Substrate-Enzyme Interactions from Modeling and Isotope Effects

Challenges and Advances in Computational Chemistry and Physics

Volumn 4, Issue , 2007, Pages 341-363

  Kwiecień, Renata A ^a   Lewandowicz, Andrzej ^b   Paneth, Piotr ^a  

^a LODZ UNIVERSITY OF TECHNOLOGY   (Poland)

^b INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

Author keywords

DADMe; Immucillin; Isotope effects; Nucleosidase; PNP; Purine nucleoside phosphorylase; QM MM calculations; Rational drug design; Transition state analogue

Indexed keywords

EID: 85000253014     PISSN: 25424491     EISSN: 25424483     Source Type: Book Series    
DOI: 10.1007/1-4020-5372-X_7     Document Type: Chapter

References (84)

1. Gherman BF, Goldberg SD, Cornish VW, Friesner RA (2004) Mixed quantum mechanical/molecular mechanical (QM/MM) study of the deacylation reaction in a penicillin binding protein (PBP) versus in a class C -lactamase. J. Am. Chem. Soc. 126:7652–7664
2. Szefczyk B, Mulholland A, Sokalski WA (2004) Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field. J. Am. Chem. Soc. 126:16148–16159
3. Klahn M, Braun-Sand S, Rosta E, Warshel A (2005) On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions. J. Phys. Chem. B 109:15645–15650
4. König PH, Hoffmann M, Frauenheim Th, Cui Q (2005) A Critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method. J. Phys. Chem. B 109:9082–9095
5. Warshel A (2003) A Computer simulations of enzyme catalysis: Methods, progress, and insights. Annu. Rev. Biophys. Biomol. Struct. 32:425–443
6. Gao J, Truhlar DG (2004) Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree-Fock Wave Functions with Molecular Mechanics. J. Phys. Chem. A 108:632–650
7. Gawlita E, Anderson VE (1994) Paneth P Semiempirical calculations of the oxygen equilibrium isotope effect on binding of oxamate to lactate dehydrogenase. Eur. Biophys. J. 23:353–360
8. 18 O]oxamate with NADH and lactate dehydrogenase. Biochemistry 34:6050–6058
9. Sicińska D, Truhlar DG, Paneth P (2005) Dependence of transition state structure on substrate: the intrinsic C-13 kinetic isotope effect is different for physiological and slow substrates of the ornithine decarboxylase reaction because of different hydrogen bonding structures. J. Am. Chem. Soc. 127:5414–5422
10. Swanson T, Brooks HB, Osterman AL, O’Leary MH, Phillips MA (1998) Carbon-13 isotope effect studies of Trypanosoma brucei ornithine decarboxylase. Biochemistry 37:14943–14947
11. Garcia-Viloca M, Gao J, Karplus M, Truhlar DG (2004) How enzymes work: analysis by modern rate theory and computer simulations. Science 303:186–195
12. Alhambra C, Wu L, Zhang Y-Z, Gao J (1998) Walden-inversion-enforced transition-state stabilization in a protein tyrosine phosphatase. J. Am. Chem. Soc. 120:3858–3866
13. Senn HM, Thiel S, Thiel H (2005) Enzymatic hydroxylation in p-hydroxybenzoate hydroxylase: a case study for QM/MM molecular dynamics. J. Chem. Theory Comput. 1:494–505
14. Hata M, Tanaka Y, Fujii Y, Neya S, Hoshino T (2005) A theoretical study on the substrate deacylation mechanism of class C -lactamase. J. Phys. Chem. B 109:16153–16160
15. Mancia F, Evans PR (1998) Conformational changes on substrate binding to methylmalonyl CoA mutase and new insights into the free radical mechanism. Structure 6:711–720
16. Pittsburgh PA (2000) GaussView 2. Gaussian, Inc.
17. − exchange reaction and gas-phase protonation of polyethers. J. Comput. Chem. 7:718–730
18. Pittsburgh PA, Frisch MJ, et al. (2003) Gaussian 03, Revision A.1, Gaussian, Inc.
19. Ahlrichs R, Bär M, Häser M, Horn H, Kölmel C (1989) Electronic structure calculations on workstation computers: The program system turbomole. Chem. Phys. Lett. 162:165–169
20. Karlsruhe Quantum Chemistry Group, Turbomole homepage (2002) http://www.turbomole.com/
21. (a) Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic behaviour. Phys. Rev. A 38:3098–3100
22. (b) Perdew JP (1986) Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys. Rev. B 33:8822–8824
23. Schaefer A, Horn H, Ahlrichs R (1992) Fully optimized contracted Gaussian basis sets for atoms Li to Kr. J. Chem. Phys. 97:2571–2577
24. Eichkorn K, Treutler O, Öhm H, Häser M, Ahlrichs R (1995) Auxiliary basis sets to approximate Coulomb potentials. Chem. Phys. Lett. 240:283–290; erratum: Chem. Phys. Lett. 242:652–660
25. Eichkorn K, Weigend F, Treutler O, Ahlrichs R (1997) Auxiliary basis sets for main row atoms and transition metals and their use to approximate Coulomb potentials. Theor. Chem. Acc. 97:119–124
26. Ahlrichs R, Elliot S, Huniar U (2000) In: J. Grotendorst J (ed) Ab Initio Treatment of Large Molecules in Modern Methods and Algorithms of Quantum Chemistry. Proceedings, 2nd edn. John von Neumann Institute for Computing, Jülich, NIC Series 3, pp 7–25
27. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179–5197
28. (a) Marques HM, Ngoma B, Egan TJ, Brown KL (2001) Parameters for the AMBER Force Field for the Molecular Mechanics Modeling of the Cobalt Corrinoids. J. Mol. Struct. 561:71–91
29. (b) Marques HM, Brown KL (1995) A molecular mechanics force field for the cobalt corrinoids, J. Mol. Struct. (THEOCHEM) 340:97–124
30. Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98:5648–5642
31. Stephens PJ, Devlin FJ, Chablowski CF, Frisch MJ (1994) Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J. Phys. Chem. 98:11623–11627
32. Ditchfield R, Hehre WJ, Pople JA (1971) Self-consistent molecular-orbital methods. IX. Extended Gaussian-type basis for molecular-orbital studies of organic molecules. J. Chem. Phys. 54:724–728
33. Hehre WJ, Ditchfield R, Pople JA (1972) Self-consistent molecular orbital methods. XII. Further extensions of Gaussian-type basis sets for use in molecular orbital studies of organic molecules. J. Chem. Phys. 56:2257–2261
34. Thomä NH, Meier TW, Evans PR, Leadlay PF (1998) Stabilization of radical intermediates by an active-site tyrosine residue in methylmalonyl-CoA mutase. Biochemistry 37:14386–14393
35. Vlasie M, Banerjee R (2003) Tyrosine 89 Accelerates Co-Carbon Bond Homolysis in Methylmalonyl-CoA Mutase. J. Am. Chem. Soc. 125:5431–5435
36. McDonald IK, Thornton IK (1994) Satisfying hydrogen-bonding potential in proteins. J. Mol. Biol. 238:777–793
37. Giblett ER, Ammann AJ, Wara DW, Sandman R, Diamond LK (1975) Nucleoside-phosphorylase deficiency in a child with severely defective T-cell immunity and normal B-cell immunity. Lancet 1:1010–1013
38. Bantia S, Ananth SL, Parker CD, Horn LL, Upshaw R (2003) Mechanism of inhibition of T-acute lymphoblastic leukemia cells by PNP inhibitor – BCX-1777. Int Immunopharmacol. 3:879–887
39. Schramm VL (2002) Development of transition state analogues of purine nucleoside phosphorylase as anti-T-cell agents. Biochim. Biophys. Acta 1587:107–117
40. Queen SA, Jagt DL, Reyes P (1990) In vitro susceptibilities of Plasmodium falciparum to compounds which inhibit nucleotide metabolism. Antimicrob Agents Chemother. 34:1393–1398
41. Kicska GA, Tyler PC, Evans GB, Furneaux RH, Schramm VL, Kim K (2003) Purine-less death in Plasmodium falciparum induced by Immucillin-H, a transition state analogue of purine nucleoside phosphorylase. J. Biol. Chem. 277:3226–3231
42. Kicska GA, Tyler PC, Evans GB, Furneaux RH, Kim K, Schramm VL (2002) Transition state analogue inhibitors of purine nucleoside phosphorylase from Plasmodium falciparum. J. Biol. Chem. 277:3219–3225
43. Kline PC, Schramm VL (1993) Purine nucleoside phosphorylase. Catalytic mechanism and transition-state analysis of the arsenolysis reaction. Biochemistry 32:13212–13219
44. Berti PJ, Tanaka KSE (2002) Transition state analysis using multiple kinetic isotope effects: mechanisms of enzymatic and non-enzymatic glycoside hydrolysis and transfer. Adv. Phys. Org. Chem. 37:239–314
45. Miles RW, Tyler PC, Furneaux RH, Bagdassarian CK, Schramm VL (1998) One-third-the-sites transition state inhibitors for purine nucleoside phosphorylase. Biochemistry 37:8615–8621
46. Furneaux RH, Limberg G, Tyler PC, Schramm VL (1997) Synthesis of transition state inhibitors for N-riboside hydrolases and transferases. Tetrahedron 53:2915–2930
47. Kline PC, Schramm VL (1995) Pre-steady-state transition-state analysis of the hydrolytic reaction catalyzed by purine nucleoside phosphorylase. Biochemistry 34:1153–1162
48. Lewandowicz A, Schramm VL (2004) Transition state analysis for human and Plasmodium falciparum purine nucleoside phosphorylases. Biochemistry 43:1458–1468
49. Pham TV, Fang Y-R, Westaway KC (1997) Using secondary deuterium kinetic isotope effects to determine the symmetry of SN2 transition states. J. Am. Chem. Soc. 119:3670–3676
50. Glad SS, Jensen F (1997) Transition state looseness and secondary kinetic isotope effects. J. Am. Chem. Soc. 119:227–232
51. Birck MR, Schramm VL (2004) Nucleophilic participation in the transition state for human thymidine phosphorylase. J. Am. Chem. Soc. 126:2447–2453
52. Shi W, Ting LM, Kicska GA, Lewandowicz A, Tyler PC, Evans GB, Furneaux RH, Kim K, Almo SC, Schramm VL (2004) Plasmodium falciparum purine nucleoside phosphorylase: crystal structures, immucillin inhibitors, and dual catalytic function. J. Biol. Chem. 279:18103–18106
53. Kicska GA, Tyler PC, Evans GB, Furneaux RH, Shi W, Fedorov A, Lewandowicz A, Cahill SM, Almo SC, Schramm VL (2002) Atomic dissection of the hydrogen bond network for transition-state analogue binding to purine nucleoside phosphorylase. Biochemistry 41:14489–14498
54. Fedorov A, Shi W, Kicska GA, Fedorov E, Tyler PC, Furneaux RH, Hanson JC, Gainsford GJ, Larese JZ, Schramm VL, Almo SC (2001) Transition state structure of purine nucleoside phosphorylase and principles of atomic motion in enzymatic catalysis. Biochemistry 40:853–860
55. Horenstein BA, Parkin DW, Estupinan B, Schramm VL (1991) Transition-state analysis of nucleoside hydrolase from Crithidia fasciculate. Biochemistry 30:10788–10795
56. Schramm VL, Purich DL (1999) In: Methods in Enzymol. Enzyme Kinetics and Mechanism Part E. Energetics of Enzyme Catalysis 308:301–355
57. Nunez S, Antoniou D, Schramm VL, Schwartz SD (2004) Promoting vibrations in human purine nucleoside phosphorylase. A molecular dynamics and hybrid quantum mechanical/molecular mechanical study. J. Am. Chem. Soc. 126:15720–15729
58. Birck MR, Schramm VL (2004) Nucleophilic participation in the transition state for human thymidine phosphorylase. J. Am. Chem. Soc. 126:2447–2453
59. 3 H]thymidine kinetic isotope effect in human thymidine phosphorylase. J. Am. Chem. Soc. 126:6882–6883
60. Lewis BE, Schramm VL (2003) Binding equilibrium isotope effects for glucose at the catalytic domain of human brain hexokinase. J. Am. Chem. Soc. 125:4785–4798
61. Miller BG, Wolfenden R (2002) Catalytic proficiency: the unusual case of OMP decarboxylase. Annu. Rev. Biochem. 71:847–885
62. Wolfenden R (1999) Conformational aspects of inhibitor design: enzyme-substrate interactions in the transition state. Bioorg. Med. Chem. 7:647–652
63. Schramm VL (1998) Enzymatic transition states and transition state analog design. Annu. Rev. Biochem. 67:693–720
64. Schramm VL (2001) Transition state variation in enzymatic reactions. Curr. Opin. Chem. Biol. 5:556–563
65. Schramm VL (2003) Enzymatic transition state poise and transition state analogues. Acc. Chem. Res. 36:588–596
66. Lewandowicz A, Shi W, Evans GB, Tyler PC, Furneaux RH, Basso LA, Santos DS, Almo SC, Schramm VL (2003) Over-the-barrier transition state analogues and crystal structure with mycobacterium tuberculosis purine nucleoside phosphorylase. Biochemistry 42:6057–6066
67. ′-methylthioadenosine phosphorylase. J. Med. Chem. 47:3275–3281
68. Lewandowicz A, Tyler PC, Evans GB, Furneaux RH, Schramm VL (2003) Achieving the ultimate goal in transition state analogues for human purine nucleoside phosphorylase. J. Biol. Chem. 278:31465–31468
69. Politzer P, Truhlar G (1981) In: Chemical Applications of Atomic and Molecular Electrostatic Potentials. Plenum Press, New York, pp 1–6
70. Horenstein BA, Schramm VL (1993) Electronic nature of the transition state for nucleoside hydrolase. A blueprint for inhibitor design. Biochemistry 32:7089–7097
71. Bagdassarian CK, Schramm VL, Schwartz SD (1996) J. Am. Chem. Soc. 118:8825–8836
72. ′-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Escherichia coli. J. Biol. Chem. 280:18265–18273
73. ′-methylthioadenosine/S-adenosylhomocysteine nucleosidase. J. Biol. Chem. 280:18274–18282
74. Sauve AA, Cahill SM, Zech SG, Basso LA, Lewandowicz A, Santos DS, Grubmeyer C, Evans GB, Furneaux RH, Tyler PC, McDermott A, Girvin ME, Schramm VL (2003) Ionic states of substrates and transition state analogues at the catalytic sites of N-ribosyltransferases. Biochemistry 42:5694–5705
75. Morrison JE, Walsh CT (1988) The behavior and significance of slow-binding enzyme inhibitors. Adv. Enzymol. Relat. Areas Mol. Biol. 61:201–301
76. Evans GB, Furneaux RH, Lewandowicz A, Schramm VL, Tyler PC (2003) Synthesis of second-generation transition state analogues of human purine nucleoside phosphorylase. J. Med. Chem. 46:5271–5276
77. Zhou G-C, Parikh SL, Tyler PC, Evans GB, Furneaux GB, Zubkova OV, Benjes PA, Schramm VL (2004) Inhibitors of ADP-ribosylating bacterial toxins based on oxacarbenium ion character at their transition states. J. Am. Chem. Soc. 126:5690–5698
78. Deng H, Lewandowicz A, Schramm VL, Callender R (2004) Activating the phosphate nucleophile at the catalytic site of purine nucleoside phosphorylase: a vibrational spectroscopic study. J. Am. Chem. Soc. 126:9516–9517
79. Ting LM, Shi W, Lewandowicz A, Singh V, Mwakingwe A, Birck MR, Taylor Ringia EA, Bench G, Madrid DC, Tyler PC, Evans GB, Furneaux RH, Schramm, VL, Kim K (2004) Targeting a novel Plasmodium falciparum purine recycling pathway with specific immucillins. J. Biol. Chem. 280:9547–9554
80. Lewandowicz A, Taylor Ringia EA, Ting LM, Kim K, Tyler PC, Evans GB, Zubkova OV, Mee S, Painter GF, Lenz DH, Furneaux RH, Schramm VL (2005) Energetic mapping of transition state analogue interactions with human and Plasmodium falciparum purine nucleoside phosphorylases. J. Biol. Chem. 280:30320–30328
81. ′-methylthioadenosine phosphorylase and X-ray structure with MT-immucillin-A. Biochemistry 43:9–18
82. ′-methylthioadenosine phosphorylase. J. Med. Chem. 48:4679–4689
83. ′-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Escherichia coli and its similarity to transition state analogues. Biochemistry 44:11647–11659
84. http://www.biocryst.com/bcx_4208.htm.