Analyzing the Red‐shift Characteristics of Azulenic, Naphthyl, Other Ring‐fused and Retinyl Pigment Analogs of Bacteriorhodopsin*

Abstract

Prompted by the near infrared-absorbing properties of some of the azulenic bacteriorhodopsin (bR) analogs, we have analyzed their absorption characteristics along with 11 new related ring-fused analogs and the corresponding Schiff bases (SB) and protonated Schiff bases (PSB). The following three factors are believed to contribute to the total red shift of each of the pigment analogs (sigma RS): perturbation of the basic chromophore (SB shift, delta SB), protonation of the SB (PSB shift, PSBS) and protein perturbation (the opsin shift, OS). For each factor, effects of structural modifications were examined. For the red-shifted pigments, percent OS has been suggested as an alternate way of measuring protein perturbation. Computer-simulated chromophores provided evidence against any explanation involving altered shapes of the binding pocket as a major cause for absorption differences. Implications of the current bR results on preparation of further red-shifted bR and possible application to visual pigment analogs are discussed.

Microbial and Animal Rhodopsins: Structures, Functions, and Molecular Mechanisms

“…Other factors defining the spectral tuning of individual rhodopsins are given by chromophore–protein interactions such as electrostatic interactions with charged and polar amino acids, termed electrostatic tuning and extensively studied, first using retinal analogues, 29−32 and, later, site-directed mutagenesis. 33−35 Electrostatic tuning was elegantly demonstrated in a model system based on cellular retinol-binding protein II.…”

The Nature of the Delocalized Cations in Azulenic Bacteriorhodopsin Analogs¶

“…The NIR absorbing bR analogs previously reported by this laboratory were generated from azulene-and guaiazulene trienals, 2a,b and 3a-c (7,9,20). The final red-shifted pigments showed the characteristic features of a sharp, narrow absorption band (W 1/2 ϳ 800 cm Ϫ1 ) and a shoulder on its blue edge.…”

“…For the purpose of these calculations (retinal) and v max (pigment) are the respective absorption maxima of retv max inal or its analog and its corresponding bR pigment in cm Ϫ1 . This refined concept simplifies an earlier version where the redshift was separated into two terms, percent PSB shift and percent OS (9). The main advantage of using a percentage value rather than an absolute energy value is that such a quantity minimizes the effect of very different excitation energies of the azulenic bR pigment compared with that of the parent bR.…”

“…In an effort to prepare near infrared (NIR) absorbing bR analogs (7)(8)(9), we reported earlier the preparation of several retinal analogs with the unsaturated side chain attached to the uniquely colored (blue) nonalternant hydrocarbon azulene. The underlying strategy merely followed the simple logic that the colored ring chromophore with its lower-lying S 1 -state relative to the colorless cyclohexenyl ring, should provide ready access to pigment analogs absorbing beyond 700 nm.…”

Bacteriorhodopsin Analogs from Diphenylpolyene Chromophores¶

“…Over the years much effort has been directed toward understanding the spectral and photochemical properties of bR. A large number of synthetic chromophore analogs have been incorporated into the binding site of bR, and the observations of the resulting opsin shifts (OS) and photochemical properties have been analyzed in terms of chromophore–protein electrostatic and conformationally restrictive interactions (5–25). It has been found that the binding site of bR is quite flexible because retinal analogs with substantially bulky groups in the ring portion of the retinal can be accommodated in the bR binding site (23,24).…”