Biology Reference
In-Depth Information
147
around 18 hydrophobic residues in a protein strongly suggests the existence
of a trans-membrane region of about 27 A in length.
For all these predictive methods, one may ask two questions:
(1) Is the prediction self-consistent?
(2) From the prediction, is it possible to display the three-dimensional
structure of the protein?
Self-consistent means that if the three-dimensional structure of a protein is
already determined experimentally, the predictive method should indeed
predict that structure. The helical wheel method is self-consistent, but most
of the other methods are not. If the locations of -helices, -strands, and
turns are all precisely predicted, it is usually not possible to generate the
three-dimensional structure of the protein. There are always amino acid
residues not in one of these three configurations.
For these reasons, we will consider a predictive method involving the
estimation of and angles as defined in the previous Chapter. As
discussed below, in principle, it is self-consistent and should be able to
provide sufficient information to construct the entire three-dimensional
structure.
REFERENCE PROTEINS
As we have discussed in the previous Chapter, there are many angles
sterically allowed for all amino acid residues. Thus, for a protein of 100
amino acid residues, for example, if there are ten possible choices of
angles for each residue, the total number of configurations to be analyzed
will be 10
100
. Even the fastest compute currently available will not be able
to handle so many different calculations. It is thus essential to reduce the
number of
choices for every position of the protein.
Furthermore, experimentally observed angles as determined from
atomic coordinates of proteins with known three-dimensional structures at
the website, http://www.rcsb.org/pdb, may not agree with those predicted
theoretically. Some of the experimentally determined angles are not
within the allowed regions based on steric hindrance calculations. On the
other hand, some of the allowed regions in the
plot are not populated
