Forces in proteins

C. Niedermeier and P. Tavan. Fast version of the structure adapted multipole method — efficient calculation of electrostatic forces in protein dynamics. Mol. Sim., 17 57-66, 1996. 

Dill, K. A. (1990). Dominant forces in protein folding. Biochemistry 29, 7133-7155. 

About 200 to 460 kJ/mol are required to break a single covalent bond, whereas weak interactions can be disrupted by a mere 4 to 30 kJ/mol. Individual covalent bonds that contribute to the native conformations of proteins, such as disulfide bonds linking separate parts of a single polypeptide chain, are clearly much stronger than individual weak interactions. Yet, because they are so numerous, it is weak interactions that predominate as a stabilizing force in protein structure. In general, the protein conformation with the lowest free energy (that is, the most stable conformation) is the one with the maximum number of weak interactions. 

Barry T. Nall and Ken A. Dill, Conformations and Forces in Protein Folding, American Association for the Advancement of Science, Washington, DC, 1991. 

Another approach to simplify the protein chain is to reduce the conformational space allowed to the protein. The argument is simply that one of the major forces in protein structure is the formation of a core, a hydrophobic core, in which the side chains are tightly packed with no free volume. It is indeed postulated to be one of the first steps in protein folding. If this is the case, the core of the protein can be simplified to the points on a lattice [43-47],... 

Proteins solubilized in aqueous solution interact more or less with hydrophilic groups of surfactants at the oil-water interface. Therefore, the type of hydrophilic group is strongly influenced by the protein extraction efficiency. Anionic and cationic surfactants interact with charged protein surfaces more strongly than non-ionic surfactants. This feature also means that the non-ionic surfactants are favourable for protein stabilization in water droplets because of the not-so-hard interaction between the protein and the surfactant. In protein extraction, such an electrostatic interaction between proteins and surfactants is the main driving force in protein transfer. 

K. A. Dill, Biochemistry, 29, 7133 (1990). Dominant Forces in Protein Folding. 

T. Determining the role of hydrahon forces in protein folding. J. 47. Phys. Chem. B 1999 103 5413-5426. 

K. A. Dill, Dominant Forces in Protein Folding, Biochemistry, 29, (1990) 7133 K. A. Dill, Theory of the Folding and Stability of Globular Proteins, Biochemistry, 24 (1985) 1501. 

The unequivocal demonstration of the importance of dispersion forces in protein-ligand association is difficult, since individual atom-atom energies are rather small and it is the sum of many atom-atom interactions which determines whether an association is given by the dispersion interactions or not. 

Although solvent exposure gets the most attention as a driving force in protein evolution, it is not the only physical parameter to be studied in this context. Multiple studies have considered the role of protein sequence length in evolution (which corresponds to the final size of the folded protein) [7,56]. Simple organisms... 

J. Clarke and P.M. Williams (2005). Unfolding induced by mechanical force. In Protein Folding Handbook. Part /, Edited by Buchner, J. and Kiefhaber, T. Wiley-VCH New York. 

This was in 1980. Since then I became convinced that Kauzmann s model, based on transferring a solute from water into an organic liquid, is inadequate for estimating the contributions of H0O groups to the overall driving forces in protein folding and protein-protein association. In these processes it is... 

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