Jérôme Hénin – Publications

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Preprints

Journal Articles

  1. Giacomo Fiorin*, Fabrizio Marinelli, , Lucy R. Forrest, Haochuan Chen, Christophe Chipot, Axel Kohlmeyer, Hubert Santuz, Jérôme Hénin*, Expanded Functionality and Portability for the Colvars Library, J. Chem. Phys. B (2024)
  2. Wu et al., (2024). alchemlyb: the simple alchemistry library. Journal of Open Source Software, 9(101), 6934
  3. Louis Lagardère*, Lise Maurin,  Olivier Adjoua, Krystel El Hage, Pierre Monmarché*, Jean-Philip Piquemal*, Jérôme Hénin*, Lambda-ABF: Simplified, Portable, Accurate, and Cost-Effective Alchemical Free-Energy Computation, J. Chem. Theory Comput. 2024, 20, 11, 4481–4498
  4. M Papadourakis, H Sinenka, P Matricon, J Hénin, G Brannigan, L Pérez-Benito, V Pande, H van Vlijmen, C de Graaf, F Deflorian, G Tresadern, M Cecchini, and Z Cournia, Alchemical Free Energy Calculations on Membrane-Associated Proteins, J. Chem. Theo. Comput. 19, 21, 7437–7458 (2023)
  5. E. StIago-McRae, M. Ebrahimi, J. Sandberg, G. Brannigan, J. Hénin, Computing absolute binding affinities by Streamlined Alchemical Free Energy Perturbation (SAFEP), LiveCOMS 5(1), 2067 (2023) [Live repository]
  6. J T Bullerjahn, S von Bülow, M Heidari, J Hénin, G Hummer, Unwrapping NPT simulations to calculate diffusion coefficients J. Chem. Theo. Comput. 19, 11, 3406–3417 (2023)
  7. A. Gagelin, C. Largeau, S. Masscheleyn, M. S. Piel, D. Calderon-Mora, F. Bouillaud, J. Hénin, B. Miroux, Molecular determinants of inhibition of UCP1-mediated respiratory uncoupling, Nature Communications 14, 2594 (2023)
  8. J Hénin, T Lelièvre, MR Shirts, O Valsson, L Delemotte, Enhanced sampling methods for molecular dynamics simulations, Living Journal of Computational Molecular Science, 4(1), 1583 (2022)
  9. J Petroff II, N Dietzen, ESantiago-McRae, B Deng , M Washington, L Chen, K Moreland, Z Deng, M Rau, J Fitzpatrick , P Yuan , T Joseph , J Hénin , G Brannigan, W Cheng, Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation. Nature Communications 13, 7017 (2022)
  10. J. Puyo-Fourtine, M. Juillé, J. Hénin, C. Clavaguéra, E. Duboué-Dijon*, Consistent picture of phosphate-divalent cation binding from models with implicit and explicit electronic polarization, J. Phys. Chem. B (2022) [preprint]
  11. M. Ebrahimi, J. Hénin, Symmetry-Adapted Restraints for Binding Free Energy Calculations, J. Chem. Theo. Comput.  (2022)
  12. J. Hénin, Laura J. S. Lopes, G. Fiorin, Human learning for molecular simulations: the Collective Variables Dashboard in VMD, J. Chem. Theo. Comput.,  (2022)
  13. Cecilia Chávez-García, Jérôme Hénin, Mikko Karttunen, Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2, J. Chem. Inf. Model. (2022)
  14. J. Hénin, Fast and Accurate Multidimensional Free Energy Integration, J. Chem. Theo. Comput. 17, 11, 6789–6798 (2021) [final preprint]
  15. E. Duboué-Dijon and J. Hénin, Building intuition for binding free energy calculations: bound state definition, restraints, and symmetry. J. Chem. Phys, 154, 204101. (2021) [final preprint]
  16. Xiaojing Wu, Jérôme Hénin, Laura Baciou, Marc Baaden, Fabien Cailliez, and Aurélien de la Lande, Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations, Front. Chem. 2021
  17. Phillips, J.; Hardy, D.; Maia, J.; Stone, J.; Ribeiro, J.; Bernardi, R.; Buch, R.; Fiorin, G.; Hénin, J.; Jiang, W.; McGreevy, R.; Melo, M. C. d. R.; Radak, B.; Skeel, R.; Singharoy, A.; Wang, Y.; Roux, B.; Aksimentiev, A.; Luthey-Schulten, Z.; Kale, L.; Schulten, K.; Chipot, C. & Tajkhorshid, E., Scalable molecular dynamics on CPU and GPU architectures with NAMD, J. Chem. Phys., 153, 044130 (2020)
  18. D. Mendes de Oliveira, S.R. Zukowski, V. Palivec, J. Hénin, H. Martinez Seara, D. Ben Amotz, P. Jungwirth, E. Duboué-Dijon*, Binding of Divalent Cations to Aqueous Acetate: Molecular Simulations Guided by Raman Spectroscopy.  Phys. Chem. Chem. Phys., 2020, 22, 24014-24027 [preprint][data]
  19. Reza Salari, Thomas Joseph, Ruchi Lohia, Jérôme Hénin, and Grace Brannigan, A streamlined, general approach for computing ligand binding free energies and its application to GPCR-bound cholesterol, J. Chem. Theo. Comput. 14 (12), pp 6560–6573 (2018) [preprint]
  20. Haohao Fu, Wensheng Cai, Jérôme Hénin, Benoît Roux, Christophe Chipot, New Coarse Variables for the Accurate Determination of Standard Binding Free Energies, J. Chem. Theo. Comput. 13, 11, 5173-5178 (2017)
  21. Dario De Vecchis, Laetitia Cavellini, Marc Baaden, Jérôme Hénin, Mickaël M. Cohen, Antoine Taly, A membrane-inserted structural model of the yeast mitofusin Fzo1, Scientific Reports (2017) [Open Access]
  22. Lesage A., Lelièvre T., Stoltz G., Hénin J., Smoothed biasing forces yield unbiased free energies with the extended-system Adaptive Biasing Force method, J. Phys. Chem. B 121 (15), 3676–3685 (2017) [Open Access]
  23. KA Woll, S Murlidaran, BJ Pinch, J Hénin, W Wang, R Salari, M Covarrubias, WP Dailey, G Brannigan, BA Garcia, RG Eckenhoff, A Novel Bifunctional Alkylphenol Anesthetic Allows Characterization of γ-Aminobutyric Acid, Type A (GABAA), Receptor Subunit Binding Selectivity in Synaptosomes, J. Biol. Chem. 291(39) 20473-20486 (2016) [Open Access]
  24. Jaiteh M, Taly A, and Hénin J, Evolution of pentameric ligand-gated ion channels: Pro-loop receptors, PLOS One 11(3): e0151934 (2016). Online dataset: phylogeny of pLGICs.
  25. Cournia Z et al., Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory, J. Membr. Biol, 248(4), 611-640 (2015)
  26. Rahaman O, Kalimeri M, Melchionna S, Hénin J, Sterpone F, Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains, J. Phys. Chem. B 119(29) 8939-49 (2015)
  27. Comer J, Gumbart JC, Hénin J, Lelièvre T, Pohorille A, Chipot C., The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask, J. Phys. Chem. B 119(3):1129-51 (2015) [Open Access]
  28. Taly A, Hénin J, Changeux J-P and Cecchini M Allosteric regulation of pentameric ligand-gated ion channels: An emerging mechanistic perspective. Channels 8(4), 350-360 (2014) [Open Access]
    Cover picture of Channels 8(4)
  29. Beaugrand M, Arnold AA, Hénin J, Warschawski DE, Williamson PT, Marcotte I. Lipid Concentration and Molar Ratio Boundaries for the Use of Isotropic Bicelles. Langmuir 30 (21), 6162–6170 (2014)
  30. J. Hénin, R. Salari, S. Murlidaran, and G. Brannigan, A predicted binding site for cholesterol on the GABA(A) receptor, Biophys. J. 106(9) 1938–1949 (2014) [Open Access]
  31. S. Lee, A. Tran, M. Allsopp, J. Lim, J. Hénin, and J. B. Klauda, CHARMM36 United-Atom Chain Model for Lipids and Surfactants, J. Phys. Chem. B 118 (2), 547–556 (2014)
  32. Y. R. Brunet, J. Hénin, H. Celia and E. Cascales, Type VI secretion and bacteriophage tail tubes share a common assembly pathway. EMBO Reports 15, 315–321 (2014)
  33. G. Fiorin, M. L. Klein, J. Hénin, Using collective variables to drive molecular dynamics simulations, Molecular Physics 111 (22-23), 3345-3362 (2013) [Open Access] [Most read]
  34. D.N. LeBard, J. Hénin, R. Eckenhoff, M. L. Klein, G. Brannigan, General anesthetics predicted to block the GLIC pore with micromolar affinity, PLoS Computational Biology 8(5): e1002532 (2012) [Open Access]
  35. G. Brannigan, D.N. LeBard, J. Hénin, R. Eckenhoff, M. L. Klein, Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain, Proc. Natl. Acad. Sci. USA 107, 14122-14127 (2010) [Open Access]
  36. P. Hubert, P. Sawma, J.P. Duneau, J. Khao, J. Hénin, D. Bagnard and J. Sturgis, Single-spanning transmembrane domains in cell growth and cell-cell interactions: More than meets the eye? Cell Adhesion and Migration, 4, 313-324 (2010) [Open Access]
  37. J. Hénin, G. Fiorin, C. Chipot, and M. L. Klein, Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables, J. Chem. Theory Comput., 6, 35-47 (2010)
  38. J. Hénin, G. Brannigan, W. Dailey, R. Eckenhoff, M. L. Klein, An atomistic model for simulations of the general anesthetic isoflurane, Journal of Physical Chemistry B, 114, 604-612 (2010)
  39. J. Hénin, W. Shinoda, M. L. Klein, Models for phosphatidylglycerol lipids put to a structural test, Journal of Physical Chemistry B, 113 , 6958-6963 (2009) [Free full text]
  40. G. Brannigan, J. Hénin, R. Law, R. Eckenhoff and M. Klein, Embedded cholesterol in the nicotinic acetylcholine receptor, Proc. Natl. Acad. Sci. USA, 105, 14418-14423 (2008) [Open Access]
  41. J. Hénin, W. Shinoda and M. Klein, United-atom acyl chains for CHARMM phospholipids, J. Phys. Chem. B 112, 7008-7015 (2008)
  42. J. Hénin, E. Tajkhorshid, K. Schulten and C. Chipot, Diffusion of Glycerol through Escherichia coli Aquaglyceroporin GlpF, Biophys. J. 94, 832-839 (2008) [Free full text]
    Biophys J cover
  43. J. Hénin, K. Schulten and C. Chipot, Conformational equilibrium in alanine-rich peptides probed by reversible stretching simulations, J. Phys. Chem. B 110, 16718-16723 (2006)
  44. J. Hénin and C. Chipot, Hydrogen-bonding patterns of cholesterol in lipid membranes, Chem. Phys. Lett. 425, 329-335 (2006)
  45. J. Hénin, B. Maigret, M. Tarek, C. Escrieut, D. Fourmy and C. Chipot, Probing a model of a GPCR/ligand complex in an explicit membrane environment. The human cholecystokinin-1 receptor, Biophys. J. 90, 1232-1240 (2006)
  46. C. Chipot and J. Hénin, Exploring the free energy landscape of a short peptide using an average force, J. Chem. Phys. 123, 244906 (2005)
  47. J. Hénin, A. Pohorille and C. Chipot, Insight into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerizatio nin glycophorin A, J. Am. Chem. Soc. 127, 8478 (2005)
    Correction to: Insight into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A, J. Am. Chem. Soc. 132, 9510 (2010)
  48. J. Hénin and C. Chipot, Overcoming free energy barriers using unconstrained molecular dynamics simulations, J. Chem. Phys. 121, 2904 (2004)

Book chapters

Hénin J, Baaden M, Taly A. Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins. Membrane Proteins Production for Structural Analysis. 347–392 (2014)

Joseph T T, Hénin J. Molecular Mechanics Parameterization of Anesthetic Molecules Methods, Enzymol. 602:61-76. (2018) (Free full text in PMC)