Flexibility of proteins

As noted earlier, the flexibility of proteins allows them to carry out a wide variety of tasks. Our cells often build about 60,000 different kinds of proteins. A bacterial cell will synthesize only a little over 1000 different kinds of proteins. 

Fig. 34. Glu-72- Zn interactions in native carboxypeptidase A and in carboxypep-tidase A-inhibitor complexes (inhibitors have been reviewed by Christianson and Lipscomb, 1989). When substrates or inhibitors bind to the enzyme active site and interact with the zinc ion, the interaction of the metal with Glu-72 tends from bidentate toward uniden-tate coordination. The flexibility of protein-zinc coordination may be an important aspect of catalysis in this system, and the Glu-72->Zn - coordination stereochemistry observed here is consistent with the stereochemical analysis of carboxylate-zinc interactions from the Cambridge Structural Database (Carrell et al., 1988 see Fig. 4).

Much information about flexibility of protein structure has also come from x-ray crystallography data. It is either in the form of atomic mean-square displacements... 

Nagayama, K. (1981). Two-dimensional NMR spectroscopy an application to the study of flexibility of protein molecules. Adv. Biophys., 14, 139-204. 

Kaivarainen, A.I. (1986) Solvent-dependent flexibility of proteins and principles of their functions. Dordrecht, Boston, London. D. Reidel Publ.Co. 

Fischer S, Verma CS. Binding of buried structural water increases the flexibility of proteins. Proc. Natl. Acad. Sci. U.S.A. 68. 1999 96 9613-9615. 

The ability of proteins to do work on the molecules they bind depends upon several factors. The active sites of enzymes bring reactive groups on both the substrate and protein together. Active sites often contain acidic or basic groups that act as chemical catalysts. They may also distort the structure of the substrate to make it resemble the transition state of the reaction being catalyzed. The flexibility of protein structures is also important because it allows the bound molecule to go through a sequence of interactions with the protein. 

Steric strain. The early idea that enzyme catalysis results from the destabilization of the ground state10 was examined and concluded that the actual amount of energy associated with steric strain is small, due to the inherent flexibility of proteins.11 Nevertheless, the strain proposal has been invoked in several recent studies. 

R 772 T, Yamamoto and K. Gekko, Study on Flexibility of Protein by Mass Spectrometry , Journal of the Mass Spectrometry Society of Japan, 2003, 51,412... 

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