gómez JD, Swartz K (2016) Structural insights into the mechanism of activation of the TRPV1 channel by a membrane-bound tarantula toxin. eLife 5:e11273 Link


42. Leone V, Pogoryelov D, Meier T, *Faraldo-Gómez JD (2015) On the principle of ion selectivity of Na(+)/H(+)-coupled membrane proteins: experimental and computational studies of an ATP-synthase rotor. Proc Natl Acad Sci USA 112:E1057-1066 Link

41. Marinelli F, *Faraldo-Gómez JD (2015) Ensemble-Biased Metadynamics: a molecular simulation method to sample experimental distributions. Biophys J 108:2779-2782 Link


40. Marinelli F, Almagor L, Hiller R, Giladi M, Khananshvili D, *Faraldo-Gómez JD (2014) Sodium recognition by the Na(+)/Ca(2+) exchanger in the outward-facing conformation. Proc Natl Acad Sci USA 111:E5354-E5362 Link

39. Eicher T, Seeger MA, Anselmi C, Zhou W, Brandstätter L, Verrey F, Diederichs K, *Faraldo-Gómez JD, Pos KM (2014). Coupling of remote alternating-access transport mechanisms for protons and substrates in the multi-drug efflux pump AcrB. eLife 3:e03145 Link

38. Matthies D, Zhou W, Klyszejko AL, Anselmi C, Yildiz O, Brandt K, Müller V, *Faraldo-Gómez JD, Meier T (2014). High-Resolution structure and mechanism of a Na(+)-coupled F/V-hybrid ATP synthase rotor ring. Nature Comm 5:5286 Link

37. Dutagaci B, Becker-Baldus Johanna, Faraldo-Gómez JD, Glaubitz C (2014) Ceramide-lipid interactions studied by MD simulations and solid-state NMR. Biochim Biophys Acta Biomem 1838:2511-2519 Link


36. Corbi-Verge C, Marinelli F, Zafra-Ruano A, Ruiz-Sanz J, Luque I, *Faraldo-Gómez JD (2013) Two-state dynamics of the SH3-SH2 tandem of Abl kinase and the allosteric role of the N-cap. Proc Natl Acad Sci USA 110:E3372-3380 Link

35. Branduardi D, *Faraldo-Gómez JD (2013) String method for calculation of minimum free-energy paths in freely-tumbling systems. J Chem Theory Comput 9:4140-4154 Link

34. Schulz S, Iglesias-Cans M, Krah A, Yildiz O, Leone V, Matthies D, Cook GM, *Faraldo-Gómez JD, Meier T (2013) A new type of Na(+)-driven ATP synthase membrane rotor with a two-carboxylate ion-coupling motif. PLoS Biol 11:e1001596 Link

33. Garzón D, Anselmi C, Bond PJ, *Faraldo-Gómez JD (2013) Dynamics of the antigen-binding grooves in CD1 proteins: reversible hydrophobic collapse in the lipid-free state. J Biol Chem 288:19528-19536 Link


32. Mayer F, Leone V, Langer JD, *Faraldo-Gómez JD, Müller V (2012) 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 287:39327-39337 Link

31. Davies KM, Anselmi C, Wittig I, Faraldo-Gómez JD, Kühlbrandt W (2012) Structure of the yeast F(1)F(o)-ATP synthase dimer and its role in shaping the mitochondrial cristae. Proc Natl Acad Sci USA 109:13602-13607 Link

30. Pogoryelov D, Klyszejko AL, Krasnoselska GO, Heller EM, Leone V, Langer JD, Vonck J, Müller DJ, Faraldo-Gómez JD, Meier T (2012) Engineering rotor ring stoichiometries in the ATP synthase. Proc Natl Acad Sci USA 109:E1599-1608 Link

29. Symersky J, Pagadala V, Osowski D, Krah A, Meier T, *Faraldo-Gómez JD, Mueller DM (2012) Structure of the c(10) ring of the yeast mitochondrial ATP synthase in the open conformation. Nat Struct Mol Biol 19:485-491 Link

28. Schlegel K, Leone V, *Faraldo-Gómez JD, Müller V (2012) Promiscuous archaeal ATP synthase concurrently coupled to Na(+) and H(+) translocation. Proc Natl Acad Sci USA 109:947-952 Link

27. Sanderson JP, Waldburger-Hauri K, Garzón D, Matulis G, Mansour S, Pumphrey NJ, Lissin N, Villiger PM, Jakobsen B, *Faraldo-Gómez JD, Gadola S (2012) Natural variations at position 93 of the invariant Vα24-Jα18 alpha chain of human iNKT TCRs strongly impact on CD1d binding. Eur J Immunol 42:248-255 Link


26. Marinelli F, Kuhlmann SI, Grell E, Kunte HJ, Ziegler C, *Faraldo-Gómez JD (2011) Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins. Proc Natl Acad Sci USA 108:E1285-E1292 Link

25. Bond PJ, *Faraldo-Gómez JD (2011) Molecular mechanism of selective recruitment of SYK kinases by the antigen-receptor membrane complex. J Biol Chem 86:25872-25881 Link

24. Staritzbichler R, Anselmi C, Forrest LR, *Faraldo-Gómez JD (2011) GRIFFIN: a versatile methodology for optimization of protein-lipid interfaces for membrane-protein simulations. J Chem Theor Comput 7:1167-1176 Link


23. 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 (2010) The 2.5 Å structure of CD1c in complex with a mycobacterial lipid reveals an open groove ideally suited for diverse antigen presentation. Immunity 33:853-862 Link

22. Pogoryelov D, Krah A, Langer JD, Yildiz O, *Faraldo-Gómez JD, Meier T (2010) Microscopic rotary mechanism of ion translocation in the F(o) complex of ATP synthases. Nature Chem Biol 6:891-89 Link

21. Anselmi C, Grininger M, Gipson P, *Faraldo-Gómez JD (2010) Mechanism of substrate shuttling by the acyl-carrier protein within fatty acid mega-synthase. J Am Chem Soc 132:12357-12364 Link

20. Leone V, Krah A, *Faraldo-Gómez JD (2010) On the question of hydronium binding to ATP synthase rotors. Biophys J 6:L53-L5 Link

19. Krah A, Pogoryelov D, Langer JD, Bond PJ, Meier T, *Faraldo-Gómez JD (2010) Structural and energetic basis for H(+) versus Na(+) binding selectivity in ATP synthase F(o) rotors. Biochim Biophys Acta 1797:763-772 Link


18. Krah A, Pogoryelov D, Meier T, *Faraldo-Gómez JD (2010) On the structure of the proton-binding site in the Fo rotor of chloroplast ATP synthases. J Mol Biol 395:20-27 Link

17. Garzón D, Bond PJ, *Faraldo-Gómez, JD (2009) Predicted structural basis for CD1c presentation of mycobacterial branched polyketides and long lipopeptide antigens. Mol Immunol 47:253-260 Link

16. Pogoryelov D, Yildiz O, Faraldo-Gómez JD, Meier T (2009) High-resolution structure of the rotor ring of a proton dependent ATP synthase. Nature Struct Mol Biol 16:1068-1073 Link

15. Meier T, Krah A, Bond PJ, Pogoryelov D, Diederichs K, *Faraldo-Gómez JD (2009) Complete ion-coordination structure in the rotor ring of Na(+)-dependent F-ATP synthases. J Mol Biol 391:498-507 Link

14. Lamoureux G, Faraldo-Gómez JD, Krupin S, Noskov SY (2009) Polarizable model of chloroform based on classical Drude oscillators. Chem Phys Lett 468:270-274 Link


13. Faraldo-Gómez JD, Roux B (2007) On the importance of a funneled energy landscape for the assembly and regulation of multidomain Src tyrosine kinases. Proc Natl Acad Sci USA 104:13643-13648 Link

12. Engh AM, Faraldo-Gómez JD, Maduke M (2007) The role of a conserved lysine in chloride- and voltage-dependent ClC-0 fast gating. J Gen Physiol 130:351-363 Link

11. Engh AM, Faraldo-Gómez JD, Maduke M (2007) The mechanism of fast-gate opening in ClC-0. J Gen Physiol 130:351-363 Link

10. Faraldo-Gómez JD, Kutluay E, Jogini V, Zhao Y, Heginbotham L, Roux B (2007) Mechanism of intracellular block of KcsA K+ channel by tetrabutylammonium: insights from X-ray crystallography, electrophysiology and replica-exchange molecular dynamics simulations. J Mol Biol 365(3):649-662 Link

9. Faraldo-Gómez JD, Roux B (2006) Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations. J Comp Chem 8:1634-1647 Link

8. Murcia M, Faraldo-Gómez JD, Maxfield FR, Roux B (2006) Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol. J Lipid Res 47:2614-2630 Link

7. Bond PJ, Faraldo-Gómez JD, Deol SS, Sansom MSP (2006) Membrane protein dynamics and detergent interactions within a crystal: a simulation study of OmpA. Proc Natl Acad Sci USA 103:9518-9523 Link

6. Faraldo-Gómez JD, Roux B (2004) Electrostatics of ion stabilization in a ClC chloride channel homologue from Escherichia coli. J Mol Biol 339:981-1000 Link

5. Faraldo-Gómez JD, Forrest LR, Baaden M, Bond PJ, Domene C, Paragias G, Cuthbertson J, Sansom MSP (2004) Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations. Proteins: Struct Funct Bioinf 57:783-791 Link

4. Faraldo-Gómez JD, Smith GR, Sansom MSP (2003) Molecular dynamics simulations of the bacterial outer membrane protein FhuA: a comparative study of the ferrichrome-free and bound states. Biophys J 85:1406-1420 Link

3. Sramala I, Lemaitre V, Faraldo-Gómez JD, Vincent S, Watts A, Fischer WB (2003) Molecular dynamics simulations of the first two helices of Vpu from HIV-1. Biophys J 84: 3276-3284 Link

2. Bond PJ, Faraldo-Gómez JD, Sansom MSP (2002) OmpA: a pore or not a pore? Simulation and modelling studies. Biophys J 83:763-775 Link

1. Faraldo-Gómez JD, Smith GR, Sansom MSP (2002) Setting up and optimization of membrane protein simulations. Eur Biophys J Biophy 31:217-227 Link

Reviews, Editorials and Book Chapters


6. Faraldo-Gómez JD (2014) Channeling your inner energy. Nature Struct Mol Biol 21:575-577 Link

5. Faraldo-Gómez JD, Forrest LR (2011) Modeling and simulation of ion-coupled and ATP-driven membrane proteins. Curr Opin Struct Biol 21:173-179 Link

4. Meier T, Faraldo-Gómez JD, Boresch M (2011). The ATP synthase: a paradigmatic molecular machine. In: Frank, J (Ed.) Molecular Machines, Cambridge University Press.


3. Faraldo-Gómez JD (2006) Protein mediated siderophore uptake in Gram-negative bacteria: a structural perpspective. In Varma A, Chincholkar S (Eds.) Microbial Siderophores. Springer-Verlag, Berlin. Link

2. Faraldo-Gómez JD Sansom MSP (2003) Acquisition of siderophores in Gram-negative bacteria. Nature Rev Mol Cell Biol 4:105-116 Link

1. Sansom MSP, Bond PJ, Beckstein O, Biggin PC, Faraldo-Gómez JD Law RJ, Patargias G & Tieleman DP (2002) Water in ion channels and pores: simulation studies. Novartis Found Symp 245:66-83 Link

Last update on 6/2017

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