Entropy contribution from individual residue

2017-06-02 10:54:47 | 日历
Figure 10
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Entropy contribution from individual residue
The entropy contribution from each individual residue in each simulation was calculated through the analysis of the cross-correlation matrices. For each RRS Dark state simulation, the relative entropy contribution from each individual residue was calculated with reference to the entropy contribution from the same residue in the unperturbed simulation of the VVD Dark state. The same calculation was also carried out for the RRS Light state simulations. The relative individual residue entropies are plotted as heat maps for RRS simulations of Dark and Light states in Fig. 11. The blue diagonal lines in both plots are due to the fact that the entropies from residues as rigid body is significantly smaller than the reference state. In addition, the averaged relative entropies of individual residues from all the RRS simulations are plotted in Fig. 12 for Dark and Light states, respectively. Most residues do not show significant entropy change upon rigid residue perturbation. However, certain residues display rather consistent but different trends in RRS simulations of Dark and Light states. The most striking case is residue Lys85, which has significantly positive entropic response in RRS simulations of Dark state and significantly negative entropic response in RRS simulations of Light state. In both Dark and LED Panel Lightstates, Lys85 forms strong hydrogen bond with the phosphate group of FAD (Fig. 13). It is notable that N-terminus residues 1 through 10 have generally positive entropic response towards rigid residue simulations in Dark state, and these positive entropic responses are further enhanced in the Light state. On the contrary, the entropic responses from residues 28 through 37 change from positive in Dark state simulations to significant negative in the Light state simulations. The individual residue entropies were also normalized with regard to the atoms number in each residue and illustrated in Figure S137. The similarity between normalized and original residue entropies plots shows that the differences of residue responses are not scaled with residue size, and therefore inherent to protein structure.
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