Biology Reference
In-Depth Information
Figure 6-11.
Stereo view of CDRH3 with seventeen amino acid residues.
As a result, depending on the number of amino acid residues, some
canonical loops (Chothia and Lesk, 1987) have been proposed without the
detailed analysis of selecting and angles. Thus, for antibodies, an
abbreviated approach of predicting backbone structures has been proposed
with the use of such standard configurations for all six CDR's (Webster and
Rees, 1995).
Proteins of Similar Functions
Many proteins have similar enzymatic functions, even though their amino
acid sequences are different. For example, as discussed in Chapter 4,
glycerol dehydrogenase uses NAD as a co-enzyme. There are many other
NAD-linked dehydrogenases and have similar three-dimensional structures
consisting of parallel -pleated sheets stabilized by -helices. Thus, it is
possible to make use of a known dehydrogenase structure as a framework to
predict the three-dimensional folding of another one.
Several of the NAD-linked dehydrogenases have an NAD domain consisting
of a -pleated sheet with six parallel -strands and a left-handed twist of
about 100
0
. That sheet is stabilized by four -helices, two on each side of
the sheet. However, there is little amino acid sequence homology among
these dehydrogenases, except that Gly residues are common at ends of
several -strands and an Asp residue is conserved for NAD binding.
Although the catalytic domains of these dehydrogenases appear somewhat
different, there are still many structural similarities.
