Skip to main content
SpringerLink
Log in

Multiple Intermediates, Diverse Conformations, and Cooperative Conformational Changes Underlie the Catalytic Hydride Transfer Reaction of Dihydrofolate Reductase

  • Chapter
  • First Online:
Dynamics in Enzyme Catalysis

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

Abstract

It has become increasingly clear that protein motions play an essential role in enzyme catalysis. However, exactly how these motions are related to an enzyme’s chemical step is still intensely debated. This chapter examines the possible role of protein motions that display a hierarchy of timescales in enzyme catalysis. The linkage between protein motions and catalysis is investigated in the context of a model enzyme, E. coli dihydrofolate reductase (DHFR), that catalyzes the hydride transfer reaction in the conversion of dihydrofolate to tetrahydrofolate. The results of extensive computer simulations probing the protein motions that are manifest during different steps along the turnover cycle of DHFR are summarized. Evidence is presented that the protein motions modulate the catalytic efficacy of DHFR by generating a conformational ensemble conducive to the hydride transfer. The alteration of the equilibrium conformational ensemble rather than any protein dynamical effects is found to be sufficient to explain the rate-diminishing effects of mutation on the kinetics of the enzyme. These data support the view that the protein motions facilitate catalysis by establishing reaction competent conformations of the enzyme, but they do not directly couple to the chemical reaction itself. These findings have broad implications for our understanding of enzyme mechanisms and the design of novel protein catalysts.

Graphical Abstract

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Fersht A (1985) Enzyme structure and mechanism. W. H. Freeman, San Francisco

    Google Scholar 

  2. Jencks WP (1987) Catalysis in chemistry and enzymology. Dover Publications, Mineola, New York

    Google Scholar 

  3. Liang JF, Li YT, Yang VC (2000) J Pharm Sci 89:979

    Article  CAS  Google Scholar 

  4. Pollard DJ, Woodley JM (2007) Trends Biotechnol 25:66

    Article  CAS  Google Scholar 

  5. Benkovic SJ, Hammes-Schiffer S (2003) Science 301:1196

    Article  CAS  Google Scholar 

  6. Garcia-Viloca M, Gao J, Karplus M, Truhlar DG (2004) Science 303:186

    Article  CAS  Google Scholar 

  7. O'Brien PJ, Hollfelder F (2010) Curr Opin Chem Biol 14:634

    Article  Google Scholar 

  8. Nagel ZD, Klinman JP (2009) Nat Chem Biol 5:543

    Article  CAS  Google Scholar 

  9. Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D (2008) Nature 453:190

    Article  Google Scholar 

  10. Frushicheva MP, Cao J, Chu ZT, Warshel A (2010) Proc Natl Acad Sci USA 107:16869

    Article  CAS  Google Scholar 

  11. Koshland DE (1994) Angew Chem Int Ed Engl 33:2375

    Article  Google Scholar 

  12. Frauenfelder H, Sligar SG, Wolynes PG (1991) Science 254:1598

    Article  CAS  Google Scholar 

  13. Gunasekaran K, Ma B, Nussinov R (2004) Proteins 57:433

    Article  CAS  Google Scholar 

  14. Karplus M, Kuryian J (2005) Proc Natl Acad Sci USA 102:6679

    Article  CAS  Google Scholar 

  15. Warshel A (1989) Computer modeling of chemical reactions in enzymes and solution. Wiley, New York

    Google Scholar 

  16. Arora K, Brooks CL III (2011) In: Frank J (ed) Molecular machines in biology. Cambridge University Press, Cambridge, p 59

    Google Scholar 

  17. Karplus M, McCammon JA (2002) Nat Struct Biol 9:788

    Article  CAS  Google Scholar 

  18. Schlick T, Collepardo-Guevara R, Halvorsen LA, Jung S, Xiao X (2011) Q Rev Biophys 44:191

    Article  CAS  Google Scholar 

  19. Arora K, Brooks CL III (2007) Proc Natl Acad Sci USA 104:18496

    Article  CAS  Google Scholar 

  20. Radhakrishnan R, Schlick T (2004) Proc Natl Acad Sci USA 101:5970

    Article  CAS  Google Scholar 

  21. Thorpe IF, Brooks CL III (2005) J Am Chem Soc 127:12997

    Article  CAS  Google Scholar 

  22. Thorpe IF, Brooks CL III (2004) Proteins Struct Funct Bioinf 57:444

    Article  CAS  Google Scholar 

  23. Thorpe IF, Brooks CL III (2003) J Phys Chem B 107:14042

    Article  CAS  Google Scholar 

  24. Rod TH, Radkiewicz JL, Brooks CL III (2003) Proc Natl Acad Sci USA 100:6980

    Article  CAS  Google Scholar 

  25. Radkiewicz JL, Brooks CL III (2000) J Am Chem Soc 122:225

    Article  CAS  Google Scholar 

  26. Khavrutskii IV, Price DJ, Lee J, Brooks CL III (2007) Protein Sci 16:1087

    Article  CAS  Google Scholar 

  27. Arora K, Brooks CL III (2009) J Am Chem Soc 131:5642

    Article  CAS  Google Scholar 

  28. Rod TH, Brooks CL III (2003) J Am Chem Soc 125:8718

    Article  CAS  Google Scholar 

  29. Hammes GG, Benkovic SJ, Hammes-Schiffer S (2011) Biochemistry 50:10422

    Article  CAS  Google Scholar 

  30. Nagel ZD, Klinman JP (2010) Chem Rev 110:PR41

    Article  Google Scholar 

  31. Blakely RL (1984) In: Blakely RL, Benkovic SJ (eds), Folate and Pteridines, vol 3. Wiley, New York, p 191

    Google Scholar 

  32. Agarwal PK, Billeter SR, Rajagopalan PTR, Benkovic SJ, Hammes-Schiffer S (2002) Proc Natl Acad Sci USA 99:2794

    Article  CAS  Google Scholar 

  33. Chen J, Dima RI, Thirumalai D (2007) J Mol Biol 374:250

    Article  CAS  Google Scholar 

  34. Adamczyk AJ, Cao J, Kamerlin SCL, Warshel A (2011) Proc Natl Acad Sci USA 108:14115

    Article  CAS  Google Scholar 

  35. Liu H, Warshel A (2007) Biochemistry 46:6011

    Article  Google Scholar 

  36. Fierke CA, Johnson KA, Benkovic SJ (1987) Biochemistry 26:4085

    Article  CAS  Google Scholar 

  37. Cannon WR, Singleton SF, Benkovic SJ (1996) Nat Struct Biol 3:821

    Article  CAS  Google Scholar 

  38. Epstein DM, Benkovic SJ, Wright PE (1995) Biochemistry 34:11037

    Article  CAS  Google Scholar 

  39. Miller GP, Benkovic SJ (1998) Biochemistry 37:6327

    Article  CAS  Google Scholar 

  40. Miller GP, Benkovic SJ (1998) Biochemistry 37:6336

    Article  CAS  Google Scholar 

  41. Miller GP, Wahnon DC, Benkovic SJ (2001) Biochemistry 40:867

    Article  CAS  Google Scholar 

  42. Rajagopalan PTR, Lutz S, Benkovic SJ (2002) Biochemistry 41:12618

    Article  CAS  Google Scholar 

  43. McElheny D, Schnell JR, Lansing JC, Dyson HJ, Wright PE (2005) Proc Natl Acad Sci USA 102:5032

    Article  CAS  Google Scholar 

  44. Schnell JR, Dyson HJ, Wright PE (2004) Biochemistry 43:374

    Article  CAS  Google Scholar 

  45. Schnell JR, Dyson HJ, Wright PE (2004) Annu Rev Biophys Biomol Struct 33:119

    Article  CAS  Google Scholar 

  46. Osborne MJ, Schnell J, Benkovic SJ, Dyson HJ, Wright PE (2001) Biochemistry 40:9846

    Article  CAS  Google Scholar 

  47. Boehr DD, McElheny D, Dyson HJ, Wright PE (2010) Proc Natl Acad Sci USA 107:1373

    Article  CAS  Google Scholar 

  48. Boehr DD, Dyson HJ, Wright PE (2008) Biochemistry 47:9227

    Article  CAS  Google Scholar 

  49. Boehr DD, McElheny D, Dyson HJ, Wright PE (2006) Science 313:1638

    Article  CAS  Google Scholar 

  50. Venkitakrishnan RP, Zaborowski E, McElheny D, Benkovic SJ, Dyson HJ, Wright PE (2004) Biochemistry 43:16046

    Article  CAS  Google Scholar 

  51. Bhabha G, Lee J, Ekiert DC, Gam J, Wilson IA, Dyson HJ, Benkovic SJ, Wright PE (2011) Science 332:234

    Article  CAS  Google Scholar 

  52. Oyeyemi OA, Sours KM, Lee T, Kohen A, Resing KA, Ahn NG, Klinman JP (2011) Biochemistry 50:8251

    Article  CAS  Google Scholar 

  53. Nagel ZD, Dong M, Bahnson BJ, Klinman JP (2011) Proc Natl Acad Sci USA 108:10520

    Article  CAS  Google Scholar 

  54. Oyeyemi OA, Sours KM, Lee T, Resing KA, Ahn NG, Klinman JP (2010) Proc Natl Acad Sci USA 107:10074

    Article  CAS  Google Scholar 

  55. Sawaya MR, Kraut J (1997) Biochemistry 36:586

    Article  CAS  Google Scholar 

  56. Benkovic SJ, Fierke CA, Naylor AM (1988) Science 239:1105

    Article  CAS  Google Scholar 

  57. Tzeng SR, Kalodimos CG (2012) Nature 488:236

    Article  CAS  Google Scholar 

  58. Frederick KK, Marlow MS, Valentine KG, Wand AJ (2007) Nature 448:325

    Article  CAS  Google Scholar 

  59. Cameron CE, Benkovic SJ (1997) Biochemistry 36:15792

    Article  CAS  Google Scholar 

  60. Warshel A, Levitt M (1976) J Mol Biol 103:227

    Article  CAS  Google Scholar 

  61. Gao JL, Truhlar DG (2002) Annu Rev Phys Chem 53:467

    Article  CAS  Google Scholar 

  62. Frauenfelder H, Parak F, Young RD (1988) Annu Rev Biophys Biophys Chem 17:451

    Article  CAS  Google Scholar 

  63. Zhang Y, Kua J, McCammon JA (2003) J Phys Chem B 107:4459

    Article  CAS  Google Scholar 

  64. Lu HP, Xun L, Xie XS (1998) Science 282:1877

    Article  CAS  Google Scholar 

  65. Zhang Z, Rajagopalan PTR, Selzer T, Benkovic SJ, Hammes GG (2004) Proc Natl Acad Sci USA 101:2764

    Article  CAS  Google Scholar 

  66. Tobias DJ, Brooks CL III (1987) Chem Phys Lett 142:472

    Article  CAS  Google Scholar 

  67. Brooks CL III, Karplus M, Pettitt BM (1988) Proteins: a theoretical perspective of dynamics, structure, and thermodynamics. Wiley, New York

    Google Scholar 

  68. Agarwal PK, Billeter SR, Hammes-Schiffer S (2002) J Phys Chem B 106:3283

    Article  CAS  Google Scholar 

  69. Knapp MJ, Klinman JP (2002) Eur J Biochem 269:3113

    Article  CAS  Google Scholar 

  70. Antoniou D, Caratzoulas S, Kalyanaraman C, Mincer JS, Schwartz SD (2002) Eur J Biochem 269:3103

    Article  CAS  Google Scholar 

  71. Loveridge EJ, Behiry EM, Guo J, Allemann RK (2012) Nat Chem 4:292

    Article  CAS  Google Scholar 

  72. Watney JB, Agarwal PK, Hammes-Schiffer S (2003) J Am Chem Soc 125:3745

    Article  CAS  Google Scholar 

  73. Morrison JF, Stone SR (1988) Biochemistry 27:5499

    Article  CAS  Google Scholar 

  74. Beard WA, Appleman JR, Delcamp TJ, Freisheim JH (1989) J Biol Chem 264:9391

    CAS  Google Scholar 

  75. Ansari A, Jones C, Henry E, Hofrichter J, Eaton W (1992) Science 256:1796

    Article  CAS  Google Scholar 

  76. Hanggi P, Talkner P, Borkovec M (1990) Rev Mod Phys 62:251

    Article  Google Scholar 

  77. Best RB, Hummer G (2006) Phys Rev Lett 96:228104

    Article  Google Scholar 

  78. Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG (1995) Proteins 21:167

    Article  CAS  Google Scholar 

  79. Schwartz SD, Basner JE (2004) J Phys Chem B 108:444

    Article  Google Scholar 

  80. Hay S, Pudney CR, Sutcliffe MJ, Scrutton NS (2008) Angew Chem Int Ed 47:537

    Article  CAS  Google Scholar 

  81. Stojković V, Perissinotti LL, Willmer D, Benkovic SJ, Kohen A (2011) J Am Chem Soc 134:1738

    Article  Google Scholar 

  82. Pisliakov AV, Cao J, Kamerlin SCL, Warshel A (2009) Proc Natl Acad Sci USA 106:17359

    Article  CAS  Google Scholar 

  83. Kamerlin SCL, Warshel A (2010) Proteins Struct Funct Bioinf 78:1339

    CAS  Google Scholar 

  84. Warshel A (1978) Proc Natl Acad Sci USA 75:5250

    Article  CAS  Google Scholar 

  85. Warshel A, Sharma PK, Kato M, Xiang Y, Liu H, Olsson MHM (2006) Chem Rev 106:3210

    Article  CAS  Google Scholar 

  86. Olsson MHM, Warshel A (2004) J Am Chem Soc 126:15167

    Article  CAS  Google Scholar 

  87. Benkovic SJ, Hammes-Schiffer S (2006) Science 312:208

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by the National Institutes of Health through the Center for Multi-Scale Modeling Tools for Structural Biology (grant RR012255) and the National Science Foundation through the Center for Theoretical Biological Physics (PHY0216576).

Author information

Authors and Affiliations

  1. Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA

    Karunesh Arora & Charles L. Brooks III

Authors
  1. Karunesh Arora
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Charles L. Brooks III
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Charles L. Brooks III .

Editor information

Editors and Affiliations

  1. Department of Chemistry Department of Molecular and Cell Biology, University of California The california institute for Quantitativ, Berkeley, CA, USA

    Judith Klinman

  2. Department of Chemistry, University of Illinois at Urbana-Champai, Urbana, Illinois, USA

    Sharon Hammes- Schiffer

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Arora, K., Brooks, C.L. (2013). Multiple Intermediates, Diverse Conformations, and Cooperative Conformational Changes Underlie the Catalytic Hydride Transfer Reaction of Dihydrofolate Reductase. In: Klinman, J., Hammes- Schiffer, S. (eds) Dynamics in Enzyme Catalysis. Topics in Current Chemistry, vol 337. Springer, Berlin, Heidelberg. https://doi.org/10.1007/128_2012_408

Download citation

Publish with us

Policies and ethics

Search

Navigation