Biology Reference
In-Depth Information
structures but also new structures that may bind this monoclonal anti-
body. The most amazing feature of the approach is that all findings can
be attained without any prior QSAR knowledge.
89-92
The specifically
active protein structures are, however, discovered rather than designed.
Peptide variants selected from the random sequence peptide library
by use of antibody binding frequently do not reproduce an exact
copy, but rather mimic natural antigenic epitopes.
93-95
The imitated
epitopes are known as mimotopes. The strategy for obtaining mimo-
topes has several important applications, including epitope mapping
within proteins.
90,96
However, the most valuable application of this
strategy is in obtaining short sequences to model conformational anti-
genic epitopes that can otherwise be reproduced only by using long
stretches of protein chains.
92-94
The limitation of the strategy is its fea-
sibility only for very short peptide sequences. A comprehensive library
of 20-mer peptides, in which each sequence variant has a chance to be
represented at least once, should contain >400 kg of peptides. Thus,
sequences in the range of 100 aa are completely out of the scope of
this approach, and the method is usually applied to peptides <10 aa in
length.
92,97
The mimotope strategy can also be used to improve natural epi-
topes in terms of characteristics such as antibody-binding affinity.
98
However, a more efficient way to accomplish this task is to use a set of
closely related sequence variants of an antigenic region for the selec-
tion of the improved variant.
99
This set can be obtained by random-
ization of the original sequence. The randomization can be achieved,
for example, by polymerase chain reaction using a low-fidelity DNA
polymerase for the amplification of a DNA fragment encoding for
the protein of interest or a region of this protein.
100,101
A significant
improvement in the protein properties can be attained by applying
several cycles of randomization and selection.
101
Several techniques can be used to implement the DE strategy.
Some techniques use recombinant DNA, whereas others use synthetic
peptides. Phage display, one of the most popular recombinant DNA
techniques, is based on the expression of a protein or its fragments
onto the surface of filamentous phages, the genome of which contains
genes encoding these proteins.
102
This versatile technique was used
