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. Author manuscript; available in PMC: 2017 Mar 9.
Published in final edited form as: Methods Enzymol. 2016 Jul 9;578:273–297. doi: 10.1016/bs.mie.2016.05.023

Figure 8. Computational method QAA allows identification of multi-scale hierarchy associated with catalysis by enzyme CypA.

Figure 8

(a) Multi-level (2 levels shown) hierarchy of conformational sub-states, each dot is a conformations. Each colored dot represents a single sampled conformation; ellipses indicate sub-states; TS′, TS″, and T indicate transition state area. (b) the free energy profile and conformations in (a) are colored according to reaction coordinate, (c) conformational change between sub-states corresponding to black arrow in (a), and (d) impact of identified motions on CypA’s mechanism. Adapted from (Ramanathan et al., 2011).