Prediction of the three‐dimensional structures of the biotinylated domain from yeast pyruvate carboxylase and of the lipoylated H‐protein from the pea leaf glycine cleavage system: A new automated method for the prediction of protein tertiary structure

Abstract

A new, automated, knowledge‐based method for the construction of three‐dimensional models of proteins is described. Geometric restraints on target structures are calculated from a consideration of homologous template structures and the wider knowledge base of unrelated protein structures. Three‐dimensional structures are calculated from initial partly folded states by high‐temperature molecular dynamics simulations followed by slow cooling of the system (simulated annealing) using nonphysical potentials. Three‐dimensional models for the biotinylated domain from the pyruvate carboxylase of yeast and the lipoylated H‐protein from the glycine cleavage system of pea leaf were constructed, based on the known structures of two lipoylated domains of 2‐oxo acid dehydrogenase multienzyme complexes. Despite their weak sequence similarity, the three proteins are predicted to have similar three‐dimensional structures, representative of a new protein module. Implications for the mechanisms of posttranslational modification of these proteins and their catalytic function are discussed.