Coarse-grain modelling of protein-protein interactions

Current Opinion in Structural Biology

Volumn 23, Issue 6, 2013, Pages 878-886

  Baaden, Marc ^a   Marrink, Siewert J ^b  

^a France   (France)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN;

BINDING AFFINITY; COARSE GRAIN MODEL; CONFORMATIONAL TRANSITION; FLUORESCENCE RESONANCE ENERGY TRANSFER; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR SIZE; NONBIOLOGICAL MODEL; NONHUMAN; PHYSICAL CHEMISTRY; PHYSICS; PREDICTION; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN CONFORMATION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW;

MEMBRANE PROTEINS; MODELS, MOLECULAR; PROTEIN INTERACTION MAPPING; SOLUBILITY;

EID: 84888825453     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2013.09.004     Document Type: Review

References (82)

1. Ellis R.J. Macromolecular crowding: an important but neglected aspect of the intracellular environment. Curr Opin Struct Biol 2001, 11:114-119.
2. Engelman D.M. Membranes are more mosaic than fluid. Nature 2005, 438:578-580.
3. Phillip Y., Schreiber G. Formation of protein complexes in crowded environments - From in vitro to in vivo. FEBS Letters 2013, 587:1046-1052.
4. Saunders M.G., Voth G.A. Coarse-graining of multiprotein assemblies. Curr Opin Struct Biol 2012, 22:144-150.
5. Shinoda W., DeVane R., Klein M.L. Computer simulation studies of self-assembling macromolecules. Curr Opin Struct Biol 2012, 22:175-186.
6. Flores S.C., Bernauer J., Shin S., Zhou R.H., Huang X.H. Multiscale modeling of macromolecular biosystems. Brief Bioinformatics 2012, 13:395-405.
7. Ingólfsson H., Lopez C.A., Uusitalo J.J., de Jong D.H., Gopal S., Periole X., Marrink S.J. The power of coarse-graining in biomolecular simulations. WIREs Comput Mol Sci 2013, in press. 10.1002/wcms.1169.
8. Kastritis P.L., Bonvin A.M.J.J. On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface 2013, 10:20120835. 10.1098/rsif.2012.0835 1742-5662.
9. Coelho E.D., Arrais J.P., Oliveira J.L. From protein-protein interactions to rational drug design: are computational methods up to the challenge?. Curr Top Med Chem 2013, 13:602-618.
10. King N.P., Sheffler W., Sawaya M.R., Vollmar B.S., Sumida J.P., Andre I., Gonen T., Yeates T.O., Baker D. Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science 2012, 336:1171-1174.
11. de Vries S.J., Zacharias M. ATTRACT-EM: a new method for the computational assembly of large molecular machines using cryo-em maps. PloS One 2012, 7:e49733.
12. Liu S., Vakser I.A. DECK: distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking. BMC Bioinformatics 2011, 12:280.
13. Ghoorah A.W., Devignes M.-D., Smail-Tabbone M., Ritchie D.W. Spatial clustering of protein binding sites for template based protein docking. Bioinformatics 2011, 27:2820-2827.
14. Andreani J., Faure G., Guerois R. InterEvScore: A novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution. Bioinformatics 2013, 29:1742-1749.
15. Karaca E., Bonvin A.M.J.J. Advances in integrative modeling of biomolecular complexes. Methods 2013, 59:372-381.
16. Schneidman-Duhovny D., Rossi A., Avila-Sakar A., Kim S.J., Velazquez-Muriel J., Strop P., Liang H., Krukenberg K.A., Liao M., Kim H.M., et al. A method for integrative structure determination of protein-protein complexes. Bioinformatics 2012, 28:3282-3289.
17. Dreyfus T., Doye V., Cazals F. Assessing the reconstruction of macromolecular assemblies with toleranced models. Proteins: Struc Funct Bioinf 2012, 80:2125-2136.
18. Zacharias M. Combining coarse-grained nonbonded and atomistic bonded interactions for protein modeling. Proteins: Struc Funct Bioinf 2013, 81:81-92.
19. Basdevant N., Borgis D., Ha-Duong T. Modeling protein-protein recognition in solution using the coarse-grained force field SCORPION. J Chem Theory Comput 2013, 9:803-813.
20. Frembgen-Kesner T., Elcock A.H. Absolute protein-protein association rate constants from flexible, coarse-grained brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association. Biophys J 2010, 99:L75-L77.
21. Solernou A., Fernandez-Recio J. pyDockCG: New coarse-grained potential for protein protein docking. J Phys Chem B 2011, 115:6032-6039.
22. Ceres N., Pasi M., Lavery R. A protein solvation model based on residue burial. J Chem Theory Comput 2012, 8:2141-2144.
23. Zheng W., Schafer N.P., Davtyan A., Papoian G.A., Wolynes P.G. Predictive energy landscapes for protein-protein association. Proc Natl Acad Sci USA 2012, 109:19244-19249.
24. Martin J., Lavery R. Arbitrary protein-protein docking targets biologically relevant interfaces. BMC Biophys 2012, 5:7.
25. De Simone A., Kitchen C., Kwan A.H., Sunde M., Dobson C.M., Frenkel D. Intrinsic disorder modulates protein self-assembly and aggregation. Proc Natl Acad Sci USA 2012, 109:6951-6956.
26. Ravikumar K.M., Huang W., Yang S. Coarse-grained simulations of protein-protein association: an energy landscape perspective. Biophys J 2012, 103:837-845.
27. Emperador A., Solernou A., Sfriso P., Pons C., Lluis Gelpi J., Fernandez-Recio J., Orozco M. Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations. J Chem Theory Comput 2013, 9:1222-1229.
28. Okazaki K-i, Sato T., Takano M. Temperature-enhanced association of proteins due to electrostatic interaction: a coarse-grained simulation of actin-myosin binding. J Am Chem Soc 2012, 134:8918-8925.
29. Saunders M.G., Voth G.A. Comparison between actin filament models: coarse-graining reveals essential differences. Structure 2012, 20:641-653.
30. Sieradzan A.K., Liwo A., Hansmann U.H.E. Folding and self-assembly of a small protein complex. J Chem Theory Comput 2012, 8:3416-3422.
31. Chaudhri A., Zarraga I.E., Yadav S., Patapoff T.W., Shire S.J., Voth G.A. The role of amino acid sequence in the self-association of therapeutic monoclonal antibodies: insights from coarse-grained modeling. J Phys Chem B 2013, 117:1269-1279.
32. Mereghetti P., Wade R.C. Atomic detail Brownian Dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions. J Phys Chem B 2012, 116:8523-8533.
33. May E.R., Feng J., Brooks C.L. Exploring the symmetry and mechanism of virus capsid maturation via an ensemble of pathways. Biophys J 2012, 102:606-612.
34. Globisch C., Krishnamani V., Deserno M., Peter C. Optimization of an elastic network augmented coarse grained model to study ccmv capsid deformation. PloS One 2013, 8:e60582.
35. Bereau T., Globisch C., Deserno M., Peter C. Coarse-grained and atomistic simulations of the salt-stable cowpea chlorotic mottle virus (ss-ccmv) subunit 26-49: beta-barrel stability of the hexamer and pentamer geometries. J Chem Theory Comput 2012, 8:3750-3758.
36. Cieplak M., Robbins M.O. Nanoindentation of 35 virus capsids in a molecular model: relating mechanical properties to structure. PloS one 2013, 8:e63640.
37. Carrasco C., Luque A., Hernando-Perez M., Miranda R., Carrascosa J.L., Serena P.A., de Ridder M., Raman A., Gomez-Herrero J., Schaap I.A.T., et al. Built-in mechanical stress in viral shells. Biophys J 2011, 100:1100-1108.
38. Grime J.M.A., Voth G.A. Early stages of the HIV-1 capsid protein lattice formation. Biophys J 2012, 103:1774-1783.
39. Zhao G., Perilla J.R., Yufenyuy E.L., Meng X., Chen B., Ning J., Ahn J., Gronenborn A.M., Schulten K., Aiken C., Zhang P. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature 2013, 497:643-646.
40. Steinbrecher T., Prock S., Reichert J., Wadhwani P., Zimpfer B., Burck J., Berditsch M., Elstner M., Ulrich A.S. Peptide-lipid interactions of the stress-response peptide TisB that induces bacterial persistence. Biophys J 2012, 103:1460-1469.
41. Marius P., Leung Y.M., Piggot T.J., Khalid S., Williamson P.T.F. Probing the oligomeric state and interaction surfaces of Fukutin-I in dilauroylphosphatidylcholine bilayers. Eur Biophys J 2012, 41:199-207.
42. Oguchi Y., Kummer E., Seyffer F., Berynskyy M., Anstett B., Zahn R., Wade R.C., Mogk A., Bukau B. A tightly regulated molecular toggle controls AAA+ disaggregase. Nat Struct Mol Biol 2012, 19:1338.
43. Kalli A.C., Campbell, Sansom M.S.P. Multiscale simulations suggest a mechanism for integrin inside-out activation. Proc Natl Acad Sci USA 2011, 108:11890-11895.
44. Davies K.M., Anselmi C., Wittig I., Faraldo-Gomez J.D., Kuhlbrandt W. Structure of the yeast F1Fo-ATP synthase dimer and its role in shaping the mitochondrial cristae. Proc Natl Acad Sci USA 2012, 109:13602-13607.
45. Casuso I., Khao J., Chami M., Paul-Gilloteaux P., Husain M., Duneau J.P., Stahlberg H., Sturgis J.N., Scheuring S. Characterization of the motion of membrane proteins using high-speed atomic force microscopy. Nat Nanotech 2012, 7:525-529.
46. Psachoulia E., Marshall D.P., Sansom M.S.P. Molecular dynamics simulations of the dimerization of transmembrane alpha-helices. Acc Chem Res 2010, 43:388-396.
47. Prakash A., Janosi L., Doxastakis M. GxxxG motifs, phenylalanine, and cholesterol guide the self-association of transmembrane domains of ErbB2 receptors. Biophys J 2011, 101:1949-1958.
48. Chng C.P., Tan S.M. Leukocyte integrin αLβ2 transmembrane association dynamics revealed by coarse-grained molecular dynamics simulations. Proteins 2011, 79:2203-2213.
49. Hall B.A., Armitage J.P., Sansom M.S.P. Mechanism of bacterial signal transduction revealed by molecular dynamics of tsr dimers and trimers of dimers in lipid vesicles. PLoS Comp Biol 2012, 8:e1002685.
50. Arnarez C., Mazat J.P., Elezgaray J., Marrink S.J., Periole X. Evidence for cardiolipin binding sites on the membrane-exposed surface of the cytochrome bc1. J Am Chem Soc 2013, 135:3112-3120.
51. Sengupta D., Marrink S.J. Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes. Phys Chem Chem Phys 2010, 12:12987-12996.
52. Castillo N., Monticelli L., Barnoud J., Tieleman D.P. Free energy of WALP23 dimer association in DMPC, DPPC, and DOPC bilayers. Chem Phys Lip 2013, 169:95-105.
53. Benjamini A., Smit B. Lipid mediated packing of transmembrane helices - a dissipative particle dynamics study. Soft Matt 2013, 9:2673-2683.
54. Yoo J., Cui Q. Membrane-mediated protein-protein interactions and connection to elastic models: a coarse-grained simulation analysis of gramicidin A association. Biophys J 2013, 104:128-138.
55. Periole X., Knepp A.M., Sakmar T.P., Marrink S.J., Huber T. Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers. J Am Chem Soc 2012, 134:10959-10965.
56. Johnston J.M., Wang H., Provasi D., Filizola M. Assessing the relative stability of dimer interfaces in G protein-coupled receptors. PLoS Comp Biol 2012, 8:e1002649.
57. Park S., Im W. Two dimensional window exchange umbrella sampling for transmembrane helix assembly. J Chem Theory Comput 2013, 9:13-17.
58. Gumbart J.C., Roux B., Chipot C.J. Efficient determination of protein-protein standard binding free energies from first principles. J Chem Theory Comput 2013, 9:3789-3798.
59. Hsin J., LaPointe L.M., Kazy A., Chipot C., Senes A., Schulten K. Oligomerization state of photosynthetic core complexes is correlated with the dimerization affinity of a transmembrane helix. J Am Chem Soc 2011, 133:14071-14081.
60. de Meyer F.J.M., Rodgers J.M., Willems T.F., Smit B. Molecular simulation of the effect of cholesterol on lipid-mediated protein-protein interactions. Biophys J 2010, 99:3629-3638.
61. Zhang L.Q., Sodt A.J., Venable R.M., Pastor R.W., Buck M. Prediction, refinement, and persistency of transmembrane helix dimers in lipid bilayers using implicit and explicit solvent/lipid representations: Microsecond molecular dynamics simulations of ErbB1/B2 and EphA1. Proteins: Struct Funct Bioinf 2013, 81:365-376.
62. Polyansky A.A., Volynsky P.E., Efremov R.G. Multistate organization of transmembrane helical protein dimers governed by the host membrane. J Am Chem Soc 2012, 134:14390-14400.
63. Marrink S.J., Tieleman D.P. Perspective on the Martini model. Chem Soc Review 2013, 42:6801-6822.
64. van den Bogaart G., Meyenberg K., Risselada H.J., Amin H., Willig K.I., Hubrich B.E., Dier M., Hell S.W., Grubmuller H., Diederichsen U., Jahn R. Membrane protein sequestering by ionic protein-lipid interactions. Nature 2011, 479:552-555.
65. Domanski J., Marrink S.J., Schäfer L.V. Transmembrane helices can induce domain formation in crowded model membranes. BBA Biomembr 2012, 1818:984-994.
66. Goose J.E., Sansom M.S.P. Reduced lateral mobility of lipids and proteins in crowded membranes. PLoS Comput Biol 2013, 9:e1003033.
67. Javanainen M., Hammaren H., Monticelli L., Jeon J.H., Miettinen M.S., Martinez-Seara H., Metzler R., Vattulainen I. Anomalous and normal diffusion of proteins and lipids in crowded lipid membranes. Farad Discuss 2013, 161:397-417.
68. Parton D.L., Tek A., Baaden M., Sansom M.S.P. Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations. PLoS Comput Biol 2013, 9:e1003034.
69. de Jong D.H., Lopez C.A., Marrink S.J. Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors. Farad Discuss 2013, 161:347-363.
70. Janosi L., Li Z., Hancock J.F., Gorfe A.A. Organization, dynamics, and segregation of Ras nanoclusters in membrane domains. Proc Natl Acad Sci USA 2012, 109:8097-8102.
71. Parton D.L., Klingelhoefer J.W., Sansom M.S.P. Aggregation of model membrane proteins, modulated by hydrophobic mismatch, membrane curvature, and protein class. Biophys J 2011, 101:691-699.
72. Kovalenko I.B., Abaturova A.M., Diakonova A.N., Knyazeva O.S., Ustinin D.M., Khruschev S.S., Riznichenko G.Y., Rubin A.B. Computer simulation of protein-protein association in photosynthesis. Math Model Nat Phenom 2011, 6:39-54.
73. Lai C.L., Jao C.C., Lyman E., Gallop J.L., Peter B.J., McMahon H.T., Langen R., Voth G.A. Membrane binding and self-association of the epsin N-terminal homology domain. J Mol Biol 2012, 423:800-817.
74. Yu H., Schulten K. Membrane sculpting by F-BAR domains studied by molecular dynamics simulations. PLoS Comput Biol 2013, 9:e1002892.
75. Tuffery P., Derreumaux P. Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches. J R Soc Interface 2012, 9:20-33.
76. Fry D.C. Small-molecule inhibitors of protein-protein interactions: how to mimic a protein partner. Curr Pharm Des 2012, 18:4679-4684.
77. Villoutreix B.O., Labbe C.M., Lagorce D., Laconde G., Sperandio O. A leap into the chemical space of protein-protein interaction inhibitors. Curr Pharm Des 2012, 18:4648-4667.
78. Wassenaar T.A., Ingólfsson H., Prieß M., Marrink S.J., Schäfer L.V. Mixing Martini: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations. J Phys Chem B 2013, 117:3516-3530.
79. Poblete S., Praprotnik M., Kremer K., Delle Site L. Coupling different levels of resolution in molecular simulations. J Chem Phys 2010, 132:114101.
80. Dama J.F., Sinitskiy A.V., McCullagh M., Weare J., Roux B., Dinner A.R., Voth G.A. The theory of ultra-coarse-graining. 1. General principles. J Chem Theory Comput 2013, 9:2466-2480.
81. Stark A.C., Andrews C.T., Elcock A.H. Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the Martini coarse-grained force field. J Chem Theory Comput 2013, 9:4176-4185.
82. Saladin A., Amourda C., Poulain P., Ferey N., Baaden M., Zacharias M., Delalande O., Prevost C. Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments. Nucleic Acids Res 2010, 38:6313-6323.