In silico detection of binding mode of J-superfamily conotoxin pl14a with Kv1.6 channel

In Silico Biology

Volumn 7, Issue 2, 2007, Pages 175-186

  Mondal, Sukanta ^a   Babu, Rajasekaran Mohan ^a   Bhavna, Rajasekaran ^a   Ramakumar, Suryanarayanarao ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Basic residues ring; Conotoxin superfamily; Docking; Functional dyad; Homology modelling; Kv1 channel inhibitor; Pore loop region

Indexed keywords

AMINO ACID; ARGININE; CONOTOXIN; CONOTOXIN P114A; LYSINE; NICOTINIC RECEPTOR; POTASSIUM CHANNEL; POTASSIUM CHANNEL KV1.2; POTASSIUM CHANNEL KV1.6; TYROSINE; UNCLASSIFIED DRUG;

AMIDATION; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CARBOXY TERMINAL SEQUENCE; COMPLEX FORMATION; COMPUTER MODEL; COMPUTER PROGRAM; CRYSTAL STRUCTURE; MOLECULAR MODEL; PHARMACOPHORE; PROTEIN BINDING; PROTEIN FAMILY; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SNAIL; VALIDATION STUDY;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; COMPUTATIONAL BIOLOGY; CONOTOXINS; CONUS SNAIL; KV1.6 POTASSIUM CHANNEL; MOLECULAR SEQUENCE DATA; NEUROTOXINS; PEPTIDE FRAGMENTS; PROTEIN BINDING; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 34548361322     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (33)

1. Bairoch, A., Boeckmann, B., Ferro, S. and Gasteiger, E. (2004). Swiss-Prot: Juggling between evolution and stability. Brief. Bioinform. 5, 39-55.
2. Buczek, O., Bulaj, G. and Olivera, B. M. (2005). Conotoxins and the posttranslational modification of secreted gene products. Cell. Mol. Life Sci. 62, 3067-3079.
3. Chinea, G., Padron, G., Hooft, R. W. W., Sander, C. and Vriend, G. (1995). The use of position specific rotamers in model building by homology. Proteins 23, 415-421.
4. Cohen, G. H. (1997). ALIGN: A program to superimpose protein coordinates, accounting for insertions and deletions. J. Appl. Crystallogr. 30, 1160-1161.
5. DeLano, W. L. (2002). The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA, USA.
6. Gasparini, S., Danse, J.-M., Lecoq, A., Pinkasfeld, S., Zinn-Justin, S., Young, L. C., de Medeiros, C. C. L., Rowan, E. G., Harvey, A. L. and Ménez, A. (1998). Delineation of the functional site of α-dendrotoxin. The functional topographies of dendrotoxins are different but share a conserved core with those of other Kv1 potassium channel-blocking toxins. J. Biol. Chem. 273, 25393-25403.
7. Huang, X., Dong, F. and Zhou, H.-X. (2005). Electrostatic recognition and induced fit in the κ-PVIIA toxin binding to Shaker potassium channel. J. Am. Chem. Soc. 127, 6836-6849.
8. Imperial, J. S., Bansal, P. S., Alewood, P. F., Daly, N. L., Craik, D. J., Sporning, A., Terlau, H., López-Vera, E., Bandyopadhyay, P. K. and Olivera, B. M. (2006). A novel conotoxin inhibitor of Kv1.6 channel and nAChR subtypes defines a new superfamily of conotoxins. Biochemistry 45, 8331-8340.
9. Jones, R. M. and Bulaj, G. (2000). Conotoxins - new vistas for peptide therapeutics. Curr. Pharm. Des. 6, 1249-1285.
10. Lew, M. J., Flinn, J. P., Pallaghy, P. K., Murphy, R., Whorlow, S. L., Wright, C. E., Norton, R. S. and Angus, J. A. (1997). Structure-function relationships of ω-conotoxin GVIA. Synthesis, structure, calcium channel binding, and functional assay of alanine-substituted analogues. J. Biol. Chem. 272, 12014-12023.
11. -channel. Science 309, 897-903.
12. Luty, B. A., Wasserman, Z. R., Stouten, P. F. W., Hodge, C. N., Zacharias, M. and McCammon, J. A. (1995). A molecular mechanics/grid method for evaluation of ligand-receptor interactions. J. Comp. Chem. 16, 454-464.
13. McIntosh, J. M. and Jones, R. M. (2001). Cone venom-from accidental stings to deliberate injection. Toxicon 39, 1447-1451.
14. Mouhat, S., Jouirou, B., Mosbah, A., De Waard, M. and Sabatier, J. M. (2004a). Diversity of folds in animal toxins acting on ion channels. Biochem. J. 378, 717-726.
15. Mouhat, S., Mosbah, A., Visan, V., Wulff, H., Delepierre, M., Darbon, H., Grissmer, S., De Waard, M. and Sabatier, J. M. (2004b). The 'functional' dyad of scorpion toxin Pil is not itself a prerequisite for toxin binding to the voltage-gated Kv1.2 potassium channels. Biochem. J. 377, 25-36.
16. Mondal, S., Vijayan, R., Shichina, K., Babu, R. M. and Ramakumar, S. (2005). I-superfamily conotoxins: Sequence and structure analysis. In Silico Biol. 5, 557-571.
17. Mondal, S., Bhavna, R., Babu, R. M. and Ramakumar, S. (2006a). Pseudo amino acid composition and multi-class support vector machines approach for conotoxin superfamily classification. J. Theor. Biol. 243, 252-260.
18. Mondal, S., Babu, R. M., Bhavna, R. and Ramakumar, S. (2006b). I-conotoxin superfamily revisited. J. Pept. Sci. 12, 679-685.
19. Mouhat, S., De Waard, M. and Sabatier, J. M. (2005). Contribution of functional dyad of animal toxins acting on voltage-gated Kv 1-type channels. J. Peptide Sci. 2, 65-68.
20. Nicholls, A., Sharp, K. A. and Honig, B. (1991). Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.
21. Norton, R. S. and Olivera, B. M. (2006). Conotoxins down under. Toxicon. 48, 780-798.
22. Olivera, B. M. (2006). Conus peptides, biodiversity-based discovery and exogenomics. J. Biol. Chem. 281, 31173-31177.
23. Pallaghy, P. K. and Norton, R. S. (1999). Refined solution structure of ω-conotoxin GVIA: Implications for calcium channel binding. J. Pept. Res. 53, 343-351.
24. Rajendra, W., Armugam, A. and Jeyaseelan, K. (2004). Toxins in anti-nociception and anti-inflammation. Toxicon 44, 1-17.
25. Savarin, P., Guenneugues, M., Gilquin, B., Lamthanh, H., Gasparini, S., Zinn-Justin, S. and Ménez, A. (1998). Three-dimensional structure of κ-conotoxin PVIIA, a novel potassium channel-blocking toxin from cone snails. Biochemistry 37, 5407-5416.
26. Skarzynski, T. (1992). Crystal structure of alpha-dendrotoxin from the green mamba venom and its comparison with the structure of bovine pancreatic trypsin inhibitor. J. Mol. Biol. 224, 671-683.
27. Sobolev, V., Sorokine, A., Prilusky, J., Abola, E. E. and Edelman, M. (1999). Automated analysis of interatomic contacts in proteins. Bioinformatics 15, 327-332.
28. Srinivasan, K. N., Sivaraja, V, Huys, L, Sasaki, T., Cheng, B., Kumar, T. K., Sato, K., Tytgat, J., Yu, C., San, B. C. C., Ranganathan, S., Bowie, H. J., Kim, R. M. and Gopalakrishnakone, P. (2002). κ-Hefutoxinl, a novel toxin from the scorpion Heterometrus fulvipes with unique structure and function. Importance of the functional diad in potassium channel selectivity. J. Biol. Chem. 277, 30040-30047.
29. Stouten, P. F. W., Frömmel, C., Nakamura, H. and Sander, C. (1993). An effective solvation term based on atomic occupancies for use in protein simulations. Molecular Simulation 10, 97-120.
30. Terlau, H. and Olivera, B. M. (2004). Conus venoms: A rich source of novel ion channel-targeted peptides. Physiol. Rev. 84, 41-68.
31. + channels. J. Biol. Chem. 280, 21246-21255.
32. Vriend, G. (1990). WHAT IF: A molecular modeling and drug design program. J. Mol. Graph. 8, 52-56.
33. Wang, C. Z. and Chi, C. W. (2004). Conus peptides - a rich pharmaceutical treasure. Acta Biochim. Biophys. Sin. (Shanghai) 36 713-723.