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Fig. 2 Ribbon representation of the crystal structure 2WUR of a GFP triple mutant determined at
0.9 ˚ resolution. The chromophore atoms are shown as yellow van der Waals spheres . The protein
ribbon is colored green , and the transparent gray surface illustrates the protein surface. Colored
spheres indicate water oxygens. Different colors are used for different parts of the active-site
hydrogen-bonding clusters identified in [ 20 ] according to the subcluster “entrance” on the right
( red ), “internal” in the middle ( blue ), and “exit” on the left ( magenta ). Amino acid residues
involved in each cluster are also labeled with the corresponding color. Note that we did not draw
residues for which only the backbone oxygen and nitrogen atoms are involved in a cluster
5 Computational Approaches to Study Biomolecular
PT Dynamics
The simple algorithm applied in [ 20 ] that was discussed above did not consider the
p K a values of the residues involved nor the energy barriers for rotating their side
chains. In contrast, Warshel and coworkers treated the dynamics of biomolecular
PT by first computing the local p K a values of titratable residues and then applying a
Marcus-type approach to get transfer rates [ 25 ]. Taraphder and Hummer presented
an algorithm that accounts for the conformational dynamics of proteins to a certain
degree by considering all possible side-chain rotamer conformations and their
torsion energies and identifying the pathway of lowest-cost for generating bridging
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