Abstract
Only with the help from (little) “friends” is it possible for the 11-cis-retinal Schiff base to compete successfully against Glu 113 for a proton (see picture). A strategically placed amino acid, Thr 94, plus a water molecule are sufficient to reduce the basicity of the glutamate and stabilize the protonated chromophore—this is the result of ab initio optimization and molecular-dynamic study of the retinal binding site in rhodopsin.
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