Hrishikesh Dhondge (CAPSID) will defend his thesis, entitled “Structural characterization of RNA binding to RNA recognition motif (RRM) domain using data integration, 3D modeling, and dynamic simulation“, on Tuesday, July 11 at 2pm in room C005.
The specific goal of this thesis was to design and develop computational tools to better exploit existing knowledge on RNA Recognition Motif (RRM) domains using 3D modeling of RRM-RNA complexes.
A central achievement of this thesis is the construction of a relational database called ‘InteR3M’ that integrates sequence, structural and functional information about RRM domains. InteR3M database contains interactions between RRM and nucleic acids.
During the data collection procedure, inconsistencies were detected in the classification of several RRM instances in the popular domain databases CATH and Pfam. This led me to propose an original approach (CroMaSt) to solve this issue, based on the cross-mapping of structural instances of RRMs between these two domain databases and on the structural alignment of domain instances with an RRM structural prototype.
Information stored in InteR3M database was then used for characterization of RNA binding to RRM domains and to model RRM-RNA complexes via anchored docking protocol. These led to the development of ‘RRMScorer’ and ‘RRM-RNA dock’ tools in the frame of collaborations.
Finally, molecular dynamic (MD) simulation is another computational tool tested in this thesis to contribute to the 3D modeling of RRM-RNA complexes. Promising preliminary MD protocols are described as attempts to distinguish between strongly and weakly binding RRM-RNA complexes.
PhD Advisors:
Reviewers:
Stanisław Dunin-Horkawicz Researcher, Université de Varsovie
Examiners:
Invited members:
