A Rigorous Framework for Calculating Protein–Protein Binding Affinities in Membranes
Open accessAbstract
Calculating the binding free energy of integral transmembrane (TM) proteins is crucial for understanding the mechanisms by which they recognize one another and reversibly associate. The glycophorin A (GpA) homodimer, composed of two α-helical segments, has long served as a model system for studying TM protein reversible association. The present work establishes a methodological framework for calculating the binding affinity of the GpA homodimer in the heterogeneous environment of a membrane. Our investigation carefully considered a variety of protocols, including the appropriate choice of the force field, rigorous standardization reflecting the experimental conditions, sampling algorithm, anisotropic environment, and collective variables, to accurately describe GpA dimerization via molecular dynamics-based approaches. Specifically, two strategies were explored: (i) an unrestrained potential mean force (PMF) calculation, which merely enhances sampling along the separation of the two binding partners without any restraint, and (ii) a so-called "geometrical route", whereby the α-helices are progressively separated with imposed restraints on their orientational, positional, and conformational degrees of freedom to accelerate convergence. Our simulations reveal that the simplified, unrestrained PMF approach is inadequate for the description of GpA dimerization. Instead, the geometrical route, tailored specifically to GpA in a membrane environment, yields excellent agreement with experimental data within a reasonable computational time. A dimerization free energy of -10.7 kcal/mol is obtained, in fairly good agreement with available experimental data. The geometrical route further helps elucidate how environmental forces drive association before helical interactions stabilize it. Our simulations also brought to light a distinct, long-lived spatial arrangement that potentially serves as an intermediate state during dimer formation. The methodological advances in the generalized geometrical route provide a powerful tool for accurate and efficient binding-affinity calculations of intricate TM protein complexes in inhomogeneous environments.
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The protocol has so far been successfully used in calculating the binding free energy of a variety of protein-protein complexes, in good agreement with experimental data, including a homodimeric α-helical complex.
“The protocol has so far been successfully used in calculating the binding free energy of a variety of protein–protein complexes, in good agreement with experimental data,54,62,64,65,67,73−76 including a homodimeric α-helical complex.69”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [69]
Since the coiled coils in the present study are all homomultimers composed of identical α-helical monomers, the effect of symmetry must be considered during the calculation of the binding free energy, and a symmetry correction must be applied.
“Since the coiled coils in the present study are all homomultimers composed of identical α-helical monomers, the effect of symmetry must also be considered during the calculation of the binding free energy.63,69 Therefore, a symmetry correction must be applied to the binding free energy as follows”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [69]
Simulations without such restraints have been reported to fail to converge and to yield binding free energies inconsistent with experimental data.
“Simulations without such restraints have been reported to fail to converge and to yield binding free energies inconsistent with experimental data.62,65,69”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [69]
Cites
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp973084f · Cited by 14,270 · see citing works
Self-citationUnified Approach for Molecular Dynamics and Density-Functional Theory
Car, R., & Parrinello, M. (1985) · Physical Review Letters · doi:10.1103/physrevlett.55.2471 · Cited by 10,737 · see citing works
Membrane lipids: where they are and how they behave
van Meer, G., Voelker, D. R., & Feigenson, G. W. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2330 · Cited by 7,157 · see citing works
Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P. E. M., Vorobyov, I., et al. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21367 · Cited by 6,986 · see citing works
CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins
Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de Groot, B. L., Grubmüller, H., & MacKerell, A. (2016) · Nature Methods · doi:10.1038/nmeth.4067 · Cited by 6,708 · see citing works
MDAnalysis: A toolkit for the analysis of molecular dynamics simulations
Michaud‐Agrawal, N., Denning, E. J., Woolf, T. B., & Beckstein, O. (2011) · Journal of Computational Chemistry · doi:10.1002/jcc.21787 · Cited by 4,549 · see citing works
Replica-exchange molecular dynamics method for protein folding
Sugita, Y., & Okamoto, Y. (1999) · Chemical Physics Letters · doi:10.1016/s0009-2614(99)01123-9 · Cited by 4,499 · see citing works
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data
Huang, J., & MacKerell, A. D. (2013) · Journal of Computational Chemistry · doi:10.1002/jcc.23354 · Cited by 4,484 · see citing works
Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types
Klauda, J. B., Venable, R., Freites, J. A., O'Connor, J. W., Tobias, D., Mondragon-Ramirez, C., Vorobyov, I., MacKerell, A. D., & Pastor, R. (2010) · Journal of Physical Chemistry B · doi:10.1021/jp101759q · Cited by 4,369 · see citing works
Evidence for the Formation of Symmetric and Asymmetric DLPC-DAPC Lipid Bilayer Domains
Ritter, M., Schmidt, S., Jakab, M., Paulmichl, M., & Henderson, R. M. (2013) · Cellular Physiology and Biochemistry · doi:10.1159/000350122 · Cited by 3,923 · see citing works
MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations
Gowers, R. J., Linke, M., Barnoud, J., Reddy, T. J., Melo, M. N., Seyler, S. L., Domański, J., Dotson, D., Buchoux, S., Kenney, I. M., et al. (2016) · Proceedings of the Python in Science Conferences · doi:10.25080/majora-629e541a-00e · Cited by 2,085 · see citing works
Martini 3: A general purpose force field for coarse-grained molecular dynamics
Souza, P. C. T., Alessandri, R., Barnoud, J., Thallmair, S., Faustino, I., Grünewald, F., Patmanidis, I., Abdizadeh, H., Bruininks, B. M. H., Wassenaar, T. A., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01098-3 · Cited by 1,551 · see citing works
The statistical-thermodynamic basis for computation of binding affinities: a critical review
Gilson, M. K., Given, J. A., Bush, B. L., & McCammon, J. A. (1997) · Biophysical Journal · doi:10.1016/s0006-3495(97)78756-3 · Cited by 1,222 · see citing works
Kučerka, N., Nieh, M., & Katsaras, J. (2011) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2011.07.022 · Cited by 1,059 · see citing works
Using collective variables to drive molecular dynamics simulations
Fiorin, G., Klein, M. L., & Hénin, J. (2013) · Molecular Physics · doi:10.1080/00268976.2013.813594 · Cited by 1,053 · see citing works
Interaction of membrane proteins and lipids with solubilizing detergents
le Maire, M., Champeil, P., & MØLLER, J. V. (2000) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/s0304-4157(00)00010-1 · Cited by 1,034 · see citing works
Constrained reaction coordinate dynamics for the simulation of rare events
Carter, E. A., Ciccotti, G., Hynes, J. T., & Kapral, R. (1989) · Chemical Physics Letters · doi:10.1016/s0009-2614(89)87314-2 · Cited by 1,023 · see citing works
Calculating free energies using average force
Darve, E. F., & Pohorille, A. (2001) · The Journal of Chemical Physics · doi:10.1063/1.1410978 · Cited by 998 · see citing works
A Transmembrane Helix Dimer: Structure and Implications
MacKenzie, K. R., Prestegard, J. H., & Engelman, D. M. (1997) · Science · doi:10.1126/science.276.5309.131 · Cited by 960 · see citing works
Membrane protein folding and oligomerization: the two-stage model
Popot, J., & Engelman, D. M. (1990) · Biochemistry · doi:10.1021/bi00469a001 · Cited by 941 · see citing works
Chipot, C. J., & Pohorille, A. (2007) · Springer series in chemical physics · doi:10.1007/978-3-540-38448-9 · Cited by 911 · see citing works
Self-citationThe spontaneous insertion of proteins into and across membranes: The helical hairpin hypothesis
Engelman, D. M., & Steitz, T. A. (1981) · Cell · doi:10.1016/0092-8674(81)90136-7 · Cited by 880 · see citing works
Bilayer Thickness and Membrane Protein Function: An Energetic Perspective
Andersen, O. S., & Koeppe, R. E. (2007) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.36.040306.132643 · Cited by 870 · see citing works
Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics
Iannuzzi, M., Laio, A., & Parrinello, M. (2003) · Physical Review Letters · doi:10.1103/physrevlett.90.238302 · Cited by 817 · see citing works
Structure of Fully Hydrated Fluid Phase Lipid Bilayers with Monounsaturated Chains
Kučerka, N., Tristram‐Nagle, S., & Nagle, J. F. (2006) · The Journal of Membrane Biology · doi:10.1007/s00232-005-7006-8 · Cited by 803 · see citing works
Adaptive biasing force method for scalar and vector free energy calculations.
Darve, E. F., Rodríguez-Gómez, D., & Pohorille, A. (2008) · Journal of Chemical Physics · doi:10.1063/1.2829861 · Cited by 793 · see citing works
An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids
Feller, S. E., & MacKerell, A. D. (2000) · The Journal of Physical Chemistry B · doi:10.1021/jp0007843 · Cited by 766 · see citing works
Enhanced sampling techniques in molecular dynamics simulations of biological systems
Bernardi, R. C., Melo, M. C. R., & Schulten, K. (2015) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2014.10.019 · Cited by 757 · see citing works
Calculation of absolute protein–ligand binding free energy from computer simulations
Woo, H.-J., & Roux, B. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409005102 · Cited by 661 · see citing works
Self-citationHelical Membrane Protein Folding, Stability, and Evolution
Popot, J., & Engelman, D. M. (2000) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.69.1.881 · Cited by 591 · see citing works
Sequence specificity in the dimerization of transmembrane .alpha.-helixes
Lemmon, M. A., Flanagan, J. M., Treutlein, H., Zhang, J., & Engelman, D. M. (1992) · Biochemistry · doi:10.1021/bi00166a002 · Cited by 495 · see citing works
The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask
Comer, J. R., Gumbart, J. C., Hénin, J., Tony Lelièvre, A., Pohorille, A., & Chipot, C. J. (2014) · The Journal of Physical Chemistry B · doi:10.1021/jp506633n · Cited by 472 · see citing works
Self-citationGlycophorin A dimerization is driven by specific interactions between transmembrane alpha-helices.
Lemmon, M. A., Flanagan, J. M., Hunt, J. F., Adair, B. D., Bormann, B. J., Dempsey, C. E., & Engelman, D. M. (1992) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)42569-0 · Cited by 468 · see citing works
Overcoming free energy barriers using unconstrained molecular dynamics simulations.
Hénin, J., & Chipot, C. (2004) · Journal of Chemical Physics · doi:10.1063/1.1773132 · Cited by 419 · see citing works
Self-citationEnhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0]
Hénin, J., Tony Lelièvre, A., Shirts, M. R., Valsson, Ó., & Delemotte, L. (2022) · Living Journal of Computational Molecular Science · doi:10.33011/livecoms.4.1.1583 · Cited by 404 · see citing works
Development of the CHARMM Force Field for Lipids
Pastor, R. W., & MacKerell, A. D. (2011) · The Journal of Physical Chemistry Letters · doi:10.1021/jz200167q · Cited by 399 · see citing works
Hénin, J., Fiorin, G., Chipot, C., & Klein, M. (2009) · Journal of Chemical Theory and Computation · doi:10.1021/ct9004432 · Cited by 397 · see citing works
Self-citationTOXCAT: A measure of transmembrane helix association in a biological membrane
Russ, W. P., & Engelman, D. M. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.3.863 · Cited by 352 · see citing works
Well-Tempered Metadynamics Converges Asymptotically
Dama, J. F., Parrinello, M., & Voth, G. A. (2014) · Physical Review Letters · doi:10.1103/physrevlett.112.240602 · Cited by 347 · see citing works
Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
Gumbart, J. C., Roux, B., & Chipot, C. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct3008099 · Cited by 343 · see citing works
Self-citationProtein modulation of lipids, and vice-versa, in membranes
Marsh, D. (2008) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2008.01.015 · Cited by 320 · see citing works
A dimerization motif for transmembrane α–helices
Lemmon, M. A., Treutlein, H., Adams, P. D., Brünger, A. T., & Engelman, D. M. (1994) · Nature Structural Biology · doi:10.1038/nsb0394-157 · Cited by 314 · see citing works
Membrane protein folding: beyond the two stage model
Engelman, D. M., Chen, Y., Chin, C., Curran, A. R., Dixon, A. M., Dupuy, A. D., Lee, A. S., Lehnert, U., Matthews, E. E., Reshetnyak, Y. K., et al. (2003) · FEBS Letters · doi:10.1016/s0014-5793(03)01106-2 · Cited by 299 · see citing works
Models of Lipid-Protein Interactions in Membranes
Mouritsen, O. G., & Bloom, M. J. (1993) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.bb.22.060193.001045 · Cited by 277 · see citing works
Free Energy Computations: A Mathematical Perspective
Lelièvre, T., Rousset, M., & Stoltz, G. (2010) · doi:10.1142/p579 · Cited by 253 · see citing works
Lipid-mediated protein interaction in membranes
Marĉelja, S. (1976) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/0005-2736(76)90149-8 · Cited by 251 · see citing works
A polytopic membrane protein displays a reversible topology dependent on membrane lipid composition
Bogdanov, M. V., Heacock, P. N., & Dowhan, W. (2002) · The EMBO Journal · doi:10.1093/emboj/21.9.2107 · Cited by 249 · see citing works
Langosch, D., Brosig, B., Kolmar, H., & Fritz, H. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0595 · Cited by 238 · see citing works
The effect of point mutations on the free energy of transmembrane α-helix dimerization
Fleming, K. G., Ackerman, A. L., & Engelman, D. M. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1236 · Cited by 235 · see citing works
Brosig, B., & Langosch, D. (1998) · Protein Science · doi:10.1002/pro.5560070423 · Cited by 234 · see citing works
Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles
Gumbart, J. C., Roux, B., & Chipot, C. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400273t · Cited by 211 · see citing works
Self-citationFolding and Stability of α-Helical Integral Membrane Proteins
MacKenzie, K. R. (2006) · Chemical Reviews · doi:10.1021/cr0404388 · Cited by 210 · see citing works
Anomalous and normal diffusion of proteins and lipids in crowded lipid membranes
Javanainen, M., Hammarén, H. M., Monticelli, L., Jeon, J., Miettinen, M. S., Martinez‐Seara, H., Metzler, R., & Vattulainen, I. (2012) · Faraday Discussions · doi:10.1039/c2fd20085f · Cited by 210 · see citing works
Specificity and promiscuity in membrane helix interactions
Lemmon, M. A., & Engelman, D. M. (1994) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583500004522 · Cited by 200 · see citing works
Detergents modulate dimerization, but not helicity, of the glycophorin A transmembrane domain
Fisher, L. E., Engelman, D. M., & Sturgis, J. N. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3126 · Cited by 183 · see citing works
Structure of the Transmembrane Dimer Interface of Glycophorin A in Membrane Bilayers
Smith, S. O., Song, D. Y., Shekar, S. C., Groesbeek, M., Ziliox, M., & Aimoto, S. (2001) · Biochemistry · doi:10.1021/bi010357v · Cited by 176 · see citing works
Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains
Klauda, J. B., Monje‐Galvan, V., Kim, T., & Im, W. (2012) · The Journal of Physical Chemistry B · doi:10.1021/jp304056p · Cited by 175 · see citing works
Fleming, K. G., & Engelman, D. M. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.251367498 · Cited by 174 · see citing works
Treutlein, H. R., Lemmon, M. A., Engelman, D. M., & Brünger, A. T. (1992) · Biochemistry · doi:10.1021/bi00166a003 · Cited by 173 · see citing works
Tilt Angle of a Trans-membrane Helix is Determined by Hydrophobic Mismatch
Park, S. H., & Opella, S. J. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.05.004 · Cited by 168 · see citing works
Taming Rugged Free Energy Landscapes Using an Average Force
Fu, H., Shao, X., Cai, W., & Chipot, C. J. (2019) · Accounts of Chemical Research · doi:10.1021/acs.accounts.9b00473 · Cited by 166 · see citing works
Self-citationLesage, A., Tony Lelièvre, A., Stoltz, G., & Hénin, J. (2016) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.6b10055 · Cited by 164 · see citing works
Pluháčková, K., Kirsch, S. A., Han, J., Sun, L., Jiang, Z., Unruh, T., & Böckmann, R. A. (2016) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.6b01870 · Cited by 156 · see citing works
Synthetic Peptides Mimic the Assembly of Transmembrane Glycoproteins
Bormann, B. J., Knowles, W. J., & Marchesi, V. T. (1989) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)84957-8 · Cited by 152 · see citing works
Accelerating Membrane Simulations with Hydrogen Mass Repartitioning
Balusek, C., Hwang, H. J., Lau, C. H., Lundquist, K. P., Hazel, A. J., Pavlova, À., Lynch, D. L., Reggio, P. H., Wang, Y., & Gumbart, J. C. (2019) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.9b00160 · Cited by 152 · see citing works
Self-citationZooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys
Fu, H., Zhang, H., Chen, H., Shao, X., Chipot, C. J., & Cai, W. (2018) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.8b01994 · Cited by 149 · see citing works
Self-citationHénin, J., Pohorille, A., & Chipot, C. J. (2005) · Journal of the American Chemical Society · doi:10.1021/ja050581y · Cited by 147 · see citing works
Self-citationMacKenzie, K. R., & Engelman, D. M. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.7.3583 · Cited by 136 · see citing works
Self-association of Transmembrane α-Helices in Model Membranes
Sparr, E., Ash, W. L., Nazarov, P. V., Rijkers, D. T. S., Hemminga, M. A., Tieleman, D. P., & Killian, J. A. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m502810200 · Cited by 132 · see citing works
Measuring the Energetics of Membrane Protein Dimerization in Mammalian Membranes
Chen, L., Novicky, L., Merzlyakov, M., Hristov, T. S., & Hristova, K. A. (2010) · Journal of the American Chemical Society · doi:10.1021/ja910692u · Cited by 131 · see citing works
Standardizing the Free Energy Change of Transmembrane Helix–Helix Interactions
Fleming, K. G. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00920-8 · Cited by 129 · see citing works
Effect of Detergents on the Association of the Glycophorin A Transmembrane Helix
Fisher, L. E., Engelman, D. M., & Sturgis, J. N. (2003) · Biophysical Journal · doi:10.1016/s0006-3495(03)74728-6 · Cited by 123 · see citing works
GALLEX, a Measurement of Heterologous Association of Transmembrane Helices in a Biological Membrane
Schneider, D., & Engelman, D. M. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m206287200 · Cited by 123 · see citing works
The Structure and Topology of α-Helical Coiled Coils
Lupas, A. N., Baßler, J., & Dunin-Horkawicz, S. (2017) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-3-319-49674-0_4 · Cited by 116 · see citing works
Sengupta, D., & Marrink, . J. (2010) · Physical Chemistry Chemical Physics · doi:10.1039/c0cp00101e · Cited by 115 · see citing works
Mueller, B. K., Subramaniam, S., & Senes, A. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319944111 · Cited by 114 · see citing works
Intramembrane Helix-Helix Association in Oligomerization and Transmembrane Signaling
Bormann, B. J., & Engelman, D. M. (1992) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.bb.21.060192.001255 · Cited by 114 · see citing works
Computation of free energy profiles with parallel adaptive dynamics.
Lelièvre, T., Rousset, M., & Stoltz, G. (2006) · Journal of Chemical Physics · doi:10.1063/1.2711185 · Cited by 110 · see citing works
Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association
Domański, J., Hedger, G., Best, R. B., Stansfeld, P. J., & Sansom, M. S. P. (2016) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.6b08445 · Cited by 110 · see citing works
In VitroStudies of Membrane Protein Folding
Booth, P. J., Templer, R. H., Meijberg, W., Allen, S. J., Curran, A. R., & Lorch, M. (2001) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/20014091074246 · Cited by 110 · see citing works
Zhuang, X., Makover, J. R., Im, W., & Klauda, J. B. (2014) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2014.06.010 · Cited by 105 · see citing works
Sequence Context Modulates the Stability of a GxxxG-mediated Transmembrane Helix–Helix Dimer
Doura, A. K., Kobus, F. J., Dubrovsky, L., Hibbard, E., & Fleming, K. G. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.06.042 · Cited by 104 · see citing works
Complex Interactions at the Helix–Helix Interface Stabilize the Glycophorin A Transmembrane Dimer
Doura, A. K., & Fleming, K. G. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.09.011 · Cited by 103 · see citing works
Error and efficiency of replica exchange molecular dynamics simulations
Rosta, E., & Hummer, G. (2009) · The Journal of Chemical Physics · doi:10.1063/1.3249608 · Cited by 100 · see citing works
Method to measure strong protein–protein interactions in lipid bilayers using a steric trap
Hong, H., Blois, T. M., Cao, Z., & Bowie, J. U. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1010348107 · Cited by 98 · see citing works
Validating lipid force fields against experimental data: Progress, challenges and perspectives
Poger, D., Caron, B., & Mark, A. E. (2016) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2016.01.029 · Cited by 96 · see citing works
Hong, H., & Bowie, J. U. (2011) · Journal of the American Chemical Society · doi:10.1021/ja204524c · Cited by 93 · see citing works
Computation of free energy profiles with parallel adaptive dynamicsPreprint
Lelièvre, T., Rousset, M., & Stoltz, G. (2007) · HAL (Le Centre pour la Communication Scientifique Directe) · Cited by 92 · see citing works
Hydrophobic Coupling of Lipid Bilayer Energetics to Channel Function
Goforth, R. L., Chi, A. K., Greathouse, D. V., Providence, L. L., Koeppe, R. E., & Andersen, O. S. (2003) · The Journal of General Physiology · doi:10.1085/jgp.200308797 · Cited by 92 · see citing works
Zheng, L.-Q., & Yang, W. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct200726v · Cited by 91 · see citing works
Exploration, Sampling, And Reconstruction of Free Energy Surfaces with Gaussian Process Regression
Mones, L., Bernstein, N., & Csányi, G. (2016) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.6b00553 · Cited by 91 · see citing works
Folding scene investigation: membrane proteins
Booth, P. J., & Curnow, P. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.12.005 · Cited by 89 · see citing works
Potential of Mean Force Calculations: A Multiple-Walker Adaptive Biasing Force Approach
Minoukadeh, K., Chipot, C. J., & Tony Lelièvre, A. (2010) · Journal of Chemical Theory and Computation · doi:10.1021/ct900524t · Cited by 87 · see citing works
Self-citationComer, J. R., Phillips, J. C., Schulten, K. J., & Chipot, C. J. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct500874p · Cited by 82 · see citing works
Self-citationLipid-Assisted Membrane Protein Folding and Topogenesis
Dowhan, W., Vitrac, H., & Bogdanov, M. V. (2019) · The Protein Journal · doi:10.1007/s10930-019-09826-7 · Cited by 81 · see citing works
Khavrutskii, I. V., Dzubiella, J., & McCammon, J. A. (2008) · The Journal of Chemical Physics · doi:10.1063/1.2825620 · Cited by 77 · see citing works
New Coarse Variables for the Accurate Determination of Standard Binding Free Energies
Fu, H., Cai, W., Hénin, J., Roux, B., & Chipot, C. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b00791 · Cited by 74 · see citing works
Self-citationControlling the Folding Efficiency of an Integral Membrane Protein
Allen, S. J., Curran, A. R., Templer, R. H., Meijberg, W., & Booth, P. J. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.07.041 · Cited by 74 · see citing works
Mingarro, I., Whitley, P. R., von HEIJNE, G., & Lemmon, M. A. (1996) · Protein Science · doi:10.1002/pro.5560050712 · Cited by 74 · see citing works
Chasis, J. A., Reid, M. E., Jensen, R. H., & Mohandas, N. (1988) · The Journal of Cell Biology · doi:10.1083/jcb.107.4.1351 · Cited by 70 · see citing works
Determination of helix-helix interactions in membranes by rotational resonance NMR.
Smith, S. O., & Bormann, B. J. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.2.488 · Cited by 69 · see citing works
Free Energy Methods for the Description of Molecular Processes
Chipot, C. J. (2023) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-062722-093258 · Cited by 69 · see citing works
Self-citationGrau-Campistany, A., Strandberg, E., Wadhwani, P., Reichert, J. C., Bürck, J., Rabanal, F., & Ulrich, A. S. (2015) · Scientific Reports · doi:10.1038/srep09388 · Cited by 68 · see citing works
Sane in the membrane: designing systems to modulate membrane proteins
Booth, P. J. (2005) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2005.06.002 · Cited by 68 · see citing works
Beck, D. A. C., White, G. W. N., & Daggett, V. (2006) · Journal of Structural Biology · doi:10.1016/j.jsb.2006.10.002 · Cited by 65 · see citing works
Membrane Protein Dynamics and Functional Implications in Mammalian Cells
Alenghat, F. J., & Golan, D. E. (2013) · Current topics in membranes · doi:10.1016/b978-0-12-417027-8.00003-9 · Cited by 64 · see citing works
The Activation Energy for Insertion of Transmembrane α-Helices is Dependent on Membrane Composition
Meijberg, W., & Booth, P. J. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00342-x · Cited by 64 · see citing works
Lipid-Modulated Sequence-Specific Association of Glycophorin A in Membranes
Janosi, L., Prakash, A., & Doxastakis, M. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2010.04.005 · Cited by 62 · see citing works
Rhodopsin/Lipid Hydrophobic Matching—Rhodopsin Oligomerization and Function
Soubias, O., Teague, W. E., Hines, K. G., & Gawrisch, K. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2015.01.006 · Cited by 61 · see citing works
Evaluation of Predicted Protein–Protein Complexes by Binding Free Energy Simulations
Siebenmorgen, T., & Zacharias, M. (2019) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.8b01022 · Cited by 59 · see citing works
Lipid enrichment and selectivity of integral membrane proteins in two-component lipid bilayers
Sperotto, M. M., & Mouritsen, O. G. (1993) · European Biophysics Journal · doi:10.1007/bf00213555 · Cited by 58 · see citing works
Arkin, I. T. (2002) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/s0005-2736(02)00580-1 · Cited by 57 · see citing works
Crystal Structure of the Glycophorin A Transmembrane Dimer in Lipidic Cubic Phase
Trenker, R., Call, M. E., & Call, M. J. (2015) · Journal of the American Chemical Society · doi:10.1021/jacs.5b11354 · Cited by 54 · see citing works
Thermodynamics of glycophorin A transmembrane helix dimerization in C14 betaine micelles
Fleming, K. G., Ren, C.-C., Doura, A. K., Eisley, M. E., Kobus, F. J., & Stanley, A. M. (2004) · Biophysical Chemistry · doi:10.1016/j.bpc.2003.10.008 · Cited by 53 · see citing works
Mean-field and Monte Carlo simulation studies of the lateral distribution of proteins in membranes
Sperotto, M. M., & Mouritsen, O. G. (1991) · European Biophysics Journal · doi:10.1007/bf00196342 · Cited by 53 · see citing works
Mondal, S., Khelashvili, G., & Weinstein, H. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.04.032 · Cited by 52 · see citing works
Navigating the Structural Landscape of De Novo α-Helical Bundles
Rhys, G. G., Wood, C. W., Beesley, J. L., Zaccai, N. R., Burton, A. J., Brady, R. L., Thomson, A. R., & Woolfson, D. N. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.8b13354 · Cited by 48 · see citing works
Wang, F., Stuart, S. J., & Latour, R. A. (2008) · Biointerphases · doi:10.1116/1.2840054 · Cited by 47 · see citing works
Balancing Force Field Protein–Lipid Interactions To Capture Transmembrane Helix–Helix Association
Domański, J., Sansom, M. S. P., Stansfeld, P. J., & Best, R. B. (2018) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b00983 · Cited by 47 · see citing works
Duboué-Dijon, E., & Hénin, J. (2021) · The Journal of Chemical Physics · doi:10.1063/5.0046853 · Cited by 46 · see citing works
Kim, H., Saura, P., Pöverlein, M. C., Gámiz‐Hernández, A. P., & Kaila, V. R. I. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.3c03086 · Cited by 46 · see citing works
Chadda, R., Bernhardt, N., Kelley, E. G., Teixeira, S., Griffith, K., Gil-Ley, A., Öztürk, T. N., Hughes, L. E., Forsythe, A. N., Krishnamani, V., et al. (2021) · eLife · doi:10.7554/elife.63288 · Cited by 45 · see citing works
Efficient preparation and analysis of membrane and membrane protein systems
Javanainen, M., & Martinez‐Seara, H. (2016) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2016.02.036 · Cited by 41 · see citing works
Helix-helix packing in a membrane-like environment
Mingarro, I., Elofsson, A., & von HEIJNE, G. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1276 · Cited by 41 · see citing works
Effects of High Pressure on Phospholipid Bilayers
Ding, W., Palaiokostas, M., Shahane, G., Wang, W., & Orsi, M. (2017) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.7b07119 · Cited by 41 · see citing works
Calculating the Free Energy of Association of Transmembrane Helices
Zhang, J., & Lazaridis, T. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.081224 · Cited by 40 · see citing works
Enhancing sampling with free-energy calculations.
Chen, H., & Chipot, C. (2022) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2022.102497 · Cited by 38 · see citing works
Self-citationChen, H., Fu, H., Chipot, C. J., Shao, X., & Cai, W. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00103 · Cited by 37 · see citing works
Self-citationLocal Bilayer Hydrophobicity Modulates Membrane Protein Stability
Marx, D. C., & Fleming, K. G. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.0c09412 · Cited by 36 · see citing works
Sarabipour, S., & Hristova, K. A. (2013) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2013.03.022 · Cited by 35 · see citing works
Folding α-helical membrane proteins: kinetic studies on bacteriorhodopsin
Booth, P. J. (1997) · Folding and Design · doi:10.1016/s1359-0278(97)00045-x · Cited by 35 · see citing works
Folding energetics and oligomerization of polytopic α-helical transmembrane proteins
Neumann, J., Klein, N., Otzen, D. E., & Schneider, D. (2014) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2014.07.017 · Cited by 32 · see citing works
Tony Lelièvre, A., Rousset, M., & Stoltz, G. (2006) · Journal of Computational Physics · doi:10.1016/j.jcp.2006.08.003 · Cited by 31 · see citing works
Whisstock, J. C., Lesk, A. M., & Carrell, R. W. (1996) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(199611)26:3 · Cited by 30 · see citing works
The biological significance of lipid–protein interactions
Findlay, H. E., & Booth, P. J. (2006) · Journal of Physics Condensed Matter · doi:10.1088/0953-8984/18/28/s11 · Cited by 30 · see citing works
Replica-Exchange Methods for Biomolecular Simulations
Sugita, Y., Kamiya, M., Oshima, H., & Re, S. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9608-7_7 · Cited by 30 · see citing works
Quantification of helix–helix binding affinities in micelles and lipid bilayers
Lomize, A. L., Pogozheva, I. D., & Mosberg, H. I. (2004) · Protein Science · doi:10.1110/ps.04850804 · Cited by 29 · see citing works
Hazardous Shortcuts in Standard Binding Free Energy Calculations
Blazhynska, M., Goulard Coderc de Lacam, E., Chen, H., Roux, B., & Chipot, C. (2022) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.2c01490 · Cited by 27 · see citing works
Self-citationMolecular Mechanism for Gramicidin Dimerization and Dissociation in Bilayers of Different Thickness
Sun, D., Peyear, T. A., Bennett, W. F., Andersen, O. S., Lightstone, F. C., & Ingólfsson, H. I. (2019) · Biophysical Journal · doi:10.1016/j.bpj.2019.09.044 · Cited by 27 · see citing works
Exploring the impact of proteins on the line tension of a phase-separating ternary lipid mixture
Bandara, A., Panahi, A., Pantelopulos, G. A., Nagai, T., & Straub, J. E. (2019) · The Journal of Chemical Physics · doi:10.1063/1.5091450 · Cited by 26 · see citing works
Free energy calculations from adaptive molecular dynamics simulations with adiabatic reweighting
Cao, L., Stoltz, G., Tony Lelièvre, A., Marinica, M., & Athènes, M. (2014) · The Journal of Chemical Physics · doi:10.1063/1.4866811 · Cited by 22 · see citing works
Chin, C., von HEIJNE, G., & de Gier, J. L. (2002) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(02)02082-0 · Cited by 22 · see citing works
On Computing Equilibrium Binding Constants for Protein–Protein Association in Membranes
Majumder, A., Kwon, S., & Straub, J. E. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c00106 · Cited by 20 · see citing works
de Lacam, E. G. C., Blazhynska, M., Chen, H., Gumbart, J. C., & Chipot, C. J. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c00604 · Cited by 19 · see citing works
Self-citationSahoo, A. R., Souza, P. C. T., Meng, Z., & Buck, M. (2023) · Structure · doi:10.1016/j.str.2023.03.014 · Cited by 19 · see citing works
Gofman, Y., Haliloǧlu, T., & Ben‐Tal, N. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300128x · Cited by 19 · see citing works
A model-free method for measuring dimerization free energies of CLC-ec1 in lipid bilayers
Chadda, R., Cliff, L., Brimberry, M., & Robertson, J. (2018) · The Journal of General Physiology · doi:10.1085/jgp.201711893 · Cited by 19 · see citing works
Methods to study folding of alpha-helical membrane proteins in lipids
Harris, N. J., Pellowe, G. A., Blackholly, L. R., Breen, S. G., Findlay, H. E., & Booth, P. J. (2022) · Open Biology · doi:10.1098/rsob.220054 · Cited by 19 · see citing works
Atomistic mechanism of transmembrane helix association
Domański, J., Sansom, M. S. P., Stansfeld, P. J., & Best, R. B. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007919 · Cited by 19 · see citing works
Nash, A., Notman, R., & Dixon, A. M. (2015) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2015.02.020 · Cited by 17 · see citing works
Host Cell Membrane Capture by the SARS-CoV-2 Spike Protein Fusion Intermediate
Su, R., Zeng, J., Marcink, T. C., Porotto, M., Moscona, A., & O’Shaughnessy, B. (2023) · ACS Central Science · doi:10.1021/acscentsci.3c00158 · Cited by 17 · see citing works
A Glycophorin A-Like Framework for the Dimerization of Photosynthetic Core Complexes
Hsin, J., Chipot, C. J., & Schulten, K. J. (2009) · Journal of the American Chemical Society · doi:10.1021/ja905903n · Cited by 16 · see citing works
Self-citationHansen, S. K., Vestergaard, M., Thøgersen, L., Schiøtt, B., Nielsen, N. C., & Vosegaard, T. (2014) · The Journal of Physical Chemistry B · doi:10.1021/jp5000304 · Cited by 15 · see citing works
The role of structural heterogeneity in the homodimerization of transmembrane proteins
Majumder, A., & Straub, J. E. (2023) · The Journal of Chemical Physics · doi:10.1063/5.0159801 · Cited by 10 · see citing works
Lipinski, K. A., McKay, M. J., Afrose, F., Martfeld, A. N., Koeppe, R. E., & Greathouse, D. V. (2019) · ChemBioChem · doi:10.1002/cbic.201900282 · Cited by 7 · see citing works
Urano, R., Kokubo, H., & Okamoto, Y. (2015) · Journal of the Physical Society of Japan · doi:10.7566/jpsj.84.084802 · Cited by 7 · see citing works
Helix-helix interactions inside membranes
Engelman, D. M., Adair, B. D., Brünger, A. T., Hunt, J. F., Kahn, T. W., Lemmon, M. A., MacKenzie, K. R., & Treutlein, H. (1995) · Birkhäuser Basel eBooks · doi:10.1007/978-3-0348-9057-1_21 · Cited by 4 · see citing works
Revealing the Key Packing Features Determining the Stability of Peptide Bilayer Membrane
Ganesan, V., & Priya, M. H. (2023) · ACS Applied Bio Materials · doi:10.1021/acsabm.2c00949 · Cited by 4 · see citing works
Srivastava, D., & Patra, N. (2023) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.3c04217 · Cited by 4 · see citing works
Cao, L., Stoltz, G., Tony Lelièvre, A., Marinica, M., & Athènes, M. (2014) · The Journal of Chemical Physics · doi:10.1063/1.4870094 · Cited by 2 · see citing works
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Machine Learning Derived Collective Variables for the Study of Protein Homodimerization in Membrane
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STIM1 transmembrane helix dimerization captured by AI-guided transition path sampling
Horvath, F., Jung, H., Grabmayr, H., Fahrner, M., Romanin, C., & Hummer, G. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2506516122 · Cited by 9 · see citing works
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- Authors
- Blazhynska, M., Gumbart, J. C., Chen, H., Tajkhorshid, E., Roux, B., & Chipot, C.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Georgia Institute of Technology (US)
- University of Illinois Urbana-Champaign (US)
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th Street W225, Chicago, Illinois 60637, United States
- University of Hawaiʻi at Mānoa (US)
- Corresponding author
- Chipot, Christophe
- ORCID
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2023-12-13
- Volume
- 19
- Issue
- 24
- Pages
- 9077-9092
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- PMC
- PMC11145395
- OpenAlex
- W4389656489
- Cited by
- 22
- References
- 160
- Citations by year
- 2026: 8 · 2025: 7 · 2024: 7
- FWCI
- 1.96
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Journal of Chemical Theory and Computation (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion, other-oa)
- Funders
- Agence Nationale de la Recherche
- National Institute of General Medical Sciences (R01-GM123169, R24-GM145965)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Keywords
- protein-protein binding affinity, transmembrane proteins, glycophorin A, homodimerization, binding free energy, potential of mean force, collective variables, membrane environment
- MeSH terms
- Membrane Proteins, Protein Binding, Entropy, Dimerization, Molecular Dynamics Simulation
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