Homology models of human γ-crystallins: Structural study of the extensive charge network in γ-crystallins

Biochemical and Biophysical Research Communications

Volumn 300, Issue 3, 2003, Pages 624-630

  Salim, Asmat ^a   Zaidi, Zafar H ^a  

^a UNIVERSITY OF KARACHI   (Pakistan)

Author keywords

Homology or comparative modeling; Ion pairs; Long lived proteins; Salt bridges; Three dimensional structure prediction

Indexed keywords

AMINO ACID; GAMMA CRYSTALLIN; ISOPROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; HUMAN; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN MOTIF; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

EID: 0037449865     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-291X(02)02895-4     Document Type: Article

References (29)

1. Breitman M.L., Lok S., Wistow G., Piatigorsky J., Treton J.A., Gold R.J.M., Tsui L.-C. γ -Crystallin family of the mouse lens: structural and evolutionary relationships Proc. Natl. Acad. Sci. USA. 81:1984;7762-7766.
2. Meakin S.O., Breitman M.L., Tsui L.-C. Structural and evolutionary relationships among five members of the human. γ -crystallin gene family Mol. Cell. Biol. 5:1985;1408-1414.
3. den Dunnen J.T., Moormann R.J.M., Lubsen N.H., Schoenmakers J.G.G. Concerted and divergent evolution within the rat. γ -crystallin gene family J. Mol. Biol. 189:1986;37-46.
4. Papaconstantinou J. Biochemistry of bovine lens proteins. II. The. γ -crystallins of adult bovine, calf and embryonic lenses Biochim. Biophys. Acta. 107:1965;81-90.
5. Francis P.J., Berry V., Moore A.T., Bhattacharya S. Lens biology: development and human cataractogenesis. Trends Genet. 15:1999;191-196.
6. Meakin S.O., Du R.P., Tsui L.-C., Breitman M.L. γ -Crystallins of the human eye lens: expression analysis of five members of the gene family Mol. Cell. Biol. 7:1987;2671-2679.
7. Schoenmakers J.G.G., den Dunnen J.T., Moormann R.J.M., Jongbloed R., van Leen R.W., Lubsen N.H. The crystallin gene families. Ciba Found. Symp. 106:1984;208-218.
8. Summers L.J., Slingsby C., Blundell T.L., den Dunnen J.T., Moormann R.J.M., Schoenmakers J.G.G. Structural variation in mammalian. γ -crystallins based on computer graphics analyses of human, rat and calf sequences. 1. Core packing and surface properties Exp. Eye Res. 43:1986;77-92.
9. c γ -crystallins, γ B and γ D Exp. Eye Res. 65:1997;609-630.
10. L. Summers, G. Wistow, M. Narebor, D. Moss, P. Lindley, C. Slingsby, T. Blundell, H. Bartunik, K. Bartels, in: M.T.W. Hearn (Ed.), Peptide and Protein Reviews, vol. 3, Marcel Dekker, 1984, pp. 147-168.
11. Chirgadze Y.N., Driessen H.P.C., Wright G., Slingsby C., Hay R.E., Lindley P.F. Structure of the bovine eye lens. γ D ( γ IIIb)-crystallin at 1.95 Å Acta Crystallogr. D. 52:1996;712-721.
12. Zarina S., Slingsby C., Jaenicke R., Zaidi Z.H., Driessen H., Srinivasan N. Three-dimensional model and quaternary structure of the human eye lens protein. γ S-crystallin based on β - and γ -crystallin X-ray coordinates and ultracentrifugation Protein Sci. 3:1994;1840-1846.
13. Goode D., Crabbe M.J. Modelling molecular stability in. γ B crystallin Comput. Chem. 19:1995;65-74.
14. Farnsworth P.N., Frauwirth H., Groth-Vasselli B., Singh K. Refinement of 3D structure of bovine lens. α A-crystallin Int. J. Biol. Macromol. 22:1998;175-185.
15. Groth-Vasselli B., Kumosinski T.F., Farnsworth P.N. Computer-generated model of the quaternary structure of. α crystallin in the lens Exp. Eye Res. 61:1995;249-253.
16. Stephan D.A., Gillanders E., Vanderveen D., Freas-Lutz D., Wistow G., Baxevanis A.D., Robbins C.M., VanAuken A., Quesenberry M.I., Bailey-Wilson J., Juo S.H., Trent J.M., Smith L., Brownstein M.J. Progressive juvenile-onset punctate cataracts caused by mutation of the. γ D-crystallin gene Proc. Natl. Acad. Sci. USA. 96:1999;1008-1012.
17. Chuang C.C., Wu S.H., Chiou S.H., Chang G.G. Homology modeling of cephalopod lens S-crystallin: a natural mutant of sigma-class glutathione transferase with diminished endogenous activity. Biophys. J. 76:1999;679-690.
18. Bairoch A., Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucleic Acids Res. 25:1997;31-36.
19. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. Nucleic Acids Res. 28:2000;235-242.
20. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
21. Najmudin S., Nalini V., Driessen H.P.C., Slingsby C., Blundell T.L., Moss D.S., Lindley P.F. Structure of the bovine eye lens protein. γ B ( γ II)-crystallin at 1.47 Å Acta Cryst. D. 49:1993;223-233.
22. Sali A., Blundell T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234:1993;779-815.
23. Laskowski R.A., McAurthur M.W., Moss D.S., Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26:1993;283-291.
24. Vriend G. A molecular modelling and drug design program. J. Mol. Graph. 8:1990;52-56.
25. Barlow D.J., Thornton J.M. Ion-pairs in proteins. J. Mol. Biol. 168:1983;867-885.
26. Borders C.L.J., Broadwater J.A., Bekeny P.A., Salmon J.E., Lee A.S., Elridge A.M., Pett V.B. A structural role for arginine in proteins: multiple hydrogen bonds to backbone carbonyl oxygens. Protein Sci. 3:1994;541-548.
27. Chirgadze Y.N., Tabolina O.Y. Alternating charge clusters of side chains: new surface structural invariants observed in calf eye lens. γ -crystallins Protein Eng. 9:1996;745-754.
28. Wistow G., Turnell B., Summers L., Slingsby C., Moss D., Miller L., Lindley P.F., Blundell T.L. X-ray analysis of the eye lens protein. γ -II crystallin at 1.9 Å resolution J. Mol. Biol. 170:1983;175-202.
29. Realini C., Rogers S.W., Rechsteiner M. KEKE motifs. Proposed roles in protein-protein association and presentation of peptides by MHC class I receptors. FEBS Lett. 348:1994;109-113.