Investigation of Allosteric Mechanism from an Evolutionary Perspective

Abstract

Allostery is fundamental to biological regulation and, consequently, understanding its molecular mechanism has many potential practical applications. Investigation of the evolution of allostery offers one approach to elucidating this mechanism. Biotin protein ligases are essential for survival in all organisms. In bacteria the Class 1 or monofunctional ligases only catalyze post-translational biotin addition while the Class 2 proteins also function as allosterically activated transcription repressors. Similar architectures are observed in structures of proteins from both classes. In this work, we used combined experimental and computational methods to identify features that distinguish allosteric from non-allosteric biotin ligases. Combined kinetic and equilibrium thermodynamic measurements reveal that residues that function in allostery in Class 2 ligases are distributed throughout the protein structure. Energy based network analysis performed on the allosterically "inactive" and "active" forms of representatives of each protein class revealed distinct residue networks that show different responses to allosteric ligand binding. Phylogenetic Mutual Information analysis revealed markedly distinct residue coevolution patterns in the Class 1 and Class 2 ligases. The combined results reveal that allostery can evolve via changes in the composition of residue networks in a protein and the patterns of interaction among these networks.