CHARACTERIZATION OF PROTEIN RNA &PROTEIN PROTEIN INTERACTIONS OF MBBP: HIV

University Of California San Francisco, San Francisco CA

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Abstract

The aim of my research is to look at RNA-protein interactions in terms of specificity. The RNA binding motif of the mammalian splicing factor mBBP (branchpoint sequence binding protein) is used as a model system in order to define whether different members of an RNA-binding protein family form similar binding surfaces, and bind RNA in a similar way. Then, similarities in RNA binding between that motif and other RNA binding motifs will be analyzed. The long term goal being to engineer novel specificities into a known RNA-binding protein fold. mBBP is a member of the STAR (signal transduction and activation of RNA) family of RNA binding proteins, which have multiple functions in developmental processes. Family members share an RNA-binding STAR domain of approximately 200 amino acids that include a maxi K homology (KH) domain and two flanking domains. In addition, most of the STAR proteins show sequence hallmarks indicative of a role in signal transduction. mBBP binds directly to the branchpoint sequence (BPS) RNA and takes part in the assembly of the spliceosomal E complex (the early mammalian U1 snRNP complex). It interacts with the splicing factor U2AF65, and with the WW domain-containing proteins FBP11 and FBP21. We are utilizing an in vivo HIV-1 Tat-fusion system in mammalian cells to study the binding of mBBP to BPS RNA, and to investigate the multiprotein-RNA complex that include mBBP, BPS, and U2AF65. The experimental results will then be used to build a model that will define the RNA and protein binding surfaces of mBBP. The model will be used to predict the amino acids requirements for specific RNA binding in other members of the STAR family, and as a basis for the design of new RNA binding specificities for the KH fold.