Evolution of graded refractive index in squid lenses

Journal of the Royal Society Interface

Volumn 4, Issue 15, 2007, Pages 685-698

  Sweeney, Alison M ^a   Des Marais, David L ^a   Ban, Yih En Andrew ^b,c   Johnsen, Sönke ^a  

^a DUKE UNIVERSITY   (United States)

^b DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Cephalopods; Graded refractive index; Lenses; Molecular evolution

Indexed keywords

CRYSTALLIN; GLUTATHIONE TRANSFERASE; S CRYSTALLIN; UNCLASSIFIED DRUG;

ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; DIMERIZATION; LENS; LIGHT SCATTERING; MOLECULAR EVOLUTION; NONHUMAN; OPTIC NERVE; PHYLOGENY; PROTEIN AGGREGATION; PROTEIN EXPRESSION; PROTEIN STABILITY; REFRACTION INDEX; SEQUENCE HOMOLOGY; SQUID; VISUAL ACUITY;

ANIMALIA; CEPHALOPODA;

EID: 34547621813     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2006.0210     Document Type: Article

References (42)

1. Baker, D. A. 2000 A surprising simplicity to protein folding. Nature 405, 39-42. (doi:10.1038/35011000)
2. Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. 2001 Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA 98, 10 037-10 041. (doi:10.1073/pnas.181342398)
3. Benedek, G. B. 1971 Theory of transparency of the eye. Appl. Opt. 10, 459-473.
4. Bettelheim, F. A. & Siew, E. L. 1983 Effect of change in concentration upon lens turbidity as predicted by the random fluctuation theory. J. Biophys. Soc. 41, 29-33.
5. Branden, C. & Tooze, J. 1999 Introduction to protein structure, 2nd edn. New York, NY: Garland Publishing.
6. Chang, B. S. W., Jönsson, M. A., Kazmi, M. J. & Donoghue, T. P. 2002 Recreating a functional ancestral archosaur visual pigment. Mol. Biol. Evol. 19, 1483-1489.
7. Clauser, K. R., Baker, P. R. & Burlingame, A. L. 1999 Role of accurate mass measurement ( + / - 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 71, 2871-2882. (doi:10. 1021/ac9810516)
8. Darwin, C. R. 1859 On the origin of species: a facsimile of the first edition. Cambridge, UK: Harvard University Press.
9. Delaye, M. 1983 A Short-range order of crystallin proteins accounts for eye lens transparency. Nature 302, 415-417. (doi:10.1038/302415a0)
10. Dolinsky, T. J., Nielsen, J. E., McCammon, J. A. & Baker, N. A. 2004 PDB2PQR.:an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 32, W665-W667.
11. Gordon, J. M. 2000 Spherical gradient-index lenses as perfect imaging and maximum power transfer devices. Appl. Opt. 39, 3825-3832.
12. Graw, J. 1997 The crystallins: genes, proteins and diseases. Biol. Chem. 378, 1331-1348.
13. Hecht, E. 1989 Optics. Boston, MA: Addison-Wesley Longman.
14. Huelsenbeck, J. P. & Ronquist, F. 2001 MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755. (doi:10.1093/bioinformatics/17.8.754)
15. Humphrey, W., Dalke, A. & Schulten, K. 1996 VMD: visual molecular dynamics. J. Mol. Graph. 14, 33-38. (doi:10. 1016/0263-7855(96) 00018-5)
16. Jagger, W. S. & Sands, P. J. 1999 A wide-angle gradient index optical model of the crystalline lens and eye of the octopus. Vis. Res. 39, 2841-2852. (doi:10.1016/S0042-6989(99) 00012-7)
17. Ji, X., von Rosenvinge, E. C., Johnson, W. W., Tomarev, S. I., Piatigorsky, J., Armstrong, R. N. & Gilliland, G. L. 1995 Three-dimensional structure, catalytic properties, and evolution of a sigma class glutathione transferase from squid, a progenitor of the lens S-crystallins of cephalopods. Biochem. 34, 5317-5328. (doi:10.1021/bi00016a003)
18. Kaplan, W., Husler, P., Klump, H., Erhardt, J., Sluis-Cremer, N. & Dirr, H. 1997 Conformational stability of pGEX-expressed Schistosoma japonicum glutathione S-transferase: a detoxification enzyme and fusion-protein affinity tag. Protein Sci. 6, 399-406.
19. Land, M. F. & Nilsson, D. E. 2002 Animal eyes. Oxford, UK: Oxford University Press.
20. Larget, B. & Simon, D. L. 1999 Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16, 750-759.
21. Luo, J.-K., Hornby, J. A. T., Wallace, L. A., Chen, J., Armstrong, R. N. & Dirr, H. 2002 Impact of domain interchange on conformational stability and equilibrum folding of chimeric class μ glutathione transferases. Protein Sci. 11, 2208-2217. (doi:10.1110/ps.0208002)
22. Matthiesen, L. 1886 Uber die Beziehungen, welche zwischen dem Brechungsindex des Kerncentrums der Krystallinse und den Dimensionen des Auges bestehen. Pflugers Archiv 27, 510-523.
23. Mei, G., Di Venere, A., Rosato, N. & Finazzi-Agro, A. 2004 The importance of being dimeric. FEBS J. 272, 16-27. (doi:10.1111/j.1432-1033.2004.04407.x)
24. Nilsson, D.-E. & Pelger, S. 1994 A pessimistic estimate of the time required for an eye to evolve. Proc. R. Soc. B 256, 53-58. (doi:10.1098/rspb.1994.0048)
25. Nilsson, D. E., Gislen, L., Coates, M. M., Skogh, C. & Garm, A. 2005 Advanced optics in a jellyfish eye. Nature 435, 201-205. (doi:10.1038/nature03484)
26. Piatigorsky, J., Horwitz, J., Kuwabara, T. & Cutress, C. E. 1989 The cellular eye lens and crystallins of cubomedusan jellyfish. J. Comp. Physiol. A 164, 577-587. (doi:10.1007/ BF00614500)
27. Piatigorsky, J., Horwitz, J. & Norman, B. L. 1993 J1-crysttallins of the cubomedusan jellyfish lens constitute a novel family encoded in at least three intronless genes. J. Biol. Chem. 268, 11 894-11 901.
28. Piatigorsky, J., Norman, B., Dishaw, L. J., Kos, L., Horwitz, J., Steinbach, P. J. & Kozmik, Z. 2001 J3-crystallin of the jellyfish lens: similarity to saposins. Proc. Natl Acad. Sci. USA 98, 12 362-12 367. (doi:10.1073/pnas.231310698)
29. Ponder, J. W. & Richards, F. M. 1987 An efficient Newton-like method for molecular mechanics energy minimization of large molecules. J. Comput. Chem. 8, 1016-1024. (doi:10.1002/jcc.540080710)
30. Schwede, T., Kopp, J., Guex, N. & Peitsch, M. C. 2003 SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 31, 3381-3385. (doi:10.1093/ nar/gkg520)
31. Sitkoff, D., Sharp, K. A. & Honig, B. 1994 Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98, 1978-1988. (doi:10. 1021/j100058a043)
32. Smith, G. 2003 The optical properties of the crystalline lens and their significance. Clin. Exp. Optom. 86, 3-18.
33. Stevens, J. M., Hornby, J. A. T., Armstrong, R. N. & Dirr, H. W. 1998 Class sigma glutathione transferase unfolds via a dimeric and a monomeric intermediate: impact of subunit interface on conformational stability in the superfamily. Biochem. 37, 15 534-15 541. (doi:10.1021/bi981044b)
34. Stevens, J. M., Armstrong, R. N. & Dirr, H. W. 2000 Electrostatic interactions affecting the active site of class sigma glutathione S-transferase. Biochem. J. 347, 193-197. (doi:10.1042/0264-6021:3470193)
35. Tomarev, S. I. & Piatigorsky, J. 1996 Lens crystallins of invertebrates-diversity and recruitment from detoxification enzymes and novel proteins. Eur. J. Biochem. 235, 449-465. (doi:10.1111/j.1432-1033. 1996.00449.x)
36. Tomarev, S. I., Chung, S. & Piatigorsky, J. 1995 Glutathione S-transferase and S-crystallins of cephalopods: evolution from active enzyme to lens-refractive proteins. J. Mol. Evol. 41, 1048-1056. (doi:10.1007/BF00173186)
37. Ugalde, J. A., Chang, B. S. W. & Matz, M. V. 2004 Evolution of coral pigments recreated. Science 305, 1433. (doi:10. 1126/science.1099597)
38. Werten, P. J. L., Roll, B., van Aalten, D. M. F. & de Jong, W. W. 2000 Gecko ι-crystallin: how cellular retinol-binding protein became an eye lens ultraviolet filter. Proc. Natl Acad. Sci. USA 97, 3282-3287. (doi:10.1073/ pnas.050500597)
39. West, J. A., Sivak, J. G. & Doughty, M. J. 1995 Microscopical evaluation of the crystalline lens of the squid (Loligo opalescens) during embryonic development. Exp. Eye Res. 60, 19-35. (doi:10.1016/S0014-4835(05)80080-6)
40. Willekens, B., Vrensen, G., Jacob, T. & Duncan, G. 1984 The ultrastructure of the lens of the cephalopod Sepiola: a scanning electron microscopic study. Tissue Cell 16, 941-950. (doi:10.1016/0040- 8166(84)90073-9)
41. Wistow, G. 1995 Molecular biology and evolution of crystallins: gene recruitment and multifunctional proteins in the eye lens. Austin, TX: Landes.
42. Yang, Z. & Nielsen, R. 2002 Codon substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19, 908-917.