Thesis Topic Details

Topic ID:
Analysis of multidomain protein structures and supramodules
Paul Curmi
Research Area:
Associated Staff
Bruno Gaeta
Topic Details
Group Suitable:
Many proteins in higher eukaryotes are composed of concatenated, functional, independently folding protein domains. Molecular evolution uses domains as building blocks that may be recombined in different arrangements to create proteins with different functions. The simplest multi-domain organization in proteins is that of a single domain repeated in tandem, which may interact with each other or remain isolated, like beads on string.

Supramodules are viewed as a specific type of multi-domain protein that is distinguished by having all constituent domains of a functional complex within one protein. Although domains within these complexes are independently stable and folded, they are likely to interact with each other in a way that affects the structure and function of the domains. For example Myosin X (MyoX), an unconventional myosin known to induce the formation and elongation of filopodia using three PH domains in its tail region.

Although the boundaries of a domain can be determined by visual inspection, construction of an automated method is not straightforward. With the advent of modern bioinformatics, the conservation of domains throughout evolution became instantly recognizable, leading to the established view that domains can be represented by a specific pattern of secondary structure elements that adopt a canonical form when in solution. However, it is much less appreciated but still important that a significant number of domains have additional elements of structure that lie almost immediately before or after the canonical domain, extending the domain, especially in supramodules with multi-domains. In this work, we will aim to use bioinformatic methods to analyze protein sequences and setup a database to identify the potential multi-domain supramodules with well-defined functional domains, such as PDZ domain, PH domain and FERM domain, to explore the new function of these supramodules.
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