Walker-Taylor, Alice; (2003) Analysis and prediction of protein-protein interactions. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

Protein-protein interactions provide a means for cells to communicate both internally and externally, and they also enable the catabolic and anabolic reactions of metabolism. To understand and predict these interactions is therefore a very important area of research. The ability to predict how two proteins interact would prove an extremely useful tool in terms of being able to block these interactions, but also as a way of understanding biological pathways in general. However, prediction of these interactions is not trivial, and there are many layers of complexity that must be considered. This thesis highlights some of these complexities and attempts prediction methods of different sorts with varying degrees of success. This study is concerned with proteins that are able to exist in isolation prior to forming a complex (non-obligatory complexes), as these are thought to form a distinct sub-class of protein-protein interaction. A representative set of protein structures is first taken for detailed analyses in terms of amino acid types at the interface, interface rigidity, secondary structure, hydrogen bonds, distances between contacting residues, etc. interaction residue potentials and hydrophobic burial potentials are then used extensively for two separate methods. The first was a method that aimed to correlate the binding free energy to a score derived from these parameter potentials. The second method was a prediction method that involved a threading type approach in order to predict binding partners from sequence profiles. This aim of this method was to find novel binding partners or to determine binding specificity/affinity of their interactions. The final method used involves docking proteins in contact space using a simulated annealing minimisation algorithm. Various scoring parameters were used to find an energy minimum to represent the correct residue pair interactions at the interface. These scoring parameters included conservation, interaction potentials, interface potentials, surface complementarity. Each of these studies has contributed to the understanding of these protein-protein interactions and from the initial results obtained, in each case the methods show potential.

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