A compact review on the comparison of conventional and non-conventional interactions on the structural stability of therapeutic proteins

Interdisciplinary Sciences – Computational Life Sciences

Volumn 3, Issue 2, 2011, Pages 144-160

  Ramanathan, K ^a   Shanthi, V ^a   Sethumadhavan, Rao ^a  

^a VIT UNIVERSITY   (India)

Author keywords

C H...... interaction; cation interaction; conservation; conventional hydrogen bonds; N H...... interaction; O H...... interaction; therapeutic protein

Indexed keywords

AMINO ACID; CATION; RECOMBINANT PROTEIN; SOLVENT;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; THERMODYNAMICS;

AMINO ACID SEQUENCE; AMINO ACIDS; CATIONS; CONSERVED SEQUENCE; DATABASES, PROTEIN; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; SOLVENTS; THERMODYNAMICS;

EID: 84859475996     PISSN: 19132751     EISSN: 18671462     Source Type: Journal    
DOI: 10.1007/s12539-011-0082-9     Document Type: Article

References (75)

1. Anand, A., Sudha, A., Lazar Mathew, T., Sethumadhavan, R. 2007. Influence of cation-π interactions on RNA-binding proteins. Int J Biol Macromol 40, 479-483.
2. Armstrong, K. M., Fairman, R., Baldwin, R. L. 1993. The (i, i + 4) Phe-His interaction studied in an alaninebased alpha-helix. J Mol Biol 230, 284-291.
3. Babu, M. M. 2003. NCI: A server to identify noncanonical interactions in protein structures. Nucleic Acid Res 31, 3345-3348.
4. Baker, E. N., Hubbard, R. E. 1984. Hydrogen bonding in globular proteins. Prog Biophys Mol Biol 44, 97-179.
5. Berman, H. M., Westrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., Bourne, P. E. 2000. The protein data bank. Nucleic Acids Res 28, 235-242.
6. Brandl, M., Weiss, M. S., Jabs, A., Sühnel, J., Hilgenfeld, R. 2001. C-H......π interactions in proteins. J Mol Biol 307, 357-377.
7. Burley, S. K., Petsko, G. A. 1985. Aromatic-aromatic interaction: A mechanism of protein structure stabilization. Science 229, 23-28.
8. Burley, S. K., Petsko, G. A. 1986. Amino-aromatic interactions in proteins. FEBS Letters 203, 139-143.
9. Burley, S. K., Petsko, G. A. 1988. Weakly polar interactions in proteins. Advan Protein Chem 39, 125-189.
10. Chakrabarti, P., Bhattacharyya, R. 2007. Geometry of nonbonded interactions involving planar groups in proteins. Prog Biophys Mol Biol 95, 83-137.
11. Chakrabarti, P., Samanta, U. 1995. CH/π interaction in the packing of the adenine ring in protein structures. J Mol Biol 251, 9-14.
12. nd Edition, W. H. Freeman and Co, New York.
13. Desiraju, G., Steiner, T. 1999. The Weak Hydrogen Bond in Structural Chemistry and Biology, Oxford University Press, Oxford.
14. Dill, K. A. 1990. Dominant forces in protein folding. Biochemistry 29, 7133-7155.
15. Dosztanyi, Z. S., Fiser, A., Simon, I. 1997. Stabilization centers in proteins: Identification, characterization and predictions. J Mol Biol 272, 597-612.
16. Dosztanyi, Z. S., Magyar, C. S., Tusnady, E., Simon, I. 2003. Scide: Indentification of stabilization centers in proteins. Bioinformatics 19, 899-900.
17. Dougherty, D. A. 1996. Cation-π interactions in chemistry and biology: A new view of benzene, Phe, Tyr, and Trp. Science 271, 163-168.
18. Gallivan, J. P., Dougherty, D. A. 1999a. Cation-π interactions in structural biology. Proc Natl Acad Sci USA 96, 9459-9464.
19. Gallivan, J. P., Dougherty, D. A. 1999b. Can Lone Pairs Bind to a pi System? The Water-Hexafluorobenzene Interaction. Org Lett 1, 103-105.
20. Gazit, E. 2002. A possible role for π-stacking in the self-assembly of amyloid fibrils. FASEB J 16, 77-83.
21. th Edition, McGraw Hill, Inc. New York.
22. Glaser, F., Pupko, T., Paz, I., Bell, R. E., Bechor, D., Martz, E., Ben-Tal, N. 2003. ConSurf: Identification of functional regions in proteins by surfacemapping of phylogenetic information. Bioinformatics 19, 163-164.
23. Gromiha, M. M. 2003. Influence of cation-π interactions in different folding types of membrane proteins. Biophys Chem 103, 251-258.
24. Gromiha, M. M., Selvaraj, S. 2004. Inter-residue interactions in protein folding and stability. Prog Biophys Mol Biol 86, 235-277.
25. Gromiha, M. M., Santhosh, C., Suwa, M. 2004a. Influence of cation-π interactions in protein-DNA complexes. Polymer 45, 633-639.
26. Gromiha, M. M., Santhosh, C., Ahmad, S. 2004b. Structural analysis of cation-π interactions in DNA binding proteins. Int J Biol Macromol 34, 203-211.
27. Gromiha, M. M., Pujadas, G., Magyar, C., Selvaraj, S., Simon, I. 2004c. Locating the stabilizing residues in (alpha/beta) 8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation. Proteins 55, 316-329.
28. Gromiha, M. M., Thomas, S., Santhosh, C. 2002. Role of cation-π interactions to the stability of thermophilic proteins. Prep Biochem Biotechnol 32, 355-362.
29. Horovitz, A., Serrano, L., Avron, B., Bycroft, M., Fersht, A. 1990. Strength and co-operativity of contributions of surface salt bridges to protein stability. J Mol Biol 216, 1031-1044.
30. Ishida, T., Doi, M., Ueda, H., Inoue, M., Scheldrick, G. M. 1988. Specific ring stacking interaction on the tryptophan-7-methylguanine system: Comparative crystallographic studies of indole derivatives-7-methylguanine base, nucleoside, and nucleotide complexes. J Am Chem Soc 110, 2286-2294.
31. Jabs, A., Weiss, M. S., Hilgenfeld, R. 1999. CH/π interactions in the crystal structure of class I MHC antigens and their complexes with peptides. J Mol Biol 286, 291-304.
32. Janiak, C. 2000. A critical account on π-π stacking in metal complexes with aromatic nitrogen-containing ligands. J Chem Soc, Dalton Trans 21, 3885-3896.
33. Jeffrey, G. A., Saenger, W. 1994. Hydrogen Bonding in Biological Structures. Springer Verlag, New York.
34. Kabsch, W., Sander, C. 1983. Dictionary of protein secondary structure pattern recognition of hydrogenbonded and geometrical features. Biopolymers 22, 2577-2637.
35. Kamiichi, K., Danshita, M., Minamino, N., Doi, M., Ishidia, T., Inoue, M. 1986. Indole ring binds to 7-methylguanine base by π-π stacking interaction: Crystal structure of 7-methylguanosine 5′-monophosphatetryptamine complex. FEBS Lett 195, 57-60.
36. Kryger, G., Silman, I., Sussman, J. L. 1999. Structure of acetylcholinesterase complexed with E2020 (Aricept®): Implications for the designs of new anti-Alzheimer drugs. Structure 7, 297-307.
37. Lakatos, S., Furesz, J., Pallinger, E., Rischak, K., Schweitzer, K., Szollar, L. 1995. Noncovalent interactions in maintaining the native structure of low density lipoprotein. Biochem Biophys Res Commun 216, 414-421.
38. Lehn, J. M. 2002. Supramolecular chemistry and selfassembly special feature: Toward complex matter: Supramolecular chemistry and self-organization. Proc Natl Acad Sci USA 99, 4763-4768.
39. Levitt, M., Perutz, M. F. 1988. Aromatic rings act as hydrogen bond acceptors. J Mol Biol 201, 751-754.
40. Lins, L., Brasseur, R. 1995. The hydrophobic effect in protein folding. FASEB J 9, 535-540.
41. Liu, S., Ji, X., Gilliland, G. L., Stevens, W. J., Armstrong, R. N. 1993. Second sphere electrostatic effects in the active site of glutathione S-transferase. Observation of an on-face hydrogen bond between the sidechains of threonine 13 and the π cloud of tyrosine 6 and its influence on catalysis. J Am Chem Soc 115, 7910-7911.
42. Liu, R., Pidikiti, R., Ha, C. E., Petersen, C. E., Bhagavan, N. V., Eckenhoff, R. G. 2002. The role of electrostatic interactions in human serum albumin binding and stabilization by halothane. J Biol Chem 277, 36373-36379.
43. Ma, J. C., Dougherty, D. A. 1997. The cation-π interaction. Chem Rev 97, 1303-1324.
44. Magyar, C., Gromiha, M. M., Pujadas, G., Tusnády, G. E., Simon, I. 2005. SRide: A server for identifying stabilizing residues in proteins. Nucleic Acids Res 33, 303-305.
45. Martis, R. L., Singh, S. K., Gromiha, M. M., Santhosh, C. 2008. Role of cation-π interactions in single chain 'all-alpha' proteins. J Theor Biol 250, 655-662.
46. Matsui, I., Matsui, E., Sakai, Y., Kikuchi, H., Kawarabayasi, Y., Ura, H., Kawaguchi, S., Kuramitsu, S., Harata, K. 2000. The molecular structure of hyperthermostable aromatic aminotransferase with novel substrate specifiity from Pyrococcus horikoshii. J Biol Chem 275, 4871-4879.
47. Maury, P. A., Reinhoudt, D. N., Huskens, J. 2008. Assembly of nanoparticles on patterned surfaces by noncovalent interactions. Curr Opin Colloid Interface Sci 13, 74-80.
48. McPhail, A. T., Sim, G. A. 1965. Hydroxyl-benzene hydrogen bonding: an X-ray-study. Chem Commun, 124-125.
49. Meyer, E. A., Castellano, R. K., Diederich, F. 2003. Interactions with aromatic rings in chemical and biological recognition. Angew Chem Int Ed Engl 42, 1210-1250.
50. Muraki, M., Harata, K., Sugita, N., Sato, K. I. 2000. Protein-carbohydrate interactions in human lysozyme probed by combining site-directed mutagenesis and affinity labeling. Biochemistry 39, 292-299.
51. Nishio, M., Hirota, M., Umezawa, Y. (Eds.) 1998. The CH/π Interaction. Wiley-VCH, New York.
52. O'Reilly, M., Watson, K. A., Schinzel, R., Palm, D., Johnson, L. N. 1997. Oligosaccharide substrate binding in Escherichia coli maltodextrin phosphorylase. Nat Struct Biol 4, 405-412.
53. Pace, C. N., Shirley, B. A., McNutt, M., Gajiwala, K. 1996. Forces contributing to the conformational stability of proteins. FASEB J 10, 75-83.
54. Parkinson, G., Gunasekara, A., Vijtechovsky, J., Zhang, X., Kunkel, T. A., Berman, H., Ebright, R. H. 1996. Aromatic hydrogen bond in sequence specific protein DNA recognition. Nat Struct Biol 3, 837-841.
55. Perutz, M. F., Fermi, G., Abraham, D. J., Poyart, C., Bursaux, E. 1986. Hemoglobin as a receptor of drugs and peptides: X-ray studies of the stereochemistry of binding. J Am Chem Soc 108, 1064-1078.
56. Ramanathan, K., Sethumadhavan, R. 2009. Exploring the role of C-H......π interactions on the structural stability of antimicrobial peptides. J Theor Comput Chem 8, 909-924.
57. Reeves, L. W., Schneider, W. G. 1957. Nuclear magnetic resonance measurements of complexes of chloroform with aromatic molecules and olefins. Can J Chem 35, 251-261.
58. Scrutton, N. S., Raine, A. R. C. 1996. Cation-π bonding and aminoaromatic interactions in the biomolecular recognition of substituted ammonium ligands. Biochem J 319, 1-8.
59. Shanthi, V., Ramanathan, K., Sethumadhavan, R. 2010. Exploring the role of C-H......π interactions on the structural stability of single chain 'all-alpha' proteins. Appl Biochem Biotechnol 160, 1473-1483.
60. Shimohigashi, Y., Maeda, I., Nose, T., Ikesue, K., Sakamoto, H., Ogawa, Y., Ide, Y., Kawahara, M., Nezu, T., Terada, Y., Kawano, K., Ohno, M. 1996. Chymotrypsin inhibitory conformation induced by amino acid side-chain-side-chain intramolecular CH/π interaction. J Chem Soc 1, 2479-2485.
61. Shimohigashi, Y., Nose, T., Yamauchi, Y., Maeda, I. 1999. Design of serine protease inhibitors with conformation restricted by amino acid sidechain side-chain CH/π interaction. Biopolymers 51, 9-17.
62. Steiner, T. 2002. The hydrogen bond in the solid state. Angew Chem Int Ed Engl 41, 48-76.
63. Steiner, T., Koellner, G. J. 2001. Hydrogen bonds with π-acceptors in proteins: Frequencies and role in stabilizing local 3D structures. J Mol Biol 305, 535-557.
64. Suzuki, S., Green, P. G., Bumgarner, R. E., Dasgupta, S., Goddard, W. A., Blake, G. A. 1992. Benzene forms hydrogen bonds with water. Science 257, 924-945.
65. Syed Ibrahim, B., Pattabhi, V. 2004. Role of weak interactions in thermal stability of proteins. Biochem Biophys Res Commun 325, 1082-1089.
66. Tamres, M. 1952. Aromatic compounds as donor molecules in hydrogen bonding. J Am Chem Soc 74, 3375-3378.
67. Tiwari, A., Panigrahi, S. K. 2007. HBAT: A complete package for analyzing strong and weak hydrogen bonds in macromolecular crystal structures. In Silico Biol 7, 0057.
68. Umezawa, Y., Nishio, M. 1998a. CH/π interactions in the crystal structure of class I MHC antigens and their complexes with peptides. Bioorg Med Chem 6, 2507-2515.
69. Umezawa, Y., Nishio, M. 1998b. CH/π interactions as demonstrated in the crystal structure of guaninenucleotide binding proteins, Src homology-2 domains and human growth hormone in complex with their specific ligands. Bioorg Med Chem 6, 493-504.
70. Umezawa, Y., Tsuboyama, S., Takahashi, H., Uzawa, J., Nishio, M. 1999. C-H......π interaction in the conformation of organic compounds-A database study. Tetrahedron 55, 10047-10056.
71. Vriend, G. 1990. WHAT IF: A molecular modeling and drug design program. J Mol Graph 8, 52-56.
72. Wlodower, A., Walter, J., Huber, R., Sjolin, L. 1984. Structure of bovine pancreatic trypsin inhibitor: Results of joint neutron and X-ray refinement of crystal form II. J Mol Biol 180, 301-329.
73. Wulf, O. R., Liddel, U., Hendricks, S. B. 1936. The effect of ortho substitution on the absorption of the OH group of phenol in the infrared. J Am Chem Soc 58, 2287-2293.
74. Zacharias, N., Dougherty, D. A. 2002. Cation-π interactions in ligand recognition and catalysis. Trends Pharmacol Sci 23, 281-287.
75. Zhong, W., Gallivan, J. P., Zhang, Y., Li, L., Lester, H. A., Dougherty, D. A. 1998. From ab initio quantum mechanics to molecular neurobiology: A cation-π binding site in the nicotinic receptor. Proc Natl Acad Sci USA 95, 12088-12093.