Biology Reference
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whether it was possible to derive novel (artificial) epitope sequences
directed against the second extracellular loop of human b
1
-adrenore-
ceptor for potential immunotherapeutic agents. Their design strategy
is described in the following four steps.
(1)
De novo design and evolutionary approach
. The researchers first
identified a sequence with a desired activity (b
1
-adrenoreceptor loop
2 epitope) that would serve as a “seed” sequence around which to
develop an
in silico
library. A common approach for such searches is
through random screening. To obtain a seed peptide, parts of the
sequence of human b
1
-adrenoreceptor encompassing loop 2 were
analyzed by epitope mapping. The ability of the peptide fragments to
bind to human anti-b
1
-adrenoreceptor antibodies was measured by
ELISA. The amino acid sequence ARRCYNDPKC (positions
107-116) was identified as a natural epitope with specific affinity to
the antibodies and was therefore selected as the seed peptide.
(2)
Focused library strategy
. Using the amino acid sequence
ARRCYNDPKC as the seed peptide, a set of 90 variants were gener-
ated by a simple algorithm describing each residue by the respective
property values for hydrophobicity
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and volume.
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Thus, a total of
ninety 20-dimensional vector representations of variants, in terms of
these two properties, were generated. These vectors were generated
using the Box-Muller formula, and were approximately gaussian-dis-
tributed around the seed peptide vector (standard deviation (
0.1);
where
g
is a gaussian-distributed random number and
i
and
j
are ran-
dom numbers in the [0, 1] interval:
σ
)
=
g
=σ√−
2 ln(
i
) sin(2
π
j
).
Eq. (1)
The rationale for obtaining vectors both close and distant from a
seed vector is that peptides with an activity similar to that of the seed
peptide are expected to be in close proximity to the seed peptide in
sequence space,
229
while those that are more distant are expected to
have decreased activity or provide new seed vectors of higher activity.
The strategy is designed, through a mathematical approach, to focus
