Recent advances in structural and biochemical studies of RFPs (red fluoroscent proteins) provide a better understanding of the molecular mechanisms of red chromophore autocatalytic synthesis. Majority of the Tyr-containing red chromophores are formed via the TagBFP-like blue intermediate containing the N-acylimine group. In RFPs, similar transitions between chromophore structures can either occur autocatalytically or be photoinduced or be blocked. Moreover, the chromophores that share the same structure can be in either fluorescent or dark states. Autocatalytical vs. photoinduced vs. blocked and fluorescent vs. chromo choices are mainly determined by amino acid residues in the chromophore and its immediate environment. The primary chromophore chemical structure, as well as the surrounding amino acids' immediate environment, predetermines the function of RFPs. Several structural features of the RFPs are translated into the RFPs functions.
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