title: On the theory of folding kinetics for short proteins.
abstract: BACKGROUND
  Recent data have suggested two principles that are central to the work we describe here. First, proteins are the result of evolutionary 'sequence selection' to optimize the energy of the native state. Second, the overlap with the native state is a qualitatively suitable reaction coordinate for modeling folding kinetics. The former principle is bolder and better established.
  
  
  RESULTS
  Employing only these two principles, we have constructed a non-phenomenological, correlated energy landscape theory that predicts single barrier protein folding kinetics. Moreover, we are able to analytically describe the nature of the free energetic barrier between the denatured and native states of a protein and to detail the nature of folding kinetics for short proteins. Our model predicts Hammond behavior and also describes how mutations can lead to drastic differences in folding times.
  
  
  CONCLUSIONS
  We find that folding and unfolding kinetics can be characterized by a single thermodynamic parameter and, moreover, that Monte Carlo simulation data on folding and unfolding rates with different temperatures and mutations collapse with this characterization. Our results also delineate a regime in which kinetics may proceed via a single unique nucleus.
authors.affiliation: Department of Physics, University of California at Berkeley 94720, USA.
authors.forename: V S
authors.initials: VS
authors.lastname: Pande
authors.lastname: Grosberg AYu
authors.forename: T
authors.initials: T
authors.lastname: Tanaka
mesh_terms: D003198:Computer Simulation; D007700:Kinetics; D008956:Models, Chemical; D009010:Monte Carlo Method; D011489:Protein Denaturation; D017510:Protein Folding; D013816:Thermodynamics