Major urinary proteins (MUPs) are present in high levels in the urine of mice, and the specific profile of MUPs varies considerably among wild-caught individuals. We have conducted a detailed study of the polymorphic variation within a geographically constrained island population, analyzing the MUP heterogeneity by isoelectric focusing and analytical ion exchange chromatography. Several MUPs were purified in sufficient quantities for analysis by electrospray ionization mass spectrometry and MALDI-TOF mass spectrometry of endopeptidase Lys-C peptide maps. The results of such analyses permitted the identification of three new MUP allelic variants. In each of these proteins, the sites of variation were located to a restricted segment of the polypeptide chain, projecting to a patch on the surface of the protein, and connected to the central lipocalin calyx through the polypeptide backbone. The restriction of the polymorphic variation to one segment of the polypeptide may be of functional significance, either in the modulation of ligand release or in communication of individuality signals within urinary scent marks.

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