Characterization of alpha helices interacting with nucleic acids

Computational Biology and Chemistry

Volumn 32, Issue 5, 2008, Pages 378-381

  Sreekanth, R ^a   Pattabhi, Vasantha ^a   Rajan, S S ^a  

^a UNIVERSITY OF MADRAS   (India)

Author keywords

Distortions; Helix bending; Helix geometry; Protein nucleic acid binding

Indexed keywords

ACIDS; BIOMOLECULES; CHLORINE COMPOUNDS; COMPLEXATION; CRYSTALLOGRAPHY; FLOW INTERACTIONS; HYDROGEN; HYDROGEN BONDS; MINERALOGY; NONMETALS; X RAY CRYSTALLOGRAPHY;

DISTORTIONS; HELIX BENDING; HELIX GEOMETRY; NON-BONDED INTERACTIONS; NUCLEIC ACID BINDING; PERPENDICULAR DIRECTIONS; PROTEIN NUCLEIC ACID BINDING; STRUCTURAL VARIATIONS;

NUCLEIC ACIDS;

NUCLEIC ACID; PROTEIN;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; PROTEIN BINDING; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE;

ALGORITHMS; DATABASES, PROTEIN; MODELS, MOLECULAR; NUCLEIC ACIDS; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 49949084015     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2008.06.002     Document Type: Article

References (36)

1. Balasubramanian R., Rajan S.S., and Srinivasan R. Analysis of protein crystallographic structural data. J. Theor. Biol. 67 (1977) 299-312
2. Bansal M., Kumar S., and Velavan R. HELANAL: a program to characterize helix geometry in proteins. J. Biomol. Struct. Dyn. 17 (2000) 811-819
3. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The protein data bank. Nucleic Acids Res. 28 (2000) 235-242
4. Christopher J.A., Swanson R., and Baldwin T.O. Algorithms for finding the axis of a helix: fast rotational and parametric least-squares methods. Comput. Chem. 20 (1996) 1-21
5. Defossez P.A., Baert J.L., Monnot M., and de Launoit Y. The ETS family member ERM contains an alpha-helical acidic activation domain that contacts TAFII60. Nucleic Acids Res. 25 (1997) 4455-4463
6. Dickerson R.E. DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res. 26 (1998) 1906-1926
7. Fortin A.S., Underhill D.A., and Gros P. Helix 2 of the paired domain plays a key role in the regulation of DNA-binding by the Pax-3 homeodomain. Nucleic Acids Res. 26 (1998) 4574-4581
8. Frishman D., and Argos P. Knowledge-based secondary structure assignment. Proteins Struct. Func. Genet. 23 (1995) 566-579
9. Gaston K., Bell A., Busby S., and Fried M. A comparison of the DNA bending activities of the DNA binding proteins CRP and TFIID. Nucleic Acids Res. 20 (1992) 3391-3396
10. Hashiguchi K., Stuart J.A., de Souza-Pinto N.C., and Bohr V.A. The C-terminal O helix of human Ogg1 is essential for 8-oxoguanine DNA glycosylase activity: the mitochondrial ß-Ogg1 lacks this domain and does not have glycosylase activity. Nucleic Acids Res. 32 (2004) 5596-5608
11. Hobohm U., and Sander C. Enlarged representative set of protein structures. Protein Sci. 3 (1994) 522-524
12. Hoffman M.M., Khrapov M.A., Cox J.C., Yao J., Tong L., and Ellington A.D. AANT: the amino acid ± nucleotide interaction database. Nucleic Acids Res. 32 (2004) D174-D181
13. Horton N.C., and Perona J.J. Crystallographic snapshots along a protein-induced DNA-bending pathway. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 5729-5734
14. Jones S., Daley D.T.A., Luscombe N.M., Berman H.M., and Thornton J.M. Protein-RNA interactions: a structural analysis. Nucleic Acids Res. 29 (2001) 943-954
15. Jones S., Shanahan H.P., Berman H.M., and Thornton J.M. Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res. 31 (2003) 7189-7198
16. Jones S., Barker J.A., Nobeli I., and Thornton J.M. Using structural motif templates to identify proteins with DNA binding function. Nucleic Acids Res. 31 (2003) 2811-2823
17. Kim J.L., Nikolov D.B., and Burley S.K. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365 (1993) 520-527
18. Luscombe N.M., Laskowski R.A., and Thornton J.M. NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions. Nucleic Acids Res. 25 (1997) 4940-4945
19. Luscombe N.M., Austin S.E., Berman H.M., and Thornton J.M. An overview of the structures of protein-DNA complexes. Genome Biol. 1 (2000) 01.1-001.37
20. Luscombe N.M., Laskowski R.A., and Thornton J.M. Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res. 29 (2001) 2860-2874
21. Nadassy K., Wodak S.J., and Janin J. Structural features of protein-nucleic acid recognition sites. Biochemistry 38 (1999) 1999-2017
22. Nobeli I., Laskowski R.A., Valdar W.S.J., and Thornton J.M. On the molecular discrimination between adenine and guanine by proteins. Nucleic Acids Res. 29 (2001) 4294-4309
23. Rajan S.S., and Srinivasan R. Helical segment analysis of alpha-helical regions in proteins. Biopolymers 16 (1977) 1617-1634
24. Rasko T., Finta C., and Kiss A. DNA bending induced by DNA (cytosine-5) methyltransferases. Nucleic Acids Res. 28 (2000) 3083-3091
25. Rice P.A., and Steitz T.A. Ribosomal protein L7/L12 has a helix-turn-helix motif similar to that found in DNA-binding regulatory proteins. Nucleic Acids Res. 17 (1989) 3757-3762
26. Sarai A., and Kono H. Protein-DNA recognition patterns and predictions. Annu. Rev. Biophys. Biomol. Struct. 34 (2005) 379-398
27. Sathyapriya R., and Vishveshwara S. Interaction of DNA with clusters of amino acids in proteins. Nucleic Acids Res. 32 (2004) 4109-4118
28. Schultz S.C., Shields G.C., and Steitz T.A. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 253 (1991) 1001-1007
29. Shao X., and Grishin N.V. Common fold in helix-hairpin-helix proteins. Nucleic Acids Res. 28 (2000) 2643-2650
30. Shanahan H.P., Garcia1 M.A., Jones S., and Thornton J.M. Identifying DNA-binding proteins using structural motifs and the electrostatic potential. Nucleic Acids Res. 32 (2004) 4732-4741
31. Sreekanth R., and Rajan S.S. The study of helical distortions due to environmental changes: choice of parameters. Biophys. Chem. 125 (2007) 191-200
32. Srinivasan R., Balasubramanian R., and Rajan S.S. Some new methods and general results of analysis of protein crystallographic structural data. J. Mol. Biol. 98 (1975) 739-747
33. Srinivasan R., and Rajan S.S. Best experimental helical parameters of alpha-helix from protein crystallographic structural data. Curr. Sci. India 46 (1977) 595-596
34. Sternberg M.J.E., Gabb H.A., and Jackson R.M. Predictive docking of protein-protein and protein-DNA complexes. Curr. Opin. Struct. Biol. 8 (1998) 250-256
35. Suzuki M. Common features in DNA recognition helices of eukaryotic transcription factors. EMBO J. 12 (1993) 3221-3226
36. van der Woerd M.J., Pelletier J.J., Xu S., and Friedman A.M. Restriction Enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis. Structure 9 (2001) 133-144