Fig. 6: Binding kinetics in the MSM.
From: A litmus test for classifying recognition mechanisms of transiently binding proteins
a On-rate kon, off-rate koff, and dissociation constant Kd of ubiquitin and SH3c calculated from the MSM for the state threshold value \({p}_{{{{{{{{\rm{bind}}}}}}}}}^{* }=0.57\) at which the experimental value for Kd is obtained. Unbound/bound states of the MSM are defined as states with \({p}_{{{{{{{{\rm{bind}}}}}}}}}^{* }\) values smaller/larger than the state threshold value. Super and sub-scripts indicate a 95% confidence interval of the posterior distribution of the MSM transition matrix. b Kd, kon, and koff, as a function of the state threshold value \({p}_{{{{{{{{\rm{bind}}}}}}}}}^{* }\). The threshold \({p}_{{{{{{{{\rm{bind}}}}}}}}}^{* }=0.57\) in (a) is located within a plausible transition state region. However, the entire range of predicted Kd values for different threshold choices is within the expected error of current state-of-the-art force field. The rates in subscript and superscript in (a) and the error regions in (b) represent 95% confidence intervals of the posterior distribution of Markov models.
