Chemistry Faculty Publications

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The effect of relocation of the W2 crystallographic water in bovine rhodopsin has been investigated by comparing and analyzing simulated resonance Raman spectra of I HZX-and 1U19-based quantum mechanics/molecular mechanics (CASSCF/MM) models. The main target is to explore the sensitivity of the simulated resonance Raman spectra to protein cavity change. In particular, we focus on a quantitative investigation of the changes in the vibrational activity of rhodopsin induced by modifications in the protein cavity structure and in the water position. Comparison of the simulated FIR spectra of the Rh-1U19 and Rh-1HZX models with the measured spectrum of rhodopsin reveals that the Rh-1U19 model provides a slightly better rhodopsin model consistently with the simulations of the absorption maxima. On the other hand, and irrespective of the comparison with the experimental data, the analysis of two different computational models for the same protein and chromophore makes it possible to investigate and disentangle the relationship between structural features and change in the FIR intensities in an unusually detailed way.

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Journal Of Chemical Theory And Computation


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