Building kit for metal cation binding sites in proteins

Abstract

Starting with conformations of calcium-binding sites in parvalbumin and integrin (representative structures of EF-hand and calcium blade zones, respectively) we introduce four new different local Ca²⁺-recognition units in proteins: a one-residue unit type I (ORI); a three-residue unit type I (TRI); a one-residue unit type II (ORII) and a three-residue unit type II (TRII). Based on the amount and nature of variable atoms, the type I and II units theoretically can have four and twelve variants, respectively. Analysis of known "Ca²⁺-bound functional niches" in proteins revealed presence of almost all possible variants of Ca²⁺-recognition units in actual structures. Parvalbumin, integrin alpha-IIb and sixteen other proteins with different Ca²⁺-bound functional niches contain various consecutively joined combinations of OR(I/II) and TR(I/II) units. Such a OR(I/II)+TR(I/II) joint unit forms a tripeptide, which uses three main-chain atoms for metal binding: nitrogen_n (Donor), oxygen_n (Acceptor) and nitrogen_n+2 (Donor). Thus, taken together, the described ORI, TRI, ORII and TRII units can serve as elementary blocks to construct more complex calcium recognizing substructures in a variety of calcium binding sites of unrelated proteins.

Keywords: Building kit; Cation; Niche motif; Protein structure; Structure motifs.