8 Enzyme Engineering and Technology 179This is done by forming -helices and -pleated
sheets, as shown in Figure 8.2. The -helix can be
thought of as having a structure similar to a coil or
spring (Surewicz and Mantsch 1988). The -sheet
can be visualized as a series of parallel strings laid
on top of an accordion-folded piece of paper. These
structures are determined by the protein’s primary
structure. Relatively small, uncharged, polar amino
acids readily organize themselves into -helices,
while relatively small, nonpolar amino acids form
-sheets. Proline is a special amino acid because of
its unique structure (Table 8.1). Introduction of pro-
line into the sequence creates a permanent bend at
that position (Garnier et al. 1990). Therefore, the
presence of proline in an -helix or a -sheet dis-
rupts the secondary structure at that point. The pres-
ence of a glycine residue confers greater than nor-
mal flexibility on a polypeptide chain. This is due to
the absence of a bulky side chain, which reduces
steric hindrance.
Another frequently observed structural unit is the
-turn (Fang and Shortle 2003). This occurs when
the main chain sharply changes direction using a
bend composed of four successive residues, often
including proline and glycine. In these units the
CuO group of residue i is hydrogen bonded to the
NH of residue i 3 instead of i 4 as in the -
helix. Many different types of -turn, which differ
in terms of the number of amino acids and in confor-
mation (e.g., Type I, Type II, Type III), have been
identified (Sibanda et al. 1989).
The three-dimensional structure of a protein com-
posed of a single polypeptide chain is known as its
tertiary structure. Tertiary structure is determined
largely by the interaction of R groups on the surface
of the protein with water and with other R groups on
the protein’s surface. The intermolecular noncova-
lent attractive forces that are involved in stabilizing
the enzyme’s structure are usually classified into
three types: ionic bonds, hydrogen bonds, and van
der Waals attractions (Matthews 1993). Hydrogen
bonding results from the formation of hydrogen
bridges between appropriate atoms; electrostatic
bonds are due to the attraction of oppositely charged
groups located on two amino acid side chains. Van
der Waals bonds are generated by the interaction
between electron clouds. Another important weak
force is created by the three-dimensional structure
of water, which tends to force hydrophobic groups
together in order to minimize their disruptive effect
on the hydrogen-bonded network of water mole-
cules. Apart from the peptide bond, the only other
type of covalent bond involved in linking amino
acids in enzymes is the disulphide (—S—S—)
bond, which can be formed between two cysteine
side chains under oxidizing conditions. The disul-
phide bond contributes significantly to the structural
stability of an enzyme and, more precisely, to terti-
ary structural stabilization (see below for details)
(Matthews 1993, Estape et al. 1998).
Detailed studies have shown that certain combi-
nations of -helices or -sheets with turns occur
in many proteins. These often-occurring structures
have been termed motifs, or supersecondary struc-
ture (Kabsch and Sander 1983, Adamson et al.
1993). Examples of motifs found in several enzymes
are shown in Figure 8.3. These protein folds repre-
sent highly stable structural units, and it is believed
that they may form nucleating centers in protein
folding (Richardson 1981).Figure 8.1.(A) The amide bond showing delocalization
of electrons. (B) A tripeptide unit of a polypeptide chain
showing the planar amide units and the relevant angles
of rotation about the bonds to the central -carbon
atom.