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OJBTM
Online
Journal of Bioinformatics©
Volume 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, Onl
J Bioinform, 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.
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