In silico homology modeling of Prophenoloxidase activating factor serine proteinase gene from the haemocytes of Fenneropenaeus indicus

Journal of Proteomics and Bioinformatics

Volumn 4, Issue 2, 2011, Pages 53-57

  Vaseeharan, Baskaralingam ^a   Sivakama Valli, J ^a  

^a ALAGAPPA UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

SERINE PROTEINASE;

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; CRYSTAL STRUCTURE; FENNEROPENAEUS INDICUS; GENE STRUCTURE; IMMUNE RESPONSE GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PENAEIDAE; PHYSICAL CHEMISTRY; PREDICTION; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; SERINE PROTEINASE GENE; STRUCTURAL HOMOLOGY; STRUCTURE ACTIVITY RELATION; VALIDATION PROCESS;

EID: 79952153361     PISSN: None     EISSN: 0974276X     Source Type: Journal    
DOI: 10.4172/jpb.1000166     Document Type: Article

References (38)

1. Rawlings RD, Barrett AJ (1993) Evolutionary families of peptidases. Biochem J 290: 205-18.
2. Krem M, Di Cera E (2002) Evolution of enzyme cascades from embryonic development to blood coagulation. Trends Biochem Sci 27: 67-74.
3. Perona JJ, Craik CS (1995) Structural basis of substrate specificity in the Serine Protease. Protein Sci 4:337-360.
4. Muta T, Iwanaga S (1996) Clotting and immune defense in Limulidae. Prog Mol Subcell Biol 15:154-189.
5. Bennett B, Ratnoff OD (1972) The normal coagulation mechanism. Med Clin North Am 56: 95-104.
6. Soderhall K, Cerenius L (1998) Role of the Prophenoloxidase-activating system in invertebrate immunity. Curr Opin Immunol 10:23-28.
7. O'Brien D, McVey J (1993) Blood coagulation, inflammation, and defense. In: Sim E (ed), The Natural Immune Systems Humoral Factors, pp 257-280.
8. Gillespie JP, Kanost MR, Trenczek T (1997) Biological mediators of insect immunity. Annu Rev Entomol 42: 611-643.
9. Cerenius L, Soderhall K (2004) The prophenoloxidase-activating system in invertebrates. Immunol Rev 198: 116-126.
10. Gollas-Galván T, Herná ndez-López J, Vargas-Albores F (1997) Effect of calcium on the Prophenoloxidase system activation of the brown shrimp (Penaeus californiensis, Holmes). Comp Biochem Physiol A 117: 419-25.
11. Wade D, Boman A, Wahlin B, Drain CM, Andreu D, et al. (1990) All-D amino acid-containing channel-forming antibiotic peptides. Proc Natl Acad Sci USA 88: 4761-4765.
12. Cociancich S, Ghazi A, Hetru C, Hoffmann JA, Letelliers L (1993) Insect defensin, an inducible antibacterial peptid forms voltage-dependent channels in Micrococcus luteus. J Biol Chem 268: 19239-19245.
13. Gill SC, Von Hippel PH (1989) Extinction coefficient. Anal Biochem 182: 319-328.
14. Guruprasad K, Reddy BVP, Pandit MW (1990) Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Prot Eng 4: 155-164.
15. Ikai AJ (1980) Thermo stability and aliphatic index of globular proteins. J Biochem 88: 1895-1898.
16. Kyte J, Doolottle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132.
17. Gasteiger E (2005) Protein Identification and Analysis Tools on the ExPASy Server. In: John M Walker ed, The Proteomics Protocols Handbook, Humana Press 571-607.
18. Falquet L, Pagni M, Bucher P, Hulo N, Sigrist CJA, et al. (2002) The PROSITE database, its status in 2002. Nucleic Acids Res 30: 235-238.
19. Sali A, Blundell TL (1993) Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 234: 779-815.
20. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
21. Marti-Renom MA, Stuart A, Fiser A, Sánchez R, Melo F, et al. (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29: 291-325.
22. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, et al. (1993) CHARMM: a program for macromolecular energy minimization and dynamics calculations. J Comput Chem 4: 187-217.
23. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereo chemical quality of protein structures. J Appl Crystallography 26: 283-291.
24. Ramachandran GN, Ramakrishnan C, Sasisekharan V (1963) Stereochemistry of polypeptide chain configurations. J Mol Biol 7: 95-99.
25. Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8: 477-486.
26. Vriend G (1990) WHAT IF: A molecular modeling and drug design program. J Mol Graph 8: 52-56.
27. Guex N, Manuel CP (1997) Data Modeling, Analysis and Classification SWISSMODEL and the Swiss-Pdb Viewer: An environment for comparative protein.
28. Weiner SJ, Kollman PA, Nguyen DT, Case DA (1986) An all atom force field for simulations of proteins and nucleic acids. J Comput Chem 7: 230-252.
29. Baker D, Sali A (2001) Protein Structure Prediction and Structural Genomics. Science 294: 93-96.
30. Ferre F, Clote P (2005) Disulfide connectivity prediction using secondary structure information and diresidue frequencies. Bioinformatics 21: 2336-2346.
31. Hirokawa T, Boon-Chieng S, Mitaku SB (1998) SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatic 14: 378-379.
32. Christian JAS, Cerutti L, Hulo N, Gattiker A, Falquet L (2002) PROSITE: A documented database using patterns and profiles as motif descriptors. Brief Bioinform 3: 265-274.
33. Eisenberg, D, Lüthy R, and Bowie JU (1997) VERIFY3D:Assessment of protein models with three-dimensional profiles. Methods Enzymol 277: 396-404.
34. Fariselli P, Casadio R (2001). Prediction of disulfide connectivity in proteins. Bioinformatics 17: 957-964.
35. Geourjon C, Deléage G (1995) SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput Appl Biosci 11: 681-684.
36. Krieger E, Nabuurs SB, Vriend G (2003) Homology modeling. Struct bioinform 44: 507-521.
37. Laskowski RA, Watson JD, Thornton JM (2005) ProFunc: A server for predicting protein function from 3D structure. Nucleic Acids Res 89-93.
38. Suresh A, Verma C (2006) Modelling study of dimerzation in mammalian defensins. BMC Bioinformatics 5: S17.