메뉴 건너뛰기




Volumn 105, Issue 12, 2008, Pages 4615-4620

A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT

Author keywords

Commitment probabilities; DNA repair; Reaction coordinates; Transition path sampling

Indexed keywords

6 O ALKYLGUANINE DNA ALKYLTRANSFERASE; ANTINEOPLASTIC AGENT; CYSTEINE; DNA BASE; GUANINE; NUCLEOTIDE; THYMINE; TYROSINE; DNA; DRUG DERIVATIVE; METHYLATED DNA PROTEIN CYSTEINE METHYLTRANSFERASE; O (6) METHYLGUANINE; O-(6)-METHYLGUANINE; UNCLASSIFIED DRUG;

EID: 42449162353     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0708058105     Document Type: Article
Times cited : (75)

References (39)
  • 1
    • 0028010888 scopus 로고
    • HhaI methyltransferase flips its target base out of the DNA helix
    • Klimasauskas S, Kumar S, Roberts RJ, Cheng X (1994) HhaI methyltransferase flips its target base out of the DNA helix. Cell 76:357-369.
    • (1994) Cell , vol.76 , pp. 357-369
    • Klimasauskas, S.1    Kumar, S.2    Roberts, R.J.3    Cheng, X.4
  • 2
    • 0029904839 scopus 로고    scopus 로고
    • A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA
    • Slupphaug G, et al. (1996) A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature 384:87-92.
    • (1996) Nature , vol.384 , pp. 87-92
    • Slupphaug, G.1
  • 3
    • 15844379169 scopus 로고    scopus 로고
    • Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA
    • Banerjee A, Yang W, Karplus M, Verdine GL (2005) Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature 434:612-618.
    • (2005) Nature , vol.434 , pp. 612-618
    • Banerjee, A.1    Yang, W.2    Karplus, M.3    Verdine, G.L.4
  • 4
    • 33644622321 scopus 로고    scopus 로고
    • Computational approaches for investigating base flipping in oligonucleotides
    • Priyamkumar UD MacKerell AD (2006) Computational approaches for investigating base flipping in oligonucleotides. Chem Rev 106:489-505.
    • (2006) Chem Rev , vol.106 , pp. 489-505
    • Priyamkumar, U.D.1    MacKerell, A.D.2
  • 5
    • 0030574226 scopus 로고    scopus 로고
    • Push and pull of base flipping
    • Kunkel TA, Wilson SH (1996) Push and pull of base flipping. Nature 384:25-26.
    • (1996) Nature , vol.384 , pp. 25-26
    • Kunkel, T.A.1    Wilson, S.H.2
  • 6
    • 0033579953 scopus 로고    scopus 로고
    • Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase
    • Stivers JT, Pankiewicz KW, Watanabe KA (1999) Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase. Biochemistry 38:952-963.
    • (1999) Biochemistry , vol.38 , pp. 952-963
    • Stivers, J.T.1    Pankiewicz, K.W.2    Watanabe, K.A.3
  • 7
    • 16544386633 scopus 로고    scopus 로고
    • Dynamic opening of DNA during the enzymatic search for a damaged base
    • Cao C, Jiang YL, Stivers JT, Song F (2004) Dynamic opening of DNA during the enzymatic search for a damaged base. Nat Struct Biol 11:1230-1236.
    • (2004) Nat Struct Biol , vol.11 , pp. 1230-1236
    • Cao, C.1    Jiang, Y.L.2    Stivers, J.T.3    Song, F.4
  • 8
    • 34848899274 scopus 로고    scopus 로고
    • Enzymatic capture of an extrahelical thymine in the search for uracil in DNA
    • Parker JB, et al. (2007) Enzymatic capture of an extrahelical thymine in the search for uracil in DNA. Nature 449:433-437.
    • (2007) Nature , vol.449 , pp. 433-437
    • Parker, J.B.1
  • 9
    • 31544464704 scopus 로고    scopus 로고
    • Targeted modulation of MGMT: Clinical implications
    • Liu LL, Gerson SL (2006) Targeted modulation of MGMT: Clinical implications. Clin Cancer Res 12:328-331.
    • (2006) Clin Cancer Res , vol.12 , pp. 328-331
    • Liu, L.L.1    Gerson, S.L.2
  • 10
    • 0037422594 scopus 로고    scopus 로고
    • Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase
    • Huang N, Banavali NK, MacKerell AD (2003) Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proc Natl Acad Sci USA 100:68-73.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 68-73
    • Huang, N.1    Banavali, N.K.2    MacKerell, A.D.3
  • 11
    • 0000729781 scopus 로고    scopus 로고
    • Transition path sampling and the calculation of rate constants
    • Dellago C, Bolhuis PG, Csajka FS, Chandler D (1998) Transition path sampling and the calculation of rate constants. J Chem Phys 108:1964-1977.
    • (1998) J Chem Phys , vol.108 , pp. 1964-1977
    • Dellago, C.1    Bolhuis, P.G.2    Csajka, F.S.3    Chandler, D.4
  • 12
    • 0036424048 scopus 로고    scopus 로고
    • Transition path sampling: Throwing ropes over rough mountain passes, in the dark
    • Bolhuis PG, Chandler D, Dellago C, Geissler PL (2002) Transition path sampling: Throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem 53:291-318.
    • (2002) Annu Rev Phys Chem , vol.53 , pp. 291-318
    • Bolhuis, P.G.1    Chandler, D.2    Dellago, C.3    Geissler, P.L.4
  • 13
    • 17544374740 scopus 로고    scopus 로고
    • Automatic method for identifying reaction coordinates in complex systems
    • Ma A, Dinner AR (2005) Automatic method for identifying reaction coordinates in complex systems. J Phys Chem B 109:6769-6779.
    • (2005) J Phys Chem B , vol.109 , pp. 6769-6779
    • Ma, A.1    Dinner, A.R.2
  • 14
    • 33749016486 scopus 로고    scopus 로고
    • Bias annealing: A method for obtaining transition paths de novo
    • Hu J, Ma A, Dinner AR (2006) Bias annealing: A method for obtaining transition paths de novo. J Chem Phys 125:114101.
    • (2006) J Chem Phys , vol.125 , pp. 114101
    • Hu, J.1    Ma, A.2    Dinner, A.R.3
  • 15
    • 33645807371 scopus 로고    scopus 로고
    • A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA
    • Blainey PC, vanOijen AM, Banerjee A, Verdine GL, Xie XS (2006) A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proc Natl Acad Sci USA 103:5752-5757.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 5752-5757
    • Blainey, P.C.1    vanOijen, A.M.2    Banerjee, A.3    Verdine, G.L.4    Xie, X.S.5
  • 17
    • 0034599723 scopus 로고    scopus 로고
    • Active and alkylated human AGT structures: A novel zinc site, inhibitor and extrahelical base binding
    • Daniels DS, et al. (2000) Active and alkylated human AGT structures: A novel zinc site, inhibitor and extrahelical base binding. EMBO J 19:1719-1730.
    • (2000) EMBO J , vol.19 , pp. 1719-1730
    • Daniels, D.S.1
  • 18
    • 0037424237 scopus 로고    scopus 로고
    • 6-alkylguanine-DNA alkyltransferase: Effects of protein and DNA alkylation on complex stability
    • 6-alkylguanine-DNA alkyltransferase: Effects of protein and DNA alkylation on complex stability. J Biol Chem 278:7973-7980.
    • (2003) J Biol Chem , vol.278 , pp. 7973-7980
    • Rasimas, J.J.1    Pegg, A.E.2    Fried, M.G.3
  • 19
    • 34047273003 scopus 로고    scopus 로고
    • 6-alkylguanine-DNA alkyltransferase (AGT) with short single-stranded DNAs
    • 6-alkylguanine-DNA alkyltransferase (AGT) with short single-stranded DNAs. J Biol Chem 282:3357-3366.
    • (2007) J Biol Chem , vol.282 , pp. 3357-3366
    • Rasimas, J.J.1    Kar, S.R.2    Pegg, A.E.3    Fried, M.G.4
  • 21
    • 3543029188 scopus 로고    scopus 로고
    • DNA binding and nucleotide flipping by the human DNA repair protein AGT
    • Daniels DS, et al. (2004) DNA binding and nucleotide flipping by the human DNA repair protein AGT. Nat Struct Mol Biol 11:714-720.
    • (2004) Nat Struct Mol Biol , vol.11 , pp. 714-720
    • Daniels, D.S.1
  • 22
    • 20544455000 scopus 로고    scopus 로고
    • The structure of the human AGT protein bound to DNA, its implications for damage detection
    • Duguid EM, Rice PA, He C (2005) The structure of the human AGT protein bound to DNA, its implications for damage detection. J Mol Biol 350:657-666.
    • (2005) J Mol Biol , vol.350 , pp. 657-666
    • Duguid, E.M.1    Rice, P.A.2    He, C.3
  • 23
    • 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 (1993) Targeted molecular-dynamics simulation of conformational change - Application to the T-R transition in insulin. Mol Simul 10:291-309.
    • (1993) Mol Simul , vol.10 , pp. 291-309
    • Schlitter, J.1    Engels, M.2    Kruger, P.3    Jacoby, E.4    Wollmer, A.5
  • 24
    • 34548175177 scopus 로고    scopus 로고
    • Activation mechanism of a signaling protein at atomic resolution from advanced computations
    • Ma L, Cui Q (2007) Activation mechanism of a signaling protein at atomic resolution from advanced computations. J Am Chem Soc 129:10261-10268.
    • (2007) J Am Chem Soc , vol.129 , pp. 10261-10268
    • Ma, L.1    Cui, Q.2
  • 25
    • 0344270866 scopus 로고    scopus 로고
    • Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA
    • Hagan MF, Dinner AR, Chandler D, Chakraborty AK (2003) Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA. Proc Natl Acad Sci USA 100:13922-13927.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 13922-13927
    • Hagan, M.F.1    Dinner, A.R.2    Chandler, D.3    Chakraborty, A.K.4
  • 26
    • 17644366825 scopus 로고    scopus 로고
    • The origins of high-affinity enzyme binding to an extrahelical DNA base
    • Krosky DJ, Song F, Stivers JT (2005) The origins of high-affinity enzyme binding to an extrahelical DNA base. Biochemistry 44:5949-5959.
    • (2005) Biochemistry , vol.44 , pp. 5949-5959
    • Krosky, D.J.1    Song, F.2    Stivers, J.T.3
  • 27
    • 0142027789 scopus 로고    scopus 로고
    • Transition-path sampling of hairpin folding
    • Bolhuis PG (2003) Transition-path sampling of hairpin folding. Proc Natl Acad Sci USA 100:12129-12134.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 12129-12134
    • Bolhuis, P.G.1
  • 28
    • 1942437505 scopus 로고    scopus 로고
    • Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase's closing
    • Radhakrishnan R, Schlick T (2004) Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase's closing. Proc Natl Acad Sci USA 101:5970-5975.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 5970-5975
    • Radhakrishnan, R.1    Schlick, T.2
  • 29
    • 34547628903 scopus 로고    scopus 로고
    • Reaction coordinate of an enzymatic reaction revealed by transition path sampling
    • Quaytman SL, Schwartz SD (2007) Reaction coordinate of an enzymatic reaction revealed by transition path sampling. Proc Natl Acad Sci USA 104:12253-12258.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 12253-12258
    • Quaytman, S.L.1    Schwartz, S.D.2
  • 31
    • 0037225952 scopus 로고    scopus 로고
    • A general method for the covalent labeling of fusion proteins with small molecules in vivo
    • Keppler A, et al. (2003) A general method for the covalent labeling of fusion proteins with small molecules in vivo. Nat Biotechnol 21:86-89.
    • (2003) Nat Biotechnol , vol.21 , pp. 86-89
    • Keppler, A.1
  • 32
    • 33749007263 scopus 로고    scopus 로고
    • Dynamic coupling between coordinates in a model for biomolecular isomerization
    • Ma A, Nag A, Dinner AR (2006) Dynamic coupling between coordinates in a model for biomolecular isomerization. J Chem Phys 124:144911.
    • (2006) J Chem Phys , vol.124 , pp. 144911
    • Ma, A.1    Nag, A.2    Dinner, A.R.3
  • 33
    • 84986512474 scopus 로고
    • CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
    • Brooks BR, et al. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187-217.
    • (1983) J Comput Chem , vol.4 , pp. 187-217
    • Brooks, B.R.1
  • 34
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of proteins
    • MacKerell AD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616.
    • (1998) J Phys Chem B , vol.102 , pp. 3586-3616
    • MacKerell, A.D.1
  • 35
    • 0348244547 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: 1. Parameter optimization based on small molecule and condensed phase macromolecular target data
    • Foloppe N, MacKerell AD (2000) All-atom empirical force field for nucleic acids: 1. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem 21:86-104.
    • (2000) J Comput Chem , vol.21 , pp. 86-104
    • Foloppe, N.1    MacKerell, A.D.2
  • 36
    • 0000214231 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: 2. Application to molecular dynamics simulations of DNA, RNA in solution
    • MacKerell AD, Banavali NK (2000) All-atom empirical force field for nucleic acids: 2. Application to molecular dynamics simulations of DNA, RNA in solution. J Comput Chem 21:105-120.
    • (2000) J Comput Chem , vol.21 , pp. 105-120
    • MacKerell, A.D.1    Banavali, N.K.2
  • 38
    • 33746899725 scopus 로고    scopus 로고
    • Obtaining reaction coordinates by likelihood maximization
    • Peters B, Trout BL (2006) Obtaining reaction coordinates by likelihood maximization. J Chem Phys 125:054108.
    • (2006) J Chem Phys , vol.125 , pp. 054108
    • Peters, B.1    Trout, B.L.2
  • 39
    • 34547354279 scopus 로고    scopus 로고
    • Extensions to the likelihood maximization approach for finding reaction coordinates
    • Peters B, Beckham GT, Trout BL (2007) Extensions to the likelihood maximization approach for finding reaction coordinates. J Chem Phys 127:034109.
    • (2007) J Chem Phys , vol.127 , pp. 034109
    • Peters, B.1    Beckham, G.T.2    Trout, B.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.