Protein Conformational Disorder and Enzyme Catalysis

Chapter
Part of the Topics in Current Chemistry book series (TOPCURRCHEM, volume 337)

Abstract

Though lacking a well-defined three-dimensional structure, intrinsically unstructured proteins are ubiquitous in nature. These molecules play crucial roles in many cellular processes, especially signaling and regulation. Surprisingly, even enzyme catalysis can tolerate substantial disorder. This observation contravenes conventional wisdom but is relevant to an understanding of how protein dynamics modulates enzyme function. This chapter reviews properties and characteristics of disordered proteins, emphasizing examples of enzymes that lack defined structures, and considers implications of structural disorder for catalytic efficiency and evolution.

Graphical Abstract

Keywords

Dynamics Evolution Intrinsic disorder Protein function Protein structure 

References

  1. 1.
    Uversky VN (2011) Intrinsically disordered proteins from A to Z. Int J Biochem Cell Biol 43:1090–1103Google Scholar
  2. 2.
    Fisher CK, Stultz CM (2011) Constructing ensembles for intrinsically disordered proteins. Curr Opin Struct Biol 21:426–431Google Scholar
  3. 3.
    Tompa P, Dosztanyi Z, Simon I (2006) Prevalent structural disorder in E. coli and S. cerevisiae proteomes. J Proteome Res 5:1996–2000Google Scholar
  4. 4.
    He B, Wang K, Liu Y, Xue B, Uversky VN, Dunker AK (2009) Predicting intrinsic disorder in proteins: an overview. Cell Res 19:929–949Google Scholar
  5. 5.
    Tompa P (2012) Intrinsically disordered proteins: a 10-year recap. Trends Biochem Sci. 37: 509–516Google Scholar
  6. 6.
    Dunker AK, Silman I, Uversky VN, Sussman JL (2008) Function and structure of inherently disordered proteins. Curr Opin Struct Biol 18:756–764Google Scholar
  7. 7.
    Uversky VN, Oldfield CJ, Dunker AK (2005) Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling. J Mol Recognit 18:343–384Google Scholar
  8. 8.
    Henzler-Wildman K, Kern D (2007) Dynamic personalities of proteins. Nature 450:964–972Google Scholar
  9. 9.
    Karplus M, McCammon JA (1981) The internal dynamics of globular proteins. CRC Crit Rev Biochem 9:293–349Google Scholar
  10. 10.
    Henzler-Wildman KA, Lei M, Thai V, Kerns SJ, Karplus M, Kern D (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450:913–916Google Scholar
  11. 11.
    Dunker AK, Oldfield CJ, Meng J, Romero P, Yang JY, Chen JW, Vacic V, Obradovic Z, Uversky VN (2008) The unfoldomics decade: an update on intrinsically disordered proteins. BMC Genomics 9(Suppl 2):S1Google Scholar
  12. 12.
    Romero P, Obradovic Z, Li XH, Garner EC, Brown CJ, Dunker AK (2001) Sequence complexity of disordered protein. Proteins 42:38–48Google Scholar
  13. 13.
    Fitzkee NC, García-Moreno EB (2008) Electrostatic effects in unfolded staphylococcal nuclease. Protein Sci 17:216–227Google Scholar
  14. 14.
    Mao AH, Crick SL, Vitalis A, Chicoine CL, Pappu RV (2010) Net charge per residue modulates conformational ensembles of intrinsically disordered proteins. Proc Natl Acad Sci USA 107:8183–8188Google Scholar
  15. 15.
    Müller-Späth S, Soranno A, Hirschfeld V, Hofmann H, Rüegger S, Reymond L, Nettels D, Schuler B (2010) Charge interactions can dominate the dimensions of intrinsically disordered proteins. Proc Natl Acad Sci USA 107:14609–14614Google Scholar
  16. 16.
    Uversky VN, Gillespie JR, Fink AL (2000) Why are “natively unfolded” proteins unstructured under physiologic conditions? Proteins 41:415–427Google Scholar
  17. 17.
    Zambelli B, Musiani F, Benini S, Ciurli S (2011) Chemistry of Ni2+ in urease: sensing, trafficking, and catalysis. Acc Chem Res 44:520–530Google Scholar
  18. 18.
    Morillas M, Eberl H, Allain FH-T, Glockshuber R, Kuennemann E (2008) Novel enzymatic activity derived from the Semliki Forest virus capsid protein. J Mol Biol 376:721–735Google Scholar
  19. 19.
    Abian O, Vega S, Neira JL, Velazquez-Campoy A (2010) Conformational stability of hepatitis C virus NS3 protease. Biophys J 99:3811–3820Google Scholar
  20. 20.
    Butz M, Neuenschwander M, Kast P, Hilvert D (2011) An N-terminal protein degradation tag enables robust selection of highly active enzymes. Biochemistry 50:8594–8602Google Scholar
  21. 21.
    Cardamone M, Puri NK (1992) Spectrofluorimetric assessment of the surface hydrophobicity of proteins. Biochem J 282(Pt 2):589–593Google Scholar
  22. 22.
    Receveur-Bréchot V, Durand D (2011) How random are intrinsically disordered proteins? A small angle scattering perspective. Curr Protein Peptide Sci 13:55–75Google Scholar
  23. 23.
    Bernadó P, Modig K, Grela P, Svergun DI, Tchorzewski M, Pons M, Akke M (2010) Structure and dynamics of ribosomal protein L12: an ensemble model based on SAXS and NMR relaxation. Biophys J 98:2374–2382Google Scholar
  24. 24.
    Pervushin K, Vamvaca K, Vögeli B, Hilvert D (2007) Structure and dynamics of a molten globular enzyme. Nat Struct Mol Biol 14:1202–1206Google Scholar
  25. 25.
    Mittag T, Forman-Kay JD (2007) Atomic-level characterization of disordered protein ensembles. Curr Opin Struct Biol 17:3–14Google Scholar
  26. 26.
    Bernadó P, Svergun DI (2011) Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering. Mol Biosyst 8:151–167Google Scholar
  27. 27.
    Zambelli B, Stola M, Musiani F, De Vriendt K, Samyn B, Devreese B, Van Beeumen J, Turano P, Dikiy A, Bryant DA et al (2005) UreG, a chaperone in the urease assembly process, is an intrinsically unstructured GTPase that specifically binds Zn2+. J Biol Chem 280: 4684–4695Google Scholar
  28. 28.
    Zotter Á, Oláh J, Hlavanda E, Bodor A, Perczel A, Szigeti K, Fidy J, Ovádi J (2011) Zn2+-induced rearrangement of the disordered TPPP/p25 affects its microtubule assembly and GTPase activity. Biochemistry 50:9568–9578Google Scholar
  29. 29.
    Fitzkee NC, Masse JE, Shen Y, Davies DR, Bax A (2010) Solution conformation and dynamics of the HIV-1 integrase core domain. J Biol Chem 285:18072–18084Google Scholar
  30. 30.
    Fitzkee NC, Torchia DA, Bax A (2011) Measuring rapid hydrogen exchange in the homodimeric 36 kDa HIV-1 integrase catalytic core domain. Protein Sci 20:500–512Google Scholar
  31. 31.
    Galea CA, Wang Y, Sivakolundu SG, Kriwacki RW (2008) Regulation of cell division by intrinsically unstructured proteins: intrinsic flexibility, modularity, and signaling conduits. Biochemistry 47:7598–7609Google Scholar
  32. 32.
    Wright PE, Dyson HJ (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 293:321–331Google Scholar
  33. 33.
    Tantos A, Han KH, Tompa P (2012) Intrinsic disorder in cell signaling and gene transcription. Mol Cell Endocrinol 348:457–465Google Scholar
  34. 34.
    Uversky VN, Oldfield CJ, Dunker AK (2008) Intrinsically disordered proteins in human diseases: introducing the D2 concept. Annu Rev Biophys 37:215–246Google Scholar
  35. 35.
    Chakrabortee S, Meersman F, Kaminski Schierle GS, Bertoncini CW, McGee B, Kaminski CF, Tunnacliffe A (2010) Catalytic and chaperone-like functions in an intrinsically disordered protein associated with desiccation tolerance. Proc Natl Acad Sci USA 107: 16084–16089Google Scholar
  36. 36.
    Reichmann D, Xu Y, Cremers CM, Ilbert M, Mittelman R, Fitzgerald MC, Jakob U (2012) Order out of disorder: working cycle of an intrinsically unfolded chaperone. Cell 148: 947–957Google Scholar
  37. 37.
    Tompa P, Csermely P (2004) The role of structural disorder in the function of RNA and protein chaperones. FASEB J 18:1169–1175Google Scholar
  38. 38.
    Wright PE, Dyson HJ (2009) Linking folding and binding. Curr Opin Struct Biol 19:31–38Google Scholar
  39. 39.
    Fuxreiter M, Simon I, Friedrich P, Tompa P (2004) Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. J Mol Biol 338:1015–1026Google Scholar
  40. 40.
    Tsai CD, Ma B, Kumar S, Wolfson H, Nussinov R (2001) Protein folding: binding of conformationally fluctuating building blocks via population selection. Crit Rev Biochem Mol Biol 36:399–433Google Scholar
  41. 41.
    Kiefhaber T, Bachmann A, Jensen KS (2012) Dynamics and mechanisms of coupled protein folding and binding reactions. Curr Opin Struct Biol 22:21–29Google Scholar
  42. 42.
    Receveur-Brechot V, Bourhis JM, Uversky VN, Canard B, Longhi S (2006) Assessing protein disorder and induced folding. Proteins 62:24–45Google Scholar
  43. 43.
    Borriello A, Cucciolla V, Oliva A, Zappia V, Della Ragione F (2007) p27Kip1 metabolism: a fascinating labyrinth. Cell Cycle 6:1053–1061Google Scholar
  44. 44.
    Lowry DF, Hausrath AC, Daughdrill GW (2008) A robust approach for analyzing a heterogeneous structural ensemble. Proteins 73:918–928Google Scholar
  45. 45.
    Sugase K, Dyson HJ, Wright PE (2007) Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447:1021–1025Google Scholar
  46. 46.
    Turjanski AG, Gutkind JS, Best RB, Hummer G (2008) Binding-induced folding of a natively unstructured transcription factor. PLoS Comput Biol 4:e1000060Google Scholar
  47. 47.
    Espinoza-Fonseca LM (2009) Reconciling binding mechanisms of intrinsically disordered proteins. Biochem Biophys Res Commun 382:479–482Google Scholar
  48. 48.
    Oldfield CJ, Meng J, Yang JY, Yang MQ, Uversky VN, Dunker AK (2008) Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics 9(Suppl 1):S1Google Scholar
  49. 49.
    Schreiber G, Keating AE (2011) Protein binding specificity versus promiscuity. Curr Opin Struct Biol 21:50–61Google Scholar
  50. 50.
    Taira N, Yoshida K (2012) Post-translational modifications of p53 tumor suppressor: determinants of its functional targets. Histol Histopathol 27:437–443Google Scholar
  51. 51.
    Vuzman D, Levy Y (2012) Intrinsically disordered regions as affinity tuners in protein-DNA interactions. Mol Biosyst 8:47–57Google Scholar
  52. 52.
    Shoemaker BA, Portman JJ, Wolynes PG (2000) Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. Proc Natl Acad Sci USA 97:8868–8873Google Scholar
  53. 53.
    Huang Y, Liu Z (2009) Kinetic advantage of intrinsically disordered proteins in coupled folding–binding process: a critical assessment of the “fly-casting” mechanism. J Mol Biol 393:1143–1159Google Scholar
  54. 54.
    Fink AL (2005) Natively unfolded proteins. Curr Opin Struct Biol 15:35–41Google Scholar
  55. 55.
    Patil A, Kinoshita K, Nakamura H (2010) Domain distribution and intrinsic disorder in hubs in the human protein–protein interaction network. Protein Sci 19:1461–1468Google Scholar
  56. 56.
    Singh GP, Ganapathi M, Dash D (2007) Role of intrinsic disorder in transient interactions of hub proteins. Proteins 66:761–765Google Scholar
  57. 57.
    Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN (2005) Flexible nets. The roles of intrinsic disorder in protein interaction networks. FEBS J 272:5129–5148Google Scholar
  58. 58.
    Pauling L (1948) Nature of forces between large molecules of biological interest. Nature 161: 707–709Google Scholar
  59. 59.
    Koshland DE (1958) Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci USA 44:98–104Google Scholar
  60. 60.
    Koshland DE (1994) The key-lock theory and the induced fit theory. Angew Chem Int Ed Engl 33:2375–2378Google Scholar
  61. 61.
    Hammes GG, Benkovic SJ, Hammes-Schiffer S (2011) Flexibility, diversity, and cooperativity: pillars of enzyme catalysis. Biochemistry 50:10422–10430Google Scholar
  62. 62.
    Redko Y, Tock MR, Adams CJ, Kaberdin VR, Grasby JA, McDowall KJ (2003) Determination of the catalytic parameters of the N-terminal half of Escherichia coli ribonuclease E and the identification of critical functional groups in RNA substrates. J Biol Chem 278: 44001–44008Google Scholar
  63. 63.
    Zhang RM, Durkin J, Windsor WT, McNemar C, Ramanathan L, Le HV (1997) Probing the substrate specificity of hepatitis C virus NS3 serine protease by using synthetic peptides. J Virol 71:6208–6213Google Scholar
  64. 64.
    Zambelli B, Musiani F, Savini M, Tucker P, Ciurli S (2007) Biochemical studies on Mycobacterium tuberculosis UreG and comparative modeling reveal structural and functional conservation among the bacterial UreG family. Biochemistry 46:3171–3182Google Scholar
  65. 65.
    Kaberdin VR, Miczak A, Jakobsen JS, Lin-Chao S, McDowall KJ, von Gabain A (1998) The endoribonucleolytic N-terminal half of Escherichia coli RNase E is evolutionarily conserved in Synechocystis sp. and other bacteria but not the C-terminal half, which is sufficient for degradosome assembly. Proc Natl Acad Sci USA 95:11637–11642Google Scholar
  66. 66.
    Callaghan AJ, Aurikko JP, Ilag LL, Günter Grossmann J, Chandran V, Kühnel K, Poljak L, Carpousis AJ, Robinson CV, Symmons MF et al (2004) Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E. J Mol Biol 340:965–979Google Scholar
  67. 67.
    Carpousis AJ (2007) The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annu Rev Microbiol 61:71–87Google Scholar
  68. 68.
    Tedbury PR, Harris M (2007) Characterisation of the role of zinc in the hepatitis C virus NS2/3 auto-cleavage and NS3 protease activities. J Mol Biol 366:1652–1660Google Scholar
  69. 69.
    Zambelli B, Cremades N, Neyroz P, Turano P, Uversky VN, Ciurli S (2012) Insights in the (un)structural organization of Bacillus pasteurii UreG, an intrinsically disordered GTPase enzyme. Mol Biosyst 8:220–228Google Scholar
  70. 70.
    Patil A, Kinoshita K, Nakamura H (2010) Hub promiscuity in protein–protein interaction networks. Int J Mol Sci 11:1930–1943Google Scholar
  71. 71.
    Tirián L, Hlavanda E, Oláh J, Horváth I, Orosz F, Szabó B, Kovács J, Szabad J, Ovádi J (2003) TPPP/p25 promotes tubulin assemblies and blocks mitotic spindle formation. Proc Natl Acad Sci USA 100:13976–13981Google Scholar
  72. 72.
    Ovádi J, Orosz F (2009) An unstructured protein with destructive potential: TPPP/p25 in neurodegeneration. Bioessays 31:676–686Google Scholar
  73. 73.
    Hlavanda E, Kovács J, Oláh J, Orosz F, Medzihradszky KF, Ovádi J (2002) Brain-specific p25 protein binds to tubulin and microtubules and induces aberrant microtubule assemblies at substoichiometric concentrations. Biochemistry 41:8657–8664Google Scholar
  74. 74.
    Kovács GG, László L, Kovács J, Jensen PH, Lindersson E, Botond G, Molnár T, Perczel A, Hudecz F, Mezo G et al (2004) Natively unfolded tubulin polymerization promoting protein TPPP/p25 is a common marker of alpha-synucleinopathies. Neurobiol Dis 17:155–162Google Scholar
  75. 75.
    Fink AL, Calciano LJ, Goto Y, Kurotsu T, Palleros DR (1994) Classification of acid denaturation of proteins: intermediates and unfolded states. Biochemistry 33:12504–12511Google Scholar
  76. 76.
    Bemporad F, Gsponer J, Hopearuoho HI, Plakoutsi G, Stati G, Stefani M, Taddei N, Vendruscolo M, Chiti F (2008) Biological function in a non-native partially folded state of a protein. EMBO J 27:1525–1535Google Scholar
  77. 77.
    Punchihewa C, Dai J, Carver M, Yang D (2007) Human topoisomerase I C-terminal domain fragment containing the active site tyrosine is a molten globule: implication for the formation of competent productive complex. J Struct Biol 159:111–121Google Scholar
  78. 78.
    Stewart L, Ireton GC, Champoux JJ (1997) Reconstitution of human topoisomerase I by fragment complementation. J Mol Biol 269:355–372Google Scholar
  79. 79.
    Olsson U, Wolf-Watz M (2010) Overlap between folding and functional energy landscapes for adenylate kinase conformational change. Nat Commun 1:111Google Scholar
  80. 80.
    Kiefhaber T, Schmid FX, Willaert K, Engelborghs Y, Chaffotte A (1992) Structure of a rapidly formed intermediate in ribonuclease T1 folding. Protein Sci 1:1162–1172Google Scholar
  81. 81.
    Ptitsyn OB, Pain RH, Semisotnov GV, Zerovnik E, Razgulyaev OI (1990) Evidence for a molten globule state as a general intermediate in protein folding. FEBS Lett 262:20–24Google Scholar
  82. 82.
    Goldberg ME, Semisotnov GV, Friguet B, Kuwajima K, Ptitsyn OB, Sugai S (1990) An early immunoreactive folding intermediate of the tryptophan synthease beta 2 subunit is a ‘molten globule’. FEBS Lett 263:51–56Google Scholar
  83. 83.
    Creighton TE (1997) How important is the molten globule for correct protein folding? Trends Biochem Sci 22:6–10Google Scholar
  84. 84.
    Hu J, Li D, Su X-D, Jin C, Xia B (2010) Solution structure and conformational heterogeneity of acylphosphatase from Bacillus subtilis. FEBS Lett 584:2852–2856Google Scholar
  85. 85.
    Schmid FX, Blaschek H (1981) A native-like intermediate on the ribonuclease A folding pathway. 2. Comparison of its properties to native ribonuclease A. Eur J Biochem 114: 111–117Google Scholar
  86. 86.
    Protasova NY, Kireeva ML, Murzina NV, Murzin AG, Uversky VN, Gryaznova OI, Gudkov AT (1994) Circularly permuted dihydrofolate-reductase of Escherichia coli has functional activity and a destabilized tertiary structure. Protein Eng 7:1373–1377Google Scholar
  87. 87.
    Smith VF, Matthews CR (2001) Testing the role of chain connectivity on the stability and structure of dihydrofolate reductase from E. coli: fragment complementation and circular permutation reveal stable, alternatively folded forms. Protein Sci 10:116–128Google Scholar
  88. 88.
    Zhang H, Huang S, Feng Y, Guo P, Jing G (2005) Effect of N-terminal deletions on the foldability, stability, and activity of staphylococcal nuclease. Arch Biochem Biophys 441: 123–131Google Scholar
  89. 89.
    Li Y, Jing G (2000) Double point mutant F34W/W140F of staphylococcal nuclease is in a molten globule state but highly competent to fold into a functional conformation. J Biochem 128:739–744Google Scholar
  90. 90.
    Huang S, Yin J, Feng Y, Jing G (2003) Effect of a specific hydrogen bond (N138ND2-Q106O) on conformational integrity, stability, and activity of staphylococcal nuclease. Arch Biochem Biophys 420:87–94Google Scholar
  91. 91.
    Shortle D, Meeker AK (1989) Residual structure in large fragments of staphylococcal nuclease: effects of amino acid substitutions. Biochemistry 28:936–944Google Scholar
  92. 92.
    Alexandrescu AT, Dames SA, Wiltscheck R (1996) A fragment of staphylococcal nuclease with an OB-fold structure shows hydrogen-exchange protection factors in the range reported for “molten globules”. Protein Sci 5:1942–1946Google Scholar
  93. 93.
    Sullivan BJ, Durani V, Magliery TJ (2011) Triosephosphate isomerase by consensus design: dramatic differences in physical properties and activity of related variants. J Mol Biol 413: 195–208Google Scholar
  94. 94.
    MacBeath G, Kast P, Hilvert D (1998) Redesigning enzyme topology by directed evolution. Science 279:1958–1961Google Scholar
  95. 95.
    Schnell JR, Dyson HJ, Wright PE (2004) Structure, dynamics, and catalytic function of dihydrofolate reductase. Annu Rev Biophys Biomol Struct 33:119–140Google Scholar
  96. 96.
    Boehr DD, McElheny D, Dyson HJ, Wright PE (2006) The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313:1638–1642Google Scholar
  97. 97.
    Sawaya MR, Kraut J (1997) Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence. Biochemistry 36: 586–603Google Scholar
  98. 98.
    Iwakura M (1998) In search of circular permuted variants of Escherichia coli dihydrofolate reductase. Biosci Biotechnol Biochem 62:778–781Google Scholar
  99. 99.
    Hu Z, Bowen D, Southerland WM, del Sol A, Pan Y, Nussinov R, Ma B (2007) Ligand binding and circular permutation modify residue interaction network in DHFR. PLoS Comput Biol 3:e117Google Scholar
  100. 100.
    Svensson A-KE, Zitzewitz JA, Matthews CR, Smith VF (2006) The relationship between chain connectivity and domain stability in the equilibrium and kinetic folding mechanisms of dihydrofolate reductase from E. coli. Protein Eng Des Sel 19:175–185Google Scholar
  101. 101.
    Uversky VN, Kutyshenko VP, Protasova NY, Rogov VV, Vassilenko KS, Gudkov AT (1996) Circularly permuted dihydrofolate reductase possesses all the properties of the molten globule state, but can resume functional tertiary structure by interaction with its ligands. Protein Sci 5:1844–1851Google Scholar
  102. 102.
    Flanagan JM, Kataoka M, Shortle D, Engelman DM (1992) Truncated staphylococcal nuclease is compact but disordered. Proc Natl Acad Sci USA 89:748–752Google Scholar
  103. 103.
    Ermácora MR, Ledman DW, Fox RO (1996) Mapping the structure of a non-native state of staphylococcal nuclease. Nat Struct Biol 3:59–66Google Scholar
  104. 104.
    Alexandrescu AT, Jahnke W, Wiltscheck R, Blommers MJ (1996) Accretion of structure in staphylococcal nuclease: an 15N NMR relaxation study. J Mol Biol 260:570–587Google Scholar
  105. 105.
    MacBeath G, Kast P, Hilvert D (1998) A small, thermostable, and monofunctional chorismate mutase from the archaeon Methanococcus jannaschii. Biochemistry 37: 10062–10073Google Scholar
  106. 106.
    Vamvaca K, Vögeli B, Kast P, Pervushin K, Hilvert D (2004) An enzymatic molten globule: efficient coupling of folding and catalysis. Proc Natl Acad Sci USA 101:12860–12864Google Scholar
  107. 107.
    Vamvaca K, Jelesarov I, Hilvert D (2008) Kinetics and thermodynamics of ligand binding to a molten globular enzyme and its native counterpart. J Mol Biol 382:971–977Google Scholar
  108. 108.
    Nagel ZD, Klinman JP (2009) A 21st century revisionist’s view at a turning point in enzymology. Nat Chem Biol 5:543–550Google Scholar
  109. 109.
    Nashine VC, Hammes-Schiffer S, Benkovic SJ (2010) Coupled motions in enzyme catalysis. Curr Opin Chem Biol 14:644–651Google Scholar
  110. 110.
    Bhabha G, Lee J, Ekiert DC, Gam J, Wilson IA, Dyson HJ, Benkovic SJ, Wright PE (2011) A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science 332:234–238Google Scholar
  111. 111.
    Adamczyk AJ, Cao J, Kamerlin SCL, Warshel A (2011) Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions. Proc Natl Acad Sci USA 108:14115–14120Google Scholar
  112. 112.
    Henzler-Wildman KA, Thai V, Lei M, Ott M, Wolf-Watz M, Fenn T, Pozharski E, Wilson MA, Petsko GA, Karplus M et al (2007) Intrinsic motions along an enzymatic reaction trajectory. Nature 450:838–844Google Scholar
  113. 113.
    Warshel A, Sharma PK, Kato M, Xiang Y, Liu H, Olsson MHM (2006) Electrostatic basis for enzyme catalysis. Chem Rev 106:3210–3235Google Scholar
  114. 114.
    Loveridge EJ, Behiry EM, Guo J, Allemann RK (2012) Evidence that a ‘dynamic knockout’ in Escherichia coli dihydrofolate reductase does not affect the chemical step of catalysis. Nat Chem 4:292–297Google Scholar
  115. 115.
    Palmer AG (2004) NMR characterization of the dynamics of biomacromolecules. Chem Rev 104:3623–3640Google Scholar
  116. 116.
    Eisenmesser EZ, Millet O, Labeikovsky W, Korzhnev DM, Wolf-Watz M, Bosco DA, Skalicky JJ, Kay LE, Kern D (2005) Intrinsic dynamics of an enzyme underlies catalysis. Nature 438:117–121Google Scholar
  117. 117.
    Schramm VL (1998) Enzymatic transition states and transition state analog design. Annu Rev Biochem 67:693–720Google Scholar
  118. 118.
    Torbeev VY, Raghuraman H, Hamelberg D, Tonelli M, Westler WM, Perozo E, Kent SB (2011) Protein conformational dynamics in the mechanism of HIV-1 protease catalysis. Proc Natl Acad Sci USA 108:20982–20987Google Scholar
  119. 119.
    Garcia-Viloca M, Gao J, Karplus M, Truhlar DG (2004) How enzymes work: analysis by modern rate theory and computer simulations. Science 303:186–195Google Scholar
  120. 120.
    Pineda JRET, Antoniou D, Schwartz SD (2010) Slow conformational motions that favor sub-picosecond motions important for catalysis. J Phys Chem B 114:15985–15990Google Scholar
  121. 121.
    Pisliakov AV, Cao J, Kamerlin SCL, Warshel A (2009) Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proc Natl Acad Sci USA 106:17359–17364Google Scholar
  122. 122.
    Schramm VL (2011) Enzymatic transition states, transition-state analogs, dynamics, thermodynamics, and lifetimes. Annu Rev Biochem 80:703–732Google Scholar
  123. 123.
    Rajagopalan PT, Benkovic SJ (2002) Preorganization and protein dynamics in enzyme catalysis. Chem Rec 2:24–36Google Scholar
  124. 124.
    Nagel ZD, Klinman JP (2006) Tunneling and dynamics in enzymatic hydride transfer. Chem Rev 106:3095–3118Google Scholar
  125. 125.
    Bar-Even A, Noor E, Savir Y, Liebermeister W, Davidi D, Tawfik DS, Milo R (2011) The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters. Biochemistry 50:4402–4410Google Scholar
  126. 126.
    Wolfenden R, Snider MJ (2001) The depth of chemical time and the power of enzymes as catalysts. Acc Chem Res 34:938–945Google Scholar
  127. 127.
    Vendruscolo M (2010) Enzymatic activity in disordered states of proteins. Curr Opin Chem Biol 14:671–675Google Scholar
  128. 128.
    Roca M, Messer B, Hilvert D, Warshel A (2008) On the relationship between folding and chemical landscapes in enzyme catalysis. Proc Natl Acad Sci USA 105:13877–13882Google Scholar
  129. 129.
    Silva RG, Murkin AS, Schramm VL (2011) Femtosecond dynamics coupled to chemical barrier crossing in a Born–Oppenheimer enzyme. Proc Natl Acad Sci USA 108:18661–18665Google Scholar
  130. 130.
    Kipp DR, Silva RG, Schramm VL (2011) Mass-dependent bond vibrational dynamics influence catalysis by HIV-1 protease. J Am Chem Soc 133:19358–19361Google Scholar
  131. 131.
    Loveridge EJ, Tey L-H, Behiry EM, Dawson WM, Evans RM, Whittaker SB-M, Günther UL, Williams C, Crump MP, Allemann RK (2011) The role of large-scale motions in catalysis by dihydrofolate reductase. J Am Chem Soc 133:20561–20570Google Scholar
  132. 132.
    Doshi U, McGowan LC, Ladani ST, Hamelberg D (2012) Resolving the complex role of enzyme conformational dynamics in catalytic function. Proc Natl Acad Sci USA 109(15): 5699–5704Google Scholar
  133. 133.
    Tokuriki N, Tawfik DS (2009) Protein dynamism and evolvability. Science 324:203–207Google Scholar
  134. 134.
    James LC, Tawfik DS (2003) Conformational diversity and protein evolution – a 60-year-old hypothesis revisited. Trends Biochem Sci 28:361–368Google Scholar
  135. 135.
    Zimmermann J, Oakman EL, Thorpe IF, Shi X, Abbyad P, Brooks CL 3rd, Boxer SG, Romesberg FE (2006) Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics. Proc Natl Acad Sci USA 103:13722–13727Google Scholar
  136. 136.
    Khersonsky O, Tawfik DS (2010) Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu Rev Biochem 79:471–505Google Scholar
  137. 137.
    Hou L, Honaker MT, Shireman LM, Balogh LM, Roberts AG, Ng KC, Nath A, Atkins WM (2007) Functional promiscuity correlates with conformational heterogeneity in A-class glutathione S-transferases. J Biol Chem 282:23264–23274Google Scholar
  138. 138.
    O'Brien PJ, Herschlag D (1999) Catalytic promiscuity and the evolution of new enzymatic activities. Chem Biol 6:R91–R105Google Scholar
  139. 139.
    Jimenez R, Salazar G, Yin J, Joo T, Romesberg FE (2004) Protein dynamics and the immunological evolution of molecular recognition. Proc Natl Acad Sci USA 101:3803–3808Google Scholar
  140. 140.
    James LC, Tawfik DS (2009) The specificity of cross-reactivity: promiscuous antibody binding involves specific hydrogen bonds rather than nonspecific hydrophobic stickiness. Protein Sci 12:2183–2193Google Scholar
  141. 141.
    Lin Y-S, Hsu W-L, Hwang J-K, Li W-H (2007) Proportion of solvent-exposed amino acids in a protein and rate of protein evolution. Mol Biol Evol 24:1005–1011Google Scholar
  142. 142.
    Jernigan RL, Kloczkowski A (2007) Packing regularities in biological structures relate to their dynamics. Methods Mol Biol 350:251–276Google Scholar
  143. 143.
    Brown CJ, Takayama S, Campen AM, Vise P, Marshall TW, Oldfield CJ, Williams CJ, Dunker AK (2002) Evolutionary rate heterogeneity in proteins with long disordered regions. J Mol Evol 55:104–110Google Scholar
  144. 144.
    Woycechowsky KJ, Choutko A, Vamvaca K, Hilvert D (2008) Relative tolerance of an enzymatic molten globule and its thermostable counterpart to point mutation. Biochemistry 47:13489–13496Google Scholar
  145. 145.
    Gould SM, Tawfik DS (2005) Directed evolution of the promiscuous esterase activity of carbonic anhydrase II. Biochemistry 44:5444–5452Google Scholar
  146. 146.
    Umeno D, Tobias AV, Arnold FH (2005) Diversifying carotenoid biosynthetic pathways by directed evolution. Microbiol Mol Biol Rev 69:51–78Google Scholar
  147. 147.
    Brustad EM, Arnold FH (2011) Optimizing non-natural protein function with directed evolution. Curr Opin Chem Biol 15:201–210Google Scholar
  148. 148.
    Williams GJ, Zhang C, Thorson JS (2007) Expanding the promiscuity of a natural-product glycosyltransferase by directed evolution. Nat Chem Biol 3:657–662Google Scholar
  149. 149.
    Jourden MJ, Clarke CN, Palmer AK, Barth EJ, Prada RC, Hale RN, Fraga D, Snider MJ, Edmiston PL (2007) Changing the substrate specificity of creatine kinase from creatine to glycocyamine: evidence for a highly evolved active site. Biochim Biophys Acta 1774: 1519–1527Google Scholar
  150. 150.
    Chen ZL, Katzenellenbogen BS, Katzenellenbogen JA, Zhao HM (2004) Directed evolution of human estrogen receptor variants with significantly enhanced androgen specificity and affinity. J Biol Chem 279:33855–33864Google Scholar
  151. 151.
    Joerger AC, Mayer S, Fersht AR (2003) Mimicking natural evolution in vitro: an N-acetylneuraminate lyase mutant with an increased dihydrodipicolinate synthase activity. Proc Natl Acad Sci USA 100:5694–5699Google Scholar
  152. 152.
    Gaille C, Kast P, Haas D (2002) Salicylate biosynthesis in Pseudomonas aeruginosa. Purification and characterization of PchB, a novel bifunctional enzyme displaying isochorismate pyruvate-lyase and chorismate mutase activities. J Biol Chem 277:21768–21775Google Scholar
  153. 153.
    DeGrado WF (1993) Peptide engineering. Catalytic molten globules. Nature 365:488–489Google Scholar
  154. 154.
    Guarnera E, Pellarin R, Caflisch A (2009) How does a simplified-sequence protein fold? Biophys J 97:1737–1746Google Scholar
  155. 155.
    Suskiewicz MJ, Sussman JL, Silman I, Shaul Y (2011) Context-dependent resistance to proteolysis of intrinsically disordered proteins. Protein Sci 20:1285–1297Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Laboratory of Organic ChemistryETH ZürichZürichSwitzerland

Personalised recommendations