Figure 5.

α₃D is a designed protein¹⁰³ for which a one-dimensional reaction coordinate cannot explain the probe-dependent kinetics using a reasonable diffusion coefficient.⁴³ (A) Structure of α₃D from PDB (2A3D). (B) A contour plot of the optimal two-dimensional free energy surface for α ₃D calculated using Langevin dynamics as described by Scott et al.¹⁷⁵ (C) Kinetic rates measured with infrared absorption spectroscopy are shown as black dots, fluorescence spectroscopy as red dots. The dashed (one-dimensional model) and solid (two-dimensional model) lines represent the fits of the data using Langevin dynamics, but the one-dimensional fit requires an unrealistic diffusion coefficient; diffusion coefficients of incorrect magnitude or with unusual coordinate dependence are a warning sign that the model underestimates the dimensionality of the dynamics. (D) Time traces of Q and C_α-RMSD for α₃D from Lindorff-Larsen et al. show strong correlation, but are not equivalent⁷. Q is the fraction of long-range native contacts. For the quantitative definition of Q see page 3 of Supplemental Materials in reference ⁷.