From structure to function: a computational study

  • Tracey Bray

    Student thesis: Phd


    The study of proteins and their function is key to understanding how the cell works in normal and disease states. Historically, the study of protein function was limited to biochemical characterisation, but as computing power and the number of available protein sequences and structures increased this allowed the relationship between sequence, structure and function to be explored. As the number of sequences and structures grows beyond the capacity for experimental groups to study them, computational approaches to inferring function become more important. Enzymes make up approximately half of the known protein sequences and structures, and most of the work in this thesis focuses on the relationship between the sequence, structure and function in enzymes.Firstly, the differences in sequence and structural features between enzymes of the six main functional classes are explored. Features that exhibited the most significant differences between the six classes were further studied to explore their link with function. This study suggested reasons as to why groups of functionally similar but non-homologous enzymes share similar sequence and structural features. A computational tool to predict EC class was then developed in an attempt to exploit the differences in these features. In order to calculate features relating to a particular active site to be used in the EC class prediction method, it was first necessary to predict the active site location. A comprehensive analysis of currently-available functional site prediction tools identified an approach previously developed by this group as amongst the best-performing methods. Here, a tool was created to deliver this approach via a publicly-available web-server, which was subsequently used in the attempt to predict EC class. The study of differences in sequence and structural features between classes revealed differences in oligomeric status between functions. High-order oligomers were linked to an increase in metabolic control in the lyases, possibly via mechanisms such as cooperativity. To further test this idea, it was necessary to be able to computationally identify oligomeric enzymes that act cooperatively. Since no such method currently exists, the degree of coupling of dynamic fluctuations between subunits was explored as a possible way of detecting cooperativity. Whilst this was unsuccessful, the study highlighted the existence of a pattern of correlated motions that were conserved over a wide range of non-homologous and functionally diverse proteins. These observations shed further light on the link between sequence, structure and function and highlight the functional importance of dynamics in protein structures.
    Date of Award31 Dec 2010
    Original languageEnglish
    Awarding Institution
    • The University of Manchester
    SupervisorAndrew Doig (Supervisor) & James Warwicker (Supervisor)


    • Bioinformatics

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