Interactions in protein folding

Aurora, R., Creamer, T, Srinivasan, R., and Rose, G. D., 1997. Local interactions in protein folding Lessons from die ci-helix. TheJournal of Biological Chemistry 272 1413-1416. 

Johnson BD, Schumacher RJ, Ross ED, Toft DO. (1998) Hop modulates Hsp70/Hsp90 interactions in protein folding. J Biol Chem. 273, 3679-3686. 

Prieto, J., M. WUmans, M.A. Jimenez, M. Rico, and L. Serrano, Non-native local interactions in protein folding and stability intro-... 

Sippl MJ, Ortner M, Jaritz M, Lackner P, Flockner H (1996) Helmholtz free energies of atom pair interactions in proteins, Fold Des, 1 289-298... 

Baldwin, R. L., Temperature dependence of the hydrophobic interaction in protein folding. Proc. Natl. Acad. Sci. USA 83, 8069-8072 (1986). 

Gromiha MM, Selveraj S. Influence of medium and long range interactions in protein folding. Prep. Biochem. Biotechnol. 1999 29 339-351. 

Gromiha MM, Selveraj S. Inter-residue interactions in protein folding and stability. Prog. Biophys. Mol. Biol. 2004 86 235-277. 

R. Aurora, T. P. Creamer, R. Srinivasan and G. D. Rose Local interactions in protein folding Lessons from theor-helix. yourao/ of Biological Chemistry 272, 1413(1997). 

Protein segments adopt only a finite number of conformations in folded proteins.This limited dictionary of templates may be due to the inherent steric constraints of the backbone and other packing and electrostatic interactions in protein folding. This was most graphically demonstrated by Jones and Thirup. They showed that the majority of the polypeptide backbone of a new structure can be built up from component pieces of other structures, whether or not they are related. Unger et al. showed, in fact, that 76% of the main chain structure of an 82 protein data set can be constructed using only 100 unique hexapeptide templates. Amino acid side chains are also found in a restricted set of conformers. Recent work in our laboratory has shown that a set of four tetrapeptide templates is sufficient to define almost all loop conformations. 

N. Go and H. Taketomi, Proc. Natl. Acad. Sci. V.S.A., 75, 559 (1978). Respective Roles of Short- and Long-Range Interactions in Protein Folding. 

SUMOylation. Figure 1 SUMOylation is a reversible and regulated process. Target protein modification by SUMO can be initiated and terminated by different cues. Sumoylation leads to changes in the behavior of the modified protein, for example, different cellular localization, enhanced/reduced activity, or increased stability. These changes are due to alterations either in protein interactions or protein folding. 

Ejtehadi MR, Avail SP, Plotkin SS. Three-body interactions improve the prediction of rate and mechanism in protein folding models. Proc Natl Acad Sci USA 2004 101 15088-93. 

Both the protein and the ligand are solvated by water when they are separated. As the two surfaces interact, water is excluded, hydrogen bonds are broken and formed, hydrophobic interactions occur, and the protein and ligand stick to each other. As in protein folding and for the same reasons, the hydrophobic interaction provides much of the free energy for the association reaction, but polar groups that are removed... 

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