Vibrational analysis of the 13-cis-retinal chromophore in dark-adapted bacteriorhodopsin

Smith, Steven O.; Pardoen, J. A.; Lugtenburg, J.; Mathies, Richard A.

doi:10.1021/j100288a011

Cited by 177 publications

(307 citation statements)

References 3 publications

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“…Overall, the similarity of the fingerprint region for AR3 and BR firmly establishes that the chromophore undergoes an all-trans to a 13-cis isomerization as previously established for BR on the basis of RRS studies of isotopic labeled retinal in BR [37,38].…”

Section: Primary Phototransition Of Ar3 Involves All-trans To 13-cis supporting

confidence: 77%

Conformational changes in the archaerhodopsin-3 proton pump: detection of conserved strongly hydrogen bonded water networks

et al. 2011

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Archaerhodopsin-3 (AR3) is a light-driven proton pump from Halorubrum sodomense, but little is known about its photocycle. Recent interest has focused on AR3 because of its ability to serve both as a high-performance, genetically-targetable optical silencer of neuronal activity and as a membrane voltage sensor. We examined light-activated structural changes of the protein, retinal chromophore, and internal water molecules during the photocycle of AR3. Low-temperature and rapid-scan time-resolved FTIR-difference spectroscopy revealed that conformational changes during formation of the K, M, and N photocycle intermediates are similar, although not identical, to bacteriorhodopsin (BR). Positive/negative bands in the region above 3,600 cm −1 , which have previously been assigned to structural changes of weakly hydrogen bonded internal water molecules, were substantially different between AR3 and BR. This included the absence of positive bands recently associated with a chain of proton transporting water molecules in the cytoplasmic channel and a weakly hydrogen bonded water (W401), which is part of a hydrogenbonded pentagonal cluster located near the retinal Schiff base. However, many of the broad IR continuum absorption changes below 3,000 cm −1 assigned to networks of water molecules involved in proton transport through cytoplasmic and extracellular portions in BR were very similar in AR3. This work and subsequent studies comparing BR and AR3 structural changes will help identify conserved elements in BR-like proton pumps as well as bioengineer AR3 to optimize neural silencing and voltage sensing.

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Section: Primary Phototransition Of Ar3 Involves All-trans To 13-cis supporting

confidence: 77%

Conformational changes in the archaerhodopsin-3 proton pump: detection of conserved strongly hydrogen bonded water networks

et al. 2011

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“…The C 14 OC 15 stretch band at 1168 cm Ϫ1 is prominent in all-trans but weak in 13-cis, while the opposite is true for the C 10 OC 11 band at 1182 cm Ϫ1 . For reasons of steric constraint in the binding pocket, the C 14 hydrogen-out-of-plane band at 800 cm Ϫ1 is strong in 13-cis,15-syn retinal but has negligible amplitude in all-trans or 13-cis,15-anti (41)(42)(43). Fig.…”

Section: Results Ph Dependence Of the Crystallographic Structure Of D85nmentioning

confidence: 97%

A local electrostatic change is the cause of the large-scale protein conformation shift in bacteriorhodopsin

Brown

Kamikubo

Zimányi

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

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During light-driven proton transport bacteriorhodopsin shuttles between two protein conformations. A large-scale structural change similar to that in the photochemical cycle is produced in the D85N mutant upon raising the pH, even without illumination. We report here that (i) the pK a values for the change in crystallographic parameters and for deprotonation of the retinal Schiff base are the same, (ii) the retinal isomeric configuration is nearly unaffected by the protein conformation, and (iii) preventing rotation of the C 13 OC 14 double bond by replacing the retinal with an all-trans locked analogue makes little difference to the Schiff base pK a . We conclude that the direct cause of the conformational shift is destabilization of the structure upon loss of interaction of the positively charged Schiff base with anionic residues that form its counter-ion.

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“…So far, Raman spectroscopy has been widely used for such systems as pigments and model chromophores and has given valuable information (5)(6)(7)(8)(9)(10)(11)(12)(13)(14). We also propose to investigate the influence of protonation and of the environment with the same technique.…”

Section: Introductionmentioning

confidence: 99%

Study of the protonation of simple Schiff bases in solvents of various polarity by means of Raman spectroscopy

Alex¹,

Turcotte²,

Fournier³

et al. 1991

Can. J. Chem.

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. 69, 239 (1991). In this study, the protonation of simple Schiff bases by organic acids in various solvents is investigated by Raman spectroscopy and the spectral response of the C=Nf stretching mode is correlated with the macroscopic properties of the medium surrounding the imine. Upon protonation, the unperturbed C=N stretch increases in frequency due to the combination of the coupling with the C=N+H bend and a partial rehybridization of the C=N bond. Depending on the proton location relative to that of its counterion, one mechanism may prevail over the other. Intensity measurements show that protonation is mostly controlled by the hydrogen bonding properties of the solvent and by the polarity of the medium. However, whatever the solvent, full proton transfer cannot be achieved with organic acids with pK, similar to the COOH of amino acids found in visual or bacterial pigments, meaning that the protonation mechanism may depend upon particular properties of the protein.Key words: imines, protonation, Raman spectroscopy, rhodopsin, Schiff base.

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Vibrational analysis of the 13-cis-retinal chromophore in dark-adapted bacteriorhodopsin

Cited by 177 publications

References 3 publications

Conformational changes in the archaerhodopsin-3 proton pump: detection of conserved strongly hydrogen bonded water networks

Conformational changes in the archaerhodopsin-3 proton pump: detection of conserved strongly hydrogen bonded water networks

A local electrostatic change is the cause of the large-scale protein conformation shift in bacteriorhodopsin

Study of the protonation of simple Schiff bases in solvents of various polarity by means of Raman spectroscopy

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