Biomedical Engineering Reference
In-Depth Information
Tabl e 3. 4
Folding
characteristics of the protein
given in EMBL-EBI and
isoforms entries in the
PDB
databases according to the
CASTOR
algorithm selected)
Protein/isoform
Length
Helix
Strand
Other (coil)
1gal
581
54
26
66
1gal
2
186
19
7
23
1gal
3
116
10
7
18
1scu
a
676
61
39
68
1scu
1
121
9
7
11
1scu
1
81
9
6
12
1scu
1
149
9
9
15
2dlin
1
306
23
16
32
2dlin
1
73
7
6
8
2dlin
3
84
7
9
9
2adm
385
29
27
47
2adm
169
15
13
31
2adm
216
14
16
21
1dpg
1
485
50
17
19
1dpg
1
177
16
9
7
1dpg
2
308
32
12
11
1rec
1
185
35
6
7
1rec
1
102
29
4
6
1rec
1
83
7
5
5
a
2 chains of proteins included
The isoform folding characteristics are for the major part not given in the
databases; therefore, to provide a partial comparison, the only given folding val-
ues for the main protein is compared to the results determined with the
CASTOR
algorithm.
Further analysis should be made to determine exactly the differences that occur,
and this research will be available in the near future. Nevertheless, the results here
indicated are deemed important as it is evident, even with these partial results, that
the secondary structure of the isoforms differ and their functional characteristics
will differ.
Thus, it is useful to determine the secondary structure of proteins and isoforms so
that the markers identified have unique characteristics and can be used as a standard
for diagnosis.
Further the prediction of secondary structure among isoforms may lead to a better
comprehension of the biological effect of mutations among the isoforms of a protein.
This might permit to determine more accurately the relationship of the biological
functions of isoforms and the protein of the class.
The analysis of secondary structures might lead to the identification of subtypes
among oncologic markers, defining also their biological implication. It is known that
subtypes of markers already identified are related to more precise prognosis and
to the eventual clinical evolution of the malignancy. The differences between two
isoforms may be as small as just one amino acid with, at the moment, totally unpre-
dictable effects on life, unless all the functional dependencies are fully determined.
This approach permits the effects to be determined more precisely, even if there
are only small modifications in the primary structure.
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