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Volumn 70, Issue 1, 2008, Pages 231-247

Exploring the role of large conformational changes in the fidelity of DNA polymerase β

Author keywords

Conformational change; Enzyme catalysis; Free energy landscape; Induced fit; Replication fidelity

Indexed keywords

DNA DIRECTED DNA POLYMERASE BETA;

EID: 37349079468     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21668     Document Type: Article
Times cited : (43)

References (81)
  • 2
    • 0035543093 scopus 로고    scopus 로고
    • The depth of chemical time and the power of enzymes as catalysts
    • Wolfenden R, Snider MJ. The depth of chemical time and the power of enzymes as catalysts. Acc Chem Res 2001;34:938-945.
    • (2001) Acc Chem Res , vol.34 , pp. 938-945
    • Wolfenden, R.1    Snider, M.J.2
  • 3
    • 0025783442 scopus 로고
    • Fidelity mechanisms in DNA replication
    • Echols H, Goodman MF. Fidelity mechanisms in DNA replication. Annu Rev Biochem 1991;60:477-511.
    • (1991) Annu Rev Biochem , vol.60 , pp. 477-511
    • Echols, H.1    Goodman, M.F.2
  • 4
    • 0027220197 scopus 로고
    • Conformational coupling in DNA polymerase fidelity
    • Johnson KA. Conformational coupling in DNA polymerase fidelity. Annu Rev Biochem 1993;62:685-713.
    • (1993) Annu Rev Biochem , vol.62 , pp. 685-713
    • Johnson, K.A.1
  • 5
    • 8544278025 scopus 로고    scopus 로고
    • DNA polymerase fidelity: Kinetics, structure, and checkpoints
    • Joyce CM, Benkovic SJ. DNA polymerase fidelity: kinetics, structure, and checkpoints. Biochemistry 2004;43:14317-14324.
    • (2004) Biochemistry , vol.43 , pp. 14317-14324
    • Joyce, C.M.1    Benkovic, S.J.2
  • 6
    • 0037566670 scopus 로고    scopus 로고
    • Structural insights into the origins of DNA polymerase fidelity
    • Beard WA, Wilson SH. Structural insights into the origins of DNA polymerase fidelity. Structure 2003;11:489-496.
    • (2003) Structure , vol.11 , pp. 489-496
    • Beard, W.A.1    Wilson, S.H.2
  • 7
    • 0037032998 scopus 로고    scopus 로고
    • Efficiency of correct nucleotide insertion governs DNA polymerase fidelity
    • Beard WA, Shock DD, Vande Berg BJ, Wilson SH. Efficiency of correct nucleotide insertion governs DNA polymerase fidelity. J Biol Chem 2002;277:47393-47398.
    • (2002) J Biol Chem , vol.277 , pp. 47393-47398
    • Beard, W.A.1    Shock, D.D.2    Vande Berg, B.J.3    Wilson, S.H.4
  • 10
    • 0035997344 scopus 로고    scopus 로고
    • Error-prone repair DNA polymerases in prokaryotes and eukaryotes
    • Goodman MF. Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu Rev Biochem 2002;71:17-50.
    • (2002) Annu Rev Biochem , vol.71 , pp. 17-50
    • Goodman, M.F.1
  • 11
    • 33644617062 scopus 로고    scopus 로고
    • Mechanistic comparison of high-fidelity and error-prone DNA polymerases and ligases involved in DNA repair
    • Showalter AK, Lamarche BJ, Bakhtina M, Su MI, Tang KH, Tsai MD. Mechanistic comparison of high-fidelity and error-prone DNA polymerases and ligases involved in DNA repair. Chem Rev 2006;106:340-360.
    • (2006) Chem Rev , vol.106 , pp. 340-360
    • Showalter, A.K.1    Lamarche, B.J.2    Bakhtina, M.3    Su, M.I.4    Tang, K.H.5    Tsai, M.D.6
  • 12
    • 0037030875 scopus 로고    scopus 로고
    • Theoretical investigation of the binding free energies and key substrate-recognition components of the replication fidelity of human DNA polymerase b
    • Florian J, Goodman MF, Warshel A. Theoretical investigation of the binding free energies and key substrate-recognition components of the replication fidelity of human DNA polymerase b. J Phys Chem B 2002;106:5739-5753.
    • (2002) J Phys Chem B , vol.106 , pp. 5739-5753
    • Florian, J.1    Goodman, M.F.2    Warshel, A.3
  • 13
    • 84961974064 scopus 로고    scopus 로고
    • Computer simulation of the chemical catalysis of DNA polymerases: Discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase
    • Florian J, Goodman MF, Warshel A. Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase. J Am Chem Soc 2003;125:8163-8177.
    • (2003) J Am Chem Soc , vol.125 , pp. 8163-8177
    • Florian, J.1    Goodman, M.F.2    Warshel, A.3
  • 14
    • 0037030879 scopus 로고    scopus 로고
    • Molecular dynamics free-energy simulations of the binding contribution to the fidelity of T7 DNA polymerase
    • Florian J, Warshel A, Goodman MF. Molecular dynamics free-energy simulations of the binding contribution to the fidelity of T7 DNA polymerase. J Phys Chem B 2002;106:5754-5760.
    • (2002) J Phys Chem B , vol.106 , pp. 5754-5760
    • Florian, J.1    Warshel, A.2    Goodman, M.F.3
  • 15
    • 0037343349 scopus 로고    scopus 로고
    • Computer simulation studies of the fidelity of DNA polymerases
    • Florian J, Goodman MF, Warshel A. Computer simulation studies of the fidelity of DNA polymerases. Biopolymers 2003;68:286-299.
    • (2003) Biopolymers , vol.68 , pp. 286-299
    • Florian, J.1    Goodman, M.F.2    Warshel, A.3
  • 16
    • 18744402486 scopus 로고    scopus 로고
    • Computer simulations of protein functions: Searching for the molecular origin of the replication fidelity of DNA polymerases
    • Florian J, Goodman MF, Warshel A. Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases. Proc Natl Acad Sci USA 2005;102:6819-6824.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 6819-6824
    • Florian, J.1    Goodman, M.F.2    Warshel, A.3
  • 18
    • 1942437505 scopus 로고    scopus 로고
    • Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing
    • Radhakrishnan R, Schlick T. Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing. Proc Natl Acad Sci USA 2004;101:5970-5975.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 5970-5975
    • Radhakrishnan, R.1    Schlick, T.2
  • 19
    • 2942666430 scopus 로고    scopus 로고
    • Highly organized but pliant active site of DNA polymerase beta: Compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses
    • Yang LJ, Beard WA, Wilson SH, Broyde S, Schlick T. Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses. Biophys J 2004;86:3392-3408.
    • (2004) Biophys J , vol.86 , pp. 3392-3408
    • Yang, L.J.1    Beard, W.A.2    Wilson, S.H.3    Broyde, S.4    Schlick, T.5
  • 20
    • 33846807511 scopus 로고    scopus 로고
    • DNA polymerase beta catalytic efficiency mirrors the Asn279-dCTP H-bonding strength
    • Martinek V, Bren U, Goodman MF, Warshel A, Florian J. DNA polymerase beta catalytic efficiency mirrors the Asn279-dCTP H-bonding strength. FEBS Lett 2007;581:775-780.
    • (2007) FEBS Lett , vol.581 , pp. 775-780
    • Martinek, V.1    Bren, U.2    Goodman, M.F.3    Warshel, A.4    Florian, J.5
  • 21
    • 33745472162 scopus 로고    scopus 로고
    • Free energy simulations of uncatalyzed DNA replication fidelity: Structure and stability of T center dot G and dTTP center dot G terminal DNA mismatches flanked by a single dangling nucleotide
    • Bren U, Martinek V, Florian J. Free energy simulations of uncatalyzed DNA replication fidelity: structure and stability of T center dot G and dTTP center dot G terminal DNA mismatches flanked by a single dangling nucleotide. J Phys Chem B 2006;110:10557-10566.
    • (2006) J Phys Chem B , vol.110 , pp. 10557-10566
    • Bren, U.1    Martinek, V.2    Florian, J.3
  • 22
    • 0034950462 scopus 로고    scopus 로고
    • Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations
    • Feig M, Zacharias M, Pettitt BM. Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations. Biophys J 2001;81:352-370.
    • (2001) Biophys J , vol.81 , pp. 352-370
    • Feig, M.1    Zacharias, M.2    Pettitt, B.M.3
  • 23
    • 1242347628 scopus 로고    scopus 로고
    • Theoretical methods for the simulation of nucleic acids
    • Orozco M, Perez A, Noy A, Luque FJ. Theoretical methods for the simulation of nucleic acids. Chem Soc Rev 2003;32:350-364.
    • (2003) Chem Soc Rev , vol.32 , pp. 350-364
    • Orozco, M.1    Perez, A.2    Noy, A.3    Luque, F.J.4
  • 24
    • 0042243498 scopus 로고    scopus 로고
    • Contribution of opening and bending dynamics to specific recognition of DNA damage
    • Seibert E, Ross JB, Osman R. Contribution of opening and bending dynamics to specific recognition of DNA damage. J Mol Biol 2003;330:687-703.
    • (2003) J Mol Biol , vol.330 , pp. 687-703
    • Seibert, E.1    Ross, J.B.2    Osman, R.3
  • 25
    • 22944481847 scopus 로고    scopus 로고
    • Efficient calculation of many stacking and pairing free energies in DNA from a few molecular dynamics simulations
    • Oostenbrink C, van Gunsteren WF. Efficient calculation of many stacking and pairing free energies in DNA from a few molecular dynamics simulations. Chemistry 2005;11:4340-4348.
    • (2005) Chemistry , vol.11 , pp. 4340-4348
    • Oostenbrink, C.1    van Gunsteren, W.F.2
  • 26
    • 26444470895 scopus 로고    scopus 로고
    • Mismatch-induced conformational distortions in polymerase support an induced-fit mechanism for fidelity
    • Arora K, Beard WA, Wilson SH, Schlick T. Mismatch-induced conformational distortions in polymerase support an induced-fit mechanism for fidelity. Biochemistry 2005;44:13328-13341.
    • (2005) Biochemistry , vol.44 , pp. 13328-13341
    • Arora, K.1    Beard, W.A.2    Wilson, S.H.3    Schlick, T.4
  • 28
    • 33745052090 scopus 로고    scopus 로고
    • Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: Evaluating amino acid group contribution and allosteric coupling for ionized residues in human pol beta
    • Xiang Y, Oelschlaeger P, Florian J, Goodman MF, Warshel A. Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: evaluating amino acid group contribution and allosteric coupling for ionized residues in human pol beta. Biochemistry 2006;45:7036-7048.
    • (2006) Biochemistry , vol.45 , pp. 7036-7048
    • Xiang, Y.1    Oelschlaeger, P.2    Florian, J.3    Goodman, M.F.4    Warshel, A.5
  • 30
    • 0033970020 scopus 로고    scopus 로고
    • Folding and binding cascades: Dynamic landscapes and population shifts
    • Kumar S, Ma BY, Tsai CJ, Sinha N, Nussinov R. Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci 2000;9:10-19.
    • (2000) Protein Sci , vol.9 , pp. 10-19
    • Kumar, S.1    Ma, B.Y.2    Tsai, C.J.3    Sinha, N.4    Nussinov, R.5
  • 31
    • 0035838382 scopus 로고    scopus 로고
    • Current topics in RNA-protein recognition: Control of specificity and biological function through induced fit and conformational capture
    • Leulliot N, Varani G. Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture. Biochemistry 2001;40:7947-7956.
    • (2001) Biochemistry , vol.40 , pp. 7947-7956
    • Leulliot, N.1    Varani, G.2
  • 33
    • 33748781457 scopus 로고    scopus 로고
    • The dynamic energy landscape of dihydrofolate reductase catalysis
    • Boehr DD, McElheny D, Dyson HJ, Wright PE. The dynamic energy landscape of dihydrofolate reductase catalysis. Science 2006;313:1638-1642.
    • (2006) Science , vol.313 , pp. 1638-1642
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wright, P.E.4
  • 34
    • 33646935697 scopus 로고    scopus 로고
    • Dynamical contributions to enzyme catalysis: Critical tests of a popular hypothesis
    • Olsson MHM, Parson WW, Warshel A. Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis. Chem Rev 2006;106:1737-1756.
    • (2006) Chem Rev , vol.106 , pp. 1737-1756
    • Olsson, M.H.M.1    Parson, W.W.2    Warshel, A.3
  • 35
    • 33750639677 scopus 로고
    • The key-lock theory and the induced fit theory
    • Koshland DE. The key-lock theory and the induced fit theory. Angew Chem Int Ed Engl 1995;33:2375-2378.
    • (1995) Angew Chem Int Ed Engl , vol.33 , pp. 2375-2378
    • Koshland, D.E.1
  • 36
    • 0036295231 scopus 로고    scopus 로고
    • Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se
    • Yang LJ, Beard WA, Wilson SH, Broyde S, Schlick T. Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se. J Mol Biol 2002;317:651-671.
    • (2002) J Mol Biol , vol.317 , pp. 651-671
    • Yang, L.J.1    Beard, W.A.2    Wilson, S.H.3    Broyde, S.4    Schlick, T.5
  • 37
    • 0035793560 scopus 로고    scopus 로고
    • DNA structure and aspartate 276 influence nucleotide binding to human DNA polymerase beta-implication for the identity of the rate-limiting conformational change
    • Van de Berg BJ, Beard WA, Wilson SH. DNA structure and aspartate 276 influence nucleotide binding to human DNA polymerase beta-implication for the identity of the rate-limiting conformational change. J Biol Chem 2001;276:3408-3416.
    • (2001) J Biol Chem , vol.276 , pp. 3408-3416
    • Van de Berg, B.J.1    Beard, W.A.2    Wilson, S.H.3
  • 38
    • 16344376908 scopus 로고    scopus 로고
    • Bakhtina M, Lee S, Wang Y, Dunlap C, Lamarche B, Tsai MD. Use of viscogens, dNTP alpha S, and rhodium(III) as probes in stopped-flow, experiments to obtain new evidence for the mechanism of catalysis by DNA polymerase beta. Biochemistry 2005;44:5177-5187.
    • Bakhtina M, Lee S, Wang Y, Dunlap C, Lamarche B, Tsai MD. Use of viscogens, dNTP alpha S, and rhodium(III) as probes in stopped-flow, experiments to obtain new evidence for the mechanism of catalysis by DNA polymerase beta. Biochemistry 2005;44:5177-5187.
  • 40
    • 23044492225 scopus 로고    scopus 로고
    • Motions of the fingers subdomain of klentaq1 are fast and not rate limiting: Implications for the molecular basis of fidelity in DNA polymerases
    • Rothwell PJ, Mitaksov V, Waksman G. Motions of the fingers subdomain of klentaq1 are fast and not rate limiting: implications for the molecular basis of fidelity in DNA polymerases. Mol Cell 2005;19:345-355.
    • (2005) Mol Cell , vol.19 , pp. 345-355
    • Rothwell, P.J.1    Mitaksov, V.2    Waksman, G.3
  • 42
    • 0001604008 scopus 로고
    • The dynamics of the primary event in rhodopsins revisited
    • Warshel A, Chu ZT, Hwang J-K. The dynamics of the primary event in rhodopsins revisited. Chem Phys 1991;158:303-314.
    • (1991) Chem Phys , vol.158 , pp. 303-314
    • Warshel, A.1    Chu, Z.T.2    Hwang, J.-K.3
  • 44
    • 0030930760 scopus 로고    scopus 로고
    • Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: Evidence for an induced fit mechanism
    • Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H. Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism. Biochemistry 1997;36:11205-11215.
    • (1997) Biochemistry , vol.36 , pp. 11205-11215
    • Sawaya, M.R.1    Prasad, R.2    Wilson, S.H.3    Kraut, J.4    Pelletier, H.5
  • 47
    • 0031883128 scopus 로고    scopus 로고
    • Structural insights into DNA polymerase beta fidelity: Hold tight if you want it right
    • Beard WA, Wilson SH. Structural insights into DNA polymerase beta fidelity: hold tight if you want it right. Chem Biol 1998;5:R7-R13.
    • (1998) Chem Biol , vol.5
    • Beard, W.A.1    Wilson, S.H.2
  • 48
    • 36549094414 scopus 로고
    • A surface constrained all-atom solvent model for effective simulations of polar solutions
    • King G, Warshel A. A surface constrained all-atom solvent model for effective simulations of polar solutions. J Chem Phys 1989;91:3647-3661.
    • (1989) J Chem Phys , vol.91 , pp. 3647-3661
    • King, G.1    Warshel, A.2
  • 49
    • 0000115003 scopus 로고
    • A Local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations
    • Lee FS, Warshel A. A Local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations. J Chem Phys 1992;97:3100-3107.
    • (1992) J Chem Phys , vol.97 , pp. 3100-3107
    • Lee, F.S.1    Warshel, A.2
  • 50
    • 0000728542 scopus 로고
    • Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs
    • Lee FS, Chu ZT, Warshel A. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs. J Comput Chem 1993;14:161-185.
    • (1993) J Comput Chem , vol.14 , pp. 161-185
    • Lee, F.S.1    Chu, Z.T.2    Warshel, A.3
  • 52
    • 0027794972 scopus 로고
    • Targeted molecular-dynamics simulation of conformational change - Application to the T-R transition in insulin
    • Schlitter J, Engels M, Kruger P, Jacoby E, Wollmer A. Targeted molecular-dynamics simulation of conformational change - Application to the T-R transition in insulin. Mol Simul 1993;10:291-308.
    • (1993) Mol Simul , vol.10 , pp. 291-308
    • Schlitter, J.1    Engels, M.2    Kruger, P.3    Jacoby, E.4    Wollmer, A.5
  • 53
    • 0019889036 scopus 로고
    • a, proton transfer reactions, and general acid catalysis reactions in enzymes
    • a, proton transfer reactions, and general acid catalysis reactions in enzymes. Biochemistry 1981;20:3167-3177.
    • (1981) Biochemistry , vol.20 , pp. 3167-3177
    • Warshel, A.1
  • 54
    • 0014022993 scopus 로고
    • Thermodynamics Of proton dissociation in dilute aqueous solution. V. An entropy titration study of adenosine pentoses hexoses and related compounds
    • Izatt RM, Rytting JH, Hansen LD, Christensen JJ. Thermodynamics Of proton dissociation in dilute aqueous solution. V. An entropy titration study of adenosine pentoses hexoses and related compounds. J Am Chem Soc 1966;88:2641-2645.
    • (1966) J Am Chem Soc , vol.88 , pp. 2641-2645
    • Izatt, R.M.1    Rytting, J.H.2    Hansen, L.D.3    Christensen, J.J.4
  • 56
    • 0030010766 scopus 로고    scopus 로고
    • DNA polymerase beta: Pre-steady-state kinetic analysis and roles of arginine-283 in catalysis and fidelity
    • Werneburg BG, Ahn J, Zhong XJ, Hondal RJ, Kraynov VS, Tsai MD. DNA polymerase beta: pre-steady-state kinetic analysis and roles of arginine-283 in catalysis and fidelity. Biochemistry 1996;35:7041-7050.
    • (1996) Biochemistry , vol.35 , pp. 7041-7050
    • Werneburg, B.G.1    Ahn, J.2    Zhong, X.J.3    Hondal, R.J.4    Kraynov, V.S.5    Tsai, M.D.6
  • 57
    • 0034719142 scopus 로고    scopus 로고
    • DNA polymerase beta: Contributions of template-positioning and dNTP triphosphate-binding residues to catalysis and fidelity
    • Kraynov VS, Showalter AK, Liu J, Zhong XJ, Tsai MD. DNA polymerase beta: contributions of template-positioning and dNTP triphosphate-binding residues to catalysis and fidelity. Biochemistry 2000;39:16008-16015.
    • (2000) Biochemistry , vol.39 , pp. 16008-16015
    • Kraynov, V.S.1    Showalter, A.K.2    Liu, J.3    Zhong, X.J.4    Tsai, M.D.5
  • 59
    • 0033597779 scopus 로고    scopus 로고
    • Base substitution specificity of DNA polymerase beta depends on interactions in the DNA minor groove
    • Osheroff WP, Beard WA, Wilson SH, Kunkel TK. Base substitution specificity of DNA polymerase beta depends on interactions in the DNA minor groove. J Biol Chem 1999;274:20749-20752.
    • (1999) J Biol Chem , vol.274 , pp. 20749-20752
    • Osheroff, W.P.1    Beard, W.A.2    Wilson, S.H.3    Kunkel, T.K.4
  • 60
    • 0037041029 scopus 로고    scopus 로고
    • Loss of DNA polymerase beta stacking interactions with templating purines, but not pyrimidines, alters catalytic efficiency and fidelity
    • Beard WA, Shock DD, Yang XP, DeLauder SF, Wilson SH. Loss of DNA polymerase beta stacking interactions with templating purines, but not pyrimidines, alters catalytic efficiency and fidelity. J Biol Chem 2002;277:8235-8242.
    • (2002) J Biol Chem , vol.277 , pp. 8235-8242
    • Beard, W.A.1    Shock, D.D.2    Yang, X.P.3    DeLauder, S.F.4    Wilson, S.H.5
  • 61
    • 0034743155 scopus 로고    scopus 로고
    • From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding
    • Shea JE, Brooks CL. From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding. Annu Rev Phys Chem 2001;52:499-535.
    • (2001) Annu Rev Phys Chem , vol.52 , pp. 499-535
    • Shea, J.E.1    Brooks, C.L.2
  • 62
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco KW, Simons KT, Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 1998;277:985-994.
    • (1998) J Mol Biol , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 63
    • 22844456329 scopus 로고    scopus 로고
    • Using simplified protein representation as a reference potential for all-atom calculations of folding free energies
    • Fan ZZ, Hwang JK, Warshel A. Using simplified protein representation as a reference potential for all-atom calculations of folding free energies. Theor Chem Acc 1999;103:77-80.
    • (1999) Theor Chem Acc , vol.103 , pp. 77-80
    • Fan, Z.Z.1    Hwang, J.K.2    Warshel, A.3
  • 64
    • 0032055511 scopus 로고    scopus 로고
    • DNA polymerase β: Effects of gapped DNA substrates of dNTP specificity, fidelity, processivity and conformational changes
    • Ahn JW, Kraynov VS, Zhong XJ, Werneburg BG, Tsai MD. DNA polymerase β: effects of gapped DNA substrates of dNTP specificity, fidelity, processivity and conformational changes. Biochem J 1998;331:79-87.
    • (1998) Biochem J , vol.331 , pp. 79-87
    • Ahn, J.W.1    Kraynov, V.S.2    Zhong, X.J.3    Werneburg, B.G.4    Tsai, M.D.5
  • 66
    • 33747462891 scopus 로고    scopus 로고
    • Tsai YC, Johnson KA. A New paradigm for DNA polymerases specificity. Biochemistry 2006;45:9675-9687.
    • Tsai YC, Johnson KA. A New paradigm for DNA polymerases specificity. Biochemistry 2006;45:9675-9687.
  • 67
    • 33748633480 scopus 로고    scopus 로고
    • Warshel A, Sharma PK, kato M, Xiang Y, Liu H, Olsson MH. Electrostatic basis for enzyme catalysis. Chem Rev 2006;106:3210-3235.
    • Warshel A, Sharma PK, kato M, Xiang Y, Liu H, Olsson MH. Electrostatic basis for enzyme catalysis. Chem Rev 2006;106:3210-3235.
  • 68
    • 0028839740 scopus 로고
    • Reexamination of induced fit as a determinant of substrate specificity in enzymatic reactions
    • Post CB, Ray WJ. Reexamination of induced fit as a determinant of substrate specificity in enzymatic reactions. Biochemistry 1995;34:15881-15885.
    • (1995) Biochemistry , vol.34 , pp. 15881-15885
    • Post, C.B.1    Ray, W.J.2
  • 70
    • 0032031405 scopus 로고    scopus 로고
    • Electrostatic contributions to protein-protein binding affinities: Application to Rap/Raf interaction
    • Muegge I, Schweins T, Warshel A. Electrostatic contributions to protein-protein binding affinities: application to Rap/Raf interaction. Proteins 1998;30:407-423.
    • (1998) Proteins , vol.30 , pp. 407-423
    • Muegge, I.1    Schweins, T.2    Warshel, A.3
  • 71
    • 34249104188 scopus 로고    scopus 로고
    • The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies
    • Liu HB, Warshel A. The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies. Biochemistry 2007;46:6011-6025.
    • (2007) Biochemistry , vol.46 , pp. 6011-6025
    • Liu, H.B.1    Warshel, A.2
  • 72
    • 37349043876 scopus 로고
    • chemistry and enzymology. New York: Dover;
    • Jencks WP. Catalysis in chemistry and enzymology. New York: Dover; 1986.
    • (1986) Catalysis
    • Jencks, W.P.1
  • 73
    • 0002724139 scopus 로고
    • The Role Of induced fit and conformational-changes of enzymes in specificity and catalysis
    • Herschlag D. The Role Of induced fit and conformational-changes of enzymes in specificity and catalysis. Bioorg Chem 1988;16:62-96.
    • (1988) Bioorg Chem , vol.16 , pp. 62-96
    • Herschlag, D.1
  • 74
    • 0035707451 scopus 로고    scopus 로고
    • Dynamics of biochemical and biophysical reactions: Insight from computer simluations
    • Warshel A, Parson WW. Dynamics of biochemical and biophysical reactions: insight from computer simluations. Q Rev Biophys 2001;34:563-670.
    • (2001) Q Rev Biophys , vol.34 , pp. 563-670
    • Warshel, A.1    Parson, W.W.2
  • 75
    • 0034663856 scopus 로고    scopus 로고
    • How does GAP catalyze the GTPase reaction of Ras? A computer simulation study
    • Glennon TM, Villa J, Warshel A. How does GAP catalyze the GTPase reaction of Ras? A computer simulation study. Biochemistry 2000;39:9641-9651.
    • (2000) Biochemistry , vol.39 , pp. 9641-9651
    • Glennon, T.M.1    Villa, J.2    Warshel, A.3
  • 76
    • 33644776045 scopus 로고    scopus 로고
    • Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions
    • Rosta E, Klahn M, Warshel A. Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions. J Phys Chem B 2006;110:2934-2941.
    • (2006) J Phys Chem B , vol.110 , pp. 2934-2941
    • Rosta, E.1    Klahn, M.2    Warshel, A.3
  • 78
    • 33751206730 scopus 로고    scopus 로고
    • Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selected
    • Radhakrishnan R, Arora K, Wang YL, Beard WA, Wilson SH, Schlick T. Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selected. Biochemistry 2006;45:15142-15156.
    • (2006) Biochemistry , vol.45 , pp. 15142-15156
    • Radhakrishnan, R.1    Arora, K.2    Wang, Y.L.3    Beard, W.A.4    Wilson, S.H.5    Schlick, T.6
  • 79
    • 0026033193 scopus 로고
    • Pre-steady-state kinetic-analysis of processive DNA-replication including complete characterization of an exonuclease-deficient mutant
    • Patel SS, Wong I, Johnson KA. Pre-steady-state kinetic-analysis of processive DNA-replication including complete characterization of an exonuclease-deficient mutant. Biochemistry 1991;30:511-525.
    • (1991) Biochemistry , vol.30 , pp. 511-525
    • Patel, S.S.1    Wong, I.2    Johnson, K.A.3
  • 80
    • 27944436617 scopus 로고    scopus 로고
    • A thymine isostere in the templating position disrupts assembly of the closed DNA polymerase beta ternary complex
    • Kirby TW, DeRose EF, Beard WA, Wilson SH, London RE. A thymine isostere in the templating position disrupts assembly of the closed DNA polymerase beta ternary complex. Biochemistry 2005;44:15230-15237.
    • (2005) Biochemistry , vol.44 , pp. 15230-15237
    • Kirby, T.W.1    DeRose, E.F.2    Beard, W.A.3    Wilson, S.H.4    London, R.E.5
  • 81
    • 3142775571 scopus 로고    scopus 로고
    • Dynamic characterization of a DNA repair enzyme: NMR studies of [methyl-C-13]methionine-labeled DNA polymerase beta
    • Bose-Basu B, DeRose EF, Kirby TW, Mueller GA, Beard WA, Wilson SH, London RE. Dynamic characterization of a DNA repair enzyme: NMR studies of [methyl-C-13]methionine-labeled DNA polymerase beta. Biochemistry 2004;43:8911-8922.
    • (2004) Biochemistry , vol.43 , pp. 8911-8922
    • Bose-Basu, B.1    DeRose, E.F.2    Kirby, T.W.3    Mueller, G.A.4    Beard, W.A.5    Wilson, S.H.6    London, R.E.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.