Patent ID: 6780598
Filing Date: 2004-08-24
Classification: A61K,C07K,G01N

Abstract:
A method for detecting a protein of known sequence comprises the steps of:determining an optimal immunobiologically active linear epitope of said protein of known sequence, wherein said protein is comprised of a plurality of amino acids, and wherein said optimal immunobiologically active linear epitope is characterized by a hydrophobic-hydrophilic-hydrophobic (Ho-Hi-Ho) motif determined by a method comprising the steps of: assigning an average hydropathy value to each of said plurality of amino acids of said protein of known sequence; generating a hydrophilicity plot using said average hydropathy value; fitting each of a plurality of curve segments of said hydrophilicity plot to one of a plurality of a negative cosine functions, wherein one of a plurality of a specific period number values of said plurality of negative cosine functions equates to a particular number of amino acids in one of said plurality of curve segments, said period number value increasing within a predetermined chosen period number range after a sequential lagging of each of said plurality of curve segments through said hydrophilicity plot thereby providing a fit-correlation value for each of said plurality of curve segments across said known sequence of said protein when using one of said plurality of said period number values; generating a potential Ho-Hi-Ho epitope set for each of said plurality of specific period number values within said chosen period number range wherein said potential Ho-Hi-Ho epitope set contains at least one potential Ho-Hi-Ho epitope in which said fit-correlation value is positive; ranking each of said potential Ho-Hi-Ho epitopes of said potential Ho-Hi-Ho epitope set and assigning a ranking value to each of said potential Ho-Hi-Ho epitopes according to said fit-correlation value wherein said potential Ho-Hi-Ho epitope with a highest positive fit-correlation value is ranked number one, thereby providing a ranked Ho-Hi-Ho potential epitope for each of said plurality of specific period number values; examining said ranking value of each of said potential Ho-Hi-Ho epitopes relative to said hydrophilicity plot to determine at least one potential Ho-Hi-Ho epitope set that exhibits alternating positioning around an equilibrium position, wherein a plurality of said ranking values of said potential Ho-Hi-Ho epitopes converge towards or diverge away from said equilibrium position; and designating each of said Ho-Hi-Ho epitopes, wherein said ranking values exhibit a most alternating ranking value that converges or diverges from said equilibrium position as said optimal immunobiologically active epitope wherein a numeric value of amino acid in said potential Ho-Hi-Ho epitopes is equal to one of said plutality of specific period number values of said negative cosine function; synthesizing at least one peptide corresponding to at least one of said optimal immunobiologically active linear epitopes; creating at least one antisera against said synthesized peptides corresponding to at least one of said optimal immunobiologically active linear epitopes; providing a sample to be analyzed for said protein of known sequence; contacting said sample with said at least one antisera; and detecting a binding of said antisera to said protein of said sample, thereby indicating presence of said protein in said sample.