Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme (original) (raw)
Lindahl, T. Instability and decay of the primary structure of DNA. Nature362, 709–715 (1993) ArticleADSCAS Google Scholar
Loeb, L. A. A mutator phenotype in cancer. Cancer Res.61, 3230–3239 (2001) CASPubMed Google Scholar
Barnes, D. E. & Lindahl, T. Repair and genetic consequences of endogenous DNA base damage in mammalian cells. Annu. Rev. Genet.38, 445–476 (2004) ArticleCAS Google Scholar
Fromme, J. C. & Verdine, G. L. Base excision repair. Adv. Protein Chem.69, 1–41 (2004) ArticleCAS Google Scholar
Grollman, A. P. & Moriya, M. Mutagenesis by 8-oxoguanine: an enemy within. Trends Genet.9, 246–249 (1993) ArticleCAS Google Scholar
Shibutani, S., Takeshita, M. & Grollman, A. P. Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG. Nature349, 431–434 (1991) ArticleADSCAS Google Scholar
Lipscomb, L. A. et al. X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine. Proc. Natl Acad. Sci. USA92, 719–723 (1995) ArticleADSCAS Google Scholar
Oda, Y. et al. NMR studies of a DNA containing 8-hydroxydeoxyguanosine. Nucleic Acids Res.19, 1407–1412 (1991) ArticleCAS Google Scholar
Plum, G. E., Grollman, A. P., Johnson, F. & Breslauer, K. J. Influence of the oxidatively damaged adduct 8-oxodeoxyguanosine on the conformation, energetics, and thermodynamic stability of a DNA duplex. Biochemistry34, 16148–16160 (1995) ArticleCAS Google Scholar
Bowman, B. R., Lee, S., Wang, S. & Verdine, G. L. Structure of the E.coli DNA glycosylase AlkA bound to the ends of duplex DNA: a system for the structure determination of lesion-containing DNA. Structure16, 1166–1174 (2008) ArticleCAS Google Scholar
Fromme, J. C. & Verdine, G. L. DNA lesion recognition by the bacterial repair enzyme MutM. J. Biol. Chem.278, 51543–51548 (2003) ArticleCAS Google Scholar
Bruner, S. D., Norman, D. P. G. & Verdine, G. L. Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. Nature403, 859–866 (2000) ArticleADSCAS Google Scholar
Zharkov, D. O. Base excision DNA repair. Cell. Mol. Life Sci.65, 1544–1565 (2008) ArticleCAS Google Scholar
Banerjee, A., Santos, W. L. & Verdine, G. L. Structure of a DNA glycosylase searching for lesions. Science311, 1153–1157 (2006) ArticleADSCAS Google Scholar
Hsu, G. W., Ober, M., Carell, T. & Beese, L. S. Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase. Nature431, 217–221 (2004) ArticleADSCAS Google Scholar
Hu, J., Ma, A. & Dinner, A. R. A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT. Proc. Natl Acad. Sci. USA105, 4615–4620 (2008) ArticleADSCAS Google Scholar
Priyakumar, U. D. & Mackerell, A. D. NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases. J. Am. Chem. Soc.128, 678–679 (2006) ArticleCAS Google Scholar
Banavali, N. K. & MacKerell, A. D. Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. J. Mol. Biol.319, 141–160 (2002) ArticleCAS Google Scholar
Cheng, X. et al. Dynamic behavior of DNA base pairs containing 8-oxoguanine. J. Am. Chem. Soc.127, 13906–13918 (2005) ArticleCAS Google Scholar
Yang, W. Poor base stacking at DNA lesions may initiate recognition by many repair proteins. DNA Repair (Amst.)5, 654–666 (2006) ArticleCAS Google Scholar
Blainey, P. C., van Oijen, A. M., Banerjee, A., Verdine, G. L. & Xie, X. S. A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proc. Natl Acad. Sci. USA103, 5752–5757 (2006) ArticleADSCAS Google Scholar
Minetti, C. A. et al. Energetics of lesion recognition by a DNA repair protein: thermodynamic characterization of formamidopyrimidine-glycosylase (Fpg) interactions with damaged DNA duplexes. J. Mol. Biol.328, 1047–1060 (2003) ArticleCAS Google Scholar
Fedorova, O. S. et al. Stopped-flow kinetic studies of the interaction between Escherichia coli Fpg protein and DNA substrates. Biochemistry41, 1520–1528 (2002) ArticleCAS Google Scholar
Ishchenko, A. A. et al. Thermodynamic, kinetic, and structural basis for recognition and repair of 8-oxoguanine in DNA by Fpg protein from Escherichia coli . Biochemistry41, 7540–7548 (2002) ArticleCAS Google Scholar
Parker, J. B. et al. Enzymatic capture of an extrahelical thymine in the search for uracil in DNA. Nature449, 433–437 (2007) ArticleADSCAS Google Scholar
MacKerell, A. D. et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B102, 3586–3616 (1998) ArticleCAS Google Scholar
Mackerell, A. D. & Banavali, N. K. All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. J. Comput. Chem.21, 105–120 (2000) ArticleCAS Google Scholar
Foloppe, N. & Mackerell, A. D. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem.21, 86–104 (2000) ArticleCAS Google Scholar
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys.79, 926–935 (1983) ArticleADSCAS Google Scholar
Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: an _N_·log(N) method for Ewald sums in large systems. J. Chem. Phys.98, 10089 (1993) ArticleCAS Google Scholar
van der Vaart, A. & Karplus, M. Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method. J. Chem. Phys.122, 114903 (2005) ArticleADS Google Scholar
Paci, E. & Karplus, M. Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations. J. Mol. Biol.288, 441–459 (1999) ArticleCAS Google Scholar
Hu, J., Ma, A. & Dinner, A. R. Bias annealing: A method for obtaining transition paths de novo . J. Chem. Phys.125, 114101 (2006) ArticleADS Google Scholar
Torrie, G. M. & Valleau, J. P. Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J. Comput. Phys.23, 187 (1977) ArticleADS Google Scholar
Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol.276, 307–326 (1997) ArticleCAS Google Scholar
Brünger, A. T. et al. Crystallography and NMR system (CNS): a new software system for macromolecular structure determination. Acta Crystallogr. D54, 905–921 (1998) Article Google Scholar
Emsley, P. & Cowan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D60, 2126–2132 (2004) Article Google Scholar
Winn, M. D., Isupov, M. N. & Murshudov, G. N. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D57, 122–133 (2001) ArticleCAS Google Scholar
Painter, J. & Merritt, E. A. Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr. D Biol. Crystallogr.62, 439–450 (2006) Article Google Scholar
Brooks, B. R. et al. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem.4, 187 (1983) ArticleCAS Google Scholar
Macke, T. & Case, D. A. in Molecular modeling of nucleic acids (eds Leontes, N. B. & SantaLucia, J. Jr) 379–393 (American Chemical Society, 1998) Google Scholar
Allen, M. P. & Tildesley, D. J. Computer simulation of liquids (Oxford Univ. Press, 1989) MATH Google Scholar
Ryckaert, J. P., Ciccotti, G. & Berendsen, H. J. C. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of _n_-alkanes. J. Comput. Phys.23, 327–341 (1977) ArticleADSCAS Google Scholar
Berendsen, H. J. C., Postma, J. P. M., Van Gunsteren, W. F., DiNola, A. & Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys.81, 3684 (1984) ArticleADSCAS Google Scholar
Schlitter, J., Engels, M., Krueger, P., Jacoby, E. & Wollmer, A. Targeted molecular dynamics simulation of conformational change-application to the T↔R transition in insulin. Mol. Simul.10, 291–308 (1993) ArticleCAS Google Scholar
Banavali, N. K. & MacKerell, A. D. Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. J. Mol. Biol.319, 141–160 (2002) ArticleCAS Google Scholar
Kumar, S., Bouzida, D., Swendsen, R. H., Kollman, P. A. & Rosenberg, J. M. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J. Comput. Chem.13, 1011–1021 (1992) ArticleCAS Google Scholar
Rajamani, R., Naidoo, K. J. & Gao, J. Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution. J. Comput. Chem.24, 1775–1781 (2003) ArticleCAS Google Scholar