Proton Travel in Green Fluorescent Protein - Fluorescent Proteins: From Understanding to Design - page 173

Fig. 3 Snapshot from a molecular dynamics simulation showing the proposed proton-entry and -
exit wires in the asFP595 protein [ 35 ]. Figure altered following [ 35 ] with permission

Proton release to the bulk solvent has also been suggested to take place for the
asFP595 protein [ 35 ]. Using molecular dynamics simulations, Sch afer and co-

workers identified a pathway from the chromophore (termed MYG here) to the
protein surface involving several titratable residues and buried water molecules
(Fig. 3 ). This pathway leading to the terminal Asp78 residue was suggested to
function as a proton-release pathway. During 20-ns long MD simulations, the
hydrogen-bonding coordination along this pathway remained intact. The authors
suggested that as the rate of proton migration along such wires is dominated by
tunneling, the proton exchange may occur by rapid one-dimensional diffusion of
protons along this wire.

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6 Outlook

Unfortunately, rational mutation work in GFP has so far been focused on the
vicinity of the chromophore with the aim of changing its fluorescence properties.
None of the mutants generated by phage display genetic evolution has targeted the
suggested proton-entry and -exit pathways. Likely, such mutations would provide
no advantage to the protein stability or folding efficiency and therefore were not
observed. However, GFP is clearly a very exciting model system for understanding
the energetic and kinetic details of internal proton transfer. We hope that some
future works will generate mutant fluorescent proteins that will affect the kinetics