Experimental and theoretical studies of linked biochemical processes

Abstract

Proteins are a class of biological macromolecules that participate in intricate chemical processes such as binding of small molecules, self-assembly, and catalysis. Often multiple chemical processes are coupled giving rise to complex biological phenomena. Characterization of the coupling between chemical processes is essential to providing an understanding of biology at the molecular level. This study is concerned with development of analytic treatments of these biochemical linkages. In particular several models of linked biochemical systems are developed. In order to apply biochemical linkage models to protein systems, experimental measurements are used to determine the model parameters. Standard parameter estimation techniques employed in biophysics and biochemistry are of limited utility here owing to the complexity of the models. Instead the robust Markov Chain Monte Carlo model fitting and parameter estimation method is used, which allows determination of the model parameter distributions that are consistent with the experimental data. Myxovirus resistance protein A (MxA) is an important part of the human innate immune response, conferring resistance to a range of viral pathogens including influenza virus. While its molecular mechanism of action is poorly understood, antiviral function appears to require linked self-assembly, mechanical switching, and catalysis. Coupling between self-assembly and catalysis of MxA is modeled based on classical kinetic theory and quantified using a range of biophysical and biochemical techniques. Coupling between catalysis and mechanical switching, known as mechano-chemical activity, is experimentally characterized using X-ray crystallography. The results provide molecular insight into how MxA may function. Many proteins, including MxA, couple small molecule binding and self-assembly to achieve biological function, however current models of this linkage are too complex for practical application. Equilibrium thermodynamic models of coupled small molecule binding and self-assembly are developed, for proteins with cyclic symmetry. These models explicitly quantify couplings that are present, and are simple enough for practical application. This method of model development is general and facilitates application to other scenarios.