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8. Enzymes and Other Proteins

Enzymes are polypeptides which use ordinary chemical mechanisms and specific binding interactions to speed up reactions. No mysterious forces need be invoked. Studies of the mechanisms by which enzymes catalyse reactions have been made by both biochemists and crystallographers, and it is when they work together that the most information is obtained. Once the three-dimensional structure has been determined by the crystallographer, further information may be obtained on the mechanism by NMR studies, chemical modification, and by X-ray crystallographic studies of enzyme-inhibitor complexes. The lock-and-key model of Emil Fischer (the enzyme is the lock and the substrate is the key), with some modification, is relevant to the interactions involved.

The building blocks are L-amino acids, NH+3--CHR--COO-, where R is a substituent which defines the particular amino acid. There are 20 that are normally found in proteins and the structures of these have been determined by X-ray and neutron diffraction methods. In proteins these amino acids are joined by a peptide linkage C--NH--CO--C. Essentially this is a planar grouping (as found in numerous peptides) and it is hinged to the next peptide group at the carbon atom to give a flexible backbone composed of planar peptide segments. Some dimensions are listed in Fig. 6. However two important types of interactions can occur as the three-dimensional structure of a protein is built up. One is hydrogen bond formation and the other is disulfide bond formation. These interactions stabilize the molecular shape. In particular hydrogen bond formation is responsible for the existence of $\alpha$-helices and $\beta$-pleated sheets, so common in enzymes.


 
Figure 6
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\includegraphics {fig6.ps}
\end{figure}

The main structural features of globular proteins may be generalized as follows (although exceptions are found):

1.
The molecule is very compact.
2.
Most of the polar or hydrophilic R groups lie on or near the surface.

3.
Most of the nonpolar or hydrophobic R groups lie in the interior, hidden from water.

4.
$\alpha$-helices, $\beta$-pleated sheets and disulfide linkages serve to stabilize the structure. In this way various points on the polypeptide chain are brought into close proximity as the polypeptide chain is folded and the active site of the enzyme (i.e. the part of the enzyme where the reaction takes place) is formed.

5.
Proline residues occur principally at bends in the polypeptide chain.

Reference

General stereoviews, Dickerson, R. E. and Geis, I., The Structure and Action of Proteins . Menlo Park, California, Benjamin (1969).

When teaching about macromolecules be sure to look up recent issues of Nature, Proceedings of the National Academy of Sciences, the Journal of Molecular Biology and the Journal of Biological Chemistry for recent advances.



 
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Next: Lysozyme Up: Elementary X-Ray Diffraction for Biologists Previous: f. Comparisons of structures using the

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