Thermodynamics and kinetics of protein folding

Mittal, J., Best, R.B. Thermodynamics and kinetics of protein folding under confinement. Proc. Natl. Acad. Sci. U.S.A. 2008,105, 20233-8. 

A. R. Dinner and M. Karplus, The thermodynamics and kinetics of protein folding A lattice model analysis of multiple pathways with intermediates. J. Phys. Chem. B 103, 7976-7994 (1999). 

A. Sali, E. Shaknovich, and M. Karplus, Thermodynamics and kinetics of protein folding, in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Vol. 23, American Mathematical Society, 1996, pp. 199-213. 

H. P. Bachinger J. Engel, The Thermodynamics and Kinetics of Collagen Folding. In Protein Folding Handbook J. Buchner,... 

Multidomain proteins may be viewed as conjugated proteins in which each domain may affect the folding dynamics and thermodynamic properties of its counterpart domain. Experimentally, the thermodynamics and kinetics of both isolated domains and conjugated constructs from several multidomain proteins were studied (a very detailed and fairly current report can be found in Reference [29]). A computational characterization of the mechanistic principles of the folding of multidomain proteins [33], utilizing native structure-based models, provides a reduced microscopic description of their folding, which in turn may enable the formulation of the forces involved in the interplay between neighboring domains. 

Friedel, M., Sheeler, D.J., Shea, J.-E. Effects of confinement and crowding on the thermodynamics and kinetics of folding of a minimalist, 6-barrel protein. J. Chem. Phys. 2003,118, 8106-13. 

Confinement and Crowding on the Thermodynamics and Kinetics of Folding of a Minimalist Beta-barrel Protein. 

Polypeptide chains exist in an equilibrium between different conformations as a function of environment (solvent, other solutes, pH) and thermodynamic (temperature, pressure) conditions. If a polypeptide adopts a structurally ordered, stable conformation, one speaks of an equilibrium between a folded state, represented by the structured, densely populated conformer, and an unfolded state, represented by diverse, sparsely populated conformers. Although this equilibrium exists for polypeptide chains of any size, its thermodynamics and kinetics are typically different for oligopeptides and proteins. This can be broadly explained with reference to the different dimensionalities of the free-energy hypersurfaces of these two types of molecules. 

Shakhnovich H. I. Theoretical studies of protein-folding thermodynamics and kinetics. Curr. Op. Str. Biol. (1997) 7(1) 29-40. 

The protein folding problem is of fundamental importance in modern structural biology. Recent advances in experimental techniques have helped to elucidate thermodynamic and kinetic mechanisms that underlie different stages of the folding process [1-6]. Computer simulations performed at various levels of molecular detail have played a central role in the interpretation of experimental studies. Molecular simulations using models based on fully atomic representations are becoming more accurate and more practical and are increasingly... 

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