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OJBTM
Online Journal of Bioinformatics©
8 (1) : 115-138,
2007
In-silico
TAT-PTD
prediction for cell penetrating peptides.
Tandon C, Aggarwal A, Goel P,
Sengupta D, Naik
P
Department
of Biotechnology and Bioinformatics,
ABSTRACT
Tandon C,
Aggarwal A,
Goel P, Sengupta D, Naik P, In-silico
TAT-PTD prediction for cell penetrating peptides, Online
J
Bioinformatics, 8 (1) : 115-138, 2007. Cell Penetrating
Peptides (CPP) enhance transport of membrane and
secretory proteins across hydrophobic membranes. Natural or synthetic CPP
water
soluble peptides translocate across cell membranes and are used for
intracellular delivery of large hydrophilic molecules. HIV-TAT PTD with
an amino
acid sequence of YGRKKRRQRRR is the
core of TAT protein in HIV, with 8 of its 11
TAT-PTD amino acids being hydrophilic yet this molecule diffuses
readily through
hydrophobic bi-lipid membranes. The effect of charged amino-acids in
TAT-PTD on
membrane transport was therefore evaluated In
silico. A dataset of 168 sequences was created mutating the
original
TAT-PTD 11-amino acid sequence. Qikprop was used to predict ADME
properties and
a correlation of R2 = 73.7% between partition coefficient
and skin
permeability was found.
Keywords: Partition Coefficient,
Skin Permeability, TAT- PTD,
Cell Penetrating Peptides, Homology
modeling.