Algorithmic Determination of Core Positions in the V_L and V_H Domains of Immunoglobulin Molecules

摘要

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 C_alpha (I) — Calpha (J) atom distances are identical in all structures of the protein family under study, where / and J are secondary structure positions in the structural units - strands, loops, or parts of them [7]. The result of applying the algorithm to 53 Ig structures lead to the identification of two geometrical core sets of Calpha atom positions for the VL and VH domains. Applications of the core sets are described.