SRSMC UMR 7565


Partenaires

CNRS


Rechercher

Sur ce site

Sur le Web du CNRS


Accueil > Pages Personnelles

Chipot Christophe

Directeur de recherche au CNRS 2ème classe

Équipe de dynamique des assemblages membranaires
Contact :Christophe.Chipot@edam.uhp-nancy.fr
Tél : 03.83.68.40.97 Fax : 03.83.68.43.87
 
Adresse :
Équipe de dynamique des assemblages membranaires
UMR CNRS 7565
Nancy –Université, BP 239
54506 Vandœuvre-lès-Nancy Cedex,France
 

Domaine de recherche


  • Mon domaine de recherche s’adresse principalement à la simulation numérique d’assemblages membranaires, en particulier ceux incluant les canaux et les transporteurs. Pour mener à bien cette thématique, le développement de nouveaux outils théoriques est nécessaire, dans le domaine des calculs d’énergie libre, mais également dans celui des potentiels intermoléculaires.


Research interests :


  • My research area is mainly focused on the numerical simulation of membrane sys-tems, in particular those embracing channels and carriers. To achieve this goal, the development of novel theoretical tools is of paramount importance, in the field of free-energy calculations, as well as in that of intermolecular potentials.


Thèmes de recherche actuels


  • Transport de l’ADP par le transporteur mitochondrial AAC (ANR avec l’IBS)


  • Nouvelles approches pour les calculs d’énergie libre (ANR avec l’ENPC)


  • Transport de chaînes peptidiques dans le translocon (Beckman Institute)


  • Développement de potentiels intermoléculaires polarisables (PICS Beckman Institute ; Universidad de Barcelona)


  • Propriétés de complexes supramoléculaires (Nankai University)


Responsabilités

  •  Responsable de l’Équipe de dynamique des assemblages membranaires.
Publications
 

2016

Gumbart, J. C., & Chipot, C. (2016). Decrypting protein insertion through the translocon with free-energy calculations. Biochimica et Biophysica Acta (BBA) – Biomembranes, 1858(7), 1663–1671.
toggle visibility
Lee, C. T., Comer, J., Herndon, C., Leung, N., Pavlova, A., Swift, R. V., Tung, C., Rowley, C. N., Amaro, R. E., Chipot, C., Wang, Y., & Gumbart, J. C. (2016). Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. Journal of Chemical Information and Modeling, 56(4), 721–733.
toggle visibility
Liu, P., Shao, X., Chipot, C., & Cai, W. (2016). The true nature of rotary movements in rotaxanes. Chem. Sci., 7(1), 457–462.
toggle visibility
Liu, Y., Chipot, C., Shao, X., & Cai, W. (2016). How Does the Solvent Modulate Shuttling in a Pillararene/Imidazolium [2]Rotaxane? Insights from Free Energy Calculations. The Journal of Physical Chemistry C, 120(11), 6287–6293.
toggle visibility
Miyagi, A., Chipot, C., Rangl, M., & Scheuring, S. (2016). High-speed atomic force microscopy shows that annexin V stabilizes membranes on the second timescale. Nature Nanotechnology, .
toggle visibility
Ramadoss, V., Dehez, F., & Chipot, C. (2016). AlaScan: A Graphical User Interface for Alanine Scanning Free-Energy Calculations. Journal of Chemical Information and Modeling, 56(6), 1122–1126.
toggle visibility
Vuković, L., Chipot, C., Makino, D. L., Conti, E., & Schulten, K. (2016). Molecular Mechanism of Processive 3′ to 5′ RNA Translocation in the Active Subunit of the RNA Exosome Complex. Journal of the American Chemical Society, 138(12), 4069–4078.
toggle visibility

2015

Comer, J., Gumbart, J. C., Hénin, J., Lelièvre, T., Pohorille, A., & Chipot, C. (2015). The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask. J. Phys. Chem. B, 119(3), 1129–1151.
toggle visibility
Fu, H., Chipot, C., Shao, X., & Cai, W. (2015). Why do the structural properties of complexes formed by glucans and carbon nanotubes differ so much? RSC Adv., 5(116), 95682–95689.
toggle visibility
Fu, H., Comer, J., Cai, W., & Chipot, C. (2015). Sonoporation at Small and Large Length Scales: Effect of Cavitation Bubble Collapse on Membranes. J. Phys. Chem. Lett., 6(3), 413–418.
toggle visibility
Jo, S., Chipot, C., & Roux, B. (2015). Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics. J. Chem. Theory Comput., 11(5), 2234–2244.
toggle visibility
Liu, Y., Chipot, C., Shao, X., & Cai, W. (2015). What causes tumbling of altro-α-CD derivatives? Insight from computer simulations. RSC Adv., 5(71), 57309–57317.
toggle visibility

2014

Chipot, C. (2014). Frontiers in free-energy calculations of biological systems. Wiley Interdisciplinary Reviews: Computational Molecular Science, 4(1), 71–89.
toggle visibility
Comer, J., Phillips, J. C., Schulten, K., & Chipot, C. (2014). Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules. J. Chem. Theory Comput., 10(12), 5276–5285.
toggle visibility
Comer, J., Roux, B., & Chipot, C. (2014). Achieving ergodic sampling using replica-exchange free-energy calculations. Molecular Simulation, 40(1-3), 218–228.
toggle visibility
Comer, J., Schulten, K., & Chipot, C. (2014). Calculation of Lipid-Bilayer Permeabilities Using an Average Force. J. Chem. Theory Comput., 10(2), 554–564.
toggle visibility
Comer, J., Schulten, K., & Chipot, C. (2014). Diffusive Models of Membrane Permeation with Explicit Orientational Freedom. J. Chem. Theory Comput., 10(7), 2710–2718.
toggle visibility
Fu, H., Liu, Y., Adrià, F., Shao, X., Cai, W., & Chipot, C. (2014). From Material Science to Avant-Garde Cuisine. The Art of Shaping Liquids into Spheres. J. Phys. Chem. B, 118(40), 11747–11756.
toggle visibility
Hazel, A., Chipot, C., & Gumbart, J. C. (2014). Thermodynamics of Deca-alanine Folding in Water. J. Chem. Theory Comput., 10(7), 2836–2844.
toggle visibility
He, J., Chipot, C., Shao, X., & Cai, W. (2014). Cooperative Recruitment of Amphotericin B Mediated by a Cyclodextrin Dimer. J. Phys. Chem. C, 118(41), 24173–24180.
toggle visibility
Liu, P., Chipot, C., Cai, W., & Shao, X. (2014). Unveiling the Underlying Mechanism for Compression and Decompression Strokes of a Molecular Engine. J. Phys. Chem. C, 118(23), 12562–12567.
toggle visibility
Liu, P., Shao, X., Chipot, C., & Cai, W. (2014). Complexation mechanism of cucurbit[6]uril with hexamethylene diammonium cations in saline solution. Phys. Chem. Chem. Phys., 16(44), 24169–24172.
toggle visibility
Liu, Y., Chipot, C., Shao, X., & Cai, W. (2014). Threading or Tumbling? Insight into the Self-Inclusion Mechanism of an altro-α-Cyclodextrin Derivative. J. Phys. Chem. C, 118(33), 19380–19386.
toggle visibility
Marquardt, R., Hénin, J., Dehez, F., & Chipot, C. (2014). Dynamiques moléculaires quantiques et classiques. L'Actualité Chimique, 382-383, 56–62.
toggle visibility

2013

Bidon-Chanal, A., Krammer, E. - M., Blot, D., Pebay-Peyroula, E., Chipot, C., Ravaud, S., & Dehez, F. (2013). How Do Membrane Transporters Sense pH? The Case of the Mitochondrial ADP–ATP Carrier. J. Phys. Chem. Lett., 4(21), 3787–3791.
toggle visibility
Cai, W., & Chipot, C. (2013). Frontiers in High-Performance, Large-Scale Molecular Dynamics. 35 Years of Molecular-Dynamics Simulations of Biological Systems. Acta Chimica Sinica, 71(2), 159.
toggle visibility
Comer, J., Chipot, C., & González-Nilo, F. D. (2013). Calculating Position-Dependent Diffusivity in Biased Molecular Dynamics Simulations. J. Chem. Theory Comput., 9(2), 876–882.
toggle visibility
Comer, J., Dehez, F., Cai, W., & Chipot, C. (2013). Water Conduction through a Peptide Nanotube. J. Phys. Chem. C, 117(50), 26797–26803.
toggle visibility
Gumbart, J. C., Roux, B., & Chipot, C. (2013). Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles. J. Chem. Theory Comput., 9(8), 3789–3798.
toggle visibility
Gumbart, J. C., Roux, B., & Chipot, C. (2013). Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy? J. Chem. Theory Comput., 9(1), 794–802.
toggle visibility
He, J., Chipot, C., Shao, X., & Cai, W. (2013). Cyclodextrin-Mediated Recruitment and Delivery of Amphotericin B. J. Phys. Chem. C, 117(22), 11750–11756.
toggle visibility
Mifsud, J., Ravaud, S., Krammer, E. - M., Chipot, C., Kunji, E. R. S., Pebay-Peyroula, E., & Dehez, F. (2013). The substrate specificity of the human ADP/ATP carrier AAC1. Molecular Membrane Biology, 30(2), 160–168.
toggle visibility
Zoonens, M., Comer, J., Masscheleyn, S., Pebay-Peyroula, E., Chipot, C., Miroux, B., & Dehez, F. (2013). Dangerous Liaisons between Detergents and Membrane Proteins. The Case of Mitochondrial Uncoupling Protein 2. J. Am. Chem. Soc., 135(40), 15174–15182.
toggle visibility

2012

Aguayo, D., González-Nilo, F. D., & Chipot, C. (2012). Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field. J. Chem. Theory Comput., 8(5), 1765–1773.
toggle visibility
Chandler, D. E., Penin, F., Schulten, K., & Chipot, C. (2012). The p7 Protein of Hepatitis C Virus Forms Structurally Plastic, Minimalist Ion Channels. PLoS Comput Biol, 8(9), e1002702.
toggle visibility
Gaborek, T. J., Chipot, C., & Madura, J. D. (2012). Conformational Free-Energy Landscapes for a Peptide in Saline Environments. Biophysical Journal, 103(12), 2513–2520.
toggle visibility
Liu, P., Chipot, C., Shao, X., & Cai, W. (2012). How Do α-Cyclodextrins Self-Organize on a Polymer Chain? J. Phys. Chem. C, 116(33), 17913–17918.
toggle visibility
Liu, P., Chipot, C., Shao, X., & Cai, W. (2012). Solvent-Controlled Shuttling in a Molecular Switch. J. Phys. Chem. C, 116(7), 4471–4476.
toggle visibility
Liu, P., Dehez, F., Cai, W., & Chipot, C. (2012). A Toolkit for the Analysis of Free-Energy Perturbation Calculations. J. Chem. Theory Comput., 8(8), 2606–2616.
toggle visibility
Liu, Y., Chipot, C., Shao, X., & Cai, W. (2012). Edge effects control helical wrapping of carbon nanotubes by polysaccharides. Nanoscale, 4(8), 2584–2589.
toggle visibility
Ravaud, S., Bidon-Chanal, A., Blesneac, I., Machillot, P., Juillan-Binard, C., Dehez, F., Chipot, C., & Pebay-Peyroula, E. (2012). Impaired Transport of Nucleotides in a Mitochondrial Carrier Explains Severe Human Genetic Diseases. ACS Chem. Biol., 7(7), 1164–1169.
toggle visibility
Vergara-Jaque, A., Poblete, H., Lee, E. H., Schulten, K., González-Nilo, F., & Chipot, C. (2012). Molecular Basis of Drug Resistance in A/H1N1 Virus. J. Chem. Inf. Model., 52(10), 2650–2656.
toggle visibility
Zou, X., Ma, W., Solov'yov, I. A., Chipot, C., & Schulten, K. (2012). Recognition of methylated DNA through methyl-CpG binding domain proteins. Nucl. Acids Res., 40(6), 2747–2758.
toggle visibility

2011

Gamini, R., Sotomayor, M., Chipot, C., & Schulten, K. (2011). Cytoplasmic Domain Filter Function in the Mechanosensitive Channel of Small Conductance. Biophysical Journal, 101, 80–89.
toggle visibility
Gumbart, J., Chipot, C., & Schulten, K. (2011). Free Energy of Nascent-Chain Folding in the Translocon. Journal of the American Chemical Society, 133(19), 7602–7607.
toggle visibility
Gumbart, J., Chipot, C., & Schulten, K. (2011). Free-energy cost for translocon-assisted insertion of membrane proteins. Proceedings of the National Academy of Sciences, 108(9), 3596–3601.
toggle visibility
Hsin, J., LaPointe, L. M., Kazy, A., Chipot, C., Senes, A., & Schulten, K. (2011). Oligomerization State of Photosynthetic Core Complexes Is Correlated with the Dimerization Affinity of a Transmembrane Helix. Journal of the American Chemical Society, 133(35), 14071–14081.
toggle visibility
Lelièvre, T., & Chipot, C. (2011). Enhanced sampling of multidimensional free-energy landscapes using adaptive biasing forces. SIAM Journal on Applied Mathematics, .
toggle visibility
Liu, Y., Chipot, C., Shao, X., & Cai, W. (2011). Free-Energy Landscape of the Helical Wrapping of a Carbon Nanotube by a Polysaccharide. Journal of Physical Chemistry C, 115(5), 1851–1856.
toggle visibility
Liu, Y., Chipot, C., Shao, X., & Cai, W. (2011). The effects of 7-dehydrocholesterol on the structural properties of membranes. Physical Biology, 8(5), 056005.
toggle visibility
Luque, F. J., Dehez, F., Chipot, C., & Orozco, M. (2011). Polarization effects in molecular interactions. Wiley Interdisciplinary Reviews: Computational Molecular Science, 1, 844–854.
toggle visibility
Sheng Cai, W., Wang, T., Zhe Liu, Y., Liu, P., Chipot, C., & Guang Shao, X. (2011). Free Energy Calculations for Cyclodextrin Inclusion Complexes. Current Organic Chemistry, 15(6), 839–847.
toggle visibility
Wang, T., Chipot, C., Shao, X., & Cai, W. (2011). Structural Characterization of Micelles Formed of Cholesteryl-Functionalized Cyclodextrins. Langmuir, 27(1), 91–97.
toggle visibility
Zúñiga, L., Márquez, V., González-Nilo, F. D., Chipot, C., Cid, L. P., Sepúlveda, F. V., & Niemeyer, M. I. (2011). Gating of a pH-Sensitive K2P Potassium Channel by an Electrostatic Effect of Basic Sensor Residues on the Selectivity Filter. PLoS ONE, 6(1).
toggle visibility

2010

Champagnat, N., Chipot, C., & Faou, E. (2010). Reconciling alternate methods for the determination of charge distributions: a probabilistic approach to high-dimensional least-squares approximations. J Math Chem, 49(1), 296–324.
toggle visibility
Chebil, L., Chipot, C., Archambault, F., Humeau, C., Engasser, J. M., Ghoul, M., & Dehez, F. (2010). Solubilities Inferred from the Combination of Experiment and Simulation. Case Study of Quercetin in a Variety of Solvents. Journal Of Physical Chemistry B, 114(38), 12308–12313.
toggle visibility
Henin, J., Fiorin, G., Chipot, C., & Klein, M. L. (2010). Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables. Journal Of Chemical Theory And Computation, 6(1), 35–47.
toggle visibility
Liu, P., Cai, W. S., Chipot, C., & Shao, X. G. (2010). Thermodynamic Insights into the Dynamic Switching of a Cyclodextrin in a Bistable Molecular Shuttle. Journal of Physical Chemistry Letters, 1(12), 1776–1780.
toggle visibility
Liu, Y. Z., Chipot, C., Shao, X. G., & Cai, W. S. (2010). Solubilizing Carbon Nanotubes through Noncovalent Functionalization. Insight from the Reversible Wrapping of Alginic Acid around a Single-Walled Carbon Nanotube. Journal Of Physical Chemistry B, 114(17), 5783–5789.
toggle visibility
Minoukadeh, K., Chipot, C., & Lelièvre, T. (2010). Potential of Mean Force Calculations: A Multiple-Walker Adaptive Biasing Force Approach. Journal of Chemical Theory and Computation, 6(4), 1008–1017.
toggle visibility
Montserret, R., Saint, N., Vanbelle, C., Salvay, A. G., Simorre, J. P., Ebel, C., Sapay, N., Renisio, J. G., Bockmann, A., Steinmann, E., Pietschmann, T., Dubuisson, J., Chipot, C., & Penin, F. (2010). NMR Structure and Ion Channel Activity of the p7 Protein from Hepatitis C Virus. Journal Of Biological Chemistry, 285(41), 31446–31461.
toggle visibility
Pohorille, A., Jarzynski, C., & Chipot, C. (2010). Good Practices in Free-Energy Calculations. Journal of Physical Chemistry B, 114(32), 10235–10253.
toggle visibility

Chapitres de Livre

2015

Chipot, C. (2015). Applications to Real Size Biological Systems. In B. Engquist (Ed.), Encyclopedia of Applied and Computational Mathematics (pp. 72–81). Springer Berlin Heidelberg.
toggle visibility