How life uses sound to reorganise matter: The role of anharmonic phonon exchange in enzyme catalysis
type: CreativeWork
description: Biological enzyme catalysis is the name for life's ability to rapidly invoke coordinated rearrangements of molecular structures using highly specialised, relatively-large functional proteins called enzymes. It is well established that enzymes reduce the activation energy barrier, which vastly accelerates the rate of reaction, however the specific dynamics and quantum mechanics are largely uncharted. Recent experimentation and modelling hints that there is a phase transition dynamic that is fundamental to enzymatic catalysis. The hypothesis that I explore in this thesis is that a mathematical model of a substrate molecule based upon anharmonic quantum vibrational modes (molecular phonons) will predict phase transition dynamics due to the presence of the appropriate enzyme. A molecular phonon is one particular individualised wave pattern in the locations of atomic nuclei from the total molecular dance that spans the low-frequency bulk swaying motions, mid-frequency bond stretches, to the high-frequency oscillations of the hydrogen bond network. In this thesis, I derive a generalised set of equations of motion for the anharmonic response behaviour of molecular phonons to enzyme stimulus via a dissipative quantum master equation, and I explore the phase transition dynamics by determining the stability bifurcation of the steady states. I then determine the critical minimum stimulus required for a molecular vibrational mode to exhibit a phase transition. The primary catalytic reaction of focus for this thesis is the cleavage of the glycosidic carbon-oxygen bond of the complex sugar isomaltose into two individual glucose molecules via the action of the enzyme MalL. Prior to this thesis, the atomic structure of MalL was obtained experimentally via X-ray diffraction crystallography of prepared MalL crystals, then digitised into the Gromacs software package and energy minimised in a simulated water bath to approximate the vibrational modes of the in vivo configuration. I obta…
abstract: Biological enzyme catalysis is the name for life's ability to rapidly invoke coordinated rearrangements of molecular structures using highly specialised, relatively-large functional proteins called enzymes. It is well established that enzymes reduce the activation energy barrier, which vastly accelerates the rate of reaction, however the specific dynamics and quantum mechanics are largely uncharted. Recent experimentation and modelling hints that there is a phase transition dynamic that is fundamental to enzymatic catalysis. The hypothesis that I explore in this thesis is that a mathematical model of a substrate molecule based upon anharmonic quantum vibrational modes (molecular phonons) will predict phase transition dynamics due to the presence of the appropriate enzyme. A molecular phonon is one particular individualised wave pattern in the locations of atomic nuclei from the total molecular dance that spans the low-frequency bulk swaying motions, mid-frequency bond stretches, to the high-frequency oscillations of the hydrogen bond network. In this thesis, I derive a generalised set of equations of motion for the anharmonic response behaviour of molecular phonons to enzyme stimulus via a dissipative quantum master equation, and I explore the phase transition dynamics by determining the stability bifurcation of the steady states. I then determine the critical minimum stimulus required for a molecular vibrational mode to exhibit a phase transition. The primary catalytic reaction of focus for this thesis is the cleavage of the glycosidic carbon-oxygen bond of the complex sugar isomaltose into two individual glucose molecules via the action of the enzyme MalL. Prior to this thesis, the atomic structure of MalL was obtained experimentally via X-ray diffraction crystallography of prepared MalL crystals, then digitised into the Gromacs software package and energy minimised in a simulated water bath to approximate the vibrational modes of the in vivo configuration. I obta…
author: Batterton, Christopher
keywords: enzyme catalysis, phonons, quantum physics, biophysics, biochemistry, mathematics, molecular dynamics, molecular vibrations, phase transition
license: https://researchcommons.waikato.ac.nz/bitstreams/4f1fa48b-fe23-4b2d-9eed-df9b586a749b/download
date published: 2024
date modified: 2026-07-24T05:57:36Z
provider: University Waikato
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: The University of Waikato