Patent ID: 6495314
Filing Date: 2002-12-17
Classification: C07K

Abstract:
A process for obtaining a molecular signature of a protein or protein domain, the protein or protein domain having an amino acid sequence with length m, each amino acid position within the sequence being represented by (aa)n where 1&lE;n&lE;m, the protein or protein domain having optimal binding conditions for binding to a target molecule and forming a binding conjugate therewith, the process comprising the following steps:Step A: providing a peptide ladder library comprising a collection of m peptides, each peptide being represented by (peptide)n, each peptide having the same amino acid sequence as the protein or protein domain except that the amino acid position (aa)n of (peptide)n is replaced by a substitute amino acid, the position of the substitute amino acid differing for each peptide within the peptide ladder library, the substitute amino acid at position (aa)n being linked to the amino acid at position (aa)n+1 by means of a selectively cleavable bond; then Step B: contacting the peptide ladder library of said Step A with the target molecule under binding conditions for forming bound peptides and unbound peptides, the bound peptides being bound to the target molecule; then Step C: separating and isolating the bound peptides from the unbound peptides of said Step B; then Step D: cleaving the selectively cleavable bond of each of the bound peptides isolated in said Step C for producing peptide cleavage products; then Step E: detecting and identifying each of the peptide cleavage products of said Step D for identifying amino acids within the amino acid sequence of the protein associated with binding to the target molecule; and then Step F: constructing a subsequence which defines the molecular signature of the protein or protein domain with respect to the target molecule using the identity of the peptide cleavage products of said Step E, the molecular signature being defined by the subsequence of the amino acid sequence selected from amongst positions (aa)n which, if individually replaced by a substitute amino acid, lead to a loss of binding affinity by the protein or protein domain with respect to the target molecule.