Modelling short peptides in solution and at the interface
type: CreativeWork
description: The way in which neighbouring particles interact with each other is fundamental to all chemical phenomena, where the specific blend of intermolecular forces and geometric conformation dictate the properties of any system. This thesis discusses the importance of intermolecular interactions to phenomena witnessed for simple systems that may hark back to the origins of life, as well as complex systems where macromolecules display high affinity for solid surfaces.In the first chapter, we explore the relationship between peptide sequence andstructure. Using the example of catalytic peptides that are able to perform amide bond condensation, we examine the possibility of short peptide sequences adopting a conformation that supports an active site analogous to that found in protease enzymes such as subtilisin using molecular dynamics (MD). In this study we define a catalytic triad by convergence of an acid, histidine and hydroxyl residue below 4 Aͦ. It was found that each of the three sequences studied could form a triad structure; however due to the flexible nature of the peptides this conformation was short-lived. We concluded that the catalytic activity of these peptides originated from their ability to form protease active site analogues and that experimentally observed Kcat rates, lower than that observed for enzymes, was a result of the flexible nature of the peptides.In Chapter two, we examine the properties of single amino acids with solid surfaces. We use Au 111 as our model since there are numerous cases of peptides with a high affinity for gold. The aim of this study was to calculate the relative binding free energies of nine amino acids that make up the gold binding peptide GBP1. Using Steered Molecular Dynamics (SMD) simulations we follow the change in free energy of each individual amino acid as it is pulled from the bound state to the bulk. We find that aromatic amino acids and those containing heteroatom side chains show greater affinity for the metal surfac…
abstract: The way in which neighbouring particles interact with each other is fundamental to all chemical phenomena, where the specific blend of intermolecular forces and geometric conformation dictate the properties of any system. This thesis discusses the importance of intermolecular interactions to phenomena witnessed for simple systems that may hark back to the origins of life, as well as complex systems where macromolecules display high affinity for solid surfaces.In the first chapter, we explore the relationship between peptide sequence andstructure. Using the example of catalytic peptides that are able to perform amide bond condensation, we examine the possibility of short peptide sequences adopting a conformation that supports an active site analogous to that found in protease enzymes such as subtilisin using molecular dynamics (MD). In this study we define a catalytic triad by convergence of an acid, histidine and hydroxyl residue below 4 Aͦ. It was found that each of the three sequences studied could form a triad structure; however due to the flexible nature of the peptides this conformation was short-lived. We concluded that the catalytic activity of these peptides originated from their ability to form protease active site analogues and that experimentally observed Kcat rates, lower than that observed for enzymes, was a result of the flexible nature of the peptides.In Chapter two, we examine the properties of single amino acids with solid surfaces. We use Au 111 as our model since there are numerous cases of peptides with a high affinity for gold. The aim of this study was to calculate the relative binding free energies of nine amino acids that make up the gold binding peptide GBP1. Using Steered Molecular Dynamics (SMD) simulations we follow the change in free energy of each individual amino acid as it is pulled from the bound state to the bulk. We find that aromatic amino acids and those containing heteroatom side chains show greater affinity for the metal surfac…
author: Cannon, Daniel Andrew
date published: 2016
date modified: 2026-07-24T04:45:26Z
provider: University of Strathclyde
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: University of Strathclyde

PropertyValue
property ID: DOI
value: 10.48730/rarj-mn48