Browsing by Author "Irvine, William A"

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    Molecular dynamics simulations of protein-membrane interactions focusing on PI3Kα and its oncogenic mutants : a thesis presented in fulfilment of the requirements for the degree of Doctor of Philosophy in Computational Biochemistry at Massey University, Albany, New Zealand
    (Massey University, 2017) Irvine, William A
    The interactions between proteins and membranes are key to many aspects of biological function. Molecular dynamics simulations can provide insight into both atomic-level structural details and energetics of protein-membrane interactions. This thesis describes the development of a physiologically accurate brain lipid bilayer, and its use in molecular dynamics simulations to characterise how proteins that are important drug targets interact with the cell membrane. A method for rapidly identifying the orientation of a protein that interacts most favourably with a membrane was also developed and tested. The first chapter provides an introduction to molecular dynamics and its role in the context of this research. The second chapter details the development of a cellular membrane with a physiologically representative brain lipid composition. This was done through the testing of simple systems prior to the construction of two more complex lipid bilayers comprising phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylserine (PS), phosphatidylinositide 4,5 bisphosphate (PIP2), sphingomyelin, and cholesterol. The third chapter implements the brain lipid bilayer in the development of a rotational interaction energy screening method designed to predict the most favourable orientation of a protein with respect to the cellular membrane. The functionality of the method was validated through application to two membrane proteins commonly implicated in cancer: the phosphatase and tensin homolog (PTEN), and the p110α-p85α phosphatidyl-inositol kinase (PI3Kα) complex. The fourth chapter corresponds to the main focus of this research, the behaviour of wild type PI3Kα and two of its oncogenic mutants (E545K and H1047R) with regards to membrane and substrate interaction. It was primarily found that H1047R’s increased membrane affinity allowed it to sample a catalytically competent orientation independently of Ras, unlike the wild type. Furthermore, it was also found that the position of the C terminal tail with regards to the substrate binding pocket was crucial in the achievement of a catalytically competent position against the cellular membrane. The fifth and final chapter describes a cytochrome P450 system embedded in a cellular membrane. It was primarily found that the properties of its ingress and egress tunnels depended on the presence or absence of a substrate in the active site.
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    Testing of parameters for a biologically accurate brain membrane and molecular dynamics simulations exploration of membrane interactions and conformational changes exhibited by p110α and its oncogenic mutants : a dissertation submitted in fulfilment of the requirements for the degree of Masters of Science in Biochemistry, Massey University, March 2014
    (Massey University, 2014) Irvine, William A
    Phosphatidylinositide 3-kinases are a family of enzymes which are involved in the regulation of cell growth and proliferation via signalling pathways. This, in turn, means they are linked with cancer development through mutations borne by the genes which encode them. One of these oncogenes, PIK3CA, encodes the catalytic subunit of p110a. This study will focus on p110a’s interaction with a phospholipid bilayer, using computational techniques, in an effort to better understand this protein and the effect the cancer-related mutations have on its activity. In order to model the phospholipid bilayer in a biologically and physiologically accurate manner, with all key components present in their correct proportions, model parameters for the components had to be produced and tested in small binary systems. The components of the membrane used include the phospholipids POPC, POPE, POPS and PIP2, as well as sphingomyelin and cholesterol. Using these new parameters for the components of a phospholipid bilayer, molecular dynamics simulations were run of the activated p110a subunit and two of its oncogenic mutants (E545K, H1047R) in the presence of a realistic brain lipid membrane. The results will pave the way to the development of drugs which will serve to inhibit the pathway when necessary, in an effort to control and reduce the incidence of cancer.