Regulation of target protein activity through modifier proteins

An isolated crystalline polypeptide, wherein the polypeptide comprising a JAM domain consisting essentially of an amino acid sequence of HXHXXXXXXXXXXD, wherein H is histidine, D is aspartate, and X is any amino acid.

An isolated monoclonal antibody that specifically binds to an epitope within a JAM domain of a polypeptide, wherein the JAM domain consists essentially of an amino acid sequence of HXHXXXXXXXXXXD, wherein H is histidine, D is aspartate, and X is any amino acid.

A method of identifying an inhibitor of a polypeptide by rational drug design wherein the polypeptide comprises a JAM domain consisting essentially of an amino acid sequence of HXHXXXXXXXXXXD, wherein H is histidine, D is aspartate, and X is any amino acid, the method comprising

• designing a potential inhibitor for the polypeptide that will form a bond with the JAM domain based upon the crystal structure co-ordinates of the polypeptide,
• synthesizing the inhibitor, and
• determining whether the potential inhibitor inhibits the activity of the polypeptide.

A method of deconjugating a modifier protein from a target protein, wherein the modifier protein is conjugated to the target protein via a peptide bond between the carboxy terminus of the modifier protein and a free amino group of the target protein comprising contacting the target protein to a polypeptide comprising a JAM domain consisting essentially of an amino acid sequence of HXHXXXXXXXXXXD, wherein H is histidine, D is aspartate, and X is any amino acid.

A method of screening for an agent that affects deconjugation of a modifier protein from a target protein, wherein the modifier protein is conjugated to the target protein via a peptide bond between the carboxy terminus of the modifier protein and a free amino group of the target protein, the method comprising

• incubating in the presence and absence of a test agent, the target protein and a polypeptide comprising a JAM domain consisting essentially of an amino acid sequence of HXHXXXXXXXXXXD wherein H is histidine, D is aspartate, and X is any amino acid,
• determining the effect of the test agent, wherein an increase or decrease in the amount of the target protein not conjugated to the modifier protein caused by the test agent is indicative of an agent affecting deconjugation of the modifier protein from the target protein.

A method of increasing conjugation of a modifier protein to a target protein, wherein the modifier protein is conjugated to the target protein via a peptide bond between the carboxy terminus of the modifier protein and a free amino group of the target protein in a cell comprising inhibiting the activity of a polypeptide comprising a JAM domain consisting essentially of an amino acid sequence of HXHXXXXXXXXXXD, wherein H is histidine, D is aspartate, and X is any amino acid, thereby increasing the conjugation of the modifier protein to the target protein.