- Fischer, E. Einfluss der configuration auf die wirkung der enzyme. Ber. Dtsch. Chem. Ges. 27, 2984–2993 (1894).
Google Scholar
- Koshland, D.E. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA 44, 98–104 (1958).
CAS PubMed Google Scholar
- Frauenfelder, H., Sligar, S.G. & Wolynes, P.G. The energy landscapes and motions of proteins. Science 254, 1598–1603 (1991).
CAS PubMed Google Scholar
- Ma, B., Kumar, S., Tsai, C.J. & Nussinov, R. Folding funnels and binding mechanisms. Protein Eng. 12, 713–720 (1999).
CAS PubMed Google Scholar
- Tsai, C.J., Kumar, S., Ma, B. & Nussinov, R. Folding funnels, binding funnels, and protein function. Protein Sci. 8, 1181–1190 (1999).
CAS PubMed PubMed Central Google Scholar
- Tsai, C.J., Ma, B. & Nussinov, R. Folding and binding cascades: shifts in energy landscapes. Proc. Natl. Acad. Sci. USA 96, 9970–9972 (1999).
CAS PubMed Google Scholar
- Foote, J. & Milstein, C. Conformational isomerism and the diversity of antibodies. Proc. Natl. Acad. Sci. USA 91, 10370–10374 (1994).
CAS PubMed Google Scholar
- Bosshard, H.R. Molecular recognition by induced fit: how fit is the concept? News Physiol. Sci. 16, 171–173 (2001).
CAS PubMed Google Scholar
- Berger, C. et al. Antigen recognition by conformational selection. FEBS Lett. 450, 149–153 (1999).
CAS PubMed Google Scholar
- Leder, L. et al. Spectroscopic, calorimetric, and kinetic demonstration of conformational adaptation in peptide-antibody recognition. Biochemistry 34, 16509–16518 (1995).
CAS PubMed Google Scholar
- Kumar, S., Ma, B., Tsai, C.J., Sinha, N. & Nussinov, R. Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci. 9, 10–19 (2000).
CAS PubMed PubMed Central Google Scholar
- Miller, D.W. & Dill, K.A. Ligand binding to proteins: the binding landscape model. Protein Sci. 6, 2166–2179 (1997).
CAS PubMed PubMed Central Google Scholar
- Dill, K.A. & Chan, H.S. From Levinthal to pathways to funnels. Nat. Struct. Biol. 4, 10–19 (1997).
CAS PubMed Google Scholar
- Ma, B., Shatsky, M., Wolfson, H.J. & Nussinov, R. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci. 11, 184–197 (2002).
CAS PubMed PubMed Central Google Scholar
- Greenleaf, W.J., Woodside, M.T. & Block, S.M. High-resolution, single-molecule measurements of biomolecular motion. Annu. Rev. Biophys. Biomol. Struct. 36, 171–190 (2007).
CAS PubMed PubMed Central Google Scholar
- Parak, F.G. Proteins in action: the physics of structural fluctuations and conformational changes. Curr. Opin. Struct. Biol. 13, 552–557 (2003).
CAS PubMed Google Scholar
- Hinterdorfer, P. & Dufrene, Y.F. Detection and localization of single molecular recognition events using atomic force microscopy. Nat. Methods 3, 347–355 (2006).
CAS PubMed Google Scholar
- Busenlehner, L.S. & Armstrong, R.N. Insights into enzyme structure and dynamics elucidated by amide H/D exchange mass spectrometry. Arch. Biochem. Biophys. 433, 34–46 (2005).
CAS PubMed Google Scholar
- Palmer, A.G. III. Nmr probes of molecular dynamics: overview and comparison with other techniques. Annu. Rev. Biophys. Biomol. Struct. 30, 129–155 (2001).
CAS PubMed Google Scholar
- Tobi, D. & Bahar, I. Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc. Natl. Acad. Sci. USA 102, 18908–18913 (2005).
CAS PubMed Google Scholar
- Keskin, O. Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies. BMC Struct. Biol. 7, 31 (2007).
PubMed PubMed Central Google Scholar
- Grunberg, R., Leckner, J. & Nilges, M. Complementarity of structure ensembles in protein-protein binding. Structure 12, 2125–2136 (2004).
CAS PubMed Google Scholar
- Austin, R.H., Beeson, K.W., Eisenstein, L., Frauenfelder, H. & Gunsalus, I.C. Dynamics of ligand binding to myoglobin. Biochemistry 14, 5355–5373 (1975).
CAS PubMed Google Scholar
- Schotte, F. et al. Watching a protein as it functions with 150-ps time-resolved x-ray crystallography. Science 300, 1944–1947 (2003).
CAS PubMed Google Scholar
- Vos, M.H. Ultrafast dynamics of ligands within heme proteins. Biochim. Biophys. Acta 1777, 15–31 (2008).
CAS PubMed Google Scholar
- Lee, A.Y., Gulnik, S.V. & Erickson, J.W. Conformational switching in an aspartic proteinase. Nat. Struct. Biol. 5, 866–871 (1998).
CAS PubMed Google Scholar
- Henzler-Wildman, K.A. et al. Intrinsic motions along an enzymatic reaction trajectory. Nature 450, 838–844 (2007). This study provides experimental support from X-ray crystallography, NMR and single-molecule fluorescence that adenylate kinase fluctuates between open and closed states in the absence of ligand.
CAS PubMed Google Scholar
- Muller, Y.A., Kelley, R.F. & de Vos, A.M. Hinge bending within the cytokine receptor superfamily revealed by the 2.4 A crystal structure of the extracellular domain of rabbit tissue factor. Protein Sci. 7, 1106–1115 (1998).
CAS PubMed PubMed Central Google Scholar
- James, L.C., Roversi, P. & Tawfik, D.S. Antibody multispecificity mediated by conformational diversity. Science 299, 1362–1367 (2003).
CAS PubMed Google Scholar
- Hanes, J., Jermutus, L., Weber-Bornhauser, S., Bosshard, H.R. & Pluckthun, A. Ribosome display efficiently selects and evolves high-affinity antibodies in vitro from immune libraries. Proc. Natl. Acad. Sci. USA 95, 14130–14135 (1998).
CAS PubMed Google Scholar
- Stella, L. et al. Flexibility of helix 2 in the human glutathione transferase P1–1. time-resolved fluorescence spectroscopy. J. Biol. Chem. 273, 23267–23273 (1998).
CAS PubMed Google Scholar
- Xu, J. & Root, D.D. Conformational selection during weak binding at the actin and myosin interface. Biophys. J. 79, 1498–1510 (2000).
CAS PubMed PubMed Central Google Scholar
- Cao, Y., Musah, R.A., Wilcox, S.K., Goodin, D.B. & McRee, D.E. Protein conformer selection by ligand binding observed with crystallography. Protein Sci. 7, 72–78 (1998).
CAS PubMed PubMed Central Google Scholar
- Mittermaier, A. & Kay, L.E. New tools provide new insights in NMR studies of protein dynamics. Science 312, 224–228 (2006).
CAS PubMed Google Scholar
- Cavalli, A., Salvatella, X., Dobson, C.M. & Vendruscolo, M. Protein structure determination from NMR chemical shifts. Proc. Natl. Acad. Sci. USA 104, 9615–9620 (2007).
CAS PubMed Google Scholar
- Vallurupalli, P., Hansen, D.F., Stollar, E., Meirovitch, E. & Kay, L.E. Measurement of bond vector orientations in invisible excited states of proteins. Proc. Natl. Acad. Sci. USA 104, 18473–18477 (2007).
CAS PubMed Google Scholar
- Igumenova, T.I., Brath, U., Akke, M. & Palmer, A.G. III. Characterization of chemical exchange using residual dipolar coupling. J. Am. Chem. Soc. 129, 13396–13397 (2007).
CAS PubMed PubMed Central Google Scholar
- Hansen, D.F., Vallurupalli, P. & Kay, L.E. Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states. J. Biomol. NMR 41, 113–120 (2008).
CAS PubMed Google Scholar
- Beach, H., Cole, R., Gill, M.L. & Loria, J.P. Conservation of mus-ms enzyme motions in the apo- and substrate-mimicked state. J. Am. Chem. Soc. 127, 9167–9176 (2005).
CAS PubMed Google Scholar
- Wolf-Watz, M. et al. Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair. Nat. Struct. Mol. Biol. 11, 945–949 (2004).
CAS PubMed Google Scholar
- Boehr, D.D., McElheny, D., Dyson, H.J. & Wright, P.E. The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313, 1638–1642 (2006). This study suggests that every functional intermediate of dihydrofolate reductase fluctuates into a higher energy conformation that is structurally similar to the next and/or previous complex in the catalytic cycle.
CAS PubMed Google Scholar
- McElheny, D., Schnell, J.R., Lansing, J.C., Dyson, H.J. & Wright, P.E. Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis. Proc. Natl. Acad. Sci. USA 102, 5032–5037 (2005).
CAS PubMed Google Scholar
- Hanson, J.A. et al. Illuminating the mechanistic roles of enzyme conformational dynamics. Proc. Natl. Acad. Sci. USA 104, 18055–18060 (2007).
CAS PubMed Google Scholar
- Eisenmesser, E.Z. et al. Intrinsic dynamics of an enzyme underlies catalysis. Nature 438, 117–121 (2005).
CAS PubMed Google Scholar
- Antikainen, N.M., Smiley, R.D., Benkovic, S.J. & Hammes, G.G. Conformation coupled enzyme catalysis: single-molecule and transient kinetics investigation of dihydrofolate reductase. Biochemistry 44, 16835–16843 (2005).
CAS PubMed Google Scholar
- Boehr, D.D., Dyson, H.J. & Wright, P.E. Conformational relaxation following hydride transfer plays a limiting role in dihydrofolate reductase catalysis. Biochemistry 47, 9227–9233 (2008).
CAS PubMed PubMed Central Google Scholar
- Kitahara, R. et al. High pressure NMR reveals active-site hinge motion of folate-bound Escherichia coli dihydrofolate reductase. Biochemistry 39, 12789–12795 (2000).
CAS PubMed Google Scholar
- Mauldin, R.V., Carroll, M.J. & Lee, A.L. Dynamic dysfunction in dihydrofolate reductase results from antifolate drug binding: modulation of dynamics within a structural state. Structure 17, 386–394 (2009).
CAS PubMed PubMed Central Google Scholar
- Tang, C., Schwieters, C.D. & Clore, G.M. Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR. Nature 449, 1078–1082 (2007).
CAS PubMed Google Scholar
- Lu, Z.L., Coetsee, M., White, C.D. & Millar, R.P. Structural determinants for ligand-receptor conformational selection in a peptide G protein-coupled receptor. J. Biol. Chem. 282, 17921–17929 (2007).
CAS PubMed Google Scholar
- Fenwick, R. et al. Solution structure and dynamics of the small GTPase RalB in its active conformation: significance for effector protein binding. Biochemistry 48, 2192–2206 (2009).
CAS PubMed Google Scholar
- Saitoh, T. et al. Tom20 recognizes mitochondrial presequences through dynamic equilibrium among multiple bound states. EMBO J. 26, 4777–4787 (2007).
CAS PubMed PubMed Central Google Scholar
- Brath, U. & Akke, M. Differential responses of the backbone and side chain conformational dynamics in FKBP12 upon binding the transition state analog FK506: implications for transition state stabilization and target protein recognition. J. Mol. Biol. 387, 233–244 (2009).
CAS PubMed Google Scholar
- Keramisanou, D. et al. Disorder-order folding transitions underlie catalysis in the helicase motor of SecA. Nat. Struct. Mol. Biol. 13, 594–602 (2006).
CAS PubMed Google Scholar
- Gsponer, J. et al. A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction. Structure 16, 736–746 (2008).
CAS PubMed PubMed Central Google Scholar
- Nevo, R. et al. A molecular switch between alternative conformational states in the complex of Ran and importin beta1. Nat. Struct. Biol. 10, 553–557 (2003).
CAS PubMed Google Scholar
- Junker, J.P., Ziegler, F. & Rief, M. Ligand-dependent equilibrium fluctuations of single calmodulin molecules. Science 323, 633–637 (2009).
CAS PubMed Google Scholar
- Koglin, A. et al. Conformational switches modulate protein interactions in peptide antibiotic synthetases. Science 312, 273–276 (2006).
CAS PubMed Google Scholar
- Koglin, A. et al. Structural basis for the selectivity of the external thioesterase of the surfactin synthetase. Nature 454, 907–911 (2008).
CAS PubMed PubMed Central Google Scholar
- Lange, O.F. et al. Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 320, 1471–1475 (2008). This report presents an NMR-derived conformational ensemble of ubiquitin that encompasses all the crystallographically determined conformations of ubiquitin.
CAS PubMed Google Scholar
- Kalodimos, C. et al. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science 305, 386–389 (2004). This study compares the structure and dynamics of the lac repressor headpiece when bound to cognate versus noncognate DNA, and demonstrates that the underlying energy landscapes are distinct.
CAS PubMed Google Scholar
- Zhang, Q., Stelzer, A.C., Fisher, C.K. & Al-Hashimi, H.M. Visualizing spatially correlated dynamics that directs RNA conformational transitions. Nature 450, 1263–1267 (2007). This study demonstrates that TAR RNA fluctuates into multiple “bound” conformations in the absence of ligands.
CAS PubMed Google Scholar
- Al-Hashimi, H.M. & Walter, N.G. RNA dynamics: it is about time. Curr. Opin. Struct. Biol. 18, 321–329 (2008).
CAS PubMed PubMed Central Google Scholar
- Mittag, T. & Forman-Kay, J.D. Atomic-level characterization of disordered protein ensembles. Curr. Opin. Struct. Biol. 17, 3–14 (2007).
CAS PubMed Google Scholar
- Lakomek, N.A. et al. Residual dipolar couplings as a tool to study molecular recognition of ubiquitin. Biochem. Soc. Trans. 36, 1433–1437 (2008).
CAS PubMed Google Scholar
- Clore, G.M., Tang, C. & Iwahara, J. Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement. Curr. Opin. Struct. Biol. 17, 603–616 (2007).
CAS PubMed PubMed Central Google Scholar
- Lindorff-Larsen, K., Best, R.B., Depristo, M.A., Dobson, C.M. & Vendruscolo, M. Simultaneous determination of protein structure and dynamics. Nature 433, 128–132 (2005).
CAS PubMed Google Scholar
- Lipari, G. & Szabo, A. Nuclear magnetic resonance relaxation in nucleic acid fragments: models for internal motion. Biochemistry 20, 6250–6256 (1981).
CAS PubMed Google Scholar
- Lakomek, N.A., Carlomagno, T., Becker, S., Griesinger, C. & Meiler, J. A thorough dynamic interpretation of residual dipolar couplings in ubiquitin. J. Biomol. NMR 34, 101–115 (2006).
CAS PubMed Google Scholar
- Esler, W.P. et al. Alzheimer's disease amyloid propagation by a template-dependent dock-lock mechanism. Biochemistry 39, 6288–6295 (2000).
CAS PubMed Google Scholar
- Tessier, P.M. & Lindquist, S. Prion recognition elements govern nucleation, strain specificity and species barriers. Nature 447, 556–561 (2007).
CAS PubMed PubMed Central Google Scholar
- Kalodimos, C., Boelens, R. & Kaptein, R. Toward an integrated model of protein−DNA recognition as inferred from NMR studies on the lac repressor system. Chem. Rev. 104, 3567–3586 (2004).
CAS PubMed Google Scholar
- von Hippel, P.H. & Berg, O.G. Facilitated target location in biological systems. J. Biol. Chem. 264, 675–678 (1989).
CAS PubMed Google Scholar
- Gorman, J. & Greene, E.C. Visualizing one-dimensional diffusion of proteins along DNA. Nat. Struct. Mol. Biol. 15, 768–774 (2008).
CAS PubMed Google Scholar
- Zhang, Q., Stelzer, A., Fisher, C. & Al-Hashimi, H. Visualizing spatially correlated dynamics that directs RNA conformational transitions. Nature 450, 1263–1267 (2007).
CAS PubMed Google Scholar
- Monod, J., Wyman, J. & Changeux, J.P. On the nature of allosteric transitions: A plausible model. J. Mol. Biol. 12, 88–118 (1965).
CAS PubMed Google Scholar
- Kantrowitz, E.R. & Lipscomb, W.N. Escherichia coli aspartate transcarbamoylase: the molecular basis for a concerted allosteric transition. Trends Biochem. Sci. 15, 53–59 (1990).
CAS PubMed Google Scholar
- Velyvis, A., Yang, Y.R., Schachman, H.K. & Kay, L.E. A solution NMR study showing that active site ligands and nucleotides directly perturb the allosteric equilibrium in aspartate transcarbamoylase. Proc. Natl. Acad. Sci. USA 104, 8815–8820 (2007).
CAS PubMed Google Scholar
- Velyvis, A., Schachman, H.K. & Kay, L.E. Application of methyl-TROSY NMR to test allosteric models describing effects of nucleotide binding to aspartate transcarbamoylase. J. Mol. Biol. 387, 540–547 (2009).
CAS PubMed Google Scholar
- Gunasekaran, K., Ma, B. & Nussinov, R. Is allostery an intrinsic property of all dynamic proteins? Proteins 57, 433–443 (2004).
CAS PubMed Google Scholar
- Volkman, B.F., Lipson, D., Wemmer, D.E. & Kern, D. Two-state allosteric behavior in a single-domain signaling protein. Science 291, 2429–2433 (2001).
CAS PubMed Google Scholar
- Yao, X., Rosen, M.K. & Gardner, K.H. Estimation of the available free energy in a LOV2-J alpha photoswitch. Nat. Chem. Biol. 4, 491–497 (2008).
CAS PubMed PubMed Central Google Scholar
- Li, P., Martins, I.R., Amarasinghe, G.K. & Rosen, M.K. Internal dynamics control activation and activity of the autoinhibited Vav DH domain. Nat. Struct. Mol. Biol. 15, 613–618 (2008). This study presents a linear correlation between biological activity and the population of the Vav DH higher energy conformation. This provides both structural and functional evidence for the involvement of a higher energy conformation in biological function.
CAS PubMed PubMed Central Google Scholar
- Boehr, D.D., Dyson, H.J. & Wright, P.E. An NMR perspective on enzyme dynamics. Chem. Rev. 106, 3055–3079 (2006).
CAS PubMed Google Scholar
- Lee, G.M. & Craik, C.S. Trapping moving targets with small molecules. Science 324, 213–215 (2009).
CAS PubMed PubMed Central Google Scholar
- Bursavich, M.G. & Rich, D.H. Designing non-peptide peptidomimetics in the 21st century: inhibitors targeting conformational ensembles. J. Med. Chem. 45, 541–558 (2002).
CAS PubMed Google Scholar
- Totrov, M. & Abagyan, R. Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr. Opin. Struct. Biol. 18, 178–184 (2008).
CAS PubMed PubMed Central Google Scholar
- Andrusier, N., Mashiach, E., Nussinov, R. & Wolfson, H.J. Principles of flexible protein-protein docking. Proteins 73, 271–289 (2008).
CAS PubMed PubMed Central Google Scholar
- Chaudhury, S. & Gray, J.J. Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles. J. Mol. Biol. 381, 1068–1087 (2008).
CAS PubMed PubMed Central Google Scholar
- Lindsley, C.W. & Emmitte, K.A. Recent progress in the discovery and development of negative allosteric modulators of mGluR5. Curr. Opin. Drug Discov. Devel. 12, 446–457 (2009).
CAS PubMed Google Scholar
- Frederick, K.K., Marlow, M.S., Valentine, K.G. & Wand, A.J. Conformational entropy in molecular recognition by proteins. Nature 448, 325–329 (2007).
CAS PubMed PubMed Central Google Scholar
- Rothlisberger, D. et al. Kemp elimination catalysts by computational enzyme design. Nature 453, 190–195 (2008).
PubMed Google Scholar
- Jiang, L. et al. De novo computational design of retro-aldol enzymes. Science 319, 1387–1391 (2008).
CAS PubMed PubMed Central Google Scholar
- Hilvert, D. Critical analysis of antibody catalysis. Annu. Rev. Biochem. 69, 751–793 (2000).
CAS PubMed Google Scholar
- Pauling, L. & Delbruck, M. The nature of the intermolecular forces operative in biological processes. Science 92, 77–79 (1940).
CAS PubMed Google Scholar
- James, L.C. & Tawfik, D.S. Conformational diversity and protein evolution—a 60-year-old hypothesis revisited. Trends Biochem. Sci. 28, 361–368 (2003).
CAS PubMed Google Scholar
- Tokuriki, N. & Tawfik, D.S. Protein dynamism and evolvability. Science 324, 203–207 (2009).
CAS PubMed Google Scholar
- Wedemayer, G.J., Patten, P.A., Wang, L.H., Schultz, P.G. & Stevens, R.C. Structural insights into the evolution of an antibody combining site. Science 276, 1665–1669 (1997).
CAS PubMed Google Scholar
- Weikl, T. & Von Deuster, C. Selected-fit versus induced-fit protein binding: kinetic differences and mutational analysis. Proteins 75, 104–110 (2009).
CAS PubMed Google Scholar