367. O'Brien P.J., Ellenberger T. (2003) Human alkyladenine DNA glycosylase uses acid-base catalysis for selective excision of damaged purines. Biochemistry, 42, p. 1241812429.
368. Hang В., Sagi J., Singer B. (1998) Correlation between sequence-dependent glycosylase repair and the thermal stability of oligonucleotide duplexes containing 1JV6-ethenoadenine. J. Biol. Chem., 273, p. 33406-33413.
369. Likhite V.S., Cass E.I., Anderson S.D., Yates J.R., Nardulli A.M. (2004) Interaction of estrogen receptor with 3-methyladenine DNA glycosylase modulates transcription and DNA repair. J. Biol. Chem., 279, p. 16875-16882.
370. Miao F., Bouziane M., Dammann R., Masutani C., Hanaoka F., Pfeifer G., O'Connor T.R. (2000) 3-Methyladenine-DNA glycosylase (MPG protein) interacts with human RAD23 proteins. J. Biol Chem., 275, p. 28433-28438.
371. Dodson M.L., Michaels M.L., Lloyd R.S. (1994) Unified catalytic mechanism for DNA glycosylases. J. Biol Chem., 269, p. 32709-32712.
372. Fuxreiter M., Warshel A., Osman R. (1999) Role of active site residues in the glycosylase step of T4 endonuclease V. Computer simulation studies on ionization states. Biochemistry, 38, p. 9577-9589.
373. Osman R., Fuxreiter M., Luo N. (2000) Specificity of damage recognition and catalysis of DNA repair. Comput. Chem., 24, p. 331-339.
374. Bianchet M.A., Seiple L.A., Jiang Y.L., Ichikawa Y„ Amzel L.M., Stivers J.T. (2003) Electrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase. Biochemistry, 42, p. 12455-12460.
375. Berti P.J., McCann J.A.B. (2006) Toward a detailed understanding of base excision repair enzymes: Transition state and mechanistic analyses of AA-glycoside hydrolysis and /»/-glycoside transfer. Chem. Rev., 106, p. 506-555.
376. Dinner A.R., Blackburn G.M., Karplus M. (2001) Uracil-DNA glycosylase acts by substrate autocatalysis. Nature, 413, p. 752-755.
377. Deng L., Scharer O.D., Verdine G.L. (1997) Unusually strong binding of a designed transition-state analog to a base-excision DNA repair protein J. Am. Chem. Soc., 119, p. 7865-7866.
378. Scharer O.D., Nash H.M., Jiricny J.,. Laval J., Verdine G.L. (1998) Specific binding of a designed pyrrolidine abasic site analog to multiple DNA glycosylases. J. Biol Chem., 273, p. 8592-8597.
379. McCullough A.K., Sanchez A., Dodson M.L., Marapaka P., Taylor J.-S., Lloyd R.S. (2001) The reaction mechanism of DNA glycosylase/AP lyases at abasic sites. Biochemistry, 40, p. 561-568.
380. Mol C.D., Arvai A.S., Slupphaug G., Kavli B., Alseth I., Krokan H.E., Tainer J.A. (1995) Crystal structure and mutational analysis of human uracil-DNA glycosylase: Structural basis for specificity and catalysis. Cell, 80, p. 869-878.
381. Sawa R., McAuley-Hecht K., Brown T., Pearl L. (1995) The structural basis of specific base-excision repair by uracil-DNA glycosylase. Nature, 373, p. 487-493.
382. Jiang Y.L., Stivers J.T. (2002) Mutational analysis of the base-flipping mechanism of uracil DNA glycosylase. Biochemistry, 41, p. 11236-11247.
383. Wong I., Lundquist A.J., Bernards A.S., Mosbaugh D.W. (2002) Presteady-state analysis of a single catalytic turnover by Escherichia coli uracil-DNA glycosylase reveals a "pinch-/7«//-push" mechanism. J. Biol. Chem., 277, p. 19424-19432.
384. Kavli B., Slupphaug G., Mol C.D., Arvai A.S., Petersen S.B., Tainer J.A., Krokan H.E. (1996) Excision of cytosine and thymine from DNA by mutants of human uracil-DNA glycosylase. EMBOJ., 15, p. 3442-3447.
385. Barrett T.E., Sawa R., Panayotou G., Barlow T., Brown T., Jiricny J., Pearl L.H. (1998) Crystal structure of a G:T/U mismatch-specific DNA glycosylase: Mismatch recognition by complementary-strand interactions. Cell, 92, p. 117-129.
386. Barrett T.E., Sawa R., Barlow T., Brown T., Jiricny J., Pearl L.H. (1998) Structure of a DNA base-excision product resembling a cisplatin inter-strand adduct Nat. Struct. Biol., 5, p. 697-701.
387. Baba D., Maita N., Jee J.-G., Uchimura Y., Saitoh H., Sugasawa K., Hanaoka F., Tochio H., Hiroaki H., Shirakawa M. (2005) Crystal structure of thymine DNA glycosylase conjugated to SUMO-1. Nature, 435, p. 979-982.
388. Hoseki J., Okamoto A., Masui R., Shibata T., Inoue Y., Yokoyama S., Kuramitsu S. (2003) Crystal structure of a family 4 uracil-DNA glycosylase from Thermus thermophilus HB8. J. Mol. Biol., 333, p. 515-526.
389. Harrison S.C., Aggarwal A.K. (1990) DNA recognition by proteins with the helix-turn-helix motif. Annu. Rev. Biochem., 59, p. 933-969.
390. Doherty A.J., Serpell L.C., Ponting C.P. (1996) The helix-hairpin-helix DNA-binding motif: A structural basis for non-sequence-specific recognition of DNA. Nucleic Acids Res., 24, p. 2488-2497.
391. Guan Y., Manuel R.C., Arvai A.S., Parikh S.S., Mol C.D., Miller J.H., Lloyd R.S., Tainer J.A. (1998) MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily. Nat. Struct. Biol., 5, p. 1058-1064.
392. Fromme J.C., Banerjee A., Huang S.J., Verdine G.L. (2004) Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase. Nature, 427, p. 652-656.
393. Bernards A.S., Miller J.K., Bao K.K., Wong I. (2002) Flipping duplex DNA inside out: A double base-flipping reaction mechanism by Escherichia coli MutY adenine glycosylase. J. Biol. Chem., 277, p. 20960-20964.
394. Wong I., Bernards A.S., Miller J.K., Wirz J.A. (2003) A dimeric mechanism for contextual target recognition by MutY glycosylase. J. Biol. Chem., 278, p. 2411-2418.
395. Mol C.D., Arvai A.S., Begley T.J., Cunningham R.P., Tainer J.A. (2002) Structure and activity of a thermostable thymine-DNA glycosylase: Evidence for base twisting to remove mismatched normal DNA bases. J. Mol. Biol., 315, p. 373-384.
396. Bruner S.D., Norman D.P.G., Verdine G.L. (2000) Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. Nature, 403, p. 859-866.
397. Norman D.P.G., Bruner S.D., Verdine G.L. (2001) Coupling of substrate recognition and catalysis by a human base-excision DNA repair protein. J. Am. Chem. Soc., 123, p. 359360.
398. Bjoras M., Seeberg E., Luna L., Pearl L.H., Barrett T.E. (2002) Reciprocal "flipping" underlies substrate recognition and catalytic activation by the human 8-oxo-guanine DNA glycosylase. J. Mol. Biol, 317, p. 171-177.
399. Norman D.P.G., Chung S.J., Verdine G.L. (2003) Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase. Biochemistry, 42, p. 15641572.
400. Fromme J.C., Bruner S.D., Yang W., Karplus M., Verdine G.L. (2003) Product-assisted catalysis in base-excision DNA repair. Nat. Struct. Biol, 10, p. 204-211.
401. Chung S.J., Verdine G.L. (2004) Structures of end products resulting from lesion processing by a DNA glycosylase/Iyase. Chem. Biol, 11, p. 1643-1649.
402. Banerjee A., Yang W., Karplus M., Verdine G.L. (2005) Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA Nature, 434, p. 612-618.
403. Labahn J., Scharer O.D., Long A., Ezaz-Nikpay K., Verdine G.L., Ellenberger T.E. (1996) Structural basis for the excision repair of alkylation-damaged DNA. Cell, 86, p. 321-329.
404. Hollis T., Ichikawa Y., Ellenberger T. (2000) DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA. EMBO J., 19, p. 758-766.
405. Pelletier H., Sawaya M.R. (1996) Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase P by X-ray structural analysis. Biochemistry, 35, p. 12778-12787.
406. Wu P., Qiu C., Sohail A., Zhang X., Bhagwat A.S., Cheng X. (2003) Mismatch repair in methylated DNA: Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4. J. Biol. Chem., 278, p. 5285-5291.
407. Ohki I., Shimotake N., Fujita N., Nakao M., Shirakawa M. (1999) Solution structure of the methyl-CpG-binding domain of the methylation-dependent transcriptional repressor MBD1. EMBO J., 18, p. 6653-6661.
408. Drohat A.C., Kwon K., Krosky D.J., Stivers J.T. (2002) 3-methyladenine DNA glycosylase I is an unexpected helix-hairpin-helix superfamily member. Nat. Struct. Biol., 9, p. 659-664.
409. Metz A.H., Hollis T., Eichman B.F. (2007) DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG). EMBO J., 26, p. 2411-2420.
410. Cao C., Kwon K., Jiang Y.L., Drohat A.C., Stivers J.T. (2003) Solution structure and base perturbation studies reveal a novel mode of alkylated base recognition by 3-methyladenine DNA glycosylase I. J. Biol. Chem., 278, p. 48012-48020.
411. Morikawa K., Matsumoto O., Tsujimoto M., Katayanagi K., Ariyoshi M., Doi T., Ikehara M., Inaoka T., Ohtsuka E. (1992) X-ray structure of T4 endonuclease V: An excision repair enzyme specific for a pyrimidine dimer. Science, 256, p. 523-526.
412. Vassylyev D.G., Kashiwagi T., Mikami Y., Ariyoshi M., Iwai S., Ohtsuka E., Morikawa K. (1995) Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: Structural basis for damaged DNA recognition. Cell, 83, p. 773-782.
413. McCullough A.K., Dodson M.L., Scharer O.D., Lloyd R.S. (1997) The role of base flipping in damage recognition and catalysis by T4 endonuclease V. J. Biol. Chem., 272, p. 27210-27217.
414. Manuel R.C., Latham K.A., Dodson M.L., Lloyd R.S. (1995) Involvement of glutamic acid 23 in the catalytic mechanism of T4 endonuclease V. J. Biol Chem., 270, p. 26522661.
415. Lau A.Y.,. Scharer O.D., Samson L., Verdine G.L., Ellenberger T. (1998) Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: Mechanisms for nucleotide flipping and base excision. Cell, 95, p. 249-258.
416. Lau A.Y., Wyatt M.D., Glassner B.J., Samson L.D., Ellenberger T. (2000) Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG. Proc. Natl Acad. Sci. U.S.A., 97, p. 13573-13578.
417. Maki H., Sekiguchi M. (1992) MutT protein specifically hydrolyses a potent mutagenic substrate for DNA synthesis. Nature, 355, p. 273-275.
418. Tajiri T., Maki H., Sekiguchi M. (1995) Functional cooperation of MutT, MutM and MutY proteins in preventing mutations caused by spontaneous oxidation of guanine nucleotide in Escherichia coli. Mutat. Res., 336, p. 257-267.
419. Sakumi K., Furuichi M., Tsuzuki T., Kakuma T., Kawabata S.-i., Maki H., Sekiguchi M. (1993) Cloning and expression of cDNA for a human enzyme that hydrolyzes 8-oxo-dGTP, a mutagenic substrate for DNA synthesis. J. Biol. Chem., 268, p. 23524-23530.
420. Boland C.R. (2004) Understanding familial colorectal cancer—finding the corner pieces and filling in the center of the puzzle. Gastroenterology, 127, p. 334-338.
421. Sampson J.R., Jones S., Dolwani S., Cheadle J.P. (2005) MutYH (MYH) and colorectal cancer. Biochem. Soc. Trans., 33, p. 679-683.
422. Wooden S.H., Bassett H.M., Wood T.G., McCullough A.K. (2004) Identification of critical residues required for the mutation avoidance function of human MutY (hMYH) and implications in colorectal cancer. Cancer Lett., 205, p. 89-95.
423. Weiss J.M., Goode E.L., Ladiges W.C., Ulrich C.M. (2005) Polymorphic variation in hOGGl and risk of cancer: A review of the functional and epidemiologic literature. Mol Carcinog., 42, p. 127-141.
424. Park J., Chen L., Tockman M.S., Elahi A., Lazarus P. (2004) The human 8-oxoguanine DNA N-glycosylase 1 (hOGGl) DNA repair enzyme and its association with lung cancer risk Pharmacogenetics, 14, p. 103-109.
425. Hill J.W., Evans M.K. (2006) Dimerization and opposite base-dependent catalytic impairment of polymorphic S326C OGG1 glycosylase. Nucleic Acids Res., 34, p. 16201632.
426. Shigenaga M.K., Hagen T.M., Ames B.N. (1994) Oxidative damage and mitochondrial decay in aging. Proc. Natl Acad. Sci. U.S.A., 91, p. 10771-10778.
427. Pinz K.G., Bogenhagen D.F. (1998) Efficient repair of abasic sites in DNA by mitochondrial enzymes. Mol. Cell Biol., 18, p. 1257-1265.
428. Stierum R.H., Dianov G.L., Bohr V.A. (1999) Single-nucleotide patch base excision repair of uracil in DNA by mitochondrial protein extracts. Nucleic Acids Res., 27, p. 3712-3719.
429. Pinz K.G., Bogenhagen D.F. (2006) The influence of the DNA polymerase y accessory subunit on base excision repair by the catalytic subunit DNA Repair, 5, p. 121-128.
430. Chen D., Yu Z., Zhu Z., Lopez C.D. (2006) The p53 pathway promotes efficient mitochondrial DNA base excision repair in colorectal cancer cells. Cancer Res., 66, p. 3485-3494.
431. Lakshmipathy U., Campbell C. (2000) Mitochondrial DNA ligase III function is independent ofXrccl. Nucleic Acids Res., 28, p. 3880-3886.
432. Takao M., Aburatani H., Kobayashi K., Yasui A. (1998) Mitochondrial targeting of human DNA glycosylases for repair of oxidative DNA damage. Nucleic Acids Res., 26, p. 2917-2922.
433. Souza-Pinto N.C., Croteau D.L., Hudson E.K., Hansford R.G., Bohr V.A. (1999) Age-associated increase in 8-oxo-deoxyguanosine glycosylase/AP lyase activity in rat mitochondria Nucleic Acids Res., 27, p. 1935-1942.
434. Audebert M., Charbonnier J.B., Boiteux S., Radiceila J.P. (2002) Mitochondrial targeting of human 8-oxoguanine DNA glycosylase hOGGl is impaired by a somatic mutation found in kidney cancer. DNA Repair, 1, p. 497-505.
435. Thibodeau L., Verly W.G. (1980) Cellular localization of the apurinic/apyrimidinic endodeoxyribonucleases in rat liver. Eur. J. Biochem., 107, p. 555-563.
436. Frossi B., Tell G., Spessotto P., Colombatti A., Vitale G., Pucill C. (2002) H202 induces translocation of APE/Ref-1 to mitochondria in the Raji B-cell line. J. Cell. Physiol., 193, p. 180-186.
437. Szczesny B., Hazra T.K., Papaconstantinou J., Mitra S., Boldogh I. (2003) Age-dependent deficiency in import of mitochondrial DNA glycosylases required for repair of oxidatively damaged bases. Proc. Natl Acad. Sei. U.S.A., 100, p. 10670-10675.
438. Englander E.W., Hu Z., Sharma A., Lee H.-M., Wu Z.-H., Greeley G.H. (2002) Rat MYH, a glycosylase for repair of oxidatively damaged DNA, has brain-specific isoforms that localize to neuronal mitochondria J. Neurochem., 83, p. 1471-1480.
439. Ikeda S., Kohmoto T., Tabata R., Seki Y. (2002) Differential intracellular localization of the human and mouse endonuclease III homologs and analysis of the sorting signals. DNA Repair, 1, p. 847-854.
440. Cool B.L., Sirover M.A. (1989) Immunocytochemical localization of the base excision repair enzyme uracil DNA glycosylase in quiescent and proliferating normal human cells. Cancer Res., 49, p. 3029-3036.
441. Lee H.-M., Hu Z„ Ma H., Greeley G.H., Jr, Wang C„ Englander E.W. (2004) Developmental changes in expression and subcellular localization of the DNA repair glycosylase, MYH, in the rat brain J. Neurochem., 88, p. 394-400.
442. Fan Z., Beresford P.J., Zhang D., Xu Z., Novina C.D., Yoshida A., Pommier Y., Lieberman J. (2003) Cleaving the oxidative repair protein Apel enhances cell death mediated by granzyme A. Nat. Immunol., 4, p. 145-153.
443. Colson P., Verly W.G. (1983) Intracellular localization of rat-liver uracil-DNA glycosylase: Purification and properties of the chromatin enzyme. Eur. J. Biochem., 134, p. 415-420.
444. Campalans A., Amouroux R., Bravard A., Epe B., Radicella J.P. (2007) UVA irradiation induces relocalisation of the DNA repair protein hOGGl to nuclear speckles. J. Cell Sci., 120, p. 23-32.
445. Nagelhus T.A., Slupphaug G., Lindmo T., Krokan H.E. (1995) Cell cycle regulation and subcellular localization of the major human uracil-DNA glycosylase. Exp. Cell Res., 220, p. 292-297.
446. Tsai-Wu J.-J., Su H.-T., Wu Y.-L., Hsu S.-M., Wu C.H.H. (2000) Nuclear localization of the human wwrFhomologue hMYH. J. Cell. Biochem., 77, p. 666-677.
447. Hayashi H., Tominaga Y., Hirano S., McKenna A.E., Nakabeppu Y., Matsumoto Y. (2002) Replication-associated repair of adenine:8-oxoguanine mispairs by MYH. Curr. Biol., 12, p. 335-339.
448. Parker A.R., Eshleman J.R. (2003) Human MutY: Gene structure, protein functions and interactions, and role in carcinogenesis. Cell. Mol. Life Sci., 60, p. 2064-2083.
449. Gerchman S.E., Graziano V., Ramakrishnan V. (1994) Expression of chicken linker histones in E. colv. Sources of problems and methods for overcoming some of the difficulties. Protein Expr. Purif, 5, p. 242-251.
450. Kuchino Y., Mori F., Kasai H., Inoue H., Iwai S., Miura K., Ohtsuka E., Nishimura S. (1987) Misreading of DNA templates containing 8-hydroxydeoxyguanosine at the modified base and at adjacent residues. Nature, 327, p. 77-79.
451. Varaprasad C.V., Bulychev N., Grollman A.P., Johnson F. (1996) Synthesis of 8-oxo-7,8 -dihydro-6-<9-methyl -2' deoxyguanosine and its use as a probe to study DNA-base excision by MutY enzyme. Tetrahedron Lett., 37, p. 9-12.
452. Morningstar M.L., Kreutzer D.A., Essigmann J.M. (1997) Synthesis of oligonucleotides containing two putatively mutagenic DNA lesions: 5-hydroxy-2'-deoxyuridine and 5-hydroxy-2'-deoxycytidine. Chem. Res. Toxicol., 10, p. 1345-1350.
453. Fasman G.D., Handbook of Biochemistry and Molecular Biology. Nucleic Acids, V. 1. 1975, GRC Press: Cleveland. 656 pp.
454. Deng C.-X., Wynshaw-Boris A., Shen M.M., Daugherty C., Ornitz D.M., Leder P. (1994) Murine FGFR-1 is required for early postimplantation growth and axial organization. Genes Dev., 8, p. 3045-3057.
455. Abbondanzo S.J., Gadi I., Stewart C.L. (1993) Derivation of embryonic stem cell lines. Methods Enzymol., 225, p. 803-823.
456. Abbotts J., SenGupta D.N., Zmudzka B., Widen S.G., Notario V., Wilson S.H. (1988) Expression of human DNA polymerase (3 in Escherichia coli and characterization of the recombinant enzyme. Biochemistry, 27, p. 901-909.
457. Beard W.A., Wilson S.H. (1995) Purification and domain-mapping of mammalian DNA polymerase p. Methods Enzymol, 262, p. 98-107.
458. Gill S.C., von Hippel P.H. (1989) Calculation of protein extinction coefficients from amino acid sequence data Anal. Biochem., 182, p. 319-326.
459. Jancarik J., Kim S.-H. (1991) Sparse matrix sampling: A screening method for crystallization of proteins. J. Appl. Crystallogr., 24, p. 409-411.
460. Hendrickson W.A., Ogata C.M. (1997) Phase determination from multiwavelength anomalous diffraction measurements. Methods Enzymol., 276, p. 494-523.
461. Otwinowski Z., Minor W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, p. 307-326.
462. Pflugrath J.W. (1999) The finer things in X-ray diffraction data collection Acta Crystallogr., D55, p. 1718-1725.
463. Terwilliger T.C., Berendzen J. (1999) Automated MAD and MIR structure solution Acta Crystallogr., D55, p. 849-861.
464. Cowtan K.D. (1994) 'dm': An automated procedure for phase improvement by density modification Joint CCP4 ESF-EACBMNewslett. Protein Crystallogr., 31, p. 34-38.
465. Wang B.C. (1985) Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol., 115, p. 90-112.
466. Number 4 Collaborative Computional Project (1994) The CCPA suite: Programs for protein crystallography. Acta Crystallogr., D50, p. 760-763.
467. Jones T.A., Zou J.-Y., Cowan S.W., Kjeldgaard M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr., A47, p. 110-119.
468. Briinger A.T. (1992) Free R value: A novel statistical quantity for assessing the accuracy of crystal structures. Nature, 355, p. 472-475.
469. Sheldrick G.M., Schneider T.R. (1997) SHELXL: High-resolution refinement. Methods Enzymol, 277, p. 319-343.
470. Navaza J., Saludjian P. (1997) AMoRe: An automated molecular replacement program package. Methods Enzymol., 276, p. 581-594.
471. Matthews B.W. (1968) Solvent content of protein crystals. J. Mol. Biol., 33, p. 491-497.
472. Tong L., Rossmann M.G. (1990) The locked rotation function Acta Crystallogr., A46, p. 783-792.
473. Tong L. (1993) REPLACE, a suite of computer programs for molecular-replacement calculations. J. Appl Crystallogr., 26, p. 748-751.
474. Vagin A., Teplyakov A. (1997) MOLREP: An automated program for molecular replacement J. Appl Crystallogr., 30, p. 1022-1025.
475. Hooft R.W.W., Vriend G., Sander C., Abola E.E. (1996) Errors in protein structures. Nature, 381, p. 272.
476. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl Crystallogr., 26, p. 283-291.
477. Sayle R.A., Milner-White E.J. (1995) RASMOL: Biomolecular graphics for all. Trends Biochem. Sci., 20, p. 374-376.
478. Guex N., Peitsch M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis, 18, p. 2714-2723.
479. DeLano W.L., The PyMOL molecular graphics system. 2002. www.pymol.org
480. Lavery R., Sklenar H. (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn., 6, p. 63-91.
481. Lavery R., Sklenar H. (1989) Defining the structure of irregular nucleic acids: Conventions and principles. J. Biomol. Struct. Dyn., 6, p. 655-667.
482. Lu X.-J., Olson W.K. (2003) 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res., 31, p. 5108-5121.
483. Nicholls A., Sharp K.A., Honig B. (1991) Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins, 11, p. 281-296.
484. Fraczkiewicz R., Braun W. (1998) Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. J. Comput. Chem., 19, p. 319-333.
485. Barnett V., Lewis T., Outliers in Statistical Data. 3rd ed. Wiley Series in Probability & Statistics. 1994, New York: John Wiley & Sons. 604 pp.
486. Ferrin T.E., Huang C.C., Jarvis L.E., Langridge R. (1988) The MIDAS display system. J. Mol. Graph, 6, p. 13-27, 36-37.
487. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., Ferrin T.E. (2005) UCSF Chimera A visualization system for exploratory research and analysis. J. Comput. Chem., 25, p. 1605-1612.
488. Kraulis P.J. (1991) MOLSCRIPT a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr., 24, p. 946-950.
489. Esnouf R.M. (1997) An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J. Mol. Graph. Model., 15, p. 132-134.
490. Christopher J.A., SPOCK: The Structural Properties Observation and Calculation Kit (Program Manual). 1998: The Center for Macromolecular Design, Texas A&M University.
491. Merrit E.A., Bacon D.J. (1997) Raster3D: Photorealistic molecular graphics. Methods Enzymol., 277, p. 505-524.
492. Cheatham T.E., III, Cieplak P., Kollman P.A. (1999) A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat J. Biomol. Struct. Dyn., 16, p. 845-862.
493. Darden T., York D., Pedersen L. (1993) Particle mesh Ewald: An N-\og(N) method for Ewald sums in large systems. J. Chem. Phys., 98, p. 10089-10092.
494. Mao H., Deng Z., Wang F., Harris T.M., Stone M.P. (1998) An intercalated and thermally stable FAPY adduct of aflatoxin Bi in a DNA duplex: Structural refinement from 'H NMR. Biochemistry, 37, p. 4374-4387.
495. Martin R.L., Fox D.J., Keith T., Al-Laham M.A., Peng C.Y., Nanayakkara A., Challacombe M., Gill P.M.W., Johnson B., Chen W., Wong M.W., Andres J.L., Gonzalez C., Head-Gordon M., Replogle E.S., Pople J.A., Gaussian 98. 2001, Gaussian: Pittsburgh. 420 pp.
496. Bayly C.I., Cieplak P., Cornell W., Kollman P.A. (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges the RESP model. J. Phys. Chem., 97, p. 10269-10280.
497. Wu X., Shapiro R., Broyde S. (1999) Conformational analysis of the major DNA adduct derived from the food mutagen 2-amino-3-methylimidazo4,5-/.quinoline. Chem. Res. Toxicol., 12, p. 895-905.
498. Hingerty B.E., Ritchie R.H., Ferrell T.L., Turner J.E. (1985) Dielectric effects in biopolymers: The theory of ionic saturation revisited. Biopolymers, 24, p. 427-439.
499. Mezei M. (1997) Optimal position of solute for simulations. J. Comput. Chem., 18, p. 812-815.
500. Pinak M. (2001) Molecular dynamics simulation of thymine glycol-lesioned DNA reveals specific hydration at the lesioa J. Comput. Chem., 22, p. 1723-1731.
501. Tovchigrechko A., Vakser I.A. (2006) GRAMM-X public web server for protein-protein docking. Nucleic Acids Res., 34, p. W310-W314.
502. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, p. 3389-3402.
503. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Wheeler D.L. (2007) GenBank. Nucleic Acids Res., 35, p. D21-D25.
504. Saitou N., Nei M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol, 4, p. 406-425.
505. Sambrook J., Russell D.W., Molecular Cloning: A Laboratory Manual. 3rd ed. 2001, Cold Spring Harbor Laboratory Press. 745 pp.
506. Kuzmic P. (1996) Program DYNAFIT for the analysis of enzyme kinetic data: Application to HIV proteinase. Anal. Biochem., 237, p. 260-273.
507. Cattell R.B. (1966) The scree test for the number of factors. Multivariate Behav. Res., 1, p. 245-276.
508. Bunker D.L., Garrett B., Kliendienst T., Long G.S., III (1974) Discrete simulation methods in combustion kinetics. Combust. Flame, 23, p. 373-379.
509. Gillespie D.T. (1976) A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys., 22, p. 403-434.
510. Carey J. (1991) Gel retardation. Methods Enzymol, 208, p. 103-117.
511. Leavitt S., Freire E. (2001) Direct measurement of protein binding energetics by isothermal titration calorimetry. Curr. Opin. Struct. Biol., 11, p. 560-566.
512. Harlow E., Lane D., Antibodies: A Laboratory Manual. 1988, Cold Spring Harbor Laboratory Press. 726 pp.
513. Conlon K.A., Grollman A.P., Berrios M. (2000) Immunolocalization of 8-oxoguanine in nutrient-deprived mammalian tissue culture cells. J. Histotechnol., 23, p. 37-44.
514. Timmons T.M., Dunbar B.S. (1990) Protein blotting and immunodetection. Methods Enzymol., 182, p. 679-688.
515. Smith D.E., Gruenbaum Y., Berrios M., Fisher P.A. (1987) Biosynthesis and interconversion of Drosophila nuclear lamin isoforms during normal growth and in response to heat shock. J. Cell Biol, 105, p. 771-790.
516. Sapir T., Cahana A., Seger R., Nekhai S., Reiner O. (1999) LISI is a microtubule-associated phosphoprotein Eur. J. Biochem., 265, p. 181-188.
517. Luzzatti V. (1952) Traitement statistique des erreurs dans la détermination des structures cristallines. Acta Crystallogr., 5, p. 802-810.
518. Mol C.D., Parikh S.S., Putnam C.D., Lo T.P., Tainer J.A. (1999) DNA repair mechanisms for the recognition and removal of damaged DNA bases. Annu. Rev. Biophys. Biomol. Struct., 28, p. 101-128.
519. Burley S.K., Petsko G.A. (1985) Aromatic-aromatic interaction: A mechanism of protein structure stabilization. Science, 229, p. 23-28.
520. Bruner S.D., Norman D.P.G., Fromme J.C., Verdine G.L. (2001) Structural and mechanistic studies on repair of 8-oxoguanine in mammalian cells. Cold Spring Harb. Symp. Quant. Biol., 65, p. 103-111.
521. McCullough A.K., Dodson M.L., Lloyd R.S. (1999) Initiation of base excision repair: Glycosylase mechanisms and structures. Annu. Rev. Biochem., 68, p. 255-285.
522. Echols N., Milburn D., Gerstein M. (2003) MolMovDB: Analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res., 31, p. 478-482.
523. Kalodimos C.G., Biris N., Bonvin A.M.J.J., Levandoski M.M., Guennuegues M., Boelens R., Kaptein R. (2004) Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science, 305, p. 386-389.
524. Ramachandran G.N., Lakshminarayanan A.V., Balasubramanian R., Tegoni G. (1970) Studies on the conformation of amino acids. XII. Energy calculations on prolyl residue. Biochim. Biophys. Acta, 221, p. 165-181.
525. Milner-White E.J., Bell L.H., Maccallum P.H. (1992) Pyrrolidine ring puckering in eis and trans-proline residues in proteins and polypeptides. Different puckers are favoured in certain situations. J. Mol. Biol., 228, p. 725-734.
526. Mace J.E., Agard D.A..(1995) Kinetic and structural characterization of mutations of glycine 216 in a-Iytic protease: A new target for engineering substrate specificity. J. Mol. Biol., 254, p. 720-736.
527. Verras A., Alian A., Ortiz de Montellano P.R. (2006) Cytochrome P450 active site plasticity: Attenuation of imidazole binding in cytochrome P450cam by an L244A mutation. Protein Eng. Des. Sel., 19, p. 491-496.
