Investigating the recognition and interactions of non-polar alpha helices in biology

UoM administered thesis: Phd

  • Authors:
  • James Baker

Abstract

Non-polar helices feature prominently in structural biology. Transmembrane alpha helix containing proteins make up around a third of all proteins, represent around 40% of drug targets, and contain some of the most critical proteins required for life as we know it. Yet they are fundamentally difficult to study experimentally. This is in part due to the very features that make them so biologically influential; their non-polar transmembrane helical regions. By leveraging large data-sets of transmembrane proteins, this thesis is focused on characterising features of transmembrane alpha helices en masse, particularly regarding their topology, membrane-protein interactions, and intramembrane protein interactions. In this study, we present statistical evidence demonstrating the `negative-outside` rule in opposition to the `positive-inside` rule. We also identify stabilising amino acid distributions in anchoring transmembrane helices compared to transmembrane helices with function beyond anchoring. Tail-anchored proteins are a group of post-translationally inserting proteins. In this thesis, we show adaptations of hydrophobicity and residue distributions through the transmembrane helices of tail-anchored proteins to different membrane environments within the cell (the mitochondria, endoplasmic reticulum, the Golgi, and the plasma membrane). However, we could not detect a hydrophobic difference between global populations of tail-anchored proteins in different species (mammals, plants, and fungi). A handful of these proteins are capable of integrating into the membrane without the need for membrane integration proteins. Structural modelling of transmembrane helices from PTP1b and cytochrome b5 reveals a 3D amphipathic arrangement of residues. This structural feature may play a role in their spontaneous membrane insertion. Finally, we find a conserved pattern of typically hydrophobic transmembrane helices neighbouring marginally hydrophobic helices in some families of transmembrane proteins. This feature corresponds to transmembrane helices that have the potential to cooperate in order to integrate the more polar, but functionally important, transmembrane helix of the pair into the membrane.

Details

Original languageEnglish
Awarding Institution
Supervisors/Advisors
Award date1 Aug 2019