Patent ID: 6070126
Filing Date: 2000-05-30
Classification: C07K

Abstract:
A method for determining an optimal length of contiguous amino acid residues of a Ho-Hi-Ho model epitope within a polypeptide, said Ho-Hi-Ho model epitope characterized by a hydrophobic-hydrophilic-hydrophobic motif, the method comprising the steps of:a) assigning a window average hydropathy value to each amino acid of the polypeptide;b) generating a hydropathy plot using said window average hydropathy value of each amino acid;c) fitting each curve segment of said hydropathy plot to a negative cosine function, wherein a specific period number value of said negative cosine function increases within a predetermined chosen period number range after each sequential lagging through said hydropathy plot thereby providing fit-correlation values for each region of amino acid sequence number ranges of said polypeptide when using said specific period number value;d) generating a potential Ho-Hi-Ho model epitope set for each specific period number value within said chosen period number range, wherein each potential Ho-Hi-Ho model epitope set contains potential Ho-Hi-Ho model epitopes with said amino acid sequence number ranges that have a positive-fit correlation value;e) ranking each potential Ho-Hi-Ho model epitope with amino acid sequence number range in said potential Ho-Hi-Ho model epitope set according to positive fit-correlation values wherein said the potential Ho-Hi-Ho model epitope with amino acid sequence number range having highest said positive-fit correlation value is ranked number one thereby providing ranked Ho-Hi-Ho model theoretical epitopes for each specific period number value;f) providing peptides that together span the length of said polypeptide, the peptides having a length from about 15 to about 25 mers;g) generating experimental data on immunobiologic reactivity of said peptides;h) ranking experiment peptides according to experimental immunobiologic reactivity thereby providing a peptide experimental ranking value for each peptide;i) comparing amino acid residue sequences of said experimental peptide with amino acid residue sequences of said ranked Ho-Hi-Ho model theoretical epitopes wherein a positive correlation of amino acid residue sequences provides the basis for assigning said experimental peptide a theoretical ranking dependent upon the ranking of a corresponding Ho-Hi-Ho model theoretical epitope thereby providing a peptide theoretical ranking for each peptide when using said potential Ho-Hi-Ho model epitope set derived from a specific period number value;j) calculating a correlation coefficient by correlating said peptide experimental ranking to said peptide theoretical ranking for each peptide when using a potential Ho-Hi-Ho model epitope set derived from a specific period number value;k) determining a statistical p-value of said correlation coefficient;l) determining said specific period number value having lowest statistical p-value; andm) determining an optimal length of a Ho-Hi-Ho model epitope by assigning said specific period number value with said lowest statistical p-value to said Ho-Hi-Ho model epitope.