Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces
Fig 2
(A) Estimated entropic contributions-TΔS to the binding free energy of the first (red) or the second (blue) cAMP binding event, and the overall entropy change for the binding of both cAMP (purple). Estimates from force covariance (FC) and quasi-harmonic (QH) analyses of either protein main chain (“MC”) or the full protein including DBD (“full”). For comparison, NMR-based estimates (“NMR”) are given for the entropy change of the first and second binding event of a truncated CAP construct (“CBD”) without DBD [8] and, respectively, for the binding of both cAMP to the full protein (“full”) [23]. (B) Functional motion of CAP for DNA binding as sampled in MD simulations. Projection of CAP X-ray structures and all simulation data from apo (black), cap1 (blue) and cap2 (orange) states on the first eigenvector obtained from a PCA of available 2 cAMP-bound X-ray structures, either solved in absence of DNA (1–6: 1GN6 [9], 1HW5 [27], and 1I6X, 3RDI, 3ROU, 1I5Z –all unpublished) or in presence of DNA (9–11: 1RUO [28], 1RUN [28] and 1CGP [26]). The two intermediate structures (PDB ids: 3QOP (unpublished) and 3KCC [29]) are not bound to DNA but to two cAMP molecules, localized in between the DBD and β-strand 5, triggering a rotation of the DBD.