The transmembrane segment of invariant chain mediates binding to MHC classII molecules in a CLIP-independent manner

Invariant chain (li) association with MHC class II molecules is strongly de pendent upon interaction of CLIP (li exon 3, residues 81-104) with the pept ide binding groove of the class II dimer. This dominant interaction does no t adequately explain, however, the efficient association of ii with class I I molecules of diverse allelic and isotypic origin, which have markedly dif ferent affinities for synthetic peptides corresponding to CLIP. In agreemen t with other recent observations, we demonstrate here that class II molecul es with occupied binding sites unable to engage CLIP maintain association w ith ii in mild detergent. The association is direct and not mediated throug h unoccupied class II chains bound to properly assembled and loaded class I I dimers, nor is it mediated through chaperones. The site of this CLIP-inde pendent binding has been mapped using truncation mutants and an ii-human tr ansferrin receptor chimeric protein to the transmembrane segment of ii. The existence of multiple low-affinity sites of interaction between MHC class II and ii helps explain how effective occupancy of all newly synthesized cl ass II molecules can occur despite substantial variations in the strength o f CLIP-dependent association that arise from class II binding domain polymo rphism. These data establishing a site of II-MHC class II association N-ter minal to CLIP also provide new insight into the possible functional relatio nship between the sequential endocytic proteolysis of ii from its C terminu s and a series of contact sites with MHC class II molecules spread from the transmembrane region through to the tip of the lumenal segment of ii.