Computational prediction of residues involved in fidelity checking for DNA synthesis in DNA polymerase i

Biochemistry

Volumn 51, Issue 12, 2012, Pages 2569-2578

  Graham, Sarah E ^a   Syeda, Fatimasultana ^a   Cisneros, G Andrés ^a  

^a WAYNE STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACILLUS STEAROTHERMOPHILUS; BASE PAIRING; COMPUTATIONAL PREDICTIONS; DNA POLYMERASE; DNA SYNTHESISS; ELECTROSTATIC FREE ENERGY; ENERGY DECOMPOSITION; KLENOW FRAGMENT; NON-COVALENT INTERACTION; POTENTIAL TARGETS; RESONANCE ENERGY TRANSFER; SINGLE-MOLECULE;

BACTERIOLOGY; ENERGY TRANSFER; ESCHERICHIA COLI; POLYMERS; SYNTHESIS (CHEMICAL);

DNA;

DNA DIRECTED DNA POLYMERASE BETA;

ARTICLE; BACTERIAL PHENOMENA AND FUNCTIONS; BASE MISPAIRING; COVALENT BOND; DNA STRUCTURE; DNA SYNTHESIS; ENERGY; ESCHERICHIA COLI; FIDELITY CHECKING SITE; GEOBACILLUS STEAROTHERMOPHILUS; HYPOTHESIS; MOLECULAR INTERACTION; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; STATIC ELECTRICITY;

AMINO ACID SEQUENCE; BASE PAIRING; DNA; DNA POLYMERASE I; ESCHERICHIA COLI; GEOBACILLUS STEAROTHERMOPHILUS; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; MUTAGENESIS; PROTEIN CONFORMATION; THERMODYNAMICS;

ESCHERICHIA COLI; GEOBACILLUS STEAROTHERMOPHILUS;

EID: 84859189016     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi201856m     Document Type: Article

References (46)

1. Thomas, A. K. (2003) Considering the cancer consequences of altered DNA polymerase function Cancer Cell 3 (2) 105-110
2. Schaaper, R. M. (1993) Base Selection, Proofreading, and Mismatch Repair during DNA Replication in Escherichia coli J. Biol. Chem. 268 (32) 23762-23765
3. Kuchta, R. D., Benkovic, P., and Benkovic, S. J. (1988) Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity Biochemistry 27 (18) 6716-6725
4. Kiefer, J. R. 1998, Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal Nature 391 (6664) 304-307
5. Bebenek, K. 1990, The fidelity of DNA synthesis catalyzed by derivatives of Escherichia coli DNA polymerase I J. Biol. Chem. 265 (23) 13878-13887
6. Carroll, S. S., Cowart, M., and Benkovic, S. J. (1991) A mutant of DNA polymerase I (Klenow fragment) with reduced fidelity Biochemistry 30 (3) 804-813
7. Loh, E., Choe, J., and Loeb, L. A. (2007) Highly Tolerated Amino Acid Substitutions Increase the Fidelity of Escherichia coli DNA Polymerase I J. Biol. Chem. 282 (16) 12201-12209
8. Thompson, E. H. Z. 2002, Determinants of DNA Mismatch Recognition within the Polymerase Domain of the Klenow Fragment Biochemistry 41 (3) 713-722
9. Suzuki, M. 2000, Thermus aquaticus DNA Polymerase I Mutants with Altered Fidelity J. Biol. Chem. 275 (42) 32728-32735
10. Tosaka, A. 2001, O-helix Mutant T664P of Thermus aquaticus DNA Polymerase I J. Biol. Chem. 276 (29) 27562-27567
11. Yoshida, K. 2001, Arg660Ser mutation in Thermus aquaticus DNA polymerase I suppresses T → C transitions: Implication of wobble base pair formation at the nucleotide incorporation step Nucleic Acids Res. 29 (20) 4206-4214
12. Christian, T. D., Romano, L. J., and Rueda, D. (2009) Single-molecule measurements of synthesis by DNA polymerase with base-pair resolution Proc. Natl. Acad. Sci. U.S.A. 106 (50) 21109-21114
13. Ibarra, B. 2009, Proofreading dynamics of a processive DNA polymerase EMBO J. 28 (18) 2794-2802
14. Florian, J., Goodman, M. F., and Warshel, A. (2002) Theoretical Investigation of the Binding Free Energies and Key Substrate-Recognition Components of the Replication Fidelity of Human DNA Polymerase β J. Phys. Chem. B 106 (22) 5739-5753
15. Florian, J., Goodman, M. F., and Warshel, A. (2003) Computer Simulation of the Chemical Catalysis of DNA Polymerases: Discriminating between Alternative Nucleotide Insertion Mechanisms for T7 DNA Polymerase J. Am. Chem. Soc. 125 (27) 8163-8177
16. Florian, J., Goodman, M. F., and Warshel, A. (2005) Computer simulations of protein functions: Searching for the molecular origin of the replication fidelity of DNA polymerases Proc. Natl. Acad. Sci. U.S.A. 102 (19) 6819-6824
17. Xiang, Y. 2008, Exploring the role of large conformational changes in the fidelity of DNA polymerase β Proteins: Struct., Funct., Bioinf. 70 (1) 231-247
18. Ishikita, H. and Warshel, A. (2008) Predicting Drug-Resistant Mutations of HIV Protease Angew. Chem., Int. Ed. 47 (4) 697-700
19. Rucker, R., Oelschlaeger, P., and Warshel, A. (2010) A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases Proteins: Struct., Funct., Bioinf. 78 (3) 671-680
20. Ram Prasad, B. and Warshel, A. (2011) Prechemistry versus preorganization in DNA replication fidelity Proteins: Struct., Funct., Bioinf. 79 (10) 2900-2919
21. Warshel, A. 2006, Electrostatic Basis for Enzyme Catalysis Chem. Rev. 106 (8) 3210-3235
22. Muegge, I., Tao, H., and Warshel, A. (1997) A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding Protein Eng. 10 (12) 1363-1372
23. Senn, H. M., O'Hagan, D., and Thiel, W. (2005) Insight into Enzymatic C-F Bond Formation from QM and QM/MM Calculations J. Am. Chem. Soc. 127 (39) 13643-13655
24. Cisneros, G. A. 2003, Ab Initio QM/MM Study Shows There Is No General Acid in the Reaction Catalyzed by 4-Oxalocrotonate Tautomerase J. Am. Chem. Soc. 125 (34) 10384-10393
25. Cisneros, G. A. 2004, The Protein Backbone Makes Important Contributions to 4-Oxalocrotonate Tautomerase Enzyme Catalysis: Understanding from Theory and Experiment Biochemistry 43 (22) 6885-6892
26. 2+ from ab initio quantum mechanical/molecular mechanical studies DNA Repair 7 (11) 1824-1834
27. Cisneros, G. A. 2009, Reaction Mechanism of the ε Subunit of E. coli DNA Polymerase III: Insights into Active Site Metal Coordination and Catalytically Significant Residues J. Am. Chem. Soc. 131 (4) 1550-1556
28. Martí, S. 2003, Preorganization and Reorganization as Related Factors in Enzyme Catalysis: The Chorismate Mutase Case Chem.-Eur. J. 9 (4) 984-991
29. Szefczyk, B. 2007, Quantum chemical analysis of reaction paths in chorismate mutase: Conformational effects and electrostatic stabilization Int. J. Quantum Chem. 107 (12) 2274-2285
30. Li, G. and Cui, Q. (2003) What Is So Special about Arg 55 in the Catalysis of Cyclophilin A? Insights from Hybrid QM/MM Simulations J. Am. Chem. Soc. 125 (49) 15028-15038
31. Cui, Q. (2003) Catalysis and specificity in enzymes: A study of triosephophate isomerase and comparison with methyl glyoxal synthase. In Advances in Protein Chemistry, pp 315-372, Academic Press, New York.
32. Metanis, N. 2004, Electrostatic Interactions Dominate the Catalytic Contribution of Arg39 in 4-Oxalocrotonate Tautomerase J. Am. Chem. Soc. 126 (40) 12726-12727
33. Bebenek, K. 2010, Loop 1 modulates the fidelity of DNA polymerase λ Nucleic Acids Res. 38 (16) 5419-5431
34. Klvaňa, M. 2011, An Abridged Transition State Model To Derive Structure, Dynamics, and Energy Components of DNA Polymerase β Fidelity Biochemistry 50 (32) 7023-7032
35. Johnson, E. R. 2010, Revealing Noncovalent Interactions J. Am. Chem. Soc. 132 (18) 6498-6506
36. Li, Y., Korolev, S., and Waksman, G. (1998) Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: Structural basis for nucleotide incorporation EMBO J. 17 (24) 7514-7525
37. Beese, L. S., Friedman, J. M., and Steitz, T. A. (1993) Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate Biochemistry 32 (51) 14095-14101
38. Case, D. A. 2005, The Amber biomolecular simulation programs J. Comput. Chem. 26 (16) 1668-1688
39. Hsu, G. W. 2004, Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase Nature 431 (7005) 217-221
40. Jorgensen, W. L., (1983) Comparison of simple potential functions for simulating liquid water, Vol. 79, pp 926-935, American Institute of Physics, College Park, MD.
41. Essmann, U. (1995) A smooth particle mesh Ewald method J. Chem. Phys. 103 (19) 8577
42. Darden, T., York, D., and Pedersen, L. (1993) Particle mesh Ewald: An N•log(N) method for Ewald sums in large systems J. Chem. Phys. 98 (12) 10089-10092
43. Contreras-García, J. 2011, NCIPLOT: A Program for Plotting Noncovalent Interaction Regions J. Chem. Theory Comput. 7 (3) 625-632
44. Minnick, D. T. 1999, Side Chains That Influence Fidelity at the Polymerase Active Site of Escherichia coli DNA Polymerase I (Klenow Fragment) J. Biol. Chem. 274 (5) 3067-3075
45. Loh, E. and Loeb, L. A. (2005) Mutability of DNA polymerase I: Implications for the creation of mutant DNA polymerases DNA Repair 4 (12) 1390-1398
46. Singh, K. and Modak, M. J. (2003) Presence of 18-Å Long Hydrogen Bond Track in the Active Site of Escherichia coli DNA Polymerase I (Klenow Fragment) J. Biol. Chem. 278 (13) 11289-11302