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José D Faraldo-Gómez

ORCID

Publication Activity (10 Years)

Years Active: 2016-2023
Publications (10 Years): 38

Top Venues

eLife

bioRxiv : the preprint server for biology

Proceedings of the National Academy of Sciences of the United States of America

Living journal of computational molecular science

This page only lists publications with an associated author ORCID identifier.

Publications

Melanie Ernst, Esam A Orabi, Randy B Stockbridge, José D Faraldo-Gómez, Janice L Robertson
Dimerization mechanism of an inverted-topology ion channel in membranes. Proceedings of the National Academy of Sciences of the United States of America 120 (47) (2023)
Giacomo Fiorin, Lucy R Forrest, José D Faraldo-Gómez
Membrane free-energy landscapes derived from atomistic dynamics explain nonuniversal cholesterol-induced stiffening. bioRxiv : the preprint server for biology (2023)
Fabrizio Marinelli, José D Faraldo-Gómez
The molecular mechanism of selective and active transport in a Na + /Ca 2+ exchanger. bioRxiv : the preprint server for biology (2023)
Yein Christina Park, Bharat Reddy, Navid Bavi, Eduardo Perozo, José D Faraldo-Gómez
State-specific morphological deformations of the lipid bilayer explain mechanosensitive gating of MscS ion channels. eLife 12 (2023)
Giacomo Fiorin, Lucy R Forrest, José D Faraldo-Gómez
Membrane free-energy landscapes derived from atomistic dynamics explain nonuniversal cholesterol-induced stiffening. PNAS nexus 2 (8) (2023)
Melanie Ernst, Esam A Orabi, Randy B Stockbridge, José D Faraldo-Gómez, Janice L Robertson
Dimerization mechanism of an inverted-topology ion channel in membranes. bioRxiv : the preprint server for biology (2023)
Giacomo Fiorin, Lucy R Forrest, José D Faraldo-Gómez
Membrane free-energy landscapes derived from atomistic dynamics explain nonuniversal cholesterol-induced stiffening. bioRxiv : the preprint server for biology (2023)
Fabrizio Marinelli, José D Faraldo-Gómez
The molecular mechanism of selective and active transport in a Na + /Ca 2+ exchanger. bioRxiv : the preprint server for biology (2023)
Yein Christina Park, Bharat Reddy, Navid Bavi, Eduardo Perozo, José D Faraldo-Gómez
State-specific morphological deformations of the lipid bilayer explain mechanosensitive gating of MscS ion channels. eLife 12 (2023)
Melanie Ernst, Esam A Orabi, Randy B Stockbridge, José D Faraldo-Gómez, Janice L Robertson
Dimerization mechanism of an inverted-topology ion channel in membranes. bioRxiv : the preprint server for biology (2023)
Fabrizio Marinelli, José D Faraldo-Gómez
The molecular mechanism of selective and active transport in a Na + /Ca 2+ exchanger. bioRxiv : the preprint server for biology (2023)
Yein Christina Park, Bharat Reddy, Navid Bavi, Eduardo Perozo, José D Faraldo-Gómez
State-specific morphological deformations of the lipid bilayer explain mechanosensitive gating of MscS ion channels. eLife 12 (2023)
Yein Christina Park, Bharat Reddy, Navid Bavi, Eduardo Perozo, José D Faraldo-Gómez
State-specific morphological deformations of the lipid bilayer explain mechanosensitive gating of MscS ion channels. eLife 12 (2023)
Giacomo Fiorin, Lucy R Forrest, José D Faraldo-Gómez
Membrane free-energy landscapes derived from atomistic dynamics explain nonuniversal cholesterol-induced stiffening. bioRxiv : the preprint server for biology (2023)
Yein Christina Park, Bharat Reddy, Navid Bavi, Eduardo Perozo, José D Faraldo-Gómez
State-specific morphological deformations of the lipid bilayer explain mechanosensitive gating of MscS ion channels. eLife 12 (2023)
Yein Christina Park, Bharat Reddy, Navid Bavi, Eduardo Perozo, José D Faraldo-Gómez
State-specific morphological deformations of the lipid bilayer explain mechanosensitive gating of MscS ion channels. eLife 12 (2023)
Wei Niu, Wenchang Zhou, Shuo Lu, Trung Vu, Vasanthi Jayaraman, José D Faraldo-Gómez, Lei Zheng
Ca 2+ efflux facilitated by co-transport of inorganic phosphate anion in the H + /Ca 2+ antiporter YfkE. Communications biology 6 (1) (2023)
Paul Suhwan Lee, Richard T Bradshaw, Fabrizio Marinelli, Kyle C Kihn, Ally K Smith, Patrick L Wintrode, Daniel J Deredge, José D Faraldo-Gómez, Lucy R Forrest
Interpreting Hydrogen-Deuterium Exchange Experiments with Molecular Simulations: Tutorials and Applications of the HDXer Ensemble Reweighting Software [Article v1.0]. Living journal of computational molecular science 3 (1) (2022)
SeCheol Oh, Robyn Stix, Wenchang Zhou, José D Faraldo-Gómez, Richard K Hite
Mechanism of 4-aminopyridine inhibition of the lysosomal channel TMEM175. Proceedings of the National Academy of Sciences of the United States of America 119 (44) (2022)
Chul-Jin Lee, Robyn Stix, Mitra Shumsher Rana, Flowreen Shikwana, R Elliot Murphy, Rodolfo Ghirlando, José D Faraldo-Gómez, Anirban Banerjee
Bivalent recognition of fatty acyl-CoA by a human integral membrane palmitoyltransferase. Proceedings of the National Academy of Sciences of the United States of America 119 (7) (2022)
Xiao-Feng Tan, Chanhyung Bae, Robyn Stix, Ana I Fernández-Mariño, Katherine E Huffer, Tsg-Hui Chang, Jiansen Jiang, José D Faraldo-Gómez, Kenton Jon Swartz
Structure of the Shaker Kv channel and mechanism of slow C-type inactivation. Science advances 8 (11) (2022)
SeCheol Oh, Fabrizio Marinelli, Wenchang Zhou, Jooyeon Lee, Ho Jeong Choi, Min Kim, José D Faraldo-Gómez, Richard K Hite
Differential ion dehydration energetics explains selectivity in the non-canonical lysosomal K + channel TMEM175. eLife 11 (2022)
Paul Suhwan Lee, Richard T Bradshaw, Fabrizio Marinelli, Kyle C Kihn, Ally K Smith, Patrick L Wintrode, Daniel J Deredge, José D Faraldo-Gómez, Lucy R Forrest
Interpreting Hydrogen-Deuterium Exchange Experiments with Molecular Simulations: Tutorials and Applications of the HDXer Ensemble Reweighting Software [Article v1.0]. Living journal of computational molecular science 3 (1) (2022)
Paul Suhwan Lee, Richard T Bradshaw, Fabrizio Marinelli, Kyle C Kihn, Ally K Smith, Patrick L Wintrode, Daniel J Deredge, José D Faraldo-Gómez, Lucy R Forrest
Interpreting Hydrogen-Deuterium Exchange Experiments with Molecular Simulations: Tutorials and Applications of the HDXer Ensemble Reweighting Software [Article v1.0]. Living journal of computational molecular science 3 (1) (2022)
Esam A Orabi, Tuǧba N Öztürk, Nathan Bernhardt, José D Faraldo-Gómez
Corrections in the CHARMM36 Parametrization of Chloride Interactions with Proteins, Lipids, and Alkali Cations, and Extension to Other Halide Anions. Journal of chemical theory and computation 17 (10) (2021)
Fabrizio Marinelli, José D Faraldo-Gómez
Force-Correction Analysis Method for Derivation of Multidimensional Free-Energy Landscapes from Adaptively Biased Replica Simulations. Journal of chemical theory and computation 17 (11) (2021)
Rahul Chadda, Nathan Bernhardt, Elizabeth G Kelley, Susana C M Teixeira, Kacie Griffith, Alejandro Gil-Ley, Tuğba N Öztürk, Lauren E Hughes, Ana Forsythe, Venkatramanan Krishnamani, José D Faraldo-Gómez, Janice L Robertson
Membrane transporter dimerization driven by differential lipid solvation energetics of dissociated and associated states. eLife 10 (2021)
Steven Castellano, Derek P Claxton, Emel Ficici, Tsukasa Kusakizako, Robyn Stix, Wenchang Zhou, Osamu Nureki, Hassane S Mchaourab, José D Faraldo-Gómez
Conserved binding site in the N-lobe of prokaryotic MATE transporters suggests a role for Na+ in ion-coupled drug efflux. The Journal of biological chemistry (2021)
Min Luo, Wenchang Zhou, Hiral Patel, Anurag P Srivastava, Jindrich Symersky, Michał M Bonar, José D Faraldo-Gómez, Maofu Liao, David M Mueller
Bedaquiline inhibits the yeast and human mitochondrial ATP synthases. Communications biology 3 (1) (2020)
Esam A Orabi, José D Faraldo-Gómez
New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology. Journal of chemical theory and computation 16 (8) (2020)
Giacomo Fiorin, Fabrizio Marinelli, José D Faraldo-Gómez
Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics. Journal of computational chemistry 41 (5) (2019)
Mufeng Li, Yao Wang, Rahul Banerjee, Fabrizio Marinelli, Shai Silberberg, José D Faraldo-Gómez, Motoyuki Hattori, Kenton Jon Swartz
Molecular mechanisms of human P2X3 receptor channel activation and modulation by divalent cation bound ATP. eLife 8 (2019)
Janice L Robertson, José D Faraldo-Gómez
Membrane physiologists of all kinds meet at Woods Hole. The Journal of general physiology 151 (3) (2019)
Wenchang Zhou, Giacomo Fiorin, Claudio Anselmi, Hossein Ali Karimi-Varzaneh, Horacio Poblete, Lucy R Forrest, José D Faraldo-Gómez
Large-scale state-dependent membrane remodeling by a transporter protein. eLife 8 (2019)
Anurag Prakash Srivastava, Min Luo, Wenchang Zhou, Jindrich Symersky, Dongyang Bai, Melissa G Chambers, José D Faraldo-Gómez, Maofu Liao, David M Mueller
High-resolution cryo-EM analysis of the yeast ATP synthase in a lipid membrane. Science (New York, N.Y.) 360 (6389) (2018)
Claudio Anselmi, Karen M Davies, José D Faraldo-Gómez
Mitochondrial ATP synthase dimers spontaneously associate due to a long-range membrane-induced force The Journal of general physiology 150 (5) (2018)
Wenchang Zhou, Fabrizio Marinelli, Corrine Nief, José D Faraldo-Gómez
Atomistic simulations indicate the c-subunit ring of the F1Fo ATP synthase is not the mitochondrial permeability transition pore. eLife 6 (2017)
Chanhyung Bae, Claudio Anselmi, Jeet Kalia, Andres Jara-Oseguera, Charles D Schwieters, Dmitriy Krepkiy, Chul Won Lee, Eun-Hee Kim, Jae Il Kim, José D Faraldo-Gómez, Kenton Jon Swartz
Structural insights into the mechanism of activation of the TRPV1 channel by a membrane-bound tarantula toxin. eLife 5 (2016)

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Publication Activity (10 Years)

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José D Faraldo-Gómez