Analysis of enzyme dynamics and calculation of activation heat capacity from simulation

Abstract

Enzymes are biological catalysts which are crucial for life and are fundamental in many important processes in organisms. The temperature dependence of enzyme-catalysed reactions is important for homeostasis, and until recently the drop-off in enzyme-catalysed reaction rates at higher temperatures has been attributed to protein denaturation. It has been shown experimentally that rate drop-off occurs in the absence of denaturation. Macromolecular rate theory (MMRT) does not assume that enthalpy and entropy changes are independent of temperature, introducing an activation heat capacity term, ∆C_p^‡ to understand the curvature of reaction rates, even in the absence of protein denaturation. Molecular dynamics (MD) simulations can provide insight into dynamical behaviours of proteins and have previously been used for the calculation of thermodynamic properties including heat capacities. In this thesis, MD simulations are used to calculate ∆C_p^‡ for two different enzyme-substrate complexes. The results show that a negative ∆C_p^‡ value is generally obtained from MD calculations for these enzymes, which agrees with the experimentally observed curvature for the enzyme-catalysed reaction rates. Principal component analysis, Kullback-Leibler divergence and hidden Markov state modelling techniques are all utilised to analyse the origin of the dynamical changes in the protein chain leading to a negative ∆C_p^‡ term. The work in this thesis shows that MD simulations can be used to provide insight into MMRT and the dynamical properties of enzymes, and points to potential future work in understanding how the optimum temperature for enzyme-catalysed reactions is influenced by the dynamics of the protein chain of an enzyme.

Date of Award	25 Jan 2022
Original language	English
Awarding Institution	University of Bristol
Supervisor	Adrian J Mulholland (Supervisor)