Biology Reference
In-Depth Information
151
Table 6-2. Some of the
angles found in reference proteins for the three di-peptides.
Val Glu
()
Val ( ) Lys
( )
Glu Lys
-46
0
,-34
0
-48
0
,-43
0
-114
0
,+180
0
-124
0
,-30
0
-99
0
,-29
0
-87
0
,-44
0
-93
0
,+22
0
-69
0
,-9
0
-82
0
,-33
0
-45
0
,-42
0
-121
0
,+134
0
-65
0
,-42
0
-29
0
,-45
0
-68
0
,-56
0
-60
0
,-39
0
-101
0
,-154
0
-128
0
,+136
0
-133
0
,+147
0
-104
0
,+125
0
-61
0
,-49
0
-67
0
,-59
0
-89
0
,+92
0
If the and values for all three di-peptides in Table 6-2 are within about
30
0
of each other, they are combined and averaged. They give a possible
choice of (-58
0
,-41
0
). Other less restrictive selections are also possible.
This procedure of matching amino acid sequences of tri-peptides and
selecting the angles of the middle amino acid residue of reference
proteins is self-consistent. Consider a protein with known three-
dimensional structure. If this protein sequence together with its angles
is included in the reference proteins, the process of matching tri-peptides
will automatically pick the known angles as possible choices. This
seemingly trivial result, however, provides a consistent scheme of selecting
and angles. A known three-dimensional structure will automatically be
included as one of the possible choices.
Consider the above mentioned case of Val Glu Lys with two possible
choices for the middle amino acid residue Val, i.e. (-75
0
,+142
0
) and
(-59
0
,-41
0
). If every residue in a protein with 100 amino acid residues has
two possible choices of angles, a total of 2
100
or roughly 10
30
possible
combinations have to be analyzed. This number, although much smaller
than 10
100
, is still too large to be processed by modern day computers. Even
though the angles of every residue together with the structure of the
standard peptide unit can in principle generate detailed three-dimensional
structures of the protein, it would be impossible to pick the correct one. In
addition, the variation of as small as 1
0
for the selected and angles can
produce extensive distortions on cumulative basis over 100 residues.
