Abstract
Simulations of protein dynamics may work on different levels of molecular detail. The levels of simplification (coarse-graining) can range from very low to atomic resolution and may concern different simulation aspects (including protein representation, interaction schemes or models of molecular motion). So-called coarse-grained (CG) models offer many advantages, unreachable by classical simulation tools, as demonstrated in numerous studies of protein dynamics. Followed by a brief introduction, we present example applications of CG models for efficient predictions of biophysical mechanisms. We discuss the following topics: mechanisms of chaperonin action, mechanical properties of proteins, membrane proteins, protein-protein interactions and intrinsically unfolded proteins. Presently, these areas represent emerging application fields of CG simulation models.
Access provided by Autonomous University of Puebla. Download to read the full chapter text
Chapter PDF
Similar content being viewed by others
Abbreviations
References
Abeln, S., Frenkel, D.: Disordered Flanks Prevent Peptide Aggregation. PLoS Comput. Biol. 4(12), e1000241 (2008), doi:10.1371/journal.pcbi.1000241
Arad-Haase, G., Chuartzman, S.G., Dagan, S., Nevo, R., Kouza, M., Mai, B.K., Nguyen, H.T., Li, M.S., Reich, Z.: Mechanical unfolding of acylphosphatase studied by single-molecule force spectroscopy and MD simulations. Biophys. J. 99(1), 238–247 (2010), doi:10.1016/j.bpj.2010.04.004
Arkhipov, A., Freddolino, P.L., Schulten, K.: Stability and dynamics of virus capsids described by coarse-grained modeling. Structure 14(12), 1767–1777 (2006), doi:10.1016/j.str.2006.10.003
Auer, S., Meersman, F., Dobson, C.M., Vendruscolo, M.: A Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric Aggregates. PLoS Comput. Biol. 4(11), e1000222 (2008), doi:10.1371/journal.pcbi.1000222
Baumketner, A., Jewett, A., Shea, J.E.: Effects of confinement in chaperonin assisted protein folding: rate enhancement by decreasing the roughness of the folding energy landscape. J. Mol. Biol. 332(3), 701–713 (2003), doi:10.1016/S0022-2836(03)00929-X
Bell, G.I.: Models for the specific adhesion of cells to cells. Science 200(4342), 618–627 (1978), doi:10.1126/science.347575
Best, R.B., Hummer, G.: Protein folding kinetics under force from molecular simulation. J. Am. Chem. Soc. 130(12), 3706–3707 (2008), doi:10.1021/ja0762691
Best, R.B., Paci, E., Hummer, G., Dudko, O.K.: Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules. Journal of Physical Chemistry B 112(19), 5968–5976 (2008), doi:10.1021/Jp075955j
Betancourt, M.R., Thirumalai, D.: Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity. J. Mol. Biol. 287(3), 627–644 (1999), doi:10.1006/jmbi.1999.2591
Bindschadler, M.: Modeling actin dynamics. Wiley Interdisciplinary Reviews: Systems Biology and Medicine 2(4), 481–488 (2010), doi:10.1002/wsbm.62
Brockwell, D.J., Paci, E., Zinober, R.C., Beddard, G.S., Olmsted, P.D., Smith, D.A., Perham, R.N., Radford, S.E.: Pulling geometry defines the mechanical resistance of a beta-sheet protein (vol 10, pg 731, 2003). Nature Structural Biology 10(10), 872–872 (2003), doi:10.1038/Nsb1003-872b
Bustamante, C., Chemla, Y.R., Forde, N.R., Izhaky, D.: Mechanical processes in biochemistry. Annu. Rev. Biochem. 73, 705–748 (2004), doi:10.1146/annurev.biochem.72.121801.161542
Caraglio, M., Imparato, A., Pelizzola, A.: Pathways of mechanical unfolding of FnIII(10): low force intermediates. J. Chem. Phys. 133(6), 065101 (2010), doi:10.1063/1.3464476
Carrion-Vazquez, M., Li, H., Lu, H., Marszalek, P.E., Oberhauser, A.F., Fernandez, J.M.: The mechanical stability of ubiquitin is linkage dependent. Nat. Struct. Biol. 10(9), 738–743 (2003), doi:10.1038/nsb965
Chang, S., Hu, J.P., Lin, P.Y., Jiao, X., Tian, X.H.: Substrate recognition and transport behavior analyses of amino acid antiporter with coarse-grained models. Mol. Biosyst. 6(12), 2430–2438 (2010), doi:10.1039/c005266c
Chetwynd, A.P., Scott, K.A., Mokrab, Y., Sansom, M.S.: CGDB: a database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations. Mol. Membr. Biol. 25(8), 662–669 (2008), doi:10.1080/09687680802446534
Chu, J.W., Voth, G.A.: Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. Biophys. J. 90(5), 1572–1582 (2006), doi:10.1529/biophysj.105.073924
Cieplak, M., Hoang, T.X., Robbins, M.O.: Folding and stretching in a Go-like model of titin. Proteins 49(1), 114–124 (2002), doi:10.1002/prot.10087
Clementi, C., Nymeyer, H., Onuchic, J.N.: Topological and energetic factors: what determines the structural details of the transition state ensemble and “en-route” intermediates for protein folding? An investigation for small globular proteins. J. Mol. Biol. 298(5), 937–953 (2000), doi:10.1006/jmbi.2000.3693
De Sancho, D., Best, R.B.: Modulation of an IDP binding mechanism and rates by helix propensity and non-native interactions: association of HIF1alpha with CBP. Mol Biosyst. 8(1), 256–267 (2012), doi:10.1039/c1mb05252g
Di Fenza, A., Rocchia, W., Tozzini, V.: Complexes of HIV-1 integrase with HAT proteins: Multiscale models, dynamics, and hypotheses on allosteric sites of inhibition. Proteins: Structure, Function, and Bioinformatics 76(4), 946–958 (2009), doi:10.1002/prot.22399
Dudko, O.K., Hummer, G., Szabo, A.: Intrinsic rates and activation free energies from single-molecule pulling experiments. Phys. Rev. Lett. 96(10), 108101 (2006), doi:10.1103/PhysRevLett.96.108101
Eliezer, D.: Biophysical characterization of intrinsically disordered proteins. Current Opinion in Structural Biology 19(1), 23–30 (2009), doi:10.1016/j.sbi.2008.12.004
Evans, E., Ritchie, K.: Dynamic strength of molecular adhesion bonds. Biophys. J. 72(4), 1541–1555 (1997), doi:10.1016/S0006-3495(97)78802-7
Fletcher, D.A., Mullins, R.D.: Cell mechanics and the cytoskeleton. Nature 463(7280), 485–492 (2010), doi:10.1038/nature08908
Florin, E.L., Moy, V.T., Gaub, H.E.: Adhesion forces between individual ligand-receptor pairs. Science 264(5157), 415–417 (1994), doi:10.1126/science.8153628
Fowler, S.B., Best, R.B., Toca Herrera, J.L., Rutherford, T.J., Steward, A., Paci, E., Karplus, M., Clarke, J.: Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering. J. Mol. Biol. 322(4), 841–849 (2002), doi:10.1016/S0022-2836(02)00805-7
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. 99(9), L75–L77 (2010), doi:10.1016/j.bpj.2010.09.006
Granzier, H.L., Labeit, S.: The giant protein titin: a major player in myocardial mechanics, signaling, and disease. Circ. Res. 94(3), 284–295 (2004), doi:10.1161/01.RES.0000117769.88862.F8
Hall, B.A., Chetwynd, A.P., Sansom, M.S.: Exploring peptide-membrane interactions with coarse-grained MD simulations. Biophys. J. 100(8), 1940–1948 (2011), doi:10.1016/j.bpj.2011.02.041
Hall, B.A., Sansom, M.S.P.: Coarse-Grained MD Simulations and Protein−Protein Interactions: The Cohesin−Dockerin System. Journal of Chemical Theory and Computation 5(9), 2465–2471 (2009), doi:10.1021/ct900140w
Hanson, P.I., Whiteheart, S.W.: AAA+ proteins: have engine, will work. Nat. Rev. Mol. Cell Biol. 6(7), 519–529 (2005), doi:10.1038/nrm1684
He, C., Genchev, G.Z., Lu, H., Li, H.: Mechanically untying a protein slipknot: multiple pathways revealed by force spectroscopy and steered molecular dynamics simulations. J. Am. Chem. Soc. 134(25), 10428–10435 (2012), doi:10.1021/ja3003205
Heath, A.P., Kavraki, L.E., Clementi, C.: From coarse-grain to all-atom: toward multiscale analysis of protein landscapes. Proteins 68(3), 646–661 (2007), doi:10.1002/prot.21371
Huang, Y., Liu, Z.: Kinetic Advantage of Intrinsically Disordered Proteins in Coupled Folding–Binding Process: A Critical Assessment of the “Fly-Casting” Mechanism. Journal of Molecular Biology 393(5), 1143–1159 (2009), doi:10.1016/j.jmb.2009.09.010
Hunte, C.: Specific protein-lipid interactions in membrane proteins. Biochem. Soc. Trans. 33(Pt. 5), 938–942 (2005), doi:10.1042/BST20050938
Irback, A., Mitternacht, S., Mohanty, S.: Dissecting the mechanical unfolding of ubiquitin. Proc. Natl. Acad. Sci. U S A 102(38), 13427–13432 (2005), doi:10.1073/pnas.0501581102
Jacob, E., Horovitz, A., Unger, R.: Different mechanistic requirements for prokaryotic and eukaryotic chaperonins: a lattice study. Bioinformatics 23(13), i240–i248 (2007), doi:10.1093/bioinformatics/btm180
Jewett, A.I., Baumketner, A., Shea, J.E.: Accelerated folding in the weak hydrophobic environment of a chaperonin cavity: creation of an alternate fast folding pathway. Proc. Natl. Acad. Sci. U S A 101(36), 13192–13197 (2004), doi:10.1073/pnas.0400720101
Jewett, A.I., Shea, J.E.: Reconciling theories of chaperonin accelerated folding with experimental evidence. Cell. Mol. Life Sci. 67(2), 255–276 (2009)
Kalli, A.C., Hall, B.A., Campbell, I.D., Sansom, M.S.: A helix heterodimer in a lipid bilayer: prediction of the structure of an integrin transmembrane domain via multiscale simulations. Structure 19(10), 1477–1484 (2011), doi:10.1016/j.str.2011.07.014
Kamerlin, S.C., Vicatos, S., Dryga, A., Warshel, A.: Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems. Annual Review of Physical Chemistry 62, 41–64 (2011), doi:10.1146/annurev-physchem-032210-103335
Kim, Y.C., Hummer, G.: Coarse-grained Models for Simulations of Multiprotein Complexes: Application to Ubiquitin Binding. Journal of Molecular Biology 375(5), 1416–1433 (2008), doi:10.1016/j.jmb.2007.11.063
Kim, Y.C., Tang, C., Clore, G.M., Hummer, G.: Replica exchange simulations of transient encounter complexes in protein-protein association. Proc. Natl. Acad. Sci. U S A 105(35), 12855–12860 (2008), doi:10.1073/pnas.0802460105
Kmiecik, S., Gront, D., Kolinski, A.: Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field. Bmc Struct. Biol. 7(43), 43 (2007), doi:10.1186/1472-6807-7-43
Kmiecik, S., Gront, D., Kouza, M., Kolinski, A.: From coarse-grained to atomic-level characterization of protein dynamics: transition state for the folding of B domain of protein A. J. Phys. Chem. B 116(23), 7026–7032 (2012), doi:10.1021/jp301720w
Kmiecik, S., Jamroz, M., Kolinski, A.: Multiscale Approach to Protein Folding Dynamics. In: Kolinski, A. (ed.) Multiscale Approaches to Protein Modeling, pp. 281–293. Springer, New York (2011), doi:10.1007/978-1-4419-6889-0_12
Kmiecik, S., Kolinski, A.: Folding pathway of the b1 domain of protein G explored by multiscale modeling. Biophys. J. 94(3), 726–736 (2008), doi:10.1529/biophysj.107.116095
Kmiecik, S., Kolinski, A.: Simulation of chaperonin effect on protein folding: a shift from nucleation-condensation to framework mechanism. J. Am. Chem. Soc. 133(26), 10283–10289 (2011), doi:10.1021/ja203275f
Knepp, A.M., Periole, X., Marrink, S.J., Sakmar, T.P., Huber, T.: Rhodopsin forms a dimer with cytoplasmic helix 8 contacts in native membranes. Biochemistry 51(9), 1819–1821 (2012), doi:10.1021/bi3001598
Koga, N., Takada, S.: Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase. Proc. Natl. Acad. Sci. U S A 103(14), 5367–5372 (2006), doi:10.1073/pnas.0509642103
Kolinski, A.: Protein modeling and structure prediction with a reduced representation. Acta Biochimica Polonica 51(2), 349–371 (2004), doi:035001349
Kolinski, A., Skolnick, J.: Reduced models of proteins and their applications. Polymer 45(2), 511–524 (2004), doi:10.1016/j.polymer.2003.10.064
Kouza, M., Hu, C.K., Li, M.S.: New force replica exchange method and protein folding pathways probed by force-clamp technique. J. Chem. Phys. 128(4), 045103 (2008), doi:10.1063/1.2822272
Kouza, M., Hu, C.K., Zung, H., Li, M.S.: Protein mechanical unfolding: Importance of non-native interactions. J. Chem. Phys. 131(21), 215103 (2009), doi:10.1063/1.3272275
Kramers, H.A.: Brownian motion in a field of force and the diffusion model of chemical reactions. Physica 7(7), 284–303 (1940), doi:10.1016/S0031-8914(40)90098-2
Kumar, S., Li, M.S.: Biomolecules under mechanical force. Phys. Rep. 486(1-2), 1–74 (2010), doi:10.1016/j.physrep.2009.11.001
Kurcinski, M., Kolinski, A.: Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acid. The Journal of Steroid Biochemistry and Molecular Biology 121(1-2), 124–129 (2010), doi:10.1016/j.jsbmb.2010.03.086
Lau, T.L., Kim, C., Ginsberg, M.H., Ulmer, T.S.: The structure of the integrin alphaIIbbeta3 transmembrane complex explains integrin transmembrane signalling. Embo. J. 28(9), 1351–1361 (2009), doi:10.1038/emboj.2009.63
Lee, A.G.: How lipids affect the activities of integral membrane proteins. Bba-Biomembranes 1666(1-2), 62–87 (2004), doi:10.1016/j.bbamem.2004.05.012
Lee, E.H., Hsin, J., Sotomayor, M., Comellas, G., Schulten, K.: Discovery Through the Computational Microscope. Structure 17(10), 1295–1306 (2009), doi:10.1016/j.str.2009.09.001
Levitt, M., Warshel, A.: Computer simulation of protein folding. Nature 253(5494), 694–698 (1975), doi:10.1038/253694a0
Li, L., Huang, H.H., Badilla, C.L., Fernandez, J.M.: Mechanical unfolding intermediates observed by single-molecule force spectroscopy in a fibronectin type III module. J. Mol. Biol. 345(4), 817–826 (2005), doi:10.1016/j.jmb.2004.11.021
Li, M.S.: Secondary structure, mechanical stability, and location of transition state of proteins. Biophys. J. 93(8), 2644–2654 (2007), doi:10.1529/biophysj.107.106138
Li, M.S., Kouza, M.: Dependence of protein mechanical unfolding pathways on pulling speeds. J. Chem. Phys. 130(14), 145102 (2009), doi:10.1063/1.3106761
Li, M.S., Kouza, M., Hu, C.K.: Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin. Biophys. J. 92(2), 547–561 (2007), doi:10.1529/biophysj.106.087684
Lichter, S., Rafferty, B., Flohr, Z., Martini, A.: Protein high-force pulling simulations yield low-force results. PLoS One 7(4), e34781 (2012), doi:10.1371/journal.pone.0034781
Liphardt, J., Onoa, B., Smith, S.B., Tinoco Jr., I., Bustamante, C.: Reversible unfolding of single RNA molecules by mechanical force. Science 292(5517), 733–737 (2001), doi:10.1126/science.1058498
Lu, H., Isralewitz, B., Krammer, A., Vogel, V., Schulten, K.: Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys. J. 75(2), 662–671 (1998), doi:10.1016/S0006-3495(98)77556-3
Lu, H., Schulten, K.: The key event in force-induced unfolding of Titin’s immunoglobulin domains. Biophys. J. 79(1), 51–65 (2000), doi:10.1016/S0006-3495(00)76273-4
Lucent, D., England, J., Pande, V.: Inside the chaperonin toolbox: theoretical and computational models for chaperonin mechanism. Physical Biology 6(1), 015003 (2009), doi:10.1088/1478-3975/6/1/015003
Marrink, S.J., Risselada, H.J., Yefimov, S., Tieleman, D.P., de Vries, A.H.: The MARTINI force field: coarse grained model for biomolecular simulations. J. Phys. Chem. B 111(27), 7812–7824 (2007), doi:10.1021/jp071097f
Marszalek, P.E., Lu, H., Li, H., Carrion-Vazquez, M., Oberhauser, A.F., Schulten, K., Fernandez, J.M.: Mechanical unfolding intermediates in titin modules. Nature 402(6757), 100–103 (1999), doi:10.1038/47083
Mittag, T., Kay, L.E., Forman-Kay, J.D.: Protein dynamics and conformational disorder in molecular recognition. Journal of Molecular Recognition 23(2), 105–116 (2010), doi:10.1002/jmr.961
Munoz, V., Henry, E.R., Hofrichter, J., Eaton, W.A.: A statistical mechanical model for beta-hairpin kinetics. Proc. Natl. Acad. Sci. U S A 95(11), 5872–5879 (1998), doi:10.1073/pnas.95.11.5872
Nilsson, J., Persson, B., von Heijne, G.: Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes. Proteins 60(4), 606–616 (2005), doi:10.1002/prot.20583
Norgaard, A.B., Ferkinghoff-Borg, J., Lindorff-Larsen, K.: Experimental Parameterization of an Energy Function for the Simulation of Unfolded Proteins. Biophys. J. 94(1), 182–192 (2008), doi:10.1529/biophysj.107.108241
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. 134(21), 8918–8925 (2012), doi:10.1021/ja301447j
Paci, E., Karplus, M.: Unfolding proteins by external forces and temperature: the importance of topology and energetics. Proc. Natl. Acad. Sci. U S A 97(12), 6521–6526 (2000), doi:10.1073/pnas.100124597
Peplowski, L., Sikora, M., Nowak, W., Cieplak, M.: Molecular jamming–the cystine slipknot mechanical clamp in all-atom simulations. J. Chem. Phys. 134(8), 085102 (2011), doi:10.1063/1.3553801
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. 134(26), 10959–10965 (2012), doi:10.1021/ja303286e
Plaxco, K.W., Simons, K.T., Baker, D.: Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277(4), 985–994 (1998), doi:10.1006/jmbi.1998.1645
Rathore, N., Knotts IV, T.A., de Pablo, J.J.: Confinement effects on the thermodynamics of protein folding: Monte Carlo simulations. Biophys J. 90(5), 1767–1773 (2006), doi:10.1529/biophysj.105.071076
Rauscher, S., Pomes, R.: Molecular simulations of protein disorder. Biochem. Cell. Biol. 88(2), 269–290 (2010), doi:10.1139/o09-169
Rauscher, S., Pomès, R.: Molecular simulations of protein disorderThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal’s usual peer review process. Biochemistry and Cell Biology 88(2), 269–290 (2010), doi:10.1139/o09-169
Rief, M., Gautel, M., Oesterhelt, F., Fernandez, J.M., Gaub, H.E.: Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276(5315), 1109–1112 (1997), doi:10.1126/science.276.5315.1109
Ruprecht, J.J., Mielke, T., Vogel, R., Villa, C., Schertler, G.F.: Electron crystallography reveals the structure of metarhodopsin I. Embo J. 23(18), 3609–3620 (2004), doi:10.1038/sj.emboj.7600374
Russel, D., Lasker, K., Phillips, J., Schneidman-Duhovny, D., Velazquez-Muriel, J.A., Sali, A.: The structural dynamics of macromolecular processes. Current Opinion in Cell Biology 21(1), 97–108 (2009), doi:10.1016/j.ceb.2009.01.022
Sansom, M.S., Scott, K.A., Bond, P.J.: Coarse-grained simulation: a high-throughput computational approach to membrane proteins. Biochem. Soc. Trans. 36(Pt. 1), 27–32 (2008), doi:10.1042/BST0360027
Saunders, M.G., Voth, G.A.: Coarse-graining of multiprotein assemblies. Current Opinion in Structural Biology 22(2), 144–150 (2012), doi:10.1016/j.sbi.2012.01.003
Scheraga, H.A., Khalili, M., Liwo, A.: Protein-folding dynamics: overview of molecular simulation techniques. Annual Review of Physical Chemistry 58, 57–83 (2007), doi:10.1146/annurev.physchem.58.032806.104614
Schlick, T., Collepardo-Guevara, R., Halvorsen, L.A., Jung, S., Xiao, X.: Biomolecularmodeling and simulation: a field coming of age. Q. Rev. Biophys. 44(2), 191–228 (2011), doi:10.1017/S0033583510000284
Schwaiger, I., Kardinal, A., Schleicher, M., Noegel, A.A., Rief, M.: A mechanical unfolding intermediate in an actin-crosslinking protein. Nat. Struct. Mol. Biol. 11(1), 81–85 (2004), doi:10.1038/nsmb705
Scott, K.A., Bond, P.J., Ivetac, A., Chetwynd, A.P., Khalid, S., Sansom, M.S.: Coarse-grained MD simulations of membrane protein-bilayer self-assembly. Structure 16(4), 621–630 (2008), doi:10.1016/j.str.2008.01.014
Sen, T.Z., Kloster, M., Jernigan, R.L., Kolinski, A., Bujnicki, J.M., Kloczkowski, A.: Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA. Biophys. J. 94(7), 2482–2491 (2008), doi:10.1529/biophysj.107.116046
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. 12(40), 12987–12996 (2010), doi:10.1039/c0cp00101e
Serohijos, A.W., Chen, Y., Ding, F., Elston, T.C., Dokholyan, N.V.: A structural model reveals energy transduction in dynein. Proc. Natl. Acad. Sci. U S A 103(49), 18540–18545 (2006), doi:10.1073/pnas.0602867103
Shoemaker, B.A., Portman, J.J., Wolynes, P.G.: Speeding molecular recognition by using the folding funnel: The fly-casting mechanism. Proceedings of the National Academy of Sciences 97(16), 8868–8873 (2000), doi:10.1073/pnas.160259697
Sieben, C., Kappel, C., Zhu, R., Wozniak, A., Rankl, C., Hinterdorfer, P., Grubmüller, H., Herrmann, A.: Influenza virus binds its host cell using multiple dynamic interactions. Proc. Natl. Acad. Sci. U S A 109(34), 13626–13631 (2012), doi:10.1073/pnas.1120265109
Sikora, M., Cieplak, M.: Mechanical stability of multidomain proteins and novel mechanical clamps. Proteins 79(6), 1786–1799 (2011), doi:10.1002/prot.23001
Sikora, M., Sulkowska, J.I., Witkowski, B.S., Cieplak, M.: BSDB: the biomolecule stretching database. Nucleic Acids Res. 39(Database Issue), D443–D450 (2011), doi:10.1093/nar/gkq851
Simmons, R.M., Finer, J.T., Chu, S., Spudich, J.A.: Quantitative measurements of force and displacement using an optical trap. Biophys. J. 70(4), 1813–1822 (1996), doi:10.1016/S0006-3495(96)79746-1
Smith, S.B., Cui, Y., Bustamante, C.: Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271(5250), 795–799 (1996), doi:10.1126/science.271.5250.795
Smith, S.O., Eilers, M., Song, D., Crocker, E., Ying, W., Groesbeek, M., Metz, G., Ziliox, M., Aimoto, S.: Implications of threonine hydrogen bonding in the glycophorin A transmembrane helix dimer. Biophys. J. 82(5), 2476–2486 (2002), doi:10.1016/S0006-3495(02)75590-2
Spijker, P., van Hoof, B., Debertrand, M., Markvoort, A.J., Vaidehi, N., Hilbers, P.A.: Coarse grained molecular dynamics simulations of transmembrane protein-lipid systems. Int. J. Mol. Sci. 11(6), 2393–2420 (2010), doi:10.3390/ijms11062393
Stossel, T.P., Condeelis, J., Cooley, L., Hartwig, J.H., Noegel, A., Schleicher, M., Shapiro, S.S.: Filamins as integrators of cell mechanics and signalling. Nat. Rev. Mol. Cell. Biol. 2(2), 138–145 (2001), doi:10.1038/35052082
Sulkowska, J.I., Cieplak, M.: Mechanical stretching of proteins - a theoretical survey of the Protein Data Bank. J. Phys.-Condens Mat. 19(28) (2007), doi:10.1088/0953-8984/19/28/283201
Sulkowska, J.I., Sulkowski, P., Onuchic, J.N.: Jamming proteins with slipknots and their free energy landscape. Phys. Rev. Lett. 103(26), 268103 (2009), doi:10.1103/PhysRevLett.103.268103
Sulkowska, J.I., Sulkowski, P., Szymczak, P., Cieplak, M.: Untying knots in proteins. J. Am. Chem. Soc. 132(40), 13954–13956 (2010), doi:10.1021/ja102441z
Szilagyi, A., Gyorffy, D., Zavodszky, P.: The twilight zone between protein order and disorder. Biophys. J. 95(4), 1612–1626 (2008), doi:10.1529/biophysj.108.131151
Szymczak, P., Janovjak, H.: Periodic forces trigger a complex mechanical response in ubiquitin. J. Mol. Biol. 390(3), 443–456 (2009), doi:10.1016/j.jmb.2009.04.071
Takada, S.: Coarse-grained molecular simulations of large biomolecules. Curr. Opin. Struct. Biol. 22(2), 130–137 (2012), doi:10.1016/j.sbi.2012.01.010
Takagi, F., Koga, N., Takada, S.: How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: Molecular simulations. Proc. Natl. Acad. Sci. USA 100(20), 11367–11372 (2003), doi:10.1073/pnas.1831920100
Taylor, W.R., Katsimitsoulia, Z.: A coarse-grained molecular model for actin-myosin simulation. J. Mol. Graph. Model. 29(2), 266–279 (2010), doi:10.1016/j.jmgm.2010.06.004
Turjanski, A.G., Gutkind, J.S., Best, R.B., Hummer, G.: Binding-Induced Folding of a Natively Unstructured Transcription Factor. PLoS Comput. Biol. 4(4), e1000060 (2008), doi:10.1371/journal.pcbi.1000060
Uversky, V.N., Gillespie, J.R., Fink, A.L.: Why are “natively unfolded” proteins unstructured under physiologic conditions? Proteins: Structure, Function, and Bioinformatics 41(3), 415–427 (2000), doi:10.1002/1097-0134(20001115)41:3<415::aid-prot130>3.0.co;2-7
Vajda, S., Kozakov, D.: Convergence and combination of methods in protein-protein docking. Curr. Opin. Struct. Biol. 19(2), 164–170 (2009), doi:10.1016/j.sbi.2009.02.008
Valbuena, A., Oroz, J., Hervas, R., Vera, A.M., Rodriguez, D., Menendez, M., Sulkowska, J.I., Cieplak, M., Carrion-Vazquez, M.: On the remarkable mechanostability of scaffoldins and the mechanical clamp motif. Proc. Natl. Acad. Sci. U S A 106(33), 13791–13796 (2009), doi:10.1073/pnas.0813093106
Vendruscolo, M., Dobson, C.M.: Protein Dynamics: Moore’s Law in Molecular Biology. Curr. Biol. 21(2), R68–R70 (2011), doi:10.1016/j.cub.2010.11.062
Verkhivker, G.M.: Protein conformational transitions coupled to binding in molecular recognition of unstructured proteins: Deciphering the effect of intermolecular interactions on computational structure prediction of the p27Kip1 protein bound to the cyclin A–cyclin-dependent kinase 2 complex. Proteins: Structure, Function, and Bioinformatics 58(3), 706–716 (2005), doi:10.1002/prot.20351
Verkhivker, G.M., Bouzida, D., Gehlhaar, D.K., Rejto, P.A., Freer, S.T., Rose, P.W.: Simulating disorder–order transitions in molecular recognition of unstructured proteins: Where folding meets binding. Proceedings of the National Academy of Sciences 100(9), 5148–5153 (2003), doi:10.1073/pnas.0531373100
Vogel, V., Sheetz, M.: Local force and geometry sensing regulate cell functions. Nat. Rev. Mol. Cell. Biol. 7(4), 265–275 (2006), doi:10.1038/nrm1890
Wang, J., Wang, Y., Chu, X., Hagen, S.J., Han, W., Wang, E.: Multi-Scaled Explorations of Binding-Induced Folding of Intrinsically Disordered Protein Inhibitor IA3 to its Target Enzyme. PLoS Comput. Biol. 7(4), e1001118 (2011), doi:10.1371/journal.pcbi.1001118
West, D.K., Olmsted, P.D., Paci, E.: Mechanical unfolding revisited through a simple but realistic model. J. Chem. Phys. 124(15) (2006), doi:10.1063/1.2185100
Wolynes, P.G., Onuchic, J.N., Thirumalai, D.: Navigating the folding routes. Science 267(5204), 1619–1620 (1995), doi:10.1126/science.7886447
Wright, P.E., Dyson, H.J.: Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 293(2), 321–331 (1999), doi:10.1006/jmbi.1999.3110
Wu, C., Shea, J.E.: Coarse-grained models for protein aggregation. Curr. Opin. Struct. Biol. 21(2), 209–220 (2011), doi:10.1016/j.sbi.2011.02.002
Yao, X.Q., Kenzaki, H., Murakami, S., Takada, S.: Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations. Nat. Commun. 1, 117 (2010), doi:10.1038/ncomms1116
Zhang, J., Muthukumar, M.: Simulations of nucleation and elongation of amyloid fibrils. J. Chem. Phys. 130(3), 035102 (2009), doi:10.1063/1.3050295
Zhmurov, A., Dima, R.I., Kholodov, Y., Barsegov, V.: Sop-GPU: accelerating biomolecular simulations in the centisecond timescale using graphics processors. Proteins 78(14), 2984–2999 (2010), doi:10.1002/prot.22824
Zhou, H.-X.: Polymer Models of Protein Stability, Folding, and Interactions†. Biochemistry 43(8), 2141–2154 (2004), doi:10.1021/bi036269n
Zhou, H.X., Dill, K.A.: Stabilization of proteins in confined spaces. Biochemistry 40(38), 11289–11293 (2001), doi:10.3410/f.1002736.29765
Zhou, J., Thorpe, I.F., Izvekov, S., Voth, G.A.: Coarse-grained peptide modeling using a systematic multiscale approach. Biophys. J. 92(12), 4289–4303 (2007), doi:10.1529/biophysj.106.094425
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Kmiecik, S., Wabik, J., Kolinski, M., Kouza, M., Kolinski, A. (2014). Coarse-Grained Modeling of Protein Dynamics. In: Liwo, A. (eds) Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. Springer Series in Bio-/Neuroinformatics, vol 1. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28554-7_3
Download citation
DOI: https://doi.org/10.1007/978-3-642-28554-7_3
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-28553-0
Online ISBN: 978-3-642-28554-7
eBook Packages: EngineeringEngineering (R0)