| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||


* Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel; and
Department of Physical Biochemistry, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse, Dortmund, Germany
Correspondence: Address reprint requests to Dr. Mudi Sheves, Dept. of Organic Chemistry, Weizmann Institute, Rehovot, Israel. Tel.: 972-8-9344320; Fax: 972-8-9343026; E-mail: mudi.sheves{at}weizmann.ac.il.
| ABSTRACT |
|---|
|
|
|---|
| INTRODUCTION |
|---|
|
|
|---|
It is widely assumed that all light-induced protein conformational alterations in retinylidene proteins are initiated by isomerization of the retinal chromophore. However, alternative approaches have been suggested in which isomerization is not the only trigger for biological activity or protein structural changes (7
). One proposal attributed protein conformational alterations to a large charge redistribution in the retinal chromophore developed after light absorption (8
10
). We have recently shown, using atomic force sensing (AFS), that protein conformational alterations are indeed induced in bR after light absorption, even when the crucial C13=C14 double bond isomerization is prevented by a rigid ring structure ("locked" pigment) (11
). In addition, we have used chemical reactions with spin-labeled artificial bR pigments derived from "locked" retinal to probe light-induced conformational changes. It was concluded that certain domains of the protein experience conformational alterations even though retinal isomerization is prevented (12
). Thus, the data questions (providing direct experimental results) the hypothesis that all primary events in retinal proteins can occur only due to an initial trans-cis isomerization. Furthermore, from examination of the light-catalyzed cleavage of the retinal-protein covalent bond by hydroxylamine (HA) (13
) it was concluded that this reaction was caused by light-induced conformational alterations extending into the µs-ms timescale. These protein changes are not correlated to an optically detectable photocycle, which is associated with C13=C14 isomerization.
In this work, we have applied the hydroxylamine reaction approach, which offers a possibility to identify protein conformational alterations in the retinal binding site after light absorption by the NpSRII system. This reaction was checked previously for the NpSRII native system at room temperature (14
). We have revealed that light absorption decreases the activation energy of the reaction as well as the frequency factor. A decrease of activation energy and frequency factor is detected also in an artificial pigment derived from a retinal analog in which isomerization around the critical C13=C14 double bond is prevented. It is concluded that after light absorption the artificial pigment experiences conformational alterations which are not associated with double bond isomerization.
| MATERIALS AND METHODS |
|---|
|
|
|---|
|
> 475 nm) cutoff filter (Schott, Mainz, Germany). The sample was passed through a PD-10 sepharose column (Amersham Pharmacia Biotech AG, Uppsala, Sweden) and the eluted sample was incubated with 1.2 equivalents of locked-trans retinal for 1 week at 25°C. Formation of the pigment was monitored by following the appearance of a characteristic absorption band at 524 nm. During this period no detectable formation of wild-type NpSRII was observed due to retinal oxime hydrolysis and retinal rebinding with the apoprotein. In addition, incubation of apomembrane at 25°C for one week did not produce detectable amount of wild-type NpSRII.
Experiments with hydroxylamine were carried out by stabilizing the temperature of the sample and the hydroxylamine for 10 min before measurement in an Agilent 4583 diode-array spectrophotometer (Agilent Technologies, Palo Alto, CA) equipped with an Agilent 89090A thermostated cuvette holder (Agilent Technologies). Since hydroxylamine is not completely thermally stable, a fresh hydroxylamine sample was used for each experiment. Irradiation was carried out with a Schott 250W cold light source (Carl Zeiss Microscopy, Jena, Germany) equipped with a heat absorbing filter and an optic fiber. The sample temperature was monitored, and the deviation in temperature did not exceed ±0.1°C, even during irradiation. Light was filtered through a long-pass cutoff filter,
> 475 nm for wild-type NpSRII, and
> 505 nm for the "locked" pigment.
The reactions with hydroxylamine were followed at various temperatures in the dark and under constant illumination by monitoring the disappearance of the main absorption band of the pigment (500 nm for the WT and 524 nm for the locked-trans pigment). Reactions in the dark showed only one component, and were fitted to the equation
; where Fdark is the fraction that did not undergo the reaction, kdark is the reaction rate in the dark, and a is a coefficient related to the total amount of pigment, which in this case should equal 1. Reactions under constant illumination were fitted to a double exponential equation, where one of the terms was the contribution of the dark reaction. Thus,
; where Flight is the fraction of remaining pigment, klight and kdark are the reaction rates of the light and dark reactions, respectively, and a is a coefficient related to the relative amount of each component. kdark was taken from the experiments in the dark, or by extrapolating the data from the Arrhenius plot for the reaction in the dark. It was necessary to conduct the experiments in the dark at higher temperatures than those required for the light reaction, since the rate of these reactions is very slow.
The reaction rates in the dark and in the light at various temperatures were fitted to the Arrhenius equation:
; where k is the reaction rate, A is the frequency factor which is a constant indicating how many collisions have the correct orientation to lead to products, Ea is the activation energy in kcal/mol, R is the gas constant and T is the temperature. A plot of ln(k) versus 1/T should be linear. From this plot it is possible to calculate the A coefficient as well as the activation energy.
| RESULTS |
|---|
|
|
|---|
|
|
0 kcal/mol. The latter change was accompanied by a significant decrease of the frequency factor by
9 orders of magnitude (Table 1). The decrease in the frequency factor indicates that after light irradiation the probability for correct collisions between the reactive molecules leading to reaction is reduced. This light effect is stronger than that detected in bR membranes (13
|
|
|
|
8 kcal/mole and five orders of magnitude relative to 17 kcal/mole and 9 orders of magnitude without transducer (Fig.4 and Table 1). In contrast, in membrane preparation the transducer increased the apparent light effect and actually the effect was similar to that observed in detergent preparation without transducer (Table 1).
It was proposed that the observed light rate acceleration of the pigment reaction with hydroxylamine is due to a greater reactivity of the reagent in the M photochemically induced intermediate of NpSRII (14
). This hypothesis was suggested for bR as well, but later it was proposed that the L intermediate (the precursor of M) is the species that is reactive to hydroxylamine (19
). Namely, the reaction is a direct consequence of a protein conformational change occurring after light-induced retinal all-trans
13-cis isomerization, but before Schiff base deprotonation. However, more recently it was shown for bR that the hydroxylamine reaction is light-catalyzed even when retinal double bond isomerization is prevented by a rigid ring structure in the chromophore (13
). This observation suggests that long-lived conformational changes occur in the protein, which are not reflected in spectroscopic changes, and enhance the reactivity of the chromophore toward hydroxylamine. Therefore, we have measured the rate of the hydroxylamine reaction both in the dark and under irradiation of an NpSRII artificial pigment derived from chromophore 2 in which isomerization around the critical C13=C14 double bond was prevented (Scheme 1). Similarly to bR, also in NpSRII artificial pigment an appreciable acceleration of the reaction rate occurred under irradiation (almost fourfold at 25°C; Table 1), which cannot be attributed to a photocycle intermediate. We note that we could not detect any photointermediate after flash-irradiation of the artificial pigment derived from chromophore 2, whereas similar irradiation of native pigment produced the well known photochemically induced intermediates. To exclude the possibility that irradiation caused rate acceleration due to temperature increase, rather than just sample light excitation, we have irradiated the sample with a cutoff filter of
> 600 nm which is not absorbed by the retinal chromophore. In this case the reaction rate was identical to the dark reaction excluding the possibility of sample warming due to irradiation. The hydroxylamine reactions were slow relative to native NpSRII (Figs. 2 and 5), due to a higher activation energy. The frequency factor was significantly higher (five orders of magnitude in the dark and two orders of magnitude under illumination), than that detected in WT, and partially compensated for the higher activation energy (Table 1). The decrease in activation energy due to irradiation was lower (
14 kcal/mol) than that detected in WT in detergent (17 kcal/mol). In the "locked" artificial pigment, it was not possible to neglect the contribution of the dark reaction under light, since the dark and light reaction rates were of comparable magnitude. Therefore, the rates of the reaction were fitted to a scheme composed of two phases. In cases where the rates of the dark and light reactions were very similar, a monophasic scheme was used instead.
| DISCUSSION |
|---|
|
|
|---|
500 fs (31
20 ps (34
500 fs). This short lifetime probably prevents atom movement but rather induces protein polarization including possible polarization of tryptophans in the retinal vicinity, bound water, or peptide dipoles. The possibility that protein polarization induces protein conformational changes on a longer time scale even in the native pigment should be the subject of future studies. In this respect it is interesting to note that bR artificial pigments derived from "locked" retinal analogs induce, after light absorption, protein conformational alterations in the same protein domains that experience changes in the native pigment, which does undergo retinal isomerization (12
The results obtained for WT NpSRII indicate that the hydroxylamine reaction in lipid reconstituted samples is not significantly different from that in detergent. In both cases light reduces the activation energy accompanied by a decrease in frequency factor. A similar light effect was detected for bR (in membranes) which may indicate that both proteins experience similar light-induced structural alterations. As detected by x-ray studies (36
39
), both proteins are characterized by a similar retinal binding structure which may lead to a similar protein response after retinal light absorption. In addition, both proteins experience similar changes in the protein cytoplasmic domain in the M intermediate. NpSRII association with its transducer did not considerably affect the rate of the reaction in the dark both in detergent and membrane preparations (in agreement with previous results (40
)), even though it reduced the energy of activation in detergent (16.9 vs. 13.5 kcal/mol). The smaller activation energy in the complex was compensated by a lower frequency factor. The small effect of the transducer binding on the hydroxylamine dark reaction is in keeping with the crystal structure of NpSRII which indicates close similarity to the structure of the transducer complex (41
). Binding of transducer to detergent preparation reduced, however, the light effect. Similarly to the free pigment, the complex experienced a significant reduction in activation energy and in frequency factor but the effect was smaller. In membranes the apparent light effect on the complex was stronger than in detergent. The effect of light on the activation energy and the frequency factor probably reflects light-induced alterations in the retinal binding site. The transducer forms in detergent a 1:1 heterodimer with the pigment whereas a 2:2 complex is detected in membrane preparations. The transducer binds to the cytoplasmic side of the protein but since the complex is different in detergent and membranes the light effect may be different. Interestingly, recent FTIR studies (42
) indicated similar secondary structure of M intermediate after transducer binding in membrane preparations. Although the light effect can originate also from other intermediates besides M, it is plausible that the light effect originates from relatively mild changes in the retinal binding site. The binding of transducer can affect differently these changes in membranes and detergent preparations. We note (as stated in the results section) that the measured rates are apparent rates since temperature change affects the intermediates' lifetime. This phenomenon may induce differences between preparations with and without transducer as well.
| ACKNOWLEDGEMENTS |
|---|
|
|
|---|
Submitted on May 3, 2005; accepted for publication July 19, 2005.
| REFERENCES |
|---|
|
|
|---|
2. Haupts, U., J. Tittor, and D. Oesterhelt. 1999. Closing in on bacteriorhodopsin: progress in understanding the molecule. Annu. Rev. Biophys. Biomol. Struct. 28:367399.[CrossRef][Medline]
3. Lanyi, J. K. 2000. Molecular mechanism of ion transport in bacteriorhodopsin: insights from crystallographic, spectroscopic, kinetic, and mutational studies. J. Phys. Chem. B. 104:1144111448.
4. Klare, J., V. Gordeliy, J. Labahn, G. Büldt, H. J. Steinhoff, and M. Engelhard. 2004. The archaeal sensory rhodopsin II/transducer complex: a model for transmembrane signal transfer. FEBS Lett. 564:219224.[CrossRef][Medline]
5. Spudich, J. L. 1998. Variations on a molecular switch: transport and sensory signalling by archaeal rhodopsins. Mol. Microbiol. 28:10511058.[CrossRef][Medline]
6. Chizhov, I., G. Schmies, R. Seidel, J. R. Sydor, B. Lüttenberg, and M. Engelhard. 1998. The photophobic receptor from Natronobacterium pharaonis: temperature and pH dependencies of the photocycle of sensory rhodopsin II. Biophys. J. 75:9991009.
7. Salem, L., and P. Bruckmann. 1975. Conversion of a photon to an electrical signal by sudden polarisation in the N-retinylidene visual chromophore. Nature. 258:526528.[CrossRef][Medline]
8. Lewis, A. 1978. The molecular mechanism of excitation in visual transduction and bacteriorhodopsin. Proc. Natl. Acad. Sci. USA. 75:549553.
9. Delaney, J. K., T. L. Brack, G. H. Atkinson, M. Ottolenghi, G. Steinberg, and M. Sheves. 1995. Primary picosecond molecular events in the photoreaction of the BR5.12 artificial bacteriorhodopsin pigment. Proc. Natl. Acad. Sci. USA. 92:21012105.
10. Xu, D., C. Martin, and K. Schulten. 1996. Molecular dynamics study of early picosecond events in the bacteriorhodopsin photocycle: dielectric response, vibrational cooling, and the J, K intermediates. Biophys. J. 70:453460.
11. Rousso, I., E. Khachatouriants, Y. Gat, I. Brodsky, M. Ottolenghi, M. Sheves, and A. Lewis. 1997. Microsecond atomic force sensing of protein conformational dynamics: implications for the primary light-induced events in bacteriorhodopsin. Proc. Natl. Acad. Sci. USA. 94:79377941.
12. Aharoni, A., L. Weiner, M. Ottolenghi, and M. Sheves. 2000. Bacteriorhodopsin experiences light-induced conformational alterations in nonisomerizable C13=C14 pigments. J. Biol. Chem. 275:2101021016.
13. Rousso, I., Y. Gat, A. Lewis, M. Sheves, and M. Ottolenghi. 1998. Effective light-induced hydroxylamine reactions occurs with C13=C14 nonisomerizable bacteriorhodopsin pigments. Biophys. J. 75:413417.
14. Iwamoto, M., Y. Sudo, K. Shimono, and N. Kamo. 2001. Selective reaction of hydroxylamine with chromophore during the photocycle of pharaonis phoborhodopsin. Biochim. Biophys. Acta. 1514:152158.[Medline]
15. Hohenfeld, I. P., A. A. Wegener, and M. Engelhard. 1999. Purification of histidine tagged bacteriorhodopsin, pharaonis halorhodopsin and pharaonis sensory rhodopsin II functionally expressed in Escherichia coli. FEBS Lett. 442:198202.[CrossRef][Medline]
16. Wegener, A. A., J. Klare, M. Engelhard, and H. J. Steinhoff. 2001. Structural insights into the early steps of receptor-transducer signal transfer in archaeal phototaxis. EMBO J. 20:53125319.[CrossRef][Medline]
17. Oesterhelt, D., L. Schumann, and H. Gruber. 1974. Light-dependent reaction of bacteriorhodopsin with hydroxylamine in cell suspensions of Halobacterium halobium: demonstration of an apo-membrane. FEBS Lett. 44:257261.[CrossRef][Medline]
18. Sudo, Y., M. Iwamoto, K. Shimono, and N. Kamo. 2001. Pharaonis phoborhodopsin binds to its cognate truncated transducer even in the presence of a detergent with a 1:1 stoichiometry. Photochem. Photobiol. 74:489494.[CrossRef][Medline]
19. Subramaniam, S., T. Marti, S. J. Rosselet, K. J. Rothschild, and H. G. Khorana. 1991. The reaction of hydroxylamine with bacteriorhodopsin studied with mutants that have altered photocycles: Selective reactivity of different photointermediates. Proc. Natl. Acad. Sci. USA. 88:25832587.
20. Huang, J., Z. Chen, and A. Lewis. 1989. Second harmonic generation in purple membrane-poly (vinyl alcohol) films: probing the dipolar characteristics of the bacteriorhodopsin chromophore in bR570 and M412. J. Phys. Chem. 93:33143319.[CrossRef]
21. Birge, R., and C. Zhang. 1990. Two photon double resonance spectroscopy of bacteriorhodopsin. Assignment of the electronic and dipolar properties of the low-lying
-like and
-like
,
* states. J. Chem. Phys. 92:71787195.[CrossRef]
22. Clays, K., E. Hendrickx, M. Triest, T. Verbiest, A. Persoons, C. Dehu, and J.-L. Bredas. 1993. Nonlinear optical properties of proteins measured by Hyper-Rayleigh scattering in solution. Science. 262:14191422.
23. Aharoni, A., A. Khatchatouriants, A. Manevitch, A. Lewis, and M. Sheves. 2003. Protein-ß-ionone interactions enhance the light induced dipole of the chromophore in bacteriorhodopsin. J. Phys. Chem. B. 107:62216225.
24. Zadok, U., A. Khatchatouriants, A. Lewis, M. Ottolenghi, and M. Sheves. 2002. Light-induced charge redistribution in the retinal chromophore is required for initiating the bacteriorhodopsin photocycle. J. Am. Chem. Soc. 124:1184411845.[CrossRef][Medline]
25. Aharoni, A., L. Weiner, A. Lewis, M. Ottolenghi, and M. Sheves. 2001. Nonisomerizable non-retinal chromophores initiate light-induced conformational alterations in bacterioopsin. J. Am. Chem. Soc. 123:66126616.[CrossRef][Medline]
26. Aharoni, A., L. Weiner, A. Lewis, M. Ottolenghi, and M. Sheves. 2001. Light induced hydrolysis in Non-isomerizable C13=C14 bacteriorhodopsin pigment. Biophys. J. 82:26172626.
27. Sheves, M., N. Friedman, and A. Albeck. 1985. Primary photochemical event in bacteriorhodopsin: study with artificial pigments. Biochemistry. 24:12601265.[CrossRef]
28. Chang, C., R. Govindjee, T. Ebrey, K. Bagley, G. Dollinger, L. Eisenstein, J. Marque, H. Rodex, J. Vittow, J. Fang, and K. Nakanishi. 1985. Trans/13-cis isomerization is essential for both the photocycle and proton pumping of bacteriorhodopsin. Biophys. J. 47:509512.
29. Bhattacharya, S., T. Marti, H. Otto, M. Heyn, and H. Khorana. 1992. A bacteriorhodopsin analog reconstituted with a nonisomerizable 13-trans retinal derivative displays light insensitivity. J. Biol. Chem. 267:67576762.
30. Uji, L., Y. Zhou, M. Sheves, M. Ottolenghi, S. Ruhman, and G. Atkinson. 2000. Vibrational spectrum of a picosecond intermediate in the artificial bR5.12 photoreaction: picosecond time resolved CARS of T-5.12. J. Am. Chem. Soc. 122:96106.[CrossRef]
31. Sharkov, S., A. Pakulev, S. Chekalin, and Y. Matveetz. 1985. Primary events in bacteriorhodopsin probed by subpicosecond spectroscopy. Biophys. Biochim. Acta. 808:94102.[CrossRef]
32. Mathies, R. A., C. H. Brito Cruz, W. T. Pollard, and C. V. Shank. 1988. Direct observation of the femtosecond excited-state cis-trans isomerization in bacteriorhodopsin. Science. 240:777779.
33. Lutz, I., A. Sieg, A. A. Wegener, M. Engelhard, I. Boche, M. Otsuka, D. Oesterhelt, J. Wachtveitl, and W. Zinth. 2001. Primary reactions of sensory rhodopsins. Proc. Natl. Acad. Sci. USA. 98:962967.
34. Zhong, Q., S. Ruhman, M. Ottolenghi, M. Sheves, N. Friedman, G. H. Atkinson, and J. K. Delaney. 1996. Reexamining the primary light-induced events in bacteriorhodopsin using a synthetic C13=C14-locked chromophore. J. Am. Chem. Soc. 118:1282812829.[CrossRef]
35. Ye, T., N. Friedman, Y. Gat, G. Atkinson, M. Sheves, M. Ottolenghi, and S. Ruhman. 1999. On the nature of the primary light-induced events in bacteriorhodopsin: ultrafast spectroscopy of native and C13=C14 locked pigments. J. Phys. Chem. B. 103:51225130.
36. Luecke, H., B. Schobert, H. T. Richter, J. P. Cartailler, and J. K. Lanyi. 1999. Structure of bacteriorhodopsin at 1.55 angstroms resolution. J. Mol. Biol. 291:899911.[CrossRef][Medline]
37. Berhali, H., P. Nollert, A. Royant, C. Menzel, J. P. Rosenbusch, E. M. Landau, and E. Pebay-Peyroula. 1999. Protein, lipid and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane at 1.9 angstroms resolution. Structure. 7:909917.[Medline]
38. Royant, A., P. Nollert, K. Edman, R. Neutze, E. M. Landau, E. Pebay-Peyroula, and J. Navarro. 2001. X-ray struture of sensory rhodopsin II at 2.1 angstroms resolution. Proc. Natl. Acad. Sci. USA.
39. Luecke, H., B. Schobert, J. K. Lanyi, E. N. Spudich, and J. L. Spudich. 2001. Crystal structure of sensory rhodopsin II at 2.4 angstroms: insight into color tuning and transducer interaction. Science. 293:14991503.
40. Sudo, Y., M. Iwamoto, K. Shimono, and N. Kamo. 2002. Association of pharaonis phoborhodopsin with its cognate tranducer decreases the photo-dependence reactivity by water-soluble reagents of azide and hydroxylamine. Biochim. Biophys. Acta. 1558:6369.[Medline]
41. Gordeliy, V., J. Labahn, R. Moukhametzianov, R. Efremov, J. Granzin, R. Schlesinger, G. Buldt, T. Savopol, A. Scheidig, J. Klare, and M. Engelhard. 2002. Molecular basis of transmembrane signaling by sensory rhodopsin II-transducer complex. Nature. 419:484487.[CrossRef][Medline]
42. Furutani, Y., K. Kamada, Y. Sudo, K. Shimono, N. Kamo, and H. Kandori. 2005. Structural changes of the complex between pharaonis phoborhodopsin and its cognate transducer upon formation of the M photointermediate. Biochemistry. 44:29092915.[CrossRef][Medline]
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |