"η6"-Type anion-π in biomolecular recognition

FEBS Letters

Volumn 586, Issue 23, 2012, Pages 4180-4185

  Chakravarty, Suvobrata ^a   Sheng, Zi Zhang ^a   Iverson, Bradley ^a   Moore, Brian ^a  

^a SOUTH DAKOTA STATE UNIVERSITY   (United States)

Author keywords

Anion ; Cation ; Evolutionary conservation; Non covalent interaction; Nucleic acid tetraloop

Indexed keywords

ANION; ARGININE; ASPARAGINE; ASPARTIC ACID; CATION; GLUTAMIC ACID; GLUTAMINE; GLYCINE; LYSINE; NUCLEIC ACID; PHENYLALANINE; TRYPTOPHAN; TYROSINE;

ARTICLE; GENETIC CONSERVATION; HUMAN; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; NONHUMAN; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE;

ANIONS; NUCLEIC ACIDS; PROTEINS;

EID: 84869493904     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2012.10.017     Document Type: Article

References (26)

1. K.S. Kim, P. Tarakeshwar, and J.Y. Lee Molecular clusters of pi-systems: theoretical studies of structures spectra, and origin of interaction energies Chem. Rev. 100 2000 4145 4186
2. A. Jain, V. Ramanathan, and R. Sankararamakrishnan Lone pair ⋯ pi interactions between water oxygens and aromatic residues: quantum chemical studies based on high-resolution protein structures and model compounds Protein Sci. (Protein Society) 18 2009 595 605
3. D.A. Dougherty Cation-pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp Science 271 1996 163 168
4. J.P. Gallivan, and D.A. Dougherty A computational study of cation-π interactions vs salt bridges in aqueous media: implications for protein engineering J. Am. Chem. Soc. 122 2000 870 874
5. V. Philip, J. Harris, R. Adams, D. Nguyen, J. Spiers, J. Baudry, E.E. Howell, and R.J. Hinde A survey of aspartate-phenylalanine and glutamate-phenylalanine interactions in the protein data bank: searching for anion-pi pairs Biochemistry 50 2011 2939 2950
6. M. Albrecht, C. Wessel, M. de Groot, K. Rissanen, and A. Luchow Structural versatility of anion-pi interactions in halide salts with pentafluorophenyl substituted cations J. Am. Chem. Soc. 130 2008 4600 4601
7. R.E. Dawson, A. Hennig, D.P. Weimann, D. Emery, V. Ravikumar, J. Montenegro, T. Takeuchi, S. Gabutti, M. Mayor, J. Mareda, C.A. Schalley, and S. Matile Experimental evidence for the functional relevance of anion-pi interactions Nat. Chem. 2 2010 533 538
8. D. Escudero, A. Frontera, D. Quinonero, and P.M. Deya Interplay between anion-pi and hydrogen bonding interactions J. Comput. Chem. 30 2009 75 82
9. G. Wang, and R.L. Dunbrack Jr. PISCES: a protein sequence culling server Bioinformatics 19 2003 1589 1591
10. M. Punta, P.C. Coggill, R.Y. Eberhardt, J. Mistry, J. Tate, C. Boursnell, N. Pang, K. Forslund, G. Ceric, J. Clements, A. Heger, L. Holm, E.L. Sonnhammer, S.R. Eddy, A. Bateman, and R.D. Finn The Pfam protein families database Nucleic Acids Res. 40 2012 D290 301
11. W. Li, and A. Godzik Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Bioinformatics 22 2006 1658 1659
12. S. Marsili, R. Chelli, V. Schettino, and P. Procacci Thermodynamics of stacking interactions in proteins Phys. Chem. Chem. Phys. 10 2008 2673 2685
13. S. Chakravarty, and R. Varadarajan Residue depth: a novel parameter for the analysis of protein structure and stability Structure 7 1999 723 732
14. P.J. Fleming, and F.M. Richards Protein packing: dependence on protein size, secondary structure and amino acid composition J. Mol. Biol. 299 2000 487 498
15. N. Pattabiraman, K.B. Ward, and P.J. Fleming Occluded molecular surface: analysis of protein packing J. Mol. Recognit. 8 1995 334 344
16. R.L. Baldwin, and G.D. Rose Is protein folding hierarchic? II. Folding intermediates and transition states (vol. 24, p. 77, 1999) Trends Biochem. Sci. 24 1999 185 186
17. T.D. Heightman, and A.T. Vasella Recent insights into inhibition, structure, and mechanism of configuration-retaining glycosidases Angew. Chem., Int. Ed. 38 1999 750 770
18. C.L. Berthold, D. Gocke, D. Wood, F.J. Leeper, M. Pohl, and G. Schneider Structure of the branched-chain keto acid decarboxylase (KdcA) from Lactococcus lactis provides insights into the structural basis for the chemoselective and enantioselective carboligation reaction Acta Crystallogr., Sect. D: Biol. Crystallogr. 63 2007 1217 1224
19. L. Jiang, E.A. Althoff, F.R. Clemente, L. Doyle, D. Rothlisberger, A. Zanghellini, J.L. Gallaher, J.L. Betker, F. Tanaka, C.F. Barbas, D. Hilvert, K.N. Houk, B.L. Stoddard, and D. Baker De novo computational design of retro-aldol enzymes Science 319 2008 1387 1391
20. C. Oubridge, N. Ito, P.R. Evans, C.H. Teo, and K. Nagai Crystal-structure at 1.92 Angstrom resolution of the RNA-binding domain of the U1a spliceosomal protein complexed with an RNA hairpin Nature 372 1994 432 438
21. S.R. Price, P.R. Evens, and K. Nagai Crystal structure of the spliceosomal U2B″-U2A′ protein complex bound to a fragment of U2 small nuclear RNA Nature 394 1998 645 650
22. P. Nissen, M. Kjeldgaard, S. Thirup, G. Polekhina, L. Reshetnikova, B.F.C. Clark, and J. Nyborg Crystal-structure of the ternary complex of Phe-Trna(Phe), Ef-Tu, and a Gtp Analog Science 270 1995 1464 1472
23. P. Nissen, S. Thirup, M. Kjeldgaard, and J. Nyborg The crystal structure of Cys-tRNA(Cys)-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA Struct. Fold. Des. 7 1999 143 156
24. M.A. Rould, J.J. Perona, and T.A. Steitz Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase Nature 352 1991 213 218
25. R.S. Prajapati, M. Sirajuddin, V. Durani, S. Sreeramulu, and R. Varadarajan Contribution of cation-pi interactions to protein stability Biochemistry 45 2006 15000 15010
26. S.W. Lockless, and R. Ranganathan Evolutionarily conserved pathways of energetic connectivity in protein families Science 286 1999 295 299