REVIEWS TIBS 24 – AUGUST 1999 detected a putative homologue (E 5 1023) an independent gene or as a domain of 3238–3241 of the bacterial smr gene in mutS2 genes. This suggests that Smr plays 3 Modrich, P. (1991) Annu. Rev. Genet. 25, an important role that is probably relevant 229–253 Saccharomyces cerevisiae (Fig. 1). 4 Pont-Kingdom, G. et al. (1998) J. Mol. Evol. 46, Eukaryotes seem to have only mutS1-type to MMR through an interaction with 419–431 genes: the presence of an smr gene is MutS1. Elucidation of the functions of 5 Fishel, R. and Wilson, T. (1997) Curr. Opin. therefore not surprising. these new proteins will require integrated Genet. Dev. 7, 105–113 The complex phylogenetic distribution biochemical and genetic approaches. 6 Fishel, R. et al. (1993) Cell 75, 1027–1038 of these proteins makes it difficult to 7 Leach, F. S. et al. (1993) Cell 75, 1215–1225 determine whether the mutS2 family arose Acknowledgements 8 Eisen, J. A. (1998) Nucleic Acids Res. 26, from an ancient fusion between a mutS1 We thank H. Brinkmann, H. Le 4291–4300 gene and an smr gene, or whether smr Guyader, P. López-García and three 9 Tomb, J. F. et al. (1997) Nature 388, genes and the mutS1 family are the result 539–547 anonymous referees for critical reading 10 Schuler, G. D. et al. (1991) Proteins 9, of splitting of a mutS2-type gene. The of the manuscript. D. M. is a postdoc- existence of the MutS2 family and Smr 180–190 toral fellow of the Spanish Ministerio de proteins suggests that the MMR pathway Educación y Cultura. involves factors other than those already DAVID MOREIRA AND HERVÉ PHILIPPE characterized, even in well known organisms such as E. coli. The smr References UPRESA Q8080-Equipe Phylogénie et 1 Lahue, R. S., Au, K. G. and Modrich, P. (1989) Evolution Moléculaires, Bâtiment 444, sequence is present in a variety of Science 245, 160–164 bacteria and also in eukaryotes, either as 2 Worth, L., Clark, S., Radman, M. and Modrich, Université Paris-Sud, 91405 Orsay Cedex, P. (1994) Proc. Natl. Acad. Sci. U. S. A. 91, France. Email: [email protected] chromophore. Although the PSB of 11- cis-retinal absorbs at 440 nm in organic How color visual pigments are solvents, vertebrate color pigments pro- vide environmental perturbations that tune the absorption maximum of the tuned retinal chromophore over a very wide range – from 360 to 635 nm8. This shift in the wavelength of maximum absorbance is called the opsin shift9. The ~60-nm Gerd G. Kochendoerfer, Steven W. Lin, shift typically observed upon proton- ation of retinal Schiff bases10 is not suffi- Thomas P. Sakmar and Richard A. Mathies cient to explain the red-shifted absorp- tion maxima of green and red visual The absorption maximum of the retinal chromophore in color visual pig- pigments. Chromophore–protein inter- ments is tuned by interactions with the protein (opsin) to which it is bound. actions that might cause this opsin shift Recent advances in the expression of rhodopsin-like transmembrane re- include: (1) a weakening of the interac- ceptors and in spectroscopic techniques have allowed us to measure res- tion between the positive charge of the onance Raman vibrational spectra of the retinal chromophore in recombi- retinal PSB and its negative counterion nant visual pigments to examine the molecular basis of this spectral or hydrogen-bonding partner11,12; (2) tuning. The dominant physical mechanism responsible for the opsin shift placement of full or partial charges13–17 18,19 in color vision is the interaction of dipolar amino acid residues with the or polarizable groups close to the ground- and excited-state charge distributions of the chromophore. polyene chain; and (3) planarization of the polyene chain caused by the protein environment20,21. THE RETINA CONTAINS two types of consist of an apoprotein (opsin) and an cells specialized for light detection: rod 11-cis-retinal chromophore that is Resonance Raman vibrational spectroscopy cells for dim-light vision and three bound to opsin by a protonated Schiff The cloning and expression of visual classes of cone cells for color vision. base (PSB) linkage4 to a specific lysine pigments and mutant pigments2,3,22 iden- The cones contain pigments absorbing residue (Lys296). Absorption of light tified Glu113 as the primary counterion in the blue (~425 nm), green (~530 nm) triggers the femtosecond isomerization of the retinal PSB chromophore23–25 as and red (~560 nm) regions of the spec- of the chromophore5, producing the ac- well as amino acids that are associated trum1–3, whose differential responses en- tive signaling state that leads to hyper- with the green-to-blue and green-to-red able color vision. These visual pigments polarization of the photoreceptor cell opsin shifts13,26–28. However, compari- membrane and generation of a visual sons of structural data on the chro- G. G. Kochendoerfer and R. A. Mathies are nerve impulse6. mophore in the relevant color pigments at the Dept of Chemistry, University of Since Isaac Newton’s famous treatise are critical to understanding the opsin- California, Berkeley, CA 94720, USA; and 7 S. W. Lin and T. P. Sakmar are at the Howard on color vision , a fundamental aim in vi- shift mechanism. By combining site- Hughes Medical Institute, Rockefeller sion research has been the elucidation directed mutagenesis with resonance University, New York, NY 10021, USA. of the factors that determine the ab- Raman vibrational spectroscopy, we can Email: [email protected] sorption maximum of the opsin-bound now compare the vibrational structures 300 0968 – 0004/99/$ – See front matter © 1999, Elsevier Science. All rights reserved. PII: S0968-0004(99)01432-2 TIBS 24 – AUGUST 1999 REVIEWS of the chromophore in differ- ent visual pigments directly and elucidate the physical mechanism underlying the opsin shift. Towards this end, we have obtained resonance Raman vibrational spectra of visual pigments absorbing in the blue, green and red by ex- ploiting preresonance and res- onance Raman microprobe techniques26,29–32. Comparison of these spectra shows that the interaction of dipolar residues with the chro- mophore ground- and excited- state charge distributions is the single most important physical interaction that de- termines the opsin shift. Figure 1 presents a compari- son of the Raman spectra of the 11-cis-retinal PSB chro- mophore in methanol (lmax = 440 nm), in a blue-rhodopsin analog (lmax = 438 nm) (Ref. 26)*, in the human green pigment (lmax = 530 nm) and in the human red pigment (lmax = 560 nm). The assignments of the retinal vibrational modes are summarized in Fig. 1, and Box 1 presents a brief tutorial on resonance Raman spec- troscopy and the concepts of vibrational structure determi- nation. A more detailed pres- entation of these assignments and of the properties of vari- ous pigment mutants is found elsewhere26,32,33. The first strik- ing observation is that the hy- drogen out-of-plane (HOOP) wagging, C–C stretch and C–H rocking, C=C stretching and C=NH Schiff-base modes of the 11-cis-retinal PSB in the blue Figure 1 pigment analog are nearly Resonance Raman vibrational spectra of the 11-cis-retinal protonated Schiff-base (PSB) chromophore in identical to those of the iso- methanol, in the blue-rhodopsin pigment analog*, in the human green cone pigment and in the human red lated PSB chromophore in cone pigment. The traces are broken at ~1600 cm–1 to facilitate presentation of expanded spectra of the † methanol . The similarity of Schiff-base region. These expanded insets also present portions of spectra recorded in D2O buffers. The the skeletal mode frequencies green and the red pigment data are reproduced, with permission, from Ref. 32. Raman spectra of the 11- cis-retinal PSB and of the blue pigment analog were obtained by focusing a 50-mW, 720-nm beam from a indicates that there are no Lexel 479 Ti:sapphire laser pumped by the all-lines output from an Ar+ laser (Spectra-Physics 2020) into strong location-specific per- ~3 ml of pigment solution in a 300 mm I.D. circular capillary cooled to ~0°C (Ref. 32). The green pigment turbations of the chromo- samples were excited similarly with 30 mW of 795 nm light. The Raman microprobe apparatus used to phore imposed by the protein obtain the low-temperature red-pigment Raman spectra was described previously29–31. *The blue absorbing (lmax = 438 nm) rhodopsin analog described in Ref. 26 was used instead of the blue cone pigment because it is easily prepared and more suit- able for Raman studies while exhibiting ~80% of the expected opsin shift. The blue-rhodopsin analog is a mutant chimera consisting of bovine rhodopsin with nine amino acid replacements (M86L/G90S/A117G/E122L/A124T/W265Y/A292S/A295S/A299C). Chromophore replacement studies with retinal analogs demon- strated that the chromophore is specifically bound to this mutant opsin. Furthermore, it is our experience that high-quality Raman spectra can only be obtained from pigments that have regenerated to form a stable native and homogeneous structure. †The lower intensity of the C-14–C-15 stretching mode at 1187 cm21 in the blue-rhodopsin pigment is due to a subtraction artifact. All reported pigment spectra are of the pigment minus a bleached background. As the spectrum of all-trans-retinal in the metarhodopsin I bleaching intermediate (see Ref. 38) exhibits a strong line at 1187 cm21, this subtraction will unavoidably reduce the 1187 cm21 band intensity. The shoulder at 960 cm21 in the red pigment spectrum originates from a small population of the 9-cis isomer that is present in the photostationary state (see Ref.