Folding funnels and conformational transitions via hinge-bending motions
In this article we focus on presenting a broad range of examples illustrating low-energy transitions via hinge-bending motions. The examples are divided according to the type of hinge-bending involved; namely, motions involving fragments of the protein chains, hinge-bending motions involving protein domains, and hinge-bending motions between the covalently unconnected subunits. We further make a distinction between allosterically and nonallosterically regulated proteins. These transitions are discussed within the general framework of folding and binding funnels. We propose that the conformers manifesting such swiveling motions are not the outcome of “induced fit” binding mechanism; instead, molecules exist in an ensemble of conformations that are in equilibrium in solution. These ensembles, which populate the bottoms of the funnels,a priori contain both the “open” and the “closed” conformational isomers. Furthermore, we argue that there are no fundamental differences among the physical principles behind the folding and binding funnels. Hence, there is no basic difference between funnels depicting ensembles of conformers of single molecules with fragment, or domain motions, as compared to subunits in multimeric quaternary structures, also showing such conformational transitions. The difference relates only to the size and complexity of the system. The larger the system, the more complex its corresponding fused funnel(s). In particular, funnels associated with allosterically regulated proteins are expected to be more complicated, because allostery is frequently involved with movements between subunits, and consequently is often observed in multichain and multimolecular complexes.
This review centers on the critical role played by flexibility and conformational fluctuations in enzyme activity. Internal motions that extend over different time scales and with different amplitudes are known to be essential for the catalytic cycle. The conformational change observed in enzyme-substrate complexes as compared to the unbound enzyme state, and in particular the hinge-bending motions observed in enzymes with two domains, have a substantial effect on the enzymatic catalytic activity. The examples we review span the lipolytic enzymes that are particularly interesting, owing to their activation at the water-oil interface; an allosterically controlled dehydrogenase (lactate dehydrogenase); a DNA methyltransferase, with a covalently-bound intermediate; large-scale flexible loop motions in a glycolytic enzyme (TIM); domain motion in PGK, an enzyme which is essential in most cells, both for ATP generation in aerobes and for fermentation in anaerobes; adenylate kinase, showing large conformational changes, owing to their need to shield their catalytic centers from water; a calcium-binding protein (calmodulin), involved in a wide range of cellular calcium-dependent signaling; diphtheria toxin, whose large domain motion has been shown to yield “domain swapping” the hexameric glutamate dehydrogenase, which has been studied both in a thermophile and in a mesophile; an allosteric enzyme, showing subunit motion between the R and the T states (aspartate transcarbamoylase), and the historically well-studied lac represoor. Nonallosteric subunit transitions are also addressed with some examples (aspartate receptor andBamHI endonuclease). Hence, using this enzyme-catalysis-centered discussion, we address energy funnel landscapes of large-scale conformational transitions, rather than the faster, quasi-harmonic, thermal fluctuations.
Index EntriesHinge-bending lock-and-key vs induced-fit conformational ensembles binding folding
Fischer, E. (1894)Ber. Dt. Chem. Ges.
, 2985–2991.CrossRefGoogle Scholar
Koshland, D. E., Jr. (1958) Application of a theory of enzyme specificity to protein synthesis.Proc. Natl. Acad. Sci. USA
, 98–123.PubMedCrossRefGoogle Scholar
Bryngelson, J. D. and Wolynes, P. G. (1989) Intermediates and barrier crossing in a random energy model (with applications to protein folding).J. Phys. Chem
, 6902–6915.CrossRefGoogle Scholar
Karplus, M. and Shakhnovitch, E. (1992) Protein folding: theoretical studies of thermodynamics and dynamics, inProtein Folding
(Creighton T. ed.), W. H. Freeman & Sons, New York, pp. 127–195.Google Scholar
Karplus, M., Sali, A., and Shakhnovitch, E. (1995) Comment: kinetics of protein folding.Nature
, 664–665.CrossRefGoogle Scholar
Wolynes, P. G., Onuchic, J. N., and Thirumalai, D. (1995) Navigating the folding routes.Science
, 1619–1620.PubMedCrossRefGoogle Scholar
Onuchic, J. N., Wolynes, P. G., Luthey-Schulten, Z., and Socci, N. D. (1995) Towards an outline of the topography of a realistic protein folding funnel.Proc. Natl. Acad. Sci. USA
, 3626–3630.PubMedCrossRefGoogle Scholar
Baldwin, R. L. (1994) Matching speed and stability.Nature
, 183–184.PubMedCrossRefGoogle Scholar
Baldwin, R. L. (1995) The nature of protein folding pathways: The classical versus the new view.J. Biomolec. NMR
, 103–109.CrossRefGoogle Scholar
Dill, K. A. and Chan, H. S. (1997) From Levinthal to pathways to funnels.Nature Struct. Biol
, 10–19.PubMedCrossRefGoogle Scholar
Karplus, M. (1997) The Levinthal paradox: yesterday and today.Folding Design
, S69-S75.PubMedCrossRefGoogle Scholar
Lazaridis, T. and Karplus, M. (1997) “New view” of protein folding reconciled with the old through multiple unfolding simulations.Science
, 1928–1931.PubMedCrossRefGoogle Scholar
Gruebele, M. and Wolynes, P. (1998) Satisfying turns in folding transitions.Nature Struct. Biol.
, 662–665.PubMedCrossRefGoogle Scholar
Tsai, C.-J., Xu, D., and Nussinov, R. (1998) Protein Folding via Binding, and vice versa.Folding & Design
, R71-R80.CrossRefGoogle Scholar
Gerstein, M., Lesk, A., and Chothia, C. (1994) Structural mechanism for domain movements in proteins.Biochemistry
, 6739–6749.PubMedCrossRefGoogle Scholar
Gerstein, M. and Krebs, W. (1998) A database of macromolecular motions.Nucleic Acids Res.
, 4280–4290.PubMedCrossRefGoogle Scholar
Derewenda, U., Brzozowski, A. M., Lawson, D. M., and Derewenda, Z. S. (1992) Catalysis at the interface: the anatomy of a conformational change in a triglyceride lipase.Biochemistry
, 1532–1541.PubMedCrossRefGoogle Scholar
Brady, L., Brzozowski, A. M., Derewenda, Z. S., Dodson, E., Dodson, G., Tolley, S., et al. (1990) A serine protease triad forms the catalytic centre of a triaclglycerol lipase.Nature
, 767–770.PubMedCrossRefGoogle Scholar
Bernstein, F., Koetzle, T., Williams, G., Meyer, E. J., Brice, M., Rodgers, J., et al. (1977) The Protein Data Bank: a computer based archival file for macromolecular structures.J. Mol. Biol.
, 535–542.PubMedCrossRefGoogle Scholar
Peters, G. H., Toxvaerd, S., Olsen, O. H., and Svendsen, A. (1997) Computational studies of the activation of lipases and the effect of a hydrophobic environment.Protein Eng.
, 137–147.PubMedCrossRefGoogle Scholar
Berg, O. G., Cajal, Y., Butterfoss, G. L., Grey, R. L., Alsina, M. A., Yu, B. Z., and Jain, M. K. (1998) Interfacial activation of triglyceride lipase from Thermomyces (Humicola) lanuginosa: kinetic parameters and a basis for control of the lid.Biochemistry
, 6615–6627.PubMedCrossRefGoogle Scholar
Lowe, M. E. (1997) Colipase stabilized the lid domain of pancreatic triglycerate lipase.J Biol. Chem.
, 9–12.PubMedGoogle Scholar
Iwata, S., Kamata, K., Yoshida, S., Minowa, T., and Ohta, T. (1994) T and R states in the crystals of bacterial L-lactate dehydrogenase reveal the mechanism for allosteric control.Struct. Biol.
, 176–185CrossRefGoogle Scholar
Klimasaukas, S., Kumar, S., Roberts, R. J., and Cheng, X. (1994) HhI methyltransferase flips its target base out of the DNA helix.Cell
, 357–369.CrossRefGoogle Scholar
Sun, J. and Sampson, N. S. (1998) Determination of the amino acid requirements for a protein hinge in triosephosphate isomerase.Protein Sci.
, 1495–1505.PubMedCrossRefGoogle Scholar
Mainfroid, V., Terpstra, P., Beauregard, M., Frere, J. M., Mande, S. C., Hol, W. G. J., Martial, J. A., and Goraj, K. (1996) 3 HTIM mutants that provide new insight on why TIM is a dimer.J. Mol. Biol
, 441–456.PubMedCrossRefGoogle Scholar
Rietveld, A. W. M. and Ferreira, S. T. (1998) Kinetics and energetics of subunit dissociation/unfolding of TIM: the importance of oligomerization for conformational persistence and chemical stability of proteins.Biochemistry
, 933–937.PubMedCrossRefGoogle Scholar
Schliebs, W., Thanki, N., Eritja, R., and Wierenga, R. (1996) Activate-site properties of monomeric triosephosphate isomerse (MONOTIM) as deduced from mutational and structural studies.Protein Sci.
, 229–239.PubMedCrossRefGoogle Scholar
Talent, J. M., Zvaigzne, A. I., Agrawal, N., and Gracy, R. W. (1997) Effect of active-site modification on the terminal marking deamidation of triosephosphate isomerase.Arc. Biochem. Biophys
, 27–35.CrossRefGoogle Scholar
Derreumaux, P. and Schlick, T. (1998) The loop opening/closing motion of the enzyme triosephosphate isomerase.Biophys. J.
, 72–81.PubMedCrossRefGoogle Scholar
Auerbach, G., Huber, R., Grattinger, M., Zaiss, K., Schurig, H., Jaenicke, R., and Jacob, U. (1997) Closed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability.Structure
, 1475–1483.PubMedCrossRefGoogle Scholar
Bernstein, B. E., Michels, P. A. M., and Hol, W. G. J. (1997) Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation.Nature
, 275–278.PubMedCrossRefGoogle Scholar
Cheung, C. W. and Mas, M. T. (1996) Substrate-induced conformational-changes in yeast 3-phosphoglycerate kinase monitored by fluorescence of single tryptophan probes.Protein Sci.
, 1144–1149.PubMedGoogle Scholar
Ritcovonsovici, M., Mouratou, B., Minard, P., Desmadril, M., Yon, J. M., Andrieux, M., Leroy, E., and Guittet, E. (1995) Role of the C-terminal helix in the folding and stability of yeast phosphoglycerate kinase.Biochemistry
, 833–841.CrossRefGoogle Scholar
Adams, B., Fowler, R., Hudson, M., and Pain, R. H. (1996) The role of the C-terminal lysine in the hinge bending mechanism of yeast phosphoglycerate kinase.Febs Lett.
, 101–104.PubMedCrossRefGoogle Scholar
Pecorari, F., Minard, P., Desmadril, M., and Yon, J. M. (1993) Structure and functional complementation of engineered fragments from yeast phosphoglycerate kinase.Protein Eng.
, 313–325.PubMedCrossRefGoogle Scholar
Pecorari, F., Guilbert, C., Minard, P., Desmadril, M., and Yon, J. M. (1996) Folding and functional complementation of engineered fragments from yeast phosphoglycerate kinase.Biochemistry
, 3465–3476PubMedCrossRefGoogle Scholar
Parker, M. J., Spencer, J., Jackson, G. S., Burston, S. G., Hosszu, L. L. P., Craven, C. J., Waltho, J. P., and Clarke, A. R. (1996) Domain behavior during the folding of a thermostable phosphoglycerate kinase.Biochemistry
, 15740–15752.PubMedCrossRefGoogle Scholar
Sherman, M. A., Beechem, J. M., and Mas, M. T. (1995). Probing intradomain and interdomain conformational-changes during equilibrium unfolding of phosphoglycerate inase-fluorescence and circuilar-dichroism study of tryptophan mutants.Biochemistry
, 13934–13942.PubMedCrossRefGoogle Scholar
Lillo, M. P., Szpikowska, B. K., Mas, M. T., Sutin, J. D., Beechem, J. M. (1997) Real-time measurement of multiple intramolecular distances during protein folding reactions: a multisite stopped-flow fluorescence energytransfer study of yeast phosphoglycerate kinase.Biochemistry
, 11273–11281.PubMedCrossRefGoogle Scholar
McPhillips, T. M., Hsu, B. T., Sherman, M. A., Mas, M. T., and Rees, D. C. (1996) Structure of the R65Q mutant of yeast 3-phosphoglycerate kinase complexed with Mg-AMP-PNP and 3-phospho-D-glyceratefe.Biochemistry
, 4118–4127PubMedCrossRefGoogle Scholar
Schulz, G. E., Muller, C. W., and Diederichs, K. (1990) Induced-fit movements in adenylate kinase.J. Mol. Biol.
, 627–630.PubMedCrossRefGoogle Scholar
Schlauderer, G. J., Proba, K., and Schulz, G. E. (1996) Structure of A Mutant Adenylate kinase ligated with an ATP-analog showing domain closure over ATP.J. Mol. Biol.
, 223–227.PubMedCrossRefGoogle Scholar
Muller, C. W, Schlauderer, G. J., Reinstein, J., and Schulz, G. E. (1996) Adenylate kinase motion during catalysis: An energetic counter-weight balancing substrate-binding.Structure
, 147–156.PubMedCrossRefGoogle Scholar
Zhang, H. J., Sheng, X. R., Pan, X. M., and Zhou, J. M. (1997) Activation of adenylate kinase by denaturants is due to the increasing conformational flexibility at its active sites.Bioch. Biophys. Res. Comm.
, 382–386.CrossRefGoogle Scholar
Ikura, M., Clore, G. M., Gronenborn, A. M., Zhu, G., Klee, C. B., and Bax, A. (1992) Solution structure of a calmodulin-target peptide complex by multidimensional NMR.Science
, 632–638.PubMedCrossRefGoogle Scholar
Bennett, M. J., Schlunegger, M. P., and Eisenberg, D. (1995) 3D domain swapping: A mechanism for oligomer assembly.Protein Sci.
, 2455–2468.PubMedCrossRefGoogle Scholar
Baker, P. J., Britton, K. L., Engel, P. C., Farrants, G. W., Lilley, K. S., Rice, D. W., and Stillman, T. J. (1992) Subunit assembly and active site location in the structure of glutamate dehydrogenase.Proteins
, 75–86.PubMedCrossRefGoogle Scholar
Kumar, S., Tsai, C. J., Ma, B., and Nussinov, R. (1999) Contribution of salt bridges toward protein thermostability.J. Biomolecular Struct. & Dynamics
. In press.Google Scholar
Braig, K., Otwinowski, Z., Hegde, R., Boisvert, D. C., Joachimiak, A., Horwich, A. L., and Sigler, P. B. (1994) The crystal structure of the bacterial chaperonin GroEL at 2.8Å.Nature
, 578–586.PubMedCrossRefGoogle Scholar
Stevens, R. C., Gouaux, J. E., and Lipscomb, W. N. (1990) Structural consequences of effector binding to the T state of aspartate carbamoyltransferase: crystal structures of the unligated and ATP- and CTP-complexed enzymes at 2.6Å resolution.Biochemistry
, 7691–7701.PubMedCrossRefGoogle Scholar
Sakash, J. B. and Kantrowitz, E. R. (1998) The N-terminus of the regulatory chain ofEscherichia coli
aspartate transcarbamoylase is important for both nucleotide binding and heterotropic effects.Biochemistry
, 281–288.CrossRefGoogle Scholar
Lewis, M., Chang, G., Horton, N. C., Kercher, M. A., Pace, H. C., Schumacher, M. A., Brennan, R. G., and Lu, P. (1996) Crystal structure of the lactose operon repressor and its complexes with the DNA and inducer.Science
, 1247–1254.PubMedCrossRefGoogle Scholar
Milburn, M. V., Prive, G. G., Milligan, D. L., Scott, W. G., Yeh, J., Jancarik, J., Koshland, D. E., and Kim, S.-H. (1991) Three dimensional structures of the ligand-binding domain of the bacterial aspartate receptor with and without a ligand.Science
, 1342–1347.PubMedCrossRefGoogle Scholar
Newman, M., Strzelecka, T., Dorner, L. F., Schildkraut, I., and Aggarwal, A. K. (1995) Structure ofBam
HI endonuclease bound to DNA: partial folding and unfolding on DNA binding.Science
, 656–663.PubMedCrossRefGoogle Scholar
Standfield, R. L., Takimoto-Kanimura, M., Rini, J. M., Profy, A. T., and Wilson, I. A. (1993) Major antigen-induced domain rearrangements in an antibody.Structure
, 83–93.CrossRefGoogle Scholar
Herron, J. N., He, X. M., Ballard, D. W., Blier, P. R., Pace, P. E., Bothwell, A. L., Voss, E. Jr., and Edmundson, A. B. (1991) An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex.Proteins
, 159–175.PubMedCrossRefGoogle Scholar
Rini, J. M., Stanfield, R. L., Stura, E. A., Salinas, P. A., Profy, A. T., and Wilson, I. A. (1993) Crystal structure of a human immunodeficiency virus type 1 neutralizing antibody 50.1, in complex with its V3 loop peptide antigen.Proc. Natl. Acad. Sci. USA
, 6325–6329.PubMedCrossRefGoogle Scholar
Marmorstein, R. and Harrison, S. C. (1994) Crystal structure of a PPR1-DNA complex: DNA recognition by proteins containing a Zn2
binuclear cluster.Gen. Dev.
, 2504–2412.CrossRefGoogle Scholar
Marques, O. and Sanejouand, Y. H. (1995) Hinge-bending motion in citrate synthase from normal-mode calculations.Proteins
, 557–560.PubMedCrossRefGoogle Scholar
Ikura, T. and Go, N. (1993) Normal-mode analysis of mouse epidermal growth-factor: characterization of the harmonic motion.Proteins
, 423–436.PubMedCrossRefGoogle Scholar
Guilbert, C., Pecorari, F., Perahia, D., and Mouawad, L. (1996) Low-frequency motions in phosphoglycerate kinase: a normal mode analysis.J. Chem. Phys.
, 327–336.CrossRefGoogle Scholar
Hayward, S., Kitao, A., and Berendsen, H. J. C. (1997) Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozymeProteins
, 425–437.PubMedCrossRefGoogle Scholar
deGroot, B. L., Hayward, S., vanAalten, D. M. F., Amadei, A., and Berendsen, H. J. C. (1998) Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data.Proteins
, 116–127.CrossRefGoogle Scholar
vanAalten, D. M. F., Grotewold, E., and Joshua Tor, L. (1998) Essential dynamics from NMR clusters: dynamic properties of the Myb DNA-binding domain and a hinge-bending enhancing variant.Methods-A Companion To Methods In Enzymology
, 318–328.CrossRefGoogle Scholar
Alexov, E. and Atanasov, B. (1995) Selective absorption of radio-frequency energy due to collective motion of charged domain: case of lysozyme crystal.J. Biomol. Struct. Dyn.
, 219–228.PubMedGoogle Scholar
Miura, N., Hayashi, Y., and Mashimo, S. (1996) Hinge-bending deformation of enzyme observed by microwave dielectric measurement.Biopolymer
, 183–187.CrossRefGoogle Scholar
Chandra, N. R., Muirhead, H., Holbrook, J. J., Bernstein, B. E., Hl, W. G. J., and Sessions, R. B. (1998) A general method of domain closure is applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme.Proteins
, 372–380.PubMedCrossRefGoogle Scholar
Hayward, S. and Berendsen, H. J. C. (1998) Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme.Proteins
, 144–154.PubMedCrossRefGoogle Scholar
Wriggers, W. and Schulten, K. (1997) Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates.Proteins
, 1–14.PubMedCrossRefGoogle Scholar
Verbitsky, G., Nussinov, R., and Wolfson, H. (1999) Structural comparison allowing hinge bending, swiveling motions.Proteins
, 232–254.PubMedCrossRefGoogle Scholar
Bahar, I., Erman, B., Haliloglu, T., and Jernigan, R. L. (1997) Identification of cooperative motions and correlated structural elements in coarse-grained proteins: application to T4 lysozyme.Biochemistry
, 13512–13523.PubMedCrossRefGoogle Scholar