Falling Down: Landscape and Kinetics of One-Dimensional Protein Folding

The capillarity picture and the kinetics of one-dimensional protein folding.

E nergy landscape theory unites the study of protein folding with the theory of phase transitions. Dimensionality, whose key role in phase transitions is well known, comes to the fore in folding repeat proteins. Repeat proteins are made of near repetitions of 20–40 residues encoding recurring structural motifs. Each repeating element interacts only with its immediate neighbors, forming extended...

Kinetics of a finite one-dimensional spin system as a model for protein folding.

Simple spin models are used to analyze the kinetic nature of lowest energy state formation of the spin systems as models of protein folding kinetics. The models employed in the present paper are based on the spin systems as models of biopolymers previously proposed by the author for the analysis of the equilibrium nature of transitions [T. Kikuchi, Biophys. Chem. 65 (1997) 109]. In particular, ...

The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein

The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying port...

Kinetics and Thermodynamics of Protein Folding

Kinetics and Thermodynamics of Membrane Protein Folding

Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins. In comparison, advances in the membrane protein folding field lag far behind. Although membrane proteins constitute about a third of the proteins encoded in k...