Protein folding thermodynamic studies

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

Karplus, M. and Shakhnovich, E. (1992) Protein folding theoretical studies of thermodynamics and dynamics. In Creighton, T. (ed.). Protein Folding, pp. 127-195. W.H. Freeman Sons, New York. 

M. Karplus and E. Shakhnovich, Protein folding Theoretical studies of thermodynamics and dynamics, in Protein Folding, T.E. Creighton, Editor. 1992, W.H.Freeman. p. 127-196. 

M. Karplus and E. Shakhnovich, Protein Folding Theoretical Studies of Thermodynamics and Dynamics , eds. M. Karplus, E. Shakhnovich and W. H. Freeman, New York, 1992, pp. 127-196. 

E. I. Shakhnovich, Curr. Opin. Struct. Biol., 7, 29 (1997). Theoretical Studies of Protein-Folding Thermodynamics and Kinetics. 

Irback A, Sjunnesson F. Folding thermodynamics of three beta-sheet peptides a model study. Proteins 2004 56 110-6. 

The substantial free energy available in the binding of hemes into natural proteins is frequently harnessed to fold or stabilize the final protein structure as observed in the differences in the apo- (77) and holo-structures (73) of cytochrome 6562 shown in Fig. 2. Although detailed thermodynamic studies of natural heme proteins are beginning... 

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... 

It is interesting to note that although apparently unaware of the development of molecular imprinting, Pande et al. [28] proposed the use of thermodynamic control for the preparation of synthetic polymer systems with a memory for a template structure. Monte Carlo computer simulations were performed to validate their hypothesis. From these calculations they identified the formation of non-random polymer sequences arising from an evolution-like preferred selection of various monomer components by similar species. These studies have since been expanded upon using statistical mechanics to examine the consequences for protein folding [29]. 

To study protein folding theoretically, simulation methods have proved indispensable. The folding transition is ultimately governed by statistical thermodynamics and hence it is paramount to use sampling methods that are able to reproduce the canonical Boltzmann distribution. Common sampling techniques are molecular dynamics (MD), Langevin or Brownian dynamics (BD) and Monte Carlo (MC). 

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