George, Richard Anthony; (2002) Predicting structural domains in proteins. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

Domains are the structural and functional units of proteins. Nature often brings several domains together to form multidomain-multifunctional proteins with the possibility of an almost infinite number of combinations. Delineation of a protein sequence into its structural domains is often an essential pre-requisite in sample preparation for structure determination, for protein engineering, site directed mutagenesis experiments and for the optimisation of structure prediction methods. Individual domains are likely to correspond to recurring functional and evolutionary units of a protein; for this reason, using individual domains to search a database for related sequences is often more successful than using the whole protein sequence. Until now there have been no accurate methods to delineate the boundaries of structural domains from sequence information alone. This thesis describes computational tools to characterise the essential properties of domains and their boundaries. Several observations render domain prediction feasible: 1) domain interfaces show an amino acid composition intermediate to those of core and surface regions; 2) domain- linking oligopeptides display distinct characteristics; 3) multidomain proteins have a larger surface area than single domain proteins of the same sequence length; and 4) the average hydrophobicity of a protein relates to the size of its domains. Based on these principles, several prediction methods have been developed and successfully applied to interesting biological examples.

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