How Metal Substitution Affects the Enzymatic Activity of Catechol-O-Methyltransferase

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Sparta, Manuel ^a   Alexandrova, Anastassia N ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM; CATECHOL METHYLTRANSFERASE; IRON; MAGNESIUM;

ARTICLE; BINDING SITE; CATALYSIS; CHEMICAL STRUCTURE; ENERGY TRANSFER; ENZYME ACTIVATION; ENZYME ACTIVITY; MOLECULAR DYNAMICS; PROTEIN BINDING; PROTEIN STRUCTURE; QUANTUM MECHANICS; SUBSTITUTION REACTION;

BINDING SITES; CALCIUM; CATECHOL O-METHYLTRANSFERASE; FERRIC COMPOUNDS; FERROUS COMPOUNDS; METALS; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84867313446     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0047172     Document Type: Article

References (49)

1. Männistö PT, Kaakkola S, (1999) Catechol-O-methyltransferase (COMT): biochemistry, molecular biology, pharmacology, and clinical efficacy of the new selective COMT inhibitors. Pharmacol. Rev. 51: 593-628.
2. Guldberg HC, Marsden CA, (1975) Catechol-O-methyl transferase: pharmacological aspects and physiological role. Pharmacol. Rev. 27: 135-20.
3. Axelrod J, Tomchick R, (1958) Enzymatic O-methylation of epinephrine and other catechols. J. Biol. Chem. 233: 702-705.
4. Lotta T, Vidgren J, Tilgmann C, Ulmanen I, Melen K, et al. (1995) Kinetics of human soluble and membrane-bound catechol O-methyltransferase: a revised mechanism and description of the thermolabile variant of the enzyme. Biochemistry 34: 4202-4210.
5. Rutherford K, Trong IL, Stenkamp R, Parson W (2008) Crystal structures of human 108V and 108M catechol O-methyltransferase. J. Mol. Biol. 380: 120-130.
6. Vidgren J, Svensson LA, Liljas A (1994) Crystal structure of catechol O-methyltransferase. Nature 368: 354-358.
7. Veser J, (1987) Kinetics and inhibition studies of catechol O-methyltransferase from the yeast Candida tropicalis. J. Bacteriol. 169: 3696-3700.
8. Tsao D, Diatchenko L, Dokholyan NV, (2011) Structural mechanism of S-adenosyl methionine binding to catechol O-methyltransferase. PLOS One 6: e24287.
9. Hegazi MF, Borchardt RT, Schowen RL, (1979) alpha.-Deuterium and carbon-13 isotope effects for methyl transfer catalyzed by catechol O-methyltransferase. SN2-like transition state. J. Am. Chem. Soc. 101: 4359-4365.
10. Zheng YJ, Bruice TC, (1997) Theoretical Examination of the Factors Controlling the Catalytic Efficiency of a Transmethylation Enzyme: Catechol O-Methyltransferase. J. Am. Chem. Soc. 119: 8137-8145.
11. Kuhn B, Kollman PA, (2000) QM-FE and Molecular Dynamics Calculations on Catechol O-Methyltransferase: Free Energy of Activation in the Enzyme and in Aqueous Solution and Regioselectivity of the Enzyme-Catalyzed Reaction. J. Am. Chem. Soc. 122: 2586-2596.
12. Lee TS, Massova I, Kuhn B, Kollman PA, (2000) QM and QM-FE simulations on reactions of relevance to enzyme catalysis: trypsin, catechol O-methyltransferase, β-lactamase and pseudouridine synthase J. Chem. Soc., Perkin Trans. 2: 409-415.
13. Roca M, Martí S, Andrés J, Moliner V, Tuñón I, et al. (2003) Theoretical modeling of enzyme catalytic power: analysis of "critic" and electrostatic factors in catechol O-methyltransferase. J. Am. Chem. Soc. 125: 7726-7737.
14. Roca M, Andrés J, Moliner V, Tuñón I, Bertrán J, (2005) On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations. J. Am. Chem. Soc. 127: 10648-10655.
15. Roca M, Moliner V, Tuñón I, Hynes JT, (2006) Coupling between protein and reaction dynamics in enzymatic processes: Application of Grote-Hynes theory to catechol O-methyltransferase. J. Am. Chem. Soc. 128: 6186-6193.
16. Roca M, Moliner V, Ruiz-Pernía JJ, Silla E, Tuñón I, (2006) Activation free energy of catechol-O-methyltransferase. J. Phys. Chem. A 110: 503-509.
17. Lau EY, Bruice TC, (1998) Importance of Correlated Motions in Forming Highly Reactive Near Attack Conformations in Catechol O Methyltransferase. J. Am. Chem. Soc. 120: 12387-12394.
18. Lau EY, Bruice TC, (2000) Comparison of the dynamics for ground-state and transition-state structures in the active site of catechol O-methyltransferase. J. Am. Chem. Soc. 122: 7165-7171.
19. Kahn K, Bruice TC, (2000) Transition state and ground state structures and their interaction with the active site residues in catechol O-methyltransferase. J. Am. Chem. Soc. 122: 46-51.
20. Ovaska M, Yliniemelä A, (1998) A semiempirical study on inhibition of catechol O-methyltransferase by substituted catechols. J. Comput.-Aided Mol. Des. 12: 301-307.
21. Sparta M, Ding F, Shirvanyants D, Dokholyan NV, Alexandrova AN (2012) Hybrid dynamics simulation engine for metalloproteins. Biophys. J. 103: 767-776.
22. Valdez C E, Alexandrova AN (2012) Why Urease is a di-Nickel Enzyme, whereas the CcrA β-Lactamase is a di-Zinc Enzyme. J. Phys. Chem. B. 116: 10649-19656
23. Warshel A, Levitt M, (1976) Theoretical Studies of Enzymatic Reactions: Dielectric Electrostatic and Steric Stabilization of the Carbonium Ion in the Reaction of Lysozyme. J. Mol. Biol. 103: 227-249.
24. Bakowies D, Thiel W, (1996) Semiempirical Treatment of Electrostatic Potentials and Partial Atomic Charges in Combined Quantum Chemical and Molecular Mechanical Approaches. J. Comput. Chem. 17: 87-108 (and references therein).
25. Svensson M, Humbel S, Froese RDJ, Matsubara T, Sieber S, et al. (1996) ONIOM: a multilayered integrated MO + MM method for geometry optimization and single point energy predictions. A test for Diels-Ander reactions and Pt(P(t-Bu)(3))(2) + H-2 oxidative addition. Phys. Chem. 100: 19357-19363.
26. Field MJ, Bash PA, Karplus M, (1990) A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations. J. Comput. Chem. 11: 700-733.
27. Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI, (1998) Molecular dynamics studies of folding of a protein-like model. Fold. Des. 3: 577-587.
28. Dokholyan NV, (2006) Studies of folding and misfolding using simplified models. Curr. Opin. Struct. Biol. 16: 79-85.
29. Ding F, Guo WH, Dokholyan NV, Shakhnovich EI, Shea JE, (2005) Reconstruction of src SH3 transition state ensemble using multiscale molecular dynamics simulations. J. Mol. Biol. 350: 1035-1050.
30. Ding F, Tsao D, Nie H, Dokholyan NV, (2008) Ab initio folding of proteins with all-atom discrete molecular dynamics. Structure 16: 1010-1018.
31. Andersen HC, (1980) Molecular dynamics simulations at constant pressure and/or temperature. J. Chem. Phys. 72: 2384.
32. Ramachandran S, Kota P, Ding F, Dokholyan NV, (2011) Automated minimization of steric clashes in protein structures. Proteins 79: 261-270.
33. Kabsch W, (1976) A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A 32: 922-923.
34. Barton GJ OC - A cluster analysis program, University of Dundee, Scotland, UK (1993, 2002), Available: www.compbio.dundee.ac.uk/downloads/oc. Accessed 2012 September 13.
35. Dirac PAM, (1929) Quantum mechanics of many-electron systems. Proc. Royal Soc. (London) A 123: 714.
36. Slater JC, (1951) A Simplification of the Hartree-Fock Method. Phys. Rev. 81: 385.
37. Vosko SH, Wilk L, Nusair M, (1980) Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis. Can. J. Phys. 80: 1200.
38. Becke AD, (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A 38: 3098-3100.
39. Perdew JP, (1986) Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys. Rev. B 33: 8822-8824.
40. Schafer A, Horn H, Ahlrichs R, (1992) Fully Optimized Contracted Gaussian Basis Sets for Atoms Li to Kr. J. Chem. Phys. 97: 2571.
41. Weigend F, Ahlrichs R, (2005) Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy. Phys. Chem. Chem. Phys. 7: 3297-3305.
42. Arnim MV, Ahlrichs R, (1998) Performance of parallel TURBOMOLE for density functional calculations. J. Comput. Chem. 19: 1746-1757.
43. Sierka M, Hogekamp A, Ahlrichs R, (2003) Fast evaluation of the coulomb potential for electron densities using multipole accelerated resolution of identity approximation. J. Chem. Phys. 118: 9136-9148.
44. Turbomole V6.3 2011, a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989-2007, Turbomole GmbH, since 2007. Available: www.turbomole.com. Accessed 2012, September 13.
45. Grimme S, (2004) Accurate description of van der waals complexes by density functional theory including empirical corrections. J. Comput. Chem. 25: 1463-1473.
46. Zhao Y, Truhlar DG, (2006) A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions. J. Chem. Phys. 125: 194101-18.
47. Valiev M, Bylaska EJ, Govind N, Kowalski K, Straatsma TP, et al. (2010) NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations. Comput. Phys. Commun. 181: 1477-1489.
48. Becke AD, (1993) Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98: 5648-5652.
49. Staroverov V, Scuseria G, Tao J, Perdew J, (2003) Comparative assessment of a new nonempirical density functional: Molecules and hydrogen-bonded complexes. J. Chem. Phys. 119: 12129-12137.