Perception of light and color permits humans to enjoy art, though the sense evolved more likely to better find ripe fruits. The recognition, centuries ago, that the wondrous sense of color comes from three visual receptors to which is added in the eye a fourth black & white one is one of the major achievements in the history of science. The visual receptors of all animals rely on one molecule for light absorption, retinal. How do the receptors tune then their spectral sensitivity? Exploiting a similarity of visual receptors to proteins in an archaebacterium, Natronobacterium pharaonis, researchers have finally been given an opportunity to answer this question quantitatively. In the bacterium, two structurally almost identical proteins absorb maximally light of 497 nm and 568 nm wavelength. X-ray crystallography and advanced quantum chemical studies could explain the difference and pinpoint to the protein side groups that actually tune the spectra.
In collaboration with E. Landau and J. Navarro at University of Texas Medical Branch, the Resource has applied a combined ab initio quantum mechanical/molecular mechanical (QM/MM) approach to examine the ground and excited state of retinal in bacteriorhodopsin (bR) and sensory rhodopsin II (sRII). The calculations include full QM/MM optimization of the retinal and its counterions at the Hartree-Fock level of theory inside the protein environment, and single point complete active space self-consistent field QM/MM computation of excitation energies of the electronically ground (S0) and the low-lying excited (S1 and S2) states of retinal. A figure at the bottom left shows a comparison of the retinal binding pockets in sRII and bR. One can recognize readily the close structural similarities between the binding pockets in the two proteins. Despite a high degree of similarity in the three-dimentional structures, electrostatic environments of the chromophore in bR and sRII differ enough to shift the absorption maximum of retinal from 568 nm in bR to 497 nm in sRII. The results of our calculations successfully explained the major part of the observed differences between the spectra in bR and sRII. The Resource has also devised the decomposition analysis which clearly identifies contributions of individual protein residues to the spectral shift, as seen in figures at the bottom right.
This material is based upon work supported by the National Science Foundation under Grant No. 0234938. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.