Figure 1.
An Illustration of Two State Cdc42-CBD Binding
The loosely bound state was presumably a subset of conformations that deviated from the bound equilibrium states, probed by the dye, without disrupting the subnanometer long-range interactions, so the overall protein complex was still associated.
Figure 2.
Single-Molecule Fluorescence and Spectroscopy Studies of Cdc42-CBD Protein–Protein Interaction Dynamics
(A) Second-order auto-correlation function, C(t), calculated from a fluorescence intensity trajectory I(t) of a single Cdc42-CBD complex. Solid curve is a bi-exponential fit. (Inset) A single-molecule fluorescence raster-scanning image of GTP-loaded Cdc42 in complex with dye-labeled CBD biosensor.
(B) The occurrence histogram of the single-complex conformational fluctuation rate for 60 individual protein complexes [19].
Figure 3.
Illustration of Flexible Binding-Folding through Two-Dimensional Free-Energy Landscape, Trajectory and Time Correlation
(A) Flexible binding-folding.
(B) Two-dimensional free-energy contour plots of the interface degree of freedom between CBD portion of WASP and Cdc42, and conformation/folding degree of freedom for CBD.
(C) Typical trajectory of fraction of native contacts of binding interface between CBD portion of WASP and Cdc42.
(D) Time correlation function of fraction of native interface contacts.
Figure 4.
Two-Dimensional Free-Energy Landscape versus Interface Binding of Cdc42 and Folding CBD for Different α
Figure 5.
Distribution of Phi Values versus Protein-Primary Sequence
(A) Distribution of phi values, and (B) phi values along the primary sequences of CBD portion of WASP and Cdc42.
Figure 6.
Distribution of Phi Values and Phi Values versus Protein-Primary Sequence for Different α
Figure 7.
Auto-Correlations of Fraction of Interface Contacts c(Δ) at Different Positions of Qb and at T = Ts
Figure 8.
Typical Structures and their Corresponding Configuration in the Free-Energy Landscape
Typical structures of loosely bound state (left structure), transition state (middle structure), and bound state (right structure) and their corresponding configuration in free-energy profiles in terms of fraction of native (interface) contacts between Cdc42 and CBD portion of WASP, as well as the fraction of native (folding) contacts of CBD itself.
Figure 9.
The simulation temperature Ts = 0.944, and melting temperature Tf = 1.0. The Tf is defined from the peak of Cv, and Ts is determined from two-dimensional free-energy profile F(Qf2,Qb). The simulation temperature was chosen so that the free-energy values at the loosely bound and bound states are equal.