Methods for identifying an epitope of a polypeptide, chlamydial antigenic polypeptides identified thereby, and methods of use thereof

A method of determining the presence of an epitope on a polypeptide encoded by a test nucleotide sequence, the method comprising:

• identifying a plurality of variable nucleotide positions in an alignment of nucleotide sequences of a plurality of variants of a polypeptide-coding sequence;
• correlating a nucleotide character state of a plurality of variable nucleotide positions with a selected immunological reactivity, to generate a plurality of correlated nucleotide character states;
• generating a plurality of reference sets comprising a plurality of correlated nucleotide states, wherein each correlated nucleotide state correlates with a selected immunological reactivity, and wherein the reference sets indicate classification of epitopes of the encoded polypeptide;
• and
• comparing the test nucleotide sequence encoding a test polypeptide to the plurality of reference sets of correlated nucleotide character states and determining the best fit of the test nucleotide sequence to a reference set from among the plurality of reference sets, wherein an identity of at least 80% to a reference set associated with a selected epitope indicates that the test polypeptide exhibits the epitope.

A method of generating a nucleotide sequence encoding an antigenic peptide that exhibits a selected epitope, the method comprising:

• identifying a plurality of variable nucleotide positions in an alignment of nucleotide sequences of a plurality of variants of a polypeptide-coding sequence;
• correlating a nucleotide character state of a plurality of variable nucleotide positions with a selected immunological reactivity, to generate a plurality of correlated nucleotide character states;
• generating a plurality of reference sets comprising a plurality of correlated nucleotide states, wherein each correlated nucleotide state correlates with a selected immunological reactivity, and wherein the reference sets indicate classification of epitopes of the encoded polypeptide;
• and
• based on the reference sets, generating a nucleotide sequence that encodes a polypeptide that exhibits one or more selected epitopes from among the classified epitopes.

An isolated polypeptide fragment of from about 5 to about 60 amino acids in length, the fragment comprising an amino acid sequence of a formula selected from:

• Formula II:
• NH2-(X1)n(A/T)GT(D/E)A(X2)m-COOH,
• (SEQ ID NO:2)
• wherein X1 and X2 are independently any amino acid, and wherein n and m are each independently zero, or an integer from 1 to about 44;
• Formula III:
• NH2—(X1)nTIAG(X2)m—COOH (SEQ ID NO:12), wherein X1 and X2 are independently any amino acid, and wherein n and m are each independently zero, or an integer from 1 to about 56;
• Formula V:
• NH2—(X1)nTTLNPTIAG(X2)m—COOH (SEQ ID NO:14), wherein X1 and X2 are independently any amino acid, and wherein n and m are each independently zero, or an integer from 1 to about 41;
• Formula VII:
• NH2—(X1)n-GAKPT(T/A)(T/D)TGN(A/S)(V/T/A)APSTLTARE-(X2)m—COOH (SEQ ID NO:44), wherein X1 and X2 are independently any amino acid, and wherein n and m are each independently zero, or an integer from 1 to about 30;
• Formula IX:
• NH2—(X1)n-TT(S/K)DVAGLQNDP-(X2)m—COOH (SEQ ID NO:53), wherein X1 and X2 are independently any amino acid, and wherein n and m are each independently zero, or an integer from 1 to about 38;
• Formula XI:
• (SEQ ID NO:65)
• NH2-(X1)n-(S/A)EFTINKPKGYVG(K/Q/A/V)E-(X2)m-COOH,
• wherein X1 and X2 are independently any amino acid, and wherein n and m are each independently zero, or an integer from 1 to about 38;
• Formula XII:
• NH2—(X1)n-ILWEGFGGDPCDPCTT-(X2)m—COOH (SEQ ID NO:70), wherein X1 and X2 are independently any amino acid, and wherein n and m are each independently zero, or an integer from 1 to about 34;
• Formula XIII:
• NH2—(X1)n-ALNIWDRFDV-(X2)m—COOH (SEQ ID NO:71), wherein X1 and X2 are independently any amino acid, and wherein n and m are each independently zero, or an integer from 1 to about 40;
• and
• Formula XIV:
• NH2—(X1)n-KMKSRKSCGIAVGTTVSADKYAVT-(X2)m—COOH (SEQ ID NO:72) where X1 and X2 are independently any amino acid, and n and m are each independently zero, or an integer from 1 to about 26.

A macromolecule comprising a polypeptide of from about 5 to about 60 amino acids in length, the fragment comprising an amino acid sequence of a formula selected from:

• Formula II:
• NH2-(X1)n(A/T)GT(D/E)A(X2)m-COOH,
• (SEQ ID NO:2)
• wherein X1 and X2 are independently any amino acid, and wherein n and m are each independently zero, or an integer from 1 to about 44;
• Formula III:
• NH2—(X1)nTIAG(X2)m—COOH (SEQ ID NO:12), wherein X1 and X2 are independently any amino acid, and wherein n and m are each independently zero, or an integer from 1 to about 56;
• Formula V:
• NH2—(X1)nTTLNPTIAG(X2)m—COOH (SEQ ID NO:14), wherein X1 and X2 are independently any amino acid, and wherein n and m are each independently zero, or an integer from 1 to about 41;
• Formula VII:
• NH2—(X1)n-GAKPT(T/A)(T/D)TGN(A/S)(V/T/A)APSTLTARE-(X2)m—COOH (SEQ ID NO:44), wherein X1 and X2 are independently any amino acid, and wherein n and m are each independently zero, or an integer from 1 to about 30;
• Formula IX:
• NH2—(X1)n-TT(S/K)DVAGLQNDP-(X2)m—COOH (SEQ ID NO:53), wherein X1 and X2 are independently any amino acid, and wherein n and m are each independently zero, or an integer from 1 to about 38;
• Formula XI:
• NH2—(X1)n-(S/A)EFTINKPKGYVG(K/Q/A/V)E-(X2)m—COOH (SEQ ID NO:65), wherein X1 and X2 are independently any amino acid, and wherein n and m are each independently zero, or an integer from 1 to about 38;
• Formula XII:
• NH2—(X1)n-ILWEGFGGDPCDPCTT-(X2)m—COOH (SEQ ID NO:70), wherein X1 and X2 are independently any amino acid, and wherein n and m are each independently zero, or an integer from 1 to about 34;
• Formula XIII:
• NH2—(X1)n-ALNIWDRFDV-(X2)m—COOH (SEQ ID NO:71), wherein X1 and X2 are independently any amino acid, and wherein n and m are each independently zero, or an integer from 1 to about 40;
• and
• Formula XIV:
• NH2—(X1)n-KMKSRKSCGIAVGTTVSADKYAVT-(X2)m—COOH (SEQ ID NO:72), where X1 and X2 are independently any amino acid, and n and m are each independently zero, or an integer from 1 to about 26.