ALGORITHMIC DETERMINATION OF CORE POSITIONS IN THE V-L AND V-H DOMAINS OF IMMUNOGLOBULIN MOLECULES

We introduce a new algorithmic method for identifying the geometrical core of proteins that does not require the usual superposition of stru ctures. A geometrical core is defined as the set of residues such that the C-alpha(I) - C-alpha(J) atom distances are identical in all struc tures of the protein family under study, where I and J are secondary s tructure positions in the structural units-strands, loops, or parts of them. The result of applying the algorithm to 53 Ig structures leads to the identification of two geometrical core sets of C-alpha atom pos itions for the V-L and V-H domains. Applications of the core sets are described.