In protein folding

Lorimer G H 1996 A quantitative assessment of the role of the ohaperonin proteins in protein folding in vivo FASEB J. 10 5-9... 

Williams S, Causgrove T P, Gilmanshin R, Fang KS, Callender R H, Woodruff WH and Dyer R B 1996 Fast events in protein folding helix melting and formation in a small peptide Biochemistry ZS 691-7... 

Li Z Q and H A Scheraga 1987. Monte Carlo Minimization Approach to the Multiple Minima Problem, in Protein Folding. Proceedings of the National Academy of Sciences USA 84 6611-6615. 

Eisenberg D and A D McLachlan 1986. Solvation Energy in Protein Folding and Binding. Nature 319 199-203. 

Noncovalent Forces Stabilizing Protein Structure. Much of protein engineering concerns attempts to alter the stmcture or function of a protein in a predefined way. An understanding of the underlying physicochemical forces that participate in protein folding and stmctural stabilization is thus important. 

AE Torda. Perspectives in protein-fold recognition. Curr Opm Struct Biol 7 200-205, 1997. 

Isomerization of proline residues can he a rate-limiting step in protein folding... 

Fersht, A.R. Characterizing transition states in protein folding an essential step in the puzzle. Curr. Opin. Struct. Biol 5 79-84, 1994. 

Enzymes assist formation of proper disulfide bonds during folding Isomerization of proline residues can be a rate-limiting step in protein folding Proteins can fold or unfold inside chaperonins GroEL is a cylindrical structure with a... 

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. 

Immunophillins are abundant proteins that catalyze the cis-trans isomerization of proline residues within proteins, generally to aid in protein folding. Immunophillins are not essential proteins, are the intracellular binding proteins of several immunosuppressive drugs. Cyclosporin A exerts its action after binding to cyclophilin. Tacrolimus and sirolimus predominantly bind to the protein FKBP-12 (FK binding protein-12). 

As stated above, the most important missing piece in protein folding theory is an accurate all-atom potential. Recently there has been much effort in this direction, and much more is needed [48,55,72-77]. The existence of a potential satisfying minimal criteria such as folding and stability for a single protein was demonstrated in [73]. It is not a realistic potential by any means, but its existence validates the all-atom, implicit solvent, Monte Carlo approach as a serious candidate for theory. The method used to derive this potential was ad hoc, and has recently been compared with other standard methods in a rigorous and illuminating study [77]. 

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. 

In mammals, peptide hormones typically contain only the a-amino acids of proteins finked by standard peptide bonds. Other peptides may, however, contain nonprotein amino acids, derivatives of the protein amino acids, or amino acids finked by an atypical peptide bond. For example, the amino terminal glutamate of glutathione, which participates in protein folding and in the metabolism of xenobiotics (Chapter 53), is finked to cysteine by a non-a peptide bond (Figure 3—3). The amino terminal glutamate of thyrotropin-... 

The studies of RNase Aand cytochrome c (Qi etal., 1998 Sosnick etal., 1997) show that caution is required in interpreting burst phenomena in protein folding. However, they do not require a reinterpretation of the cases in which the molten globule character of the burst-intermediate has been established (Arai and Kuwajima, 2000 Chamberlain and Marqusee, 2000). 

Callender, R. H., Dyer, R. B., Gilmanshin, R., and Woodruff, W. H. (1998). Fast events in protein folding The time evolution of primary processes. Annu. Rev. Phys. Chem. 49, 173-202. 

Parodi, A.J. (2000) Protein glucosylation and its role in protein folding. Annual Review of Biochemistry, 69, 69-93. 

Li, Z.Q. Scheraga, H.A., Monte-Carlo-minimization approach to the multiple-minima problem in protein folding, Proc. Natl Acad. Sci. USA 1987, 84, 6611-6615... 

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... 

D. Eisenberg and A. D. McLachlan, Solvation energy in protein folding and binding. Nature 319 199 (1986). 

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