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【交流】Aromatic-Aromatic Interaction Database 文献
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Aromatic-Aromatic Interaction Database References: 1. McGaughey GB, Gagne M, Rappe AK. p-Stacking Interactions ALIVE AND WELL IN PROTEINS. J. Biol. Chem., 1998; 273:15458-15463. 2. Burley SK, Petsko GA. Amino-aromatic interactions in proteins. FEBS., 1986; 203:139-143. 3. Hunter CA, Singh J, Thornton JM. Pi-pi interactions: the geometry and energetics of phenylalanine-phenylalanine interactions in proteins. J. Mol. Biol., 1991; 20:837-846. 4. Tatko CD, Nanda V, Lear JD, DeGrado WF. Polar Networks Control Oligomeric Assembly in Membranes. J. Am. Chem. Soc., 2006; 128:4170-4171. 5. Baud F, Karlin S. Measures of residue density in protein structures. Proc. Nat. Acad. Sci., 1999; 96:12494-12499. 6. Baker CM, Grant GH. Role of Aromatic Amino Acids in Protein-Nucleic Acid Recognition. Biopolymers, 2007; 85:456-470. 7. Sathyapriya R, Vishveshwara S. Interaction of DNA with clusters of amino acids in proteins. Nuc. Acids Res., 2004; 32:4109-4118. 8. Kannan N, Vishveshwara S. Aromatic clusters: a determinant of thermal stability of thermophilic proteins. Prot. Engg., 2000; 13:753-761. 9. Waters ML. Aromatic interactions in model systems. Curr. Opin. Chem. Biol., 2002; 6:736-741. 10. Sugimoto Y, Nakato T, Kita A, Takahashi Y, Hatae N, Tabata H, Tanaka S, Ichikawa A. A cluster of aromatic amino acids in the i2 loop plays a key role for Gs coupling in prostaglandin EP2 and EP3 receptors. J. Biol. Chem., 2004; 279:11016-11026. 11. Ma B, Elkayam T, Wolfson H, Nussinov R. Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc. Nat. Acad. Sci., 2003; 100:5772-5777. 12. Brinda KV, Vishveshwara S. Oligomeric protein structure networks: insights into protein-protein interactions. BMC Bioinfo., 2005; 6:296-311. 13. Porschke D, Jung M. Stability decrease of RNA double helices by phenylalanine-, tyrosine- and tryptophane-amides. Analysis in terms of site binding and relation to melting proteins. Nuc. Acids Res., 1982; 10:6163-6176. 14. Chourasia M, Sastry GM, Sastry GN. Proton binding sites and conformational analysis of H+K+-ATPase. Biophys. Biochem. Res. Commun., 2005; 336:961-966. 15. Adams P, East JM, Lee AG, O'connor CD. Mutational analysis of trans-membrane helices M3, M4, M5 and M7 of the fast-twitch Ca2+-ATPase. Biochem. J., 1998; 335:131-138. 16. Vasiliskov VA, Prokopenko DV, Mirzabekov AD. Parallel multiplex thermodynamic analysis of coaxial base stacking in DNA duplexes by oligodeoxyribonucleotide microchips. Nuc. Acids Res., 2001; 29:2303-2313. 17. Sivakova S, Rowan SJ. Nucleobases as supramolecular motifs. Chem. Soc. Rev., 2005; 34:9-21. 18. Serrano L, Bycroft M, Fersht AR. Aromatic-aromatic interactions and protein stability Investigation by double-mutant cycles. J. Mol. Biol., 1991; 218:465-475. 19. Watanabe T, Ariga Y, Sato U, Toratani T, Hashimoto M, Nikaidou N, Kezuka Y, Nonaka T, Sugiyama J. Aromatic residues within the substrate-binding cleft of Bacillus circulans chitinase A1 are essential for hydrolysis of crystalline chitin. Biochem. J., 2003; 376:237-244. 20. Cotte N, lle Balestre M-N, Aumelas A, MaheA E, Phalipou S, Morin D, Hibert M, Manning M, Durroux T, Barberis C, Mouillac B. Conserved aromatic residues in the transmembrane region VI of the V1a vasopressin receptor differentiate agonist vs. antagonist ligand binding. Eur. J. Biochem., 2000; 267:4253-4263. 21. Li J, Lester HA. Functional Roles of Aromatic Residues in the Ligand-Binding Domain of Cyclic Nucleotide-Gated Channels. Mole. Pharm., 1999; 55:873-882. 22. Sansom MS, Berendsen HJ. Lipid properties and the orientation of aromatic residues in OmpF, influenza M2, and alamethicin systems: molecular dynamics simulations. Biochemistry, 1998; 37:17554-61. 23. Dong G, Chakshusmathi G, Wolin SL, Reinisch KM. Structure of the La motif: a winged helix domain mediates RNA binding via a conserved aromatic patch. EMBO J., 2004; 23:1000-1007. 24. Burley SK, Petsko GA. Aromatic-Aromatic Interaction: A Mechanism of Protein Structure Stabilization. Science, 1985; 229:23-28. 25. Brooks DJ, Fresco JR. Increased frequency of cysteine, tyrosine, and phenylalanine residues since the last universal ancestor. Mol. Cell. Prot., 2002; 1:125-131. 26. Samanta U, Pal D, Chakrabarti P. Packing of aromatic rings against tryptophan residues in proteins. Acta Cryst., 1999; D55:1421-1427. 27. Janiak C. A critical account on p-p stacking in metal complexes with aromatic nitrogen-containing ligands. J. Chem. Soc., Dalton Trans., 2000; 3885-3896. 28. Sinnokrot MO, Sherrill CD. Substituent effects in p-p interactions: Sandwich and T-shaped configurations. J. Am. Chem. Soc., 2004; 126:7690-7697. 29. Tatko CD, Waters ML. Comparison of C-H...p and Hydrophobic Interactions in a beta-Hairpin Peptide: Impact on Stability and Specificity. J. Am. Chem. Soc., 2004; 126:2028-2034. 30. Cramer CJ. Essentials of computational chemistry theories and models. Second edition, John Wiley and sons Ltd, 2004. 31. Jansen F. Introduction to Computational Chemistry. Second edition, John Wiley and sons Ltd, 2007. 32. Reddy AS, Vijay D, Sastry GM, Sastry GN. From subtle to substantial: Role of metal ions on p-p interactions. J. Phys. Chem. B, 2006; 110:2479-2481. 33. Lee EC, Kim D, Jurecka P, Tarakeshwar P, Hobza P, Kim KS. Understanding of Assembly Phenomenon by Aromatic-Aromatic Interactions: Benzene Dimer and the Substituted Systems. J. Phys. Chem. A, 2007; 111:3446-3457. 34. Takeuchi H. Novel Method for Geometry Optimization of Molecular Clusters: Application to Benzene Clusters. Chem. Inf. Model., 2007; 47:104-109. 35. Sinnokrot MO, Sherrill CD. High-accuracy quantum mechanical studies of p-p interactions in benzene dimers. J. Phys. Chem. A, 2006; 110:10656-68. 36. Tauer TP, Sherrill CD. Beyond the Benzene Dimer: An Investigation of the Additivity of p-p Interactions. J. Phys. Chem. A, 2005; 109:10475-10478. 37. Gonzalez C, Lim EC. Ab Initio Study of the Intermolecular Interactions in Small Benzene Clusters: The Equillibrium Structures of Trimer, Tetramer, and Pentamer. J. Phys. Chem. A, 2001; 105:1904-1908. 38. Andreeva A, Howorth D, Brenner SE, Hubbard TJP, Chothia C, Murzin AG. SCOP database in 2004: refinements integrate structure and sequence family data. Nuc. Acids Res., 2004; 32  226-D229.39. aAlison L. Cuff; Ian Sillitoe; Tony Lewis; Oliver C. Redfern; Richard Garratt; Janet Thornton; Christine A. Orengo The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies. Nucleic Acids Research 2008; 1-5. bOrengo CA, Michie AD, Jones DT, Swindells MB, Thornton JM. CATH: A Hierarchic Classification of Protein Domain Structures. Structure, 1997; 5:1093-1108. 40. Enzyme Nomenclature 1992 [Academic Press, San Diego, California, ISBN 0-12-227164-5 (hardback), 0-12-227165-3 (paperback)] with Supplement 1 (1993), Supplement 2 (1994), Supplement 3 (1995), Supplement 4 (1997) and Supplement 5 (in Eur. J. Biochem., 1994; 223:1-5; Eur. J. Biochem., 1995; 232:1-6; Eur. J. Biochem., 1996: 237:1-5; Eur. J. Biochem., 1997; 250:1-6, and Eur. J. Biochem., 1999; 264: |
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