morecomplex thenativeprotein is, themoredifficult
it
is to find a good antigenie site that could be
recognized by the antibodies raised against the
sequence.
Predietionofgoodantigeniesitesfrom theamino
acid sequence
The physical andbiochemical characters featuring
an antigenie site along the amino acid sequence
(Table l) are quite weil understood (Maksyutov
number andpotentiallocationof the alfa- andbeta
tums, and the prohability at the sequence to be
recognizedas an antigen.Fig
l
shows the outcome
ofa typical analysis applied tohumanosteocalcin.
The antigenie index in this case is calculated
according to the
J
arneson andWolf
(J
arneson and
Wolf 1988) algorithm. The analysis indicates the
possibly surface-oriented antigenie sites offering
feasible sequences for antibody production. The
aminoacidsequence in thiscasewasobtainedfrom
Table l: Evaluatian of the methods available to prediet antigenicity
Method
Hydropathicity
Surface topography
Secondary structure
Mobility
Antigenicity
Combined protocols
Amphipaticity
Actvantages
uses sequence
weil correlated
uses sequence
weil correlated
uses sequence
Shortcomings
not a determinant of
antigenicity
need three dimensional
protein structure
not reliable
need three dimensional
protein structure
poorly correlated
improvement over individual methods
useful for
T
-cell antigens limited use
and Zagrebelnya 1993; Stern 1991; Wolf and
Modrow 1988;Westhofetal1988;HopandWoods
1981). The orientation of the amino acid chain to
the intemal (hydrophobicity) or externa! (hydro–
hilicity) parts of the rnature protein can be
approximated by the means of hydrophaticity in–
dex. Themore hydrophilic the sequence, themore
probably it is oriented towards the external part of
the protein. On the contrary, the hydrophobic
sequences are probably found from the intemal
parts of the protein. Using these characteristics
combinedto theexperimentaldataongoodantigenie
sites, algorithms predieting antigenie sites from
amino acid sequencehavebeenconstructed. Table
2 summarizes the currently available computer
programs, which can be used in calculation of
antigenie indexesand thephysicalparameters. The
computer analysis usually plats the prohability of
the orientation of a given amino acid sequence to
intemal or external parts of the native protein, the
the Swiss-Prot data service bank and the program
was run in theUnix computing systemofMinistry
ofEducation, Finland.
48
Table
2.
Programmes available for predieting
antigenie sites
author
name
language
Hopp andWoods
Hydra
HP-Basic
Hopp
Hydro4
HP-Basic
Jameson andWolf
Proteale
VAX/Fortran
Kyte andDoclite
SOAP
c
Karplus and Schulz Flexplot
Fortran
Maksyutov and
ADEPT
Zagrebelnaya
KliniskKemi iNorden2, /995
