A Linear-Scaling Quantum Mechanical Investigation of Cytidine Deaminase

Journal of Computational Physics

Volumn 151, Issue 1, 1999, Pages 242-263

  Lewis, James P ^a,b   Liu, Shubin ^a   Lee, Tai Sung ^b   Yang, Weitao ^b  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COORDINATION REACTIONS; ENZYMES; QUANTUM THEORY; X RAY CRYSTALLOGRAPHY;

ACTIVE SITE; CYTIDINE DEAMINASE; DIVIDE-AND-CONQUER TECHNIQUE; LARGE SCALE SIMULATIONS; LINEAR-SCALING; MINIMISATION; QUANTUM MECHANICAL; QUANTUM-MECHANICAL CALCULATION; SEMI-EMPIRICAL; TRANSITION-STATE ANALOGUES;

GROUND STATE;

EID: 0011746913     PISSN: 00219991     EISSN: None     Source Type: Journal    
DOI: 10.1006/jcph.1999.6219     Document Type: Article

References (89)

1. Cohen R. M., Wolfenden R. Cytidine deaminase fromEscherichia coli: J. Biol. Chem. 246:1971;7561.
2. 4. J. Biol. Chem. 246:1971;7566.
3. Marquez V. E., Liu P. S., Kelley J. A., Driscoll J. S., McCormick J. J. Synthesis of 1,3-diazepin-2-one nucleosides as transition state inhibitors of cytidine deaminase. J. Med. Chem. 23:1980;713.
4. Liu P. S., Marquez V. E., Driscoll J. S., Fuller R. W., McCormick J. J. Cyclic urea nucleosids. Cytidine deaminase activity as a function of aglycon ring size. J. Med. Chem. 24:1981;662.
5. Ashley G. W., Bartlett P. A. Inhibition ofEscherichia coli. J. Biol. Chem. 259:1984;13,621.
6. Kim C. H., Marquez V. E., Mao D. T., Haines D. R., McCormick J. J. Synthesis of pyrimidine-2-one nucleosides as acid-stable inhibitors of cytidine deaminase. J. Med. Chem. 29:1986;1374.
7. Wilson D. K., Rudolph F. B., Quiocho F. A. Atomic structure of adenosine deaminase complexed with a transition state analog: Understanding catalysis and immunodeficiency mutations. Biochemistry. 252:1991;1278.
8. Betts L., Xiang S., Short S. A., Wolfenden R., Carter C. W. Jr. Cytidine deaminase: The 2.3 Å crystal structure of an enzyme: Transition-state analog complex. J. Mol. Biol. 235:1994;635.
9. Carlow D. C., Smith A. A., Yang C. C., Short S. A., Wolfenden R. Major contribution of a carboxymethyl group to transition-state stabilization by cytidine deaminase: Mutation and rescue. Biochemistry. 34:1995;4220.
10. Xiang S., Short S. A., Wolfenden R., Carter C. W. Jr. Transition-state selectivity for a single hydroxyl group during catalysis by cytidine deaminase. Biochemistry. 34:1995;4516.
11. Carlow D. C., Short S. A., Wolfenden R. Role of glutamate-104 in generating a transition state analogue inhibitor at the active site of cytidine deaminase. Biochemistry. 35:1996;948.
12. Xiang S., Short S. A., Wolfenden R., Carter C. W. Jr. Cytidine deaminase complexed to 3-deazacytidine: A "valence buffer" in zinc enzyme catalysis. Biochemistry. 35:1996;1335.
13. Xiang S., Short S. A., Wolfenden R., Carter C. W. Jr. The structure of the cytidine deaminase-product complex provides evidence for efficient proton transfer and ground-state destabilization. Biochemistry. 36:1997;4768.
14. Frick L., Neela J. P. M., Wolfenden R. Transition state stabilization by deaminases: Rates of nonenzymatic hydrolysis of adenosine and cytidine. Bioorg. Chem. 15:1987;100.
15. Marquez V. E. Developments in Cancer Chemotherapy. 1984;91.
16. Chandrasekaren B., Capizzi R. L., Kute T. E., Morgan T., Dimling J. Modulation of the metabolism and pharacokinetics of 1-β-D-arabinofuranosyluracil in leukemic mice. Cancer Res. 49:1989;3259.
17. Kohn W., Sham L. Self-consistent equations including exchange and correlation effects. Phys. Rev. A. 140:1965;1133.
18. Parr R., Yang W. Density-Functional Theory of Atoms and Molecules. 1989.
19. Yang W. Direct calculation of electron density in density-functional theory. Phys. Rev. Lett. 66:1991;1438.
20. Yang W., Lee T.-S. A density-matrix divide-and-conquer approach for electronic structure calculations of large molecules. J. Chem. Phys. 163:1995;5674.
21. Baroni S., Giannozzi P. Towards very large scale electronic structure calculations. Europhys. Lett. 17:1992;547.
22. Galli G., Parrinello M. Large scale electronic structure calculations. Phys. Rev. Lett. 69:1992;3547.
23. Mauri F., Galli G., Car R. Orbital formulation for electronic-structure calculations with linear system-size scaling. Phys. Rev. B. 47:1993;9973.
24. Ordejón P., Drabold D., Grumbach M., Martin R. M. Unconstrained minimization approach for electronic computations that scales linearly with system size. Phys. Rev. B. 48:1993;14,646.
25. Ordejón P., Artacho E., Soler J. M. Self-consistent order-N density functional calculations for very large systems. Phys. Rev. B. 53:1996;R10,441.
26. Kim J., Mauri F., Galli G. Total energy global optimizations using nonorthogonal localized orbitals. Phys. Rev. B. 52:1995;1640.
27. Li X.-P., Nunes R. W., Vanderbilt D. Density-matrix electronic-structure method with linear system-size scaling. Phys. Rev. B. 47:1993;10,891.
28. Daw M. S. Model for energetics of solids based on the density matrix. Phys. Rev. B. 47:1993;10,895.
29. Drabold D. A., Sankey O. F. Maximum entropy approach for linear scaling in the electronic structure problem. Phys. Rev. Lett. 70:1993;3631.
30. Zhong W., Tománek D., Bertsch G. F. Total energy calculations for extremely large clusters: The recursive method. Solid State Comm. 86:1993;607.
31. Aoki M. Rapidly convergent bond order expansion for atomistic simulations. Phys. Rev. Lett. 71:1993;3842.
32. Horsfield A. P., Bratkovsky A. M., Fearn M., Pettifor D. G., Aoki M. Bond-order potentials: Theory and implementation. Phys. Rev. B. 53:1996;12,694.
33. Goedecker S., Colombo L. Efficient linear scaling algorithm for tight-binding molecular dynamics. Phys. Rev. Lett. 73:1994;122.
34. Stechel E. B., Williams A. R., Feibelman P. J. N-scaling algorithms for density-functional calculations of metals and insulators. Phys. Rev. B. 49:1994;10,088.
35. Hierse W., Stechel E. B. Order-N methods in self-consistent density-functional calculations. Phys. Rev. B. 50:1994;17,811.
36. Hernández E., Gillan M. J. Self-consistent first-principles techniques with linear scaling. Phys. Rev. B. 51:1994;10,157.
37. Hernández E., Gillan M. J., Goringe C. M. Linear-scaling density-functional-theory technique: The density-matrix approach. Phys. Rev. B. 53:1996;7147.
38. W. Yang, J. M. Pérez-Jordá, Encyclopedia of Computational Chemistry, P. Schleyer, Wiley, New York.
39. Yang W. Direct calculation of electron density in density-functional theory: Implementation for benzene and a tetrapeptide. Phys. Rev. A. 44:1991;7823.
40. Dixon S. L., Merz K. M. Jr. Semiempirical molecular orbital calculations with linear system size scaling. J. Chem. Phys. 104:1996;6643.
41. Dixon S. L., Merz K. M. Jr. Fast, accurate semiempirical molecular orbital calculations for macromolecules. J. Chem. Phys. 107:1997;879.
42. Gallant R. T., St-Amant A. Linear scaling for the charge density fitting procedure of the linear combination of Gaussian-type orbitals density functional method. Chem. Phys. Lett. 256:1996;569.
43. Goh S. K., St-Amant A. Using a fitted electronic density to improve the efficiency of a linear combination of Gaussian-type orbitals calculation. Chem. Phys. Lett. 264:1997;9.
44. Thiel W. Semiempirical methods: Current status and perspectives. Tetrahedron. 44:1988;7393.
45. Stewart J. J. P. Review in Computational Chemistry. 1:1990;45.
46. Stewart J. J. P. MOPAC: A semiempirical molecular orbital program. J. Comput. Aided Mol. Design. 4:1990;1.
47. Lee T.-S., York D., Yang W. Linear-scaling semiempirical quantum calculations for macromolecules. J. Chem. Phys. 105:1996;2744.
48. Stewart J. J. P. Application of localized molecular orbitals to the solution of the semiempirical self-consistent field equations. Int. J. Quantum Chem. 58:1996;133.
49. Daniels A. D., Willam J. M., Scuseria G. E. Semiempirical methods with conjugate gradient density matrix search to replace diagonalization for molecular systems containing thousands of atoms. J. Chem. Phys. 107:1997;425.
50. Dewar M. J. S., Thiel W. Ground states of molecules, 38, the MNDO method: Approximations and parameters. J. Am. Chem. Soc. 99:1977;4899.
51. Dewar M. J. S., Zoebisch E. G., Healy E. F., Stewart J. J. P. AM1: A new general purpose quantum mechanical model. J. Am. Chem. Soc. 107:1985;3902.
52. Stewart J. J. P. Optimization of parameters for semiempirical methods. I. Method. J. Comp. Chem. 10:1989;209.
53. Stewart J. J. P. Optimization of parameters for semiempirical methods. I. Applications. J. Comp. Chem. 10:1989;221.
54. Dewar M. J. S., Thiel W. A. semiempirical model for the two-center repulsion integrals in the NDDO approximation. Theor. Chem. Acta. 46:1977;89.
55. Mulliken R. S. Criteria for the construction of good self-consistent-field molecular orbital wave functions, and the significance of LCAO-MO population analysis. J. Chem. Phys. 36:1962;3428.
56. Zhao Q., Yang W. Analytical energy gradients and geometry optimization in the divide-and-conquer method for large molecules. J. Chem. Phys. 102:1995;9598.
57. Stewart J. J. P. MOPAC7 Version 2 Manual. 1993.
58. Press W. H., Teukolsky S. A., Vetterling W. T., Flannery B. P. Numerical Recipes. 1992.
59. Dewar M. J. S., Yamaguchi Y. Analytical first derivatives of the energy in MNDO. Comput. Chem. 2:1978;25.
60. Lee C., Yang W. The divide-and-conquer density-functional approach: Molecular internal rotation and density of states. J. Chem. Phys. 96:1992;2408.
61. York D., Lee T.-S., Yang W. Parameterization and efficient implementation of a solvent model for linear-scaling semiempirical quantum mechanical calculations of biological macromolecules. Chem. Phys. Lett. 263:1996;297.
62. York D. M., Lee T.-S., Yang W. Quantum mechanical study of aqueous polarization effects on biological macromolecules. J. Am. Chem. Soc. Comm. 118:1996;10,940.
63. York D. M., Lee T.-S., Yang W. Quantum mechanical treatment of biological macromolecules in solution using linear-scaling electronic structure methods. Phys. Rev. Lett. 118:1998;5011.
64. Klamt A., Shuurmann G. COSMO: A new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. Perkins Trans. 2:1993;799.
65. Warshel A., Levitt M. Theoretic studies of enzymic reactions: Dielectric electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103:1976;227.
66. -. J. Comp. Chem. 7:1986;718.
67. Field M. J., Bash P. A., Karplus M. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comp. Chem. 11:1990;700.
68. Gao J., Xia X. A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations. Science. 258:1992;631.
69. Warshel A. Computer simulations of enzymatic reactions. Curr. Opin. Struct. Bio. 2:1992;230.
70. Stanton R. V., Hartsough D. S., Merz K. M. Jr. Calculation of solvation free energies using a density functional/molecular dynamics coupled potential. J. Phys. Chem. 97:1993;11,868.
71. Wei D., Salahub D. R. A combined density-functional and molecular dynamics simulation of a quantum water molecule in aqueous solution. Chem. Phys. Lett. 224:1994;291.
72. Thery V., Rinaldi D., Rivail J. L. Quantum mechanical computations on very large molecular systems: The local self-consistent field method. J. Comp. Chem. 15:1994;269.
73. Gao J. A combined QM/MM simulation study of the claisen rearrangement of allyl vinyl ether in aqueous solution. J. Am. Chem. Soc. 116:1994;1563.
74. Maseras F., Morokuma K. IMOMM: A new integrated ab initio+molecular mechanics geometry optimization scheme of equilibrium structures and transition states. J. Comp. Chem. 16:1995;1170.
75. Humbel S., Sieber S., Morokuma K. The IMOMO method: Integration of different levels of molecular orbital approximations for geometry optimization of large systems: Test for n-butane conformation and SN2 reaction: RCI+CI-. J. Chem. Phys. 105:1996;1959.
76. Assfeld X., Rivail J. L. Quantum chemical computations on parts of large molecules: Theab initio. Chem. Phys. Lett. 263:1996;100.
77. Merz K. M. Jr., Banci L. Binding of bicarbonate to human carbonic anhydrase II: A continuum of binding states. J. Am. Chem. Soc. 119:1997;863.
78. Peräkyla M., Kollman P. A. A simulation of the catalytic mechanism of aspartyl-glucosaminidase usingab initio. J. Am. Chem. Soc. 119:1997;1189.
79. Stewart J. J. P. Optimization of parameters for semi-empirical methods. III. Extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, TI, Pb, and Bi. J. Comp. Chem. 12:1991;320.
80. aof zinc-bound water and nucleophilicity of hydroxo- containing species:Ab initio. Inorg. Chem. 29:1990;1460.
81. San Diego, CA, 92121.
82. Lewis J. P., Carter C. W. Jr., Hermans J., Pan W., Lee T. S., Yang W. Active species for the ground-state complex of cytidine deaminase: A linear-scaling quantum mechanical investigation. J. Am. Chem. Soc. 120:1998;5407.
83. J. Erkmann, J. C. W. Carter, J. P. Lewis, J. Hermans, W. Yang, Low-pH studies of cytidine deaminase.
84. J. P. Lewis, S. Liu, C. W. Carter, Jr. J. Hermans, T. S. Lee, W. Yang, A linear-scaling quantum mechanical investigation of the "valence-buffer" effect in cytidine deaminase.
85. Brown I. D., Shannon R. D. Empirical bond-strength-bond-length curves for oxides. Acta Crystallogr. A. 29:1973;266.
86. Brown I. D. Chemical and steric constraints in inorganic solids. Acta Crystallogr. B. 48:1992;553.
87. Becke A. D. A multicenter numerical integration scheme for polyatomic molecules. J. Chem. Phys. 88:1988;2547.
88. Perdew J. P., Wang Y. Accurate and simple analytic representation of the electron-gas correlation energy. Phys. Rev. B. 45:1992;13,244.
89. Becke A. D. Density-functional thermochemistry. II. The effect of the Perdew-Wang generalized-gradient correlation correction. J. Chem. Phys. 97:1992;9173.