scholarly journals Statistical Mechanics Model for Protein Folding

2009 ◽  
Author(s):  
Alexander Yakubovich ◽  
Andrey V. Solov’yov ◽  
Walter Greiner ◽  
Andrey Solov́yov ◽  
Eugene Surdutovich
Keyword(s):  
Protein Folding ◽  
Statistical Mechanics ◽  
Mechanics Model

STATISTICAL MECHANICAL FOUNDATION FOR THE TWO-STATE TRANSITION IN PROTEIN FOLDING OF SMALL GLOBULAR PROTEINS

2002 ◽  
Vol 16 (13) ◽  
pp. 1807-1839 ◽  
Author(s):  
KAZUMOTO IGUCHI
Keyword(s):  
Protein Folding ◽  
Statistical Mechanics ◽  
State Transition ◽  
Globular Proteins ◽  
Globular Protein ◽  
Prototype Model ◽  
Folding Model ◽  
Mechanics Model ◽  
Contact Order ◽  
Statistical Mechanical

We discuss the statistical mechanical foundation for the two-state transition in the protein folding of small globular proteins. In the standard arguments of protein folding, the statistical search for the ground state is carried out from astronomically many conformations in the configuration space. This leads us to the famous Levinthal's paradox. To resolve the paradox, Gō first postulated that the two-state transition — all-or-none type transition — is very crucial for the protein folding of small globular proteins and used the Gō's lattice model to show the two-state transition nature. Recently, there have been accumulated many experimental results that support the two-state transition for small globular proteins. Stimulated by such recent experiments, Zwanzig has introduced a minimal statistical mechanical model that exhibits the two-state transition. Also, Finkelstein and coworkers have discussed the solution of the paradox by considering the sequential folding of a small globular protein. On the other hand, recently Iguchi have introduced a toy model of protein folding using the Rubik's magic snake model, in which all folded structures are exactly known and mathematically represented in terms of the four types of conformations: cis-, trans-, left and right gauche-configurations between the unit polyhedrons. In this paper, we study the relationship between the Gō's two-state transition, the Zwanzig's statistical mechanics model and the Finkelsteinapos;s sequential folding model by applying them to the Rubik's magic snake models. We show that the foundation of the Gō's two-state transition model relies on the search within the equienergy surface that is labeled by the contact order of the hydrophobic condensation. This idea reproduces the Zwanzig's statistical model as a special case, realizes the Finkelstein's sequential folding model and fits together to understand the nature of the two-state transition of a small globular protein by calculating the physical quantities such as the free energy, the contact order and the specific heat. We point out the similarity between the liquid-gas transition in statistical mechanics and the two-state transition of protein folding. We also study morphology of the Rubik's magic snake models to give a prototype model for understanding the differences between α-helices proteins and β-sheets proteins.

scholarly journals Statistical mechanics of simple models of protein folding and design

1997 ◽  
Vol 73 (6) ◽  
pp. 3192-3210 ◽  
Author(s):  
V.S. Pande ◽  
A.Y. Grosberg ◽  
T. Tanaka
Keyword(s):  
Protein Folding ◽  
Statistical Mechanics ◽  
Simple Models
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