Reaction coordinates, protein folding

Transition state theory (Chapter 2, section A) was derived for chemical bonds that obey quantum theory. An equation analogous to that for transition state theory may be derived even more simply for protein folding because classical low energy interactions are involved and we can use the Boltzmann equation to calculate the fraction of molecules in the transition state i.e., = exp(— AG -D/RT), where A G D is the mean difference in energy between the conformations at the saddle point of the reaction and the ground state. Then, if v is a characteristic vibration frequency along the reaction coordinate at the saddle point, and k is a transmission coefficient, then... 

In chemical reactions, orbits on stable and unstable manifolds of NHIMs describe movements of reaction coordinates. In some cases, these reaction coordinates are those degrees of freedom describing the behavior of individual nuclei such as a bond length between a pair of atoms. In other cases such as protein folding, reaction coordinates describe collective behavior where multiple nuclei participate. In either case, the processes of leaving a NHIM and approaching another one involve reformulation of reaction coordinates. In particular, when reaction coordinates are collective variables, reformulation processes themselves are of interest. We think that the study of intersections is crucial to understand how a certain collective movement is replaced by another one. 

Proteins. The questions, What kinds of mechanisms carry a protein into an unique native state and What is the best reaction coordinate to describe the dynamics of protein folding have been among the most intriguing subjects over the past decades in biological physics [35,36]. The process of protein folding may be interpreted as a normal Brownian process of a few collective... 

---