Algorithmic Determination of Core Positions in the V L and V H Domains of Immunoglobulin Molecules

ABSTRACT

We introduce a new algorithmic method for identifying the geometrical core of proteins that does not require the usual superposition of structures. A geometrical core is defined as the set of residues such that the Cα(I) – Cα(J) atom distances are identical in all structures of the protein family under study, where I and J are secondary structure 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 Cα atom positions for the V _L and V _H domains. Applications of the core sets are described.