Decomposition of Proteins into Functionally and Evolutionarily Independent Cooperative Units

Understanding cooperative interactions within proteins is an important goal because cooperativity underlies protein functions such as catalysis, allostery, ligand binding and folding. Cooperative units within proteins can be revealed via an evolution based method called statistical coupling analysis that quantifies the correlations between positions in a multiple sequence alignment of a protein family. In this work, coupling analysis and experimental studies were used to analyze two protein families - the TonB dependent receptors and the S1A serine proteases. The TonB dependent receptor family members are membrane bound siderophore transporters. Ligand binding on the extracellular side of the transporter transmits a signal to the periplasmic side where another protein (TonB) provides the energy for transport. Coupling analysis, based on a diverse alignment of 541 family members revealed a network of physically contiguous positions extending close to 50 angstroms from the ligand binding pocket to the putative periplasmic interaction sites. A mutational analysis of FecA, a representative member of this family, confirmed the functional significance of the coupled positions. The S1A serine protease family members are involved in diverse functions such as digestion, coagulation, immunity and reproduction. Coupling analysis on 1470 serine proteases revealed at least three sets of independently evolving positions. Each set of positions is called a sector. Structural analysis revealed that each sector is physically contiguous suggesting mechanical independence. Extensive data in the literature on this protein family allowed the assignment of function to two of the sectors. One sector comprised positions making up the catalytic machinery, while another sector comprised positions important for substrate binding. To determine the function of the sector with unknown function, mutations were done on positions making up this sector and tested for catalytic and stability effects on proteins. The data showed that the positions in the unknown function sector affected stability but not catalysis. Each sector therefore performs a different and independent cooperative function: one sector for catalysis, one for substrate binding and one for fold stability.