Patent ID: 7176035

Claim:
A method for identifying a polypeptide that binds with a high affinity to a peptide region in a chosen protein, the peptide region being adjacent to a repulsive peptide region of the chosen protein, the method comprising: (a) providing a set of short overlapping peptides spanning a complete sequence of at least a domain of the chosen protein, the set of short overlapping peptides being covalently attached to a support; (b) contacting the support to which the overlapping peptides are covalently attached with a mixture of polypeptides under conditions enabling binding between the peptides on the support and a polypeptide of the mixture; (c) washing the support to remove unbound polypeptides of the mixture; (d) identifying a first set of contiguous overlapping peptides that bind the polypeptide, the first set comprising a first region that binds to the polypeptide with a high affinity; (e) identifying a second set of contiguous overlapping peptides that bind the polypeptide, the second set comprising a second region that binds to the polypeptide with a high affinity, the second set being discontinuous from the first set; and (f) identifying the segment between the first set and the second set, the segment comprising the repulsive peptide region of the chosen protein, the repulsive peptide region being adjacent to the high affinity peptide regions, the polypeptide that binds to the first peptide region and the second peptide region being the polypeptide that binds with a high affinity to the peptide region that is adjacent to the repulsive peptide region of the chosen protein.