Конформационная динамика нуклеиновых кислот при взаимодействии с лигандами (1098269), страница 40
Текст из файла (страница 40)
— 2010. — Dec. — Vol. 114, no. 48. — Pp. 15723–41.21. Zirbel C. [et al.] Classification and energetics of the base-phosphate interactions in RNA. // Nucleic Acids Res. — 2009. — Aug. — Vol. 37, no. 15. —Pp. 4898–918.22. Noller H. RNA structure: reading the ribosome.
// Science. — 2005. —Sept. — Vol. 309, no. 5740. — Pp. 1508–14.26523. Dickerson R. DNA bending: the prevalence of kinkiness and the virtues of normality. // Nucleic Acids Res. — 1998. — Apr. — Vol. 26, no. 8. — Pp. 1906–26.24. El Hassan M., Calladine C. Two distinct modes of protein-induced bendingin DNA.
// J Mol Biol. — 1998. — Sept. — Vol. 282, no. 2. — Pp. 331–43.25. Olson W. [et al.] DNA sequence-dependent deformability deduced fromprotein-DNA crystal complexes. // Proc Natl Acad Sci U S A. — 1998. —Sept. — Vol. 95, no. 19. — Pp. 11163–8.26. Srinivasan A., Olson W. Nucleic acid model building: the multiple backbonesolutions associated with a given base morphology. // J Biomol Struct Dyn. —1987. — June. — Vol. 4, no.
6. — Pp. 895–938.27. Suzuki M. [et al.] Use of a 3D structure data base for understanding sequencedependent conformational aspects of DNA. // J Mol Biol. — 1997. — Dec. —Vol. 274, no. 3. — Pp. 421–35.28. Olson W. [et al.] A standard reference frame for the description of nucleic acidbase-pair geometry. // J Mol Biol. — 2001. — Oct. — Vol. 313, no.
1. —Pp. 229–37.29. Lu X., Olson W. 3DNA: a software package for the analysis, rebuilding andvisualization of three-dimensional nucleic acid structures. // Nucleic AcidsRes. — 2003. — Sept. — Vol. 31, no. 17. — Pp. 5108–21.30. Sponer J., Leszczynski J., Hobza P. Electronic properties, hydrogen bonding,stacking, and cation binding of DNA and RNA bases. // Biopolymers. —2002. — Aug. — Vol. 61, no. 1. — Pp. 3–31.26631. Pérez A. [et al.] Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. // Biophys J. — 2007. —June. — Vol.
92, no. 11. — Pp. 3817–29.32. Fürtig B. [et al.] NMR spectroscopy of RNA. // Chembiochem. — 2003. —Oct. — Vol. 4, no. 10. — Pp. 936–62.33. Sponer J., Kypr J. Relationships among rise, cup, roll and stagger in DNAsuggested by empirical potential studies of base stacking. // J Biomol StructDyn. — 1993. — Aug. — Vol. 11, no. 1. — Pp. 27–41.34. Neidle S. Principles of Nucleic Acid Structure. — Elsevier Science, 2010.35.
Altona C., Sundaralingam M. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. // J Am Chem Soc. — 1972. — Nov. — Vol. 94, no. 23. — Pp. 8205–12.36. Privé G., Yanagi K., Dickerson R. Structure of the B-DNA decamer C-C-AA-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-AT-T-G-G and C-C-A-G-G-C-C-T-G-G. // J Mol Biol.
— 1991. — Jan. — Vol.217, no. 1. — Pp. 177–99.37. Svozil D. [et al.] DNA conformations and their sequence preferences. // Nucleic Acids Res. — 2008. — June. — Vol. 36, no. 11. — Pp. 3690–706.38. Schneider B., Neidle S., Berman H. Conformations of the sugar-phosphatebackbone in helical DNA crystal structures. // Biopolymers. — 1997. —July. — Vol. 42, no. 1. — Pp. 113–24.39. Várnai P. [et al.] Alpha/gamma transitions in the B-DNA backbone. // NucleicAcids Res. — 2002. — Dec. — Vol. 30, no. 24. — Pp. 5398–406.26740. Krepl M.
[et al.] Reference simulations of noncanonical nucleic acids withdifferent variants of the AMBER force field: quadruplex DNA, quadruplexRNA and Z-DNA. // J Chem Theory Comput. — 2012. — July. — Vol. 8,no. 7. — Pp. 2506–2520.41. Jones S. [et al.] Protein-DNA interactions: A structural analysis. // J MolBiol. — 1999. — Apr. — Vol. 287, no. 5. — Pp. 877–96.42.
Lu X., Shakked Z., Olson W. A-form conformational motifs in ligand-boundDNA structures. // J Mol Biol. — 2000. — July. — Vol. 300, no. 4. — Pp. 819–40.43. Matthews B. Protein-DNA interaction. No code for recognition. // Nature. —1988. — Sept. — Vol. 335, no. 6188. — Pp. 294–5.44. Pabo C., Nekludova L. Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? // J Mol Biol. — 2000.
—Aug. — Vol. 301, no. 3. — Pp. 597–624.45. Rohs R. [et al.] Nuance in the double-helix and its role in protein-DNA recognition. // Curr Opin Struct Biol. — 2009. — Apr. — Vol. 19, no. 2. — Pp. 171–7.46. Richardson J. [et al.] RNA backbone: consensus all-angle conformers andmodular string nomenclature (an RNA Ontology Consortium contribution). //RNA. — 2008. — Mar. — Vol.
14, no. 3. — Pp. 465–81.47. Murray L. [et al.] RNA backbone is rotameric. // Proc Natl Acad Sci U S A. —2003. — Nov. — Vol. 100, no. 24. — Pp. 13904–9.48. Schneider B., Morávek Z., Berman H. RNA conformational classes. // NucleicAcids Res. — 2004. — June. — Vol. 32, no. 5. — Pp.
1666–77.26849. Duarte C., Pyle A. Stepping through an RNA structure: A novel approach toconformational analysis. // J Mol Biol. — 1998. — Dec. — Vol. 284, no. 5. —Pp. 1465–78.50. Hershkovitz E. [et al.] Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA. // Nucleic Acids Res. —2003. — Nov. — Vol. 31, no. 21. — Pp.
6249–57.51. Le Faucheur X. [et al.] Nonparametric clustering for studying RNA conformations. // IEEE/ACM Trans Comput Biol Bioinform. — 2013. — June. —Vol. 8, no. 6. — Pp. 1604–19.52. Hershkovitz E. [et al.] Statistical analysis of RNA backbone. // IEEE/ACMTrans Comput Biol Bioinform. — 2006. — Nov.
— Vol. 3, no. 1. — Pp. 33–46.53. Banás P. [et al.] Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. // Methods. — 2009. — Oct. —Vol. 49, no. 2. — Pp. 202–16.54. Lavery R. [et al.] A systematic molecular dynamics study of nearest-neighboreffects on base pair and base pair step conformations and fluctuations in BDNA. // Nucleic Acids Res. — 2010.
— Jan. — Vol. 38, no. 1. — Pp. 299–313.55. Vokacova Z. [et al.] Structure and dynamics of the ApA, ApC, CpA, and CpCRNA dinucleoside monophosphates resolved with NMR scalar spin-spin couplings. // J Phys Chem B. — 2009. — Jan. — Vol. 113, no. 4. — Pp. 1182–91.56.
Beveridge D. [et al.] Molecular dynamics simulations of the 136 uniquetetranucleotide sequences of DNA oligonucleotides. I. Research design and269results on d(CpG) steps. // Biophys J. — 2004. — Dec. — Vol. 87, no. 6. —Pp. 3799–813.57. Mlídek A. [et al.] Conformational Energies of DNA Sugar−Phosphate Backbone: Reference QM Calculations and a Comparison with Density FunctionalTheory and Molecular Mechanics // Journal of Chemical Theory and Computation. — 2010.
— Vol. 6, no. 12. — Pp. 3817–3835. — eprint: http ://pubs.acs.org/doi/pdf/10.1021/ct1004593.58. Sychrovský V. [et al.] Calculation of structural behavior of indirect NMR spinspin couplings in the backbone of nucleic acids. // J Phys Chem B. — 2006. —Nov. — Vol. 110, no. 45. — Pp. 22894–902.59. Krasovska M. [et al.] Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme. // Biophys J. — 2006. — July. —Vol. 91, no. 2. — Pp. 626–38.60.
Denning E., MacKerell A. Intrinsic contribution of the 2'-hydroxyl to RNAconformational heterogeneity. // J Am Chem Soc. — 2012. — Feb. — Vol.134, no. 5. — Pp. 2800–6.61. Cheatham T., Cieplak P., Kollman P. A modified version of the Cornell et al.force field with improved sugar pucker phases and helical repeat. // J BiomolStruct Dyn.
— 1999. — Feb. — Vol. 16, no. 4. — Pp. 845–62.62. Hart K. [et al.] Optimization of the CHARMM additive force field for DNA:Improved treatment of the BI/BII conformational equilibrium. // J Chem Theory Comput. — 2012. — Jan. — Vol. 8, no. 1. — Pp. 348–362.63. Mlýnský V.
[et al.] Extensive molecular dynamics simulations showing thatcanonical G8 and protonated A38H+ forms are most consistent with crystal270structures of hairpin ribozyme. // J Phys Chem B. — 2010. — May. — Vol.114, no. 19. — Pp. 6642–52.64. Zgarbova M. [et al.] Refinement of the Cornell et al. Nucleic Acids Force FieldBased on Reference Quantum Chemical Calculations of Glycosidic TorsionProfiles. // J Chem Theory Comput. — 2011. — Sept. — Vol. 7, no.
9. —Pp. 2886–2902.65. Jurecka P. [et al.] Density functional theory augmented with an empiricaldispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations. // J ComputChem. — 2007. — Jan.
— Vol. 28, no. 2. — Pp. 555–69.66. Zgarboví M. [et al.] A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects //Journal of Chemical Theory and Computation. — 2012. — Vol. 8, no. 9. —Pp. 3232–3242. — eprint: http://pubs.acs.org/doi/pdf/10.1021/ct3001987.67. Wolfe-Simon F. [et al.] A bacterium that can grow by using arsenic instead ofphosphorus. // Science.
— 2011. — June. — Vol. 332, no. 6034. — Pp. 1163–6.68. Mlídek A. [et al.] On the Geometry and Electronic Structure of the As-DNABackbone // The Journal of Physical Chemistry Letters. — 2011. — Vol. 2,no. 5. — Pp. 389–392. — eprint: http://pubs.acs.org/doi/pdf/10.1021/jz200015n.69. Denning E., Mackerell A. Impact of arsenic/phosphorus substitution on theintrinsic conformational properties of the phosphodiester backbone of DNA271investigated using ab initio quantum mechanical calculations. // J Am ChemSoc. — 2011.
— Apr. — Vol. 133, no. 15. — Pp. 5770–2.70. Long J. W., Ray W. J. Kinetics and thermodynamics of the formation of glucose arsenate. Reaction of glucose arsenate with phosphoglucomutase // Biochemistry. — 1973. — Vol. 12, no. 20. — Pp. 3932–3937. — eprint: http://pubs.acs.org/doi/pdf/10.1021/bi00744a023.71. Baer C. D., Edwards J. O., Rieger P. H. Kinetics of the hydrolysis of arsenate(V) triesters // Inorganic Chemistry.
— 1981. — Vol. 20, no. 3. — Pp. 905–907. — eprint: http://pubs.acs.org/doi/pdf/10.1021/ic50217a052.72. Baer C. D. [et al.] Kinetics of an associative ligand-exchange process: alcohol exchange with arsenate(V) triesters // Journal of the American ChemicalSociety. — 1980. — Vol. 102, no. 18. — Pp. 5793–5798. — eprint: http://pubs.acs.org/doi/pdf/10.1021/ja00538a016.73. Reaves M. [et al.] Absence of detectable arsenate in DNA from arsenate-grownGFAJ-1 cells. // Science. — 2012. — July. — Vol. 337, no. 6093.