On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules

Journal of Molecular Biology

Volumn 279, Issue 5, 1998, Pages 1123-1136

  Luisi, Ben ^a   Orozco, Modesto ^b   Sponer, Jiri ^c   Luque, Francisco J ^b   Shakked, Zippora ^d  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF BARCELONA   (Spain)

^c J HEYROVSKÝ INSTITUTE OF PHYSICAL CHEMISTRY   (Czech Republic)

^d WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

Ab initio calculations; Amino group; DNA; Hydrogen bond; Structural database analysis

Indexed keywords

ADENINE; GUANINE; NITROGEN;

ARTICLE; CHEMICAL STRUCTURE; CRYSTAL STRUCTURE; DNA CONFORMATION; GEOMETRY; HYDROGEN BOND; MACROMOLECULE; POLARIZATION; PRIORITY JOURNAL; PROTEIN DNA INTERACTION;

EID: 0032568852     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1833     Document Type: Article

References (63)

1. Abola E.E., Bernstein F.C., Bryant S.H., Koetzle T.F., Weng J. Protein Data Bank. Allen F.H., Bergerhoff G., Sievers R. Crystallographic Databases: Information Content, Software Systems, Scientific Applications. 1987;107-132 Data Commission of the International Union of Crystallography, Bonn, Cambridge, Chester
2. Alhambra C., Luque F.J., Gago F., Orozco M. Ab initio study of stacking interactions in A- and B-DNA. J. Phys. Chem. ser. B. 101:1997;3846-3853
3. Allen F.H., Davies J.E., Galloy J.J., Johnson O., Kennard O., Macrae C.F., Mitchell E., Mitchell G.F., Smith J.M., Watson D.G. The development of versions 3 and 4 of the Cambridge Structural Database System. J. Chem. Inf. Comput. Sci. 31:1991;187
4. 3 substructures reaction pathway for the protonation of nitrogen. Acta Crystallog. sect. B. 51:1995;1068-1081
5. Bader R.F.W. Atoms in Molecules. A Quantum Theory. 1990;Clarendon, Oxford
6. Bader R.F.W. A quantum theory of molecular structure and its applications. Chem. Rev. 91:1991;893-928
7. α-H...O=C hydrogen bonds in a collagen triple helix. J. Mol. Biol. 264:1996;734-742
8. Berman H.M., Olson W.K., Beveridge D.L., Westbrook J., Gelbin A., Demeny T., Hsieh S.-H., Srinivasan A.R., Schneider B. The Nucleic Acid Database a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63:1992;751-759
9. Birnbaum G.I., Cygler M., Dudycz L., Stolarski R., Shugar D. Comparison of solid state and solution conformations of R and S epimers of 8,5′-cycloadenosine and their relevance to some enzymatic reactions. Biochemistry. 20:1981;3294-3301
10. Bludsky O., Sponer J., Leszczynski J., Spirko V., Hobza P. Amino groups in nucleic acid bases, aniline, aminopyridines, and aminotriazine are non-planar results of correlated ab initio quantum chemical calculations and anharmonic analysis of the aniline inversion motion. J. Chem. Phys. 105:1996;11042-11050
11. Bondi A. Van der Waals volume and radii. J. Phys. Chem. 68:1964;441-451
12. Brenner C., Garrison P., Gilmour J., Peisach D., Ringe D., Petsko G.A., Lowenstein J.M. Crystal structures of HINT demonstrate that histidine triad proteins are GALT-related nucleotide-binding proteins. Nature Struct. Biol. 4:1997;231
13. Bruno I.J., Cole J.C., Lommerse J.P.M., Rowland R.S., Taylor R., Verdonk M.L. Isostar-a library of information about non-bonded interactions. J. Comp. Aid. Mol. Des. 1998;. In the press
14. Busetti V., Crisma M., Toniolo C., Salvadori S., Balboni G. Alpha-beta-dehydro-amino acid residues in the design of peptide structures. Molecular and crystal structures of two folded dehydro peptides. Int. J. Biol. Macromol. 14:1992;23-28
15. Getting Started with the CSD. 1994;Cambridge Crystallographic Data Center, 12 Union Road, Cambridge, England
16. 2O), a dinucleoside monophosphate with neutral phosphodiester backbone. An X-ray crystal study. Nucl. Acids Res. 11:1983;2801-2814
17. Coll M., Frederick C.A., Wang A.H-J., Rich A. A bifurcated hydrogen-bonded conformation in the d(A·T) base-pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. Proc. Natl Acad. Sci, USA. 84:1987;8385-8389
18. Cornell W.D., Cieplak P., Bayley C.L., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. A second generation force-filled for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 117:1995;5179-5197
19. Declercq R., Herdewijn P., Van Meervelt L. 1,5-Anhydro-2,3-dideoxy-2-(guanin-9-y1)D-arabino-hexitol. Acta Crystallog. sect C. 52:1996;1213-1215
20. Derewanda Z.S., Lee L., Derewenda U. The occurrence of C-H...O hydrogen bonds in protein. J. Mol. Biol. 252:1995;248-262
21. DeWinter H.L., Blaton N.M., Peeters O.M., De Ranter C.J., Van Aetschot A., Heredewijn P. Structure of the modified nucleoside 2′,3′-dideoxy-3′-fluorocytidine. Acta Crystallog. sect C. 47:1991;832-835
22. DiGabriele A.D., Steitz T.A. A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend. J. Mol. Biol. 321:1993;1024-1039
23. DiGabriele A.D., Sanderson M.R., Steitz T.A. Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. Proc. Natl Acad. Sci. USA. 86:1989;1816-1819
24. Exall A.M., Jones M.F., Mo C.L., Myers P.L., Paternoster I.L., Singh H., Storer R., Weingarten G.G., Williamson C., Brodie A.C., Cook J., Lake D.E., Meerholz C.A., Turnbull P.J., Highcock R.M. Synthesis from (-)-aristeromycin and X-ray structure of (-)-carbovir. J. Chem. Soc. Perkin Trans. 1:1991;2467-2477
25. Fujita S., Takenaka A., Sasada Y. Model for interactions of amino acid side-chains with Watson-Crick base-pair of guanine and cytosine. Crystal structure of 9-(2-carbamoylethyl)guanine and 1-methylcytosine complex. Biochemistry. 24:1985;508-512
26. Gadre S.R., Pundlik S.S. Complementary electrostatics for the study of DNA base-pair interaction. J. Phys. Chem. sect. B. 101:1997;3298-3303
27. Hagerman P.J. Sequence-directed curvature of DNA. Nature. 321:1986;449-450
28. Haisa M., Kashino S., Yuasa T., Akigawa K. Topochemical studies. IX. The crystal and molecular structure of p-aminoacetophenone. Acta Crystallog. sect. B. 32:1976;1326-1328
29. Haran T., Crothers D.M. Cooperativity in A-tract structure and bending properties of composite TnAn blocks. Biochemistry. 28:1989;2763-2767
30. Haromy T.P., Raleigh J., Sundaraligam M. Enzyme-bound conformations of nucleotide substrates. X-ray structure and absolute configuration of 8,5′-cycloadenosine monohydrate. Biochemistry. 19:1980;1718-1722
31. Hecht H.J., Kalisz H.M., Hendle J., Schmid R.D., Schomberg D. Crystal structure of glucose oxidase from Aspergillus niger refined at 2.3 Å resolution. J. Mol. Biol. 229:1993;153-172
32. Ishida T., Doi M., Ueda H., Inoue M., Sheldrick G.M. Structural studies of the interaction between indole-derivatives and biologically important aromatic compounds. Specific ring stacking interaction on the tryptophan 7-methylguanine system comparative crystallographic studies of indole-derivatives 7-methylguanine base, nucleoside and nucleotide complexes. J. Am. Chem. Soc. 110:1988;2286-2294
33. Juo Z.S., Chiu T.K., Leiberman P.M., Baikalov I., Berk A.J., Dickerson R.E. How proteins recognize the TATA-box. J. Mol. Biol. 261:1996;239-254
34. Kim J.-J.P., Wang M., Paschke R. Crystal structures of medium chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate. Proc. Natl Acad. Sci. USA. 90:1993;7523-7527
35. Kim J.L., Burely S.K. 1.9 Å resolution structure of TBP recognizing the minor groove of TATAAAAG. Nature Struct. Biol. 1:1994;638-645
36. Koole L.H., Buck H.M., Kanters J.A., Schouten A. Molecular conformation of 2′-deoxy-3′,5′-di-O-acetyl guanosine. Crystal structure and high resolution proton nuclear magnetic resonance investigations. Can. J. Chem. 66:1988;2634-2639
37. Kraulis P.J. MOLSCRIPT a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950
38. Lai T.F., Marsh R.E. The crystal structure of adenosine. Acta Crystallog. sect B. 28:1972;1982-1989
39. Leroy J.L., Charretier E., Kochoyan M., Gueron M. Evidence from base-pair kinetics for two types of adenine tract structures in solution their relation to DNA curvature. Biochemistry. 27:1988;8894-8898
40. Lipanov A., Kopka M.L., Kaczor-Grzeskowiak M., Quintana J., Dickerson R.E. Structure of the B-DNA decamer C-C-A-A-C-I-T-T-G-G in two different space groups conformational flexibility of B-DNA. Biochemistry. 32:1993;1373-1389
41. MacKerell A.D., Wiorkiewicz-Kuczera J., Karplus M. An all-atom empirical energy function for the simulation of nucleic acids. J. Am. Chem. Soc. 117:1995;11946-11975
42. 3F. Acta Crystallog. sect. C. 40:1984;434-436
43. Nelson H.C.M., Finch J.T., Luisi B.F., Klug A. The structure of an oligo(dA)-oligo(dT) tract and its biological implications. Nature. 330:1987;221-226
44. 2O). Zh. Strukt. Khim. 28:1987;84-91
45. Perlman D.A., Kim S-H. Atomic charges for DNA constituents derived from single-crystal X-ray diffraction data. J. Mol. Biol. 211:1990;171-187
46. Shatzky-Schwartz M., Arbuckle N.D., Eisenstein M., Rabinovich D., Bareket-Samish A., Haran T.E., Luisi B.F., Shakked Z. X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature. J. Mol. Biol. 267:1997;595-623
47. Sheldrick W.S., Morr M. The stereochemistry of 3′-N-substituted 3′-deoxyadenosines. Acta Crystallog. sect. B. 36:1980;2328-23333
48. Shishkin O.V., Kolos N.N., Orlov V.D. Molecular and crystal structure of N,N′-dimethyl-5,6-diaminouracil. Kristallografiya. 42:1997;293-295
49. Sponer J., Burcl R., Hobza P. Interactions between amino groups in DNA an ab initio study and a comparison with the empirical potentials. J. Biomol. Struct. Dynam. 11:1994;1357-1376
50. Sponer J., Hobza P. Bifurcated hydrogen bonds in DNA crystal structures. An ab initio quantum chemical study. J. Am. Chem. Soc. 116:1994;709-714
51. Sponer J., Hobza P. Non-planar geometries of DNA bases. Ab initio second-order Møller-Plesset study. J. Phys. Chem. 98:1994;3161-3164
52. Sponer J., Kypr J. Close mutual contacts of the amino groups in DNA. Int. J. Biol. Macromol. 16:1994;3-6
53. Sponer J., Florian J., Leszczynski J., Hobza P. Non-planar DNA base pairs. J. Biomol. Struct. Dynam. 13:1996;827-833
54. Sponer J., Leszczynski J., Hobza P. Hydrogen bonding and stacking of DNA bases a review of quantum-chemical ab initio studies. J. Biomol. Struct. Dynam. 14:1996;117-135
55. Steiner T., Saenger W. Crystallographic evidence for the existence of C-H...O, C-H...N and C-H...C1 hydrogen bonds. J. Am. Chem. Soc. 104:1993;5063-5070
56. Takahashi S., Nakagawa F., Kawazoe K., Furukawa Y., Sato S., Tamura C., Naito A. Griseolic acid, an inhibitor of cyclic adenosine 3′-5′-monophosphate phosphodiesterase II. The structure of griseolic acid. J. Antibiot. 38:1985;830-834
57. Taylor R., Kennard O. Crystallographic evidence for the existence of C-H...O, C-H...N and C-H...C1 hydrogen bonds. J. Am. Chem. Soc. 104:1982;5063-5070
58. van der Helm D. Crystal structure of the charge transfer complex 9-cyclohexyladenine-iodine. J. Cryst. Mol. Struct. 3:1973;249-258
59. Wahl M.C., Sundaralingam M. C-H...O hydrogen bonding in biology. Trends Biochem. Sci. 22:1997;97-102
60. Wahl M.C., Rao S.T., Sundaralingam M. Crystal structure of the B-DNA hexamer d(CTCGAG) model for a A-to-B transition. Biophys. J. 70:1996;2857
61. Yamagata Y., Fukumoto S., Hamada K., Fujiwara T., Tomita K.-I. A novel guanine base-pairing. Crystal structure of a complex between 7-methylguanosine and its iodide. Nucl. Acids Res. 11:1983;6475-6486
62. Yamagata Y., Tomita K., Marubayashi N., Ueda I., Sakata S., Matsuda A., Takenuki K., Ueda ?. Molecular conformation of 2′-deoxy-2′-methylidenecytidine. A potent antineoplastic nucleoside. Nucleosid. Nucleotid. 11:1992;835-853
63. Yuan H., Quintana J.R., Dickerson R.E. Alternative structures for alternating poly(dA-dT) tracts the structure of the B-DNA decamer C-G-A-T-A-T-A-T-C-G. Biochemistry. 31:1992;8009-8021