Investigations on unconventional hydrogen bonds in RNA binding proteins: The role of CH⋯O{double bond, long}C interactions

BioSystems

Volumn 90, Issue 3, 2007, Pages 792-801

  Anbarasu, Anand ^a   Anand, Sudha ^a   Rao, Sethumadhavan ^a  

^a VIT UNIVERSITY   (India)

Author keywords

C single bond H O double bond, long C interactions; Long range interactions; Secondary structure; Solvent accessibility; Stabilization centers; Stabilizing residues

Indexed keywords

HYDROGEN; RNA BINDING PROTEIN;

AMINO ACID; CHEMICAL BONDING; HYDROGEN; MOLECULAR ANALYSIS; PROTEIN; RNA; SOLVENT;

ARTICLE; HYDROGEN BOND; MOLECULAR INTERACTION; PREDICTION; PROTEIN CONFORMATION; PROTEIN RNA BINDING; PROTEIN SECONDARY STRUCTURE; REACTION ANALYSIS; RNA STABILITY; STRUCTURE ANALYSIS;

EID: 35649025798     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2007.04.002     Document Type: Article

References (51)

1. Anbarasu A., Anand S., Mathew L., and Sethu Madhavan R. Influence of cation-π interactions on RNA-binding proteins. Int. J. Biol. Macromol. 40 (2007) 479-483
2. Auffinger P., and Westhof E. Rules governing the orientation of the 2′-hydroxyl group in RNA. J. Mol. Biol. 274 (1997) 54-63
3. Babu M.M., Singh K.S., and Balaram P. C{single bond}H⋯O hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins. J. Mol. Biol. 322 (2002) 871-880
4. Babu M.M. NCI: a server to identify non-canonical interactions in protein structures. Nucl. Acids Res. 31 (2003) 3345-3348
5. Berger I., Egli M., and Rich A. Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 12116-12121
6. Berman H.M., Westbrook J.Z., Feng G., Gilliland T.N., Bhat H., Weissig I.N., et al. The protein data bank. Nucl. Acids Res. 28 (2000) 235-242
7. Biswas R., and Sundaralingam M. J. Mol. Biol. 270 (1997) 511-519
8. Boeckman B., Bairoch A., Apweiler R., Blatter M.C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I., Pilbout S., and Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL. Nucl. Acids Res. 31 (2003) 365-370
9. Brandl M., Lindauer K., Meyer M., and Suhnel J. Theor. Chem. Acc. 101 (1999) 103-113
10. Desiraju G.R. The C{single bond}H⋯O hydrogen bond: structural implications and supramolecular design. Acc. Chem. Soc. 29 (1996) 441-449
11. Desiraju G.R. Crystal gazing: structure prediction and polymorphism. Science 278 (1997) 404-405
12. Desiraju G.R., and Steiner T. The Weak Hydrogen Bond In Structural Chemistry and Biology (1999), Oxford University Press, New York 29-121
13. Dostanyi Z.S., Fiser A., and Simon I. Stabilization centers in proteins: identification, characterization and predictions. J. Mol. Biol. 272 (1997) 597-612
14. Dosztanyi Z.S., Magyar C.S., Tusnady E.G., and Simon I. SCide: identification of stabilization centers in proteins. Bioinformatics 19 (2003) 899-900
15. Duan G., Smith V.H., and Weaver D.F. An ab initio and data mining study on aromatic-amide interactions. Chem. Phys. Lett. 310 (1999) 323-332
16. Fabiola G.F., Krishnaswamy S., Nagarajan V., and Pattabi V. C{single bond}H⋯O hydrogen bonds in beta sheets. Acta Crystallogr. Sect. D 53 (1997) 316-320
17. Gilis D., and Rooman M. Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials. J. Mol. Biol. 257 (1996) 1112-1126
18. Gilis D., and Rooman M. Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence. J. Mol. Biol. 272 (1997) 276-290
19. Glaser F., Pupko T., Paz I., Bell R.E., Bechor D., Martz E., and Ben-Tal N. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19 (2003) 163-164
20. Glusker J.P. Acta Crystallogr. D51 (1995) 418-427
21. Gray N.S., Wodicka L., Thunnissen A.W.H., Norman T.C., Kwon S., Espinoza F.H., Morgan D.O., Barnes G., LeClerc S., Meijer L., Kim S.H., Lockhart D.J., and Schultz P.G. Science 281 (1998) 533-538
22. Gromiha M.M., and Selvaraj S. Influence of medium- and long-range interaction in different structural classes of globular proteins. J. Biol. Phys. 23 (1997) 151-162
23. Gromiha M.M., and Selvaraj S. Inter-residue interactions in protein folding and stability. Prog. Biophys. Mol. Biol. 86 (2004) 235-277
24. Gromiha M.M., Santhosh C., and Shandar A. Structural analysis of cation π interactions in DNA binding proteins. Int. J. Biol. Macromol. 34 (2004) 203-211
25. 8 barrel proteins based on hydorphobicity, long range interactions and sequence conservation. Proteins 55 (2004) 316-329
26. Harakas G., Vu T., Knobler C.B., and Hawthorne M.F. J. Am. Chem. Soc. 120 (1998) 6405-6406
27. Ibrahim B.S., and Pattabhi V. Role of weak interactions in thermal stability of proteins. Biochem. Biophys. Res. Commun. 325 (2004) 1082-1089
28. Jeffrey G.A., and Saenger W. Hydrogen Bonding in Biological Structures (1991), Springer-Verlag, Berlin
29. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
30. Kuduva S.S., Craig D.C., Nangia A., and Desiraju G.R. Cubane carboxylic acids. Crystal engineering considerations and the role of C{single bond}H⋯O hydrogen bonds in determining O{single bond}H⋯O networks. J. Am. Chem. Soc. 121 (1999) 1936-1944
31. Leonard G.A., McAuley-Hecht K., Brown T., and Hunter W.N. Acta Crystallogr. D51 (1995) 136-139
32. Levitt M., and Perutz M.F. Aromatic rings act as hydrogen bond acceptors. J. Mol. Biol. 201 (1998) 751-754
33. Mandel-Gutfreund Y., Margalit H., Jernigan R.L., and Zhurkin V.B. A role for CH⋯O interactions in protein-DNA recognition. J. Mol. Biol. 277 (1998) 1129-1140
34. Meadows E.S., De Wall S.L., Barbour L.J., Fronczek F.R., Kim M.S., and Gokel G.W. Structural and dynamic evidence for CH⋯O hydrogen bonding in lariat ethers: implications for protein structure. J. Am. Chem. Soc. 122 (2000) 3325-3335
35. Pascard C. Small molecule crystal structures as a structural basis for drug design. Acta Crystallogr. D51 (1995) 407-417
36. Rubin J., Brennan T., and Sundaralingam M. Biochemistry 11 (1972) 3112-3128
37. Saenger W. Structure and function of nucleosides and nucleotides. Angew. Chem. Int. Ed. Engl. 12 (1973) 591-601
38. Selvaraj S., and Gromiha M.M. Role of hydrophobic clusters and long-range contact networks in the folding of (alpha/beta) 8 barrel proteins. Biophys. J. 84 (2003) 1919-1925
39. Scheiner S. Hydrogen Bonding: A Theoretical Perspective (1997), Oxford University Press, New York pp. 52-290
40. Scheiner S., Kar T., and Gu Y. Strength of the C{single bond}H⋯O hydrogen bond of amino acid residues. J. Biol. Chem. 276 (2001) 9832-9837
41. Smith D.A. Am. Chem. Soc. Symp. Ser. 569 (1994) 82-219
42. Steiner T., and Saenger W. Geometry of CH{single bond}O hydrogen bonds in carbohydrate crystal structures. Analysis of neutron diffraction data. J. Am. Chem. Soc. 114 (1992) 10146-10154
43. Steiner T. Influence of CH⋯O interactions on the conformation of methyl groups quantified from neutron diffraction data. J. Phys. Chem. A 104 (2000) 433-435
44. Sussman J.L., Seeman N.C., and Berman H.M. The crystal structure of a naturally occurring dinucleotide phosphate Uridylyl 3′,5′-adenosine phosphate. Models for RNA chain folding. J. Mol. Biol. 66 (1972) 403-421
45. Takahara P.M., Frederick C.A., and Lippard S.J. Crystal structure of the anticancer drug cisplatin bound to duplex DNA. J. Am. Chem. Soc. 118 (1996) 12309-12321
46. Taylor R., and Kennard O. Crystallographic evidence for the existence of C{single bond}H. ⋯Cl hydrogen bonds. J. Am. Chem. Soc. 104 (1982) 5063-5070
47. Umezawa Y., and Nishio M. CH/π interactions as demonstrated in the crystal structure of guanine-nucleotide binding proteins, Src homology-2 domains and human growth hormone in complex with their specific ligands. Bioorg. Med. Chem. 6 (1988) 493-504
48. Umezawa Y., and Nishio M. CH/π interactions in the crystal structure of TATA-Box binding protein/DNA complexes. Bioorg. Med. Chem. 8 (2000) 2643-2650
49. Vargas R., Garza J., Dixon D.A., and Hay B.P. How strong is the C{single bond}H⋯O{double bond, long}C hydrogen bond?. J. Am. Chem. Soc. 122 (2000) 4750-4755
50. Wahl M.C., Rao S.T., and Sundaralingam M. Structure of the RNA Hexamer, r(UUCGCG), ⋯Hoogsteen-Like trans U-U Base Pairs. Nat. Struct. Biol. 3 (1996) 24-31
51. Wahl M.C., and Sundaralingam M. CH⋯O hydrogen bonding in biology. Trends Biochem. Sci. 22 (1997) 97-102