A novel and simple interpretation of the three-dimensional structure of globular proteins based on quantum mechanical computations on small model molecules. II. The clusters of myoglobin.

Abstract

AbstractWe show that the bridges and clusters of the kind found earlier in rubredoxin also occur in myoglobin. The familiar acid–base(salt) bridges are at the heart of many of the clusters. The data reported by Takano [(1977) J. Mol. Biol., 110, 537–508] on sperm whale metmyoglobin reveals ten clusters together with the heme structure and some unidentified fragments. The data reported by Hanson and Schoenborn [(1981) J. Mol. Biol. 153, 117–146] on carbonmonoxymyoglobin shows numerous bridges that generally fit into the cluster picture derived from Takano's data. The data reported by S. E. V. Phillips (personal communication) on oxymyoglobin also fits into the same pattern of cluster. All but one of the myoglobin clusters are formed from two pieces of local structure each of which covers up to fifteen consecutive aminoacid residues. A “long‐range” union joins the two pieces of local structure. The clusters are generally involved with the nonhelical structure and with the junctions of the two helices. Two applications of the theory are suggested. First, the clusters offer an explanation for the formation of the α‐helices and second the unfolding of the myoglobin molecule at pH 3.8 to 5.3 is readily interpreted as the protonation at this pH of the carboxylate ions that generate the clusters that in turn support the α‐helices.