Structural stability studies in adhesion molecules—role of cation–π interactions

Albeda SM (1993) Role of integrins and other cell adhesion molecules in tumor progression and metastasis. Lab Invest 68(1):4–17 Albelda SM, Buck CA (1990) Integrins and other cell adhesion molecules. FASEB J 4:2868–2880 Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25(17):3389–3402 Anbarasu A, Sethumadhavan R (2007) Exploring the role of cation–pi interactions in glycoproteins, lipid-binding proteins and RNA-binding proteins. J Theor Biol 247(2):346–353 Baldwin RL (2007) Energetics of protein folding. J Mol Biol 371(2):283–301 Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucl Acids Res 28(1):235–242 Blankenberg S, Barbaux S, Tiret L (2003) Adhesion molecules and atherosclerosis. Atherosclerosis 170(2):191–203 Boeckman B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O’Donovan C, Phan I, Pilbout S, Schneider M (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL. Nucl Acids Res 31(1):365–370 Burghardt TP, Juranic N, Macura S, Ajtai K (2002) Cation–π interaction in a folded polypeptide. Biopolymers 63(4):261–272 Chakravarty S, Varadarajan R (2002) Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study. Biochemistry 41(25):8152–8161 Chou PY, Fasman GD (1974) Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry 13(2):211–222 Chou PY, Fasman GD (1978) Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol 47:145–148 Dosztányi Z, Fiser A, Simon I (1997) Stabilization centers in proteins: identification, characterization and predictions. J Mol Biol 272(4):597–612 Dosztányi Z, Magyar C, Tusnady G, Simon I (2003) SCide: identification of stabilization centers in proteins. Bioinformatics 19(7):899–900 Dougherty DA (1996) Cation–π interactions in chemistry and biology: a new view of benzene, Phe, Tyr and Trp. Science 271(5246):163–168 Fitzkee N, Fleming PJ, Gong H, Panasik N, Street TO, Rose GD (2005) Are proteins made from a limited parts list? Biochem Sci 30(2):73–80 Fleming PJ, Gong H, Rose GD (2006) Secondary structure determines protein topology. Prot Sci 15:1829–1834 Gallivan JP, Dougherty DA (1999) Cation–π interactions in structural biology. Proc Natl Acad Sci USA 96(17):9459–9464 Gilis D, Rooman M (1996) Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials. J Mol Biol 257(5):1112–1126 Gilis D, Rooman M (1997) 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(2):276–290 Glaser F, Pupko T, Paz I, Bell RE, Bechor D, Martz E, Tal NB (2003) ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19(1):163–164 Goridis C, Brunet JF (1992) NCAM: structural diversity, function and regulation of expression. Semin Cell Biol 3(3):189–197 Gromiha MM (1999) A simple method for predicting transmembrane alpha helices with better accuracy. Protein Eng 12:557–561 Gromiha MM (2003) Influence of cation–pi interactions in different folding types of membrane proteins. Biophys Chem 103(3):251–258 Gromiha MM, Selvaraj S (1997) Role of structural and sequence information in the prediction of protein stability changes: comparison between buried and partially buried mutations. J Biol Phys 23:151–162 Gromiha MM, Suwa M (2003) Variation of amino acid properties in all β-globular and outer membrane protein structures. Int J Biol Macromol 32:93–98 Gromiha MM, Suwa M (2005) Structural analysis of residues involving cation–π interactions in different folding types of membrane proteins. Int J Biol Macromol 35:55–62 Gromiha MM, Majumdar R, Ponnuswamy PK (1997) Identification of membrane spanning β strands in bacterial porins. Protein Eng 10:497–500 Gromiha MM, Thomas S, Santhosh C (2002) Role of cation–π interactions to the stability of thermophilic proteins. Prep Biochem Biotechnol 32(4):355–362 Gromiha MM, Santhosh C, Shandar A (2004) Influence of cation–π interactions to the structural stability of proteins. Int J Biol Macromol 34:203–211 Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637 Kloczkowski A, Ting KL, Jernigan RL, Garnier J (2002) Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence. Proteins 49(2):154–166 Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, Pupko T, Tal NB (2005) ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 33:W299–W302 Ma JC, Dougherty DA (1997) The cation–π interaction. Chem Rev 97(5):1303–1324 Malkov SN, Zivkovic MV, Beljanski MV, Hall MB, Zaric SD (2008) A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure. J Mol Model 14(8):769–775 Mayrose I, Graur D, Tal NB, Pupko T (2004) Comparison of site-specific rate-inference methods for sequences. Mol Biol Evol 21(9):1781–1791 Mitchell JBO, Nandi CL, McDonald IK, Thornton JM, Price SL (1994) Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding? J Mol Biol 239(2):315–331 Mulhern TD, Lopez AF, Andrea RJD, Gaunt C, Vandeleur L, Vadas MA, Booker GW, Bagley CJ (2000) The solution structure of the cytokine-binding domain of the common β-chain of the receptors for granulocyte-macrophage colony-stimulating factor, interleukin-3 and interleukin-5. J Mol Biol 297:989–1001 Munoz V, Serrano L (1994) Elucidating the folding problem of helical peptides using empirical parameters. Prot Struct Funct Genet 20:301–311 Munoz V, Serrano L (1996) Local versus nonlocal interactions in protein folding and stability—an experimentalist’s point of view. Fold Des 1(4):R71–R77 Nelson DL, Cox MM (2005) Principles of biochemistry, 4th edn. W.H. Freeman, New York Padmanabhan S, Marqusee S, Ridgeway T, Laue TM, Baldwin RL (1990) Relative helix-forming tendencies of nonpolar amino acids. Nature 344(6263):268–270 Pignatelli M, Vessey CJ, Protein (1994) Adhesion molecules: novel molecular tools in tumor pathology. Hum Pathol 25:849–856 Pupko T, Bell RE, Mayrose I, Glaser F, Tal NB (2002) Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18:S71–S77 Raines DE (2005) Cation–π interactions modulate the NMDA receptor inhibitory potencies of inhaled aromatic anesthetics. Int Congr Ser 1283:85–89 Roche PH, Branger DF, Daniel L, Bianco N, Pellet W, Pellissier JF (1997) Expression of cell adhesion molecules in normal nerves, chronic axonal neuropathies and Schwann cell tumors. Neurol Sci 151(2):127–133 Rose GD, Fleming PJ, Banavar JR, Maritan A (2006) A backbone-based theory of protein folding. Proc Natl Acad Sci USA 103(45):16623–16633 Rost B (2001) Review: protein secondary structure prediction continues to rise. J Str Biol 134(2–3):204–218 Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425 Sander C, Schneider R (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Prot Struct Funct Genet 9(1):56–68 Selvaraj S, Gromiha MM (2003) Role of hydrophobic clusters and long-range contact networks in the folding of (alpha/beta) 8 barrel proteins. Biophys J 84(3):1919–1925 Shi Z, Olson CA, Kallenbach NR (2002) Cation–π interaction in model α -helical peptides. J Am Chem Soc 124:3284–3291 Sippl MJ (1995) Knowledge based potentials for proteins. Curr Opin Struct Biol 5:229–235 Sussman JL, Harel M, Frolow F, Oefner C, Goldman A, Toker L, Silman I (1991) Atomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein. Science 253(5022):872–879 Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 22(22):4673–4680 Ward SD, Curtis CA, Hulme EC (1999) Alanine-scanning mutagenesis of trans-membrane domain 6 of the M (1) muscarinic acetylcholine receptor suggests that Tyr381 plays key roles in receptor function. Mol Pharmacol 56:1031–1041 Zhong W, Gallivan JP, Zhang Y, Li L, Lester HA, Dougherty DA (1998) From ab initio quantum mechanics to molecular neurobiology: a cation–π binding site in the nicotinic receptor. Proc Natl Acad Sci USA 95(21):12088–12093