Dynamic control of metabolism through engineering ligand-induced allosteric regulation based on a new concept of thermodynamic cycle of protein dynamics

Cheng-Wei Ma, Feng Geng, Sugima Rappert and An-Ping Zeng
Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestrasse 15, D-21073 Hamburg, Germany

Abstract

Allosteric regulation is the regulation of an enzyme or other protein by binding an effector molecule at the protein's allosteric site, a site other than the protein's active site. It is a natural example of control loops, such as feedback from downstream products or feed- forward from upstream substrates. Control of allosteric regulation is required in order to drive metabolic flux toward desired levels. Although static structures are known for many proteins, the functions of proteins are governed ultimately by their dynamical characteristics. Here, a novel strategy to engineer the ligand-induced allosteric regulation is proposed based on a new concept of thermodynamic cycle of protein dynamics. In this concept, allosteric process is considered as a thermodynamic process which is the energetic development of a thermodynamic system proceeding from an initial state to a final state. The thermodynamic cycle consists of a linked sequence of thermodynamic processes: conformational change, ligand binding and the allosteric process. A serial of computational approaches are employed to obtain the state parameter of solvated free energy under different allosteric states. For the ligand binding process, the state parameter is calculated from molecular dynamics simulation. Contributions of each residue can be illustrated through energy decomposition. The allosteric process is simulated by steered molecular dynamics followed by dynamic correlation analysis and fluctuation analysis. Three key enzymes in the biosynthesis of amino acids, E. coli aspartokinase III (AK III), E. coli 3-Deoxy-d- arabino-heptulosonate-7-phosphate synthase (DAHPS) and C. glutamicum homoserine dehydrogenase (HSDH) are used as model systems to demonstrate the novel strategy with totally 14 metabolites as non-natural ligands. This strategy makes it possible to rational design of allosteric regulations useful in the dynamic control of metabolism.