Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

Trends in Biochemical Sciences - Tập 35 - Trang 539-546 - 2010
Peter Csermely1, Robin Palotai1, Ruth Nussinov2,3
1Department of Medical Chemistry, Semmelweis University, PO Box 260, H-1444, Budapest 8, Hungary
2Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA
3Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel

Tài liệu tham khảo

Fischer, 1894, Einfluss der Configuration auf die Wirkung der Enzyme, Ber. Dtsch. Chem. Ges., 27, 2984 Koshland, 1958, Application of a theory of enzyme specificity to protein synthesis, Proc. Natl. Acad. Sci. U. S. A., 44, 98, 10.1073/pnas.44.2.98 Straub, F. B. and Szabolcsi, G. (1964) O dinamicseszkij aszpektah sztukturü fermentov. (On the dynamic aspects of protein structure) In: Molecular Biology, Problems and Perspectives (Braunstein, A. E., ed.), pp. 182–187 (in Russian), Izdat. Nauka Závodszky, 1966, Structure of glyceraldehyde-3-phosphate dehydrogenase and its alteration by coenzyme binding, Acta Biochim. Biophys. Acad. Sci. Hung., 1, 389 Frauenfelder, 1991, The energy landscapes and motions of proteins, Science, 254, 1598, 10.1126/science.1749933 Ma, 1999, Folding funnels and binding mechanisms, Protein Eng., 12, 713, 10.1093/protein/12.9.713 Tsai, 1999, Folding funnels, binding funnels, and protein function, Protein Sci., 8, 1181, 10.1110/ps.8.6.1181 Lange, 2008, Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution, Science, 320, 1471, 10.1126/science.1157092 Wu, 2009, Amplification and detection of single-molecule conformational fluctuation through a protein interaction network with bimodal distributions, J. Phys. Chem. B, 113, 12375, 10.1021/jp903548d Boehr, 2009, The role of dynamic conformational ensembles in biomolecular recognition, Nat. Chem. Biol., 5, 789, 10.1038/nchembio.232 Koshland, 1966, Comparison of experimental binding data and theoretical models in proteins containing subunits, Biochemistry, 5, 365, 10.1021/bi00865a047 Monod, 1965, On the nature of allosteric transitions: a plausible model, J. Mol. Biol., 12, 88, 10.1016/S0022-2836(65)80285-6 Tsai, 2008, Allostery: absence of a change in shape does not imply that allostery is not at play, J. Mol. Biol., 378, 1, 10.1016/j.jmb.2008.02.034 Schrank, 2009, Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins, Proc. Natl. Acad. Sci. U. S. A., 106, 16984, 10.1073/pnas.0906510106 Závodszky, 1972, Effect of thiol blocking and substrate binding on the conformation and conformational stability of rabbit muscle aldolase, Acta Biochim. Biophys. Acad. Sci. Hung., 7, 1 Boehr, 2010, Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands, Proc. Natl. Acad. Sci. U. S. A., 107, 1373, 10.1073/pnas.0914163107 Grünberg, 2004, Complementarity of structure ensembles in protein-protein binding, Structure, 12, 2125, 10.1016/j.str.2004.09.014 Wlodarski, 2009, Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin, Proc. Natl. Acad. Sci. U. S. A., 106, 19346, 10.1073/pnas.0906966106 Reichheld, 2009, The induction of folding cooperativity by ligand binding drives the allosteric response of tetracycline repressor, Proc. Natl. Acad. Sci. U. S. A., 106, 22263, 10.1073/pnas.0911566106 Gorfe, 2008, Water-membrane partition thermodynamics of an amphiphilic lipopeptide: an enthalpy-driven hydrophobic effect, Biophys. J., 95, 3269, 10.1529/biophysj.108.136481 Bailor, 2010, Topology links RNA secondary structure with global conformation, dynamics, and adaptation, Science, 327, 202, 10.1126/science.1181085 Solomatin, 2010, Multiple native states reveal persistent ruggedness of an RNA folding landscape, Nature, 463, 681, 10.1038/nature08717 Kovacs, 2005, Water and molecular chaperones act as weak links of protein folding networks: energy landscape and punctuated equilibrium changes point towards a game theory of proteins, FEBS Lett., 579, 2254, 10.1016/j.febslet.2005.03.056 Antal, 2009, Perturbation waves in proteins and protein networks: Applications of percolation and game theories in signaling and drug design, Curr. Protein Pept. Sci., 10, 161, 10.2174/138920309787847617 Mar, 2009, Decomposition of gene expression state space trajectories, PLoS Comput. Biol., 5, e1000626, 10.1371/journal.pcbi.1000626 Formaneck, 2006, Reconciling the “old” and “new” views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY), Proteins: Struct. Funct. Bioinformatics, 63, 846, 10.1002/prot.20893 Okazaki, 2008, Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms, Proc. Natl. Acad. Sci. U. S. A., 105, 11182, 10.1073/pnas.0802524105 Weikl, 2009, Selected-fit versus induced-fit protein binding: kinetic differences and mutational analysis, Proteins, 75, 104, 10.1002/prot.22223 Junker, 2009, Ligand-dependent equilibrium fluctuations of single calmodulin molecules, Science, 323, 633, 10.1126/science.1166191 Pereira-Leal, 2006, The origins and evolution of functional modules: lessons from protein complexes, Phil. Trans. Roy. Soc. B, 361, 507, 10.1098/rstb.2005.1807 Levy, 2005, A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes, J. Mol. Biol., 346, 1121, 10.1016/j.jmb.2004.12.021 Tang, 2006, Visualization of transient encounter complexes in protein-protein association, Nature, 444, 383, 10.1038/nature05201 Bashir, 2010, Visualization of the encounter ensemble of the transient electron transfer complex of cytochrome c and cytochrome c peroxidase, J. Am. Chem. Soc., 132, 241, 10.1021/ja9064574 Rajamani, 2004, Anchor residues in protein-protein interactions, Proc. Natl. Acad. Sci. U. S. A., 101, 11287, 10.1073/pnas.0401942101 Ma, 2002, Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations, Protein Sci., 11, 184, 10.1110/ps.21302 Böde, 2007, Network analysis of protein dynamics, FEBS Lett., 581, 2776, 10.1016/j.febslet.2007.05.021 del Sol, 2007, Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages, Genome Biol., 8, R92, 10.1186/gb-2007-8-5-r92 Csermely, 2008, Creative elements: network-based predictions of active centres in proteins, cellular and social networks, Trends Biochem. Sci., 33, 569, 10.1016/j.tibs.2008.09.006 Sethi, 2009, Dynamical networks in tRNA:protein complexes, Proc. Natl. Acad. Sci. U. S. A., 106, 6620, 10.1073/pnas.0810961106 Piazza, 2008, Discrete breathers in protein structures, Phys. Biol., 5, 26001, 10.1088/1478-3975/5/2/026001 Piazza, 2009, Long-range energy transfer in proteins, Phys. Biol., 6, 46014, 10.1088/1478-3975/6/4/046014 Haliloglu, 2005, How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues, Biophys. J., 88, 1552, 10.1529/biophysj.104.051342 Halabi, 2009, Protein sectors: evolutionary units of three-dimensional structure, Cell, 138, 774, 10.1016/j.cell.2009.07.038 Materese, 2008, Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions, Proc. Natl. Acad. Sci. U. S. A., 105, 10659, 10.1073/pnas.0801850105 Pal, 2004, Dynamics of water in biological recognition, Chem. Rev., 104, 2099, 10.1021/cr020689l Fernández, 2002, Desolvation shell of hydrogen bonds in folded proteins, protein complexes and folding pathways, FEBS Lett., 527, 166, 10.1016/S0014-5793(02)03204-0 Fernández, 2003, Insufficiently dehydrated hydrogen bonds as determinants of protein interactions, Proc. Natl. Acad. Sci. U. S. A., 100, 113, 10.1073/pnas.0136888100 Gardino, 2009, Transient non-native hydrogen bonds promote activation of a signaling protein, Cell, 139, 1109, 10.1016/j.cell.2009.11.022 Tompa, 2002, Intrinsically unstructured proteins, Trends Biochem. Sci., 27, 527, 10.1016/S0968-0004(02)02169-2 Tsai, 2001, Structured disorder and conformational selection, Proteins: Struct. Funct. Genet., 44, 418, 10.1002/prot.1107 Uversky, 2010, Understanding protein non-folding, Biochim. Biophys. Acta, 1804, 1231, 10.1016/j.bbapap.2010.01.017 Trizac, 2010, Capillarity theory for the fly-casting mechanism, Proc. Natl. Acad. Sci. U. S. A., 107, 2746, 10.1073/pnas.0914727107 Liu, 2009, Toward a quantitative theory of intrinsically disordered proteins and their function, Proc. Natl. Acad. Sci. U. S. A., 106, 19819, 10.1073/pnas.0907710106 Pechmann, 2009, Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins, Proc. Natl. Acad. Sci. U. S. A., 106, 10159, 10.1073/pnas.0812414106 Ellis, 2001, Macromolecular crowding: obvious but underappreciated, Trends Biochem. Sci., 26, 597, 10.1016/S0968-0004(01)01938-7 Tompa, 2004, The role of structural disorder in RNA- and protein chaperone function, FASEB J., 18, 1169, 10.1096/fj.04-1584rev Ellis, 2006, Protein aggregation in crowded environments, Biol. Chem., 387, 485, 10.1515/BC.2006.064 Dix, 2008, Crowding effects on diffusion in solutions and cells, Annu. Rev. Biophys., 37, 247, 10.1146/annurev.biophys.37.032807.125824 Zhou, 2008, Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences, Annu. Rev. Biophys., 37, 375, 10.1146/annurev.biophys.37.032807.125817 Wang, 2009, Confinement effects on the kinetics and thermodynamics of protein dimerization, Proc. Natl. Acad. Sci. U. S. A., 106, 5517, 10.1073/pnas.0809649106 Xing, 2008, The Goldbeter-Koshland switch in the first-order region and its response to dynamic disorder, PLoS ONE, 3, e2140, 10.1371/journal.pone.0002140 Gsponer, 2008, A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction, Structure, 16, 736, 10.1016/j.str.2008.02.017 Smock, 2009, Sending signals dynamically, Science, 324, 198, 10.1126/science.1169377 Tzeng, 2009, Dynamic activation of an allosteric regulatory protein, Nature, 462, 368, 10.1038/nature08560 Paulsson, 2000, Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation, Proc. Natl. Acad. Sci. U. S. A., 97, 7148, 10.1073/pnas.110057697 Bathe, 2008, A finite element framework for computation of protein normal modes and mechanical response, Proteins: Struct. Funct. Bioinformatics, 70, 1595, 10.1002/prot.21708 Kim, 2010, Finite element framework for mechanics and dynamics of supramolecular protein assemblies Zhong, 2009, Edgetic perturbation models of human inherited disorders, Mol. Syst. Biol., 5, 321, 10.1038/msb.2009.80 Schuster, 2008, Use of game-theoretical methods in biochemistry and biophysics, J. Biol. Phys., 34, 1, 10.1007/s10867-008-9101-4 Chettaoui, 2007, Games network and application to PAs system, Biosystems, 87, 136, 10.1016/j.biosystems.2006.09.006