Laurea, University of Rome “La Sapienza”, 1995
Ph.D., Boston University , 2002
Postdoctoral Fellow, Columbia University, 2002-2007
From protein dynamics to protein function and stability using NMR spectroscopy and computer simulation.
Proteins are flexible molecules that often undergo conformational changes to perform biological functions. For this reason, knowledge of the internal dynamics of proteins is crucial to an understanding of the details of their functions and mechanisms of action.
The focus of my laboratory is to understand the relationship between structure, stability, and dynamics of proteins. In particular we investigate how the structure and dynamics of a protein affect molecular recognition, allostery and stability. To this end, we take a multi-disciplinary approach combining the strengths of biophysical, biochemical and in vivo techniques, with particular emphasis on solution NMR spectroscopic and computational methods.
Specific targets of our research program:
1. The TTP protein family regulates cytokine mRNA turnover: Regulation of gene expression is central to efficient biological function. Two key aspects of this process are the synthesis of mRNA (transcription) and control of its stability. This process provides an important mechanism for reducing the synthesis of key cancer-related proteins, including a number of cytokines, such as tumor necrosis factor-α (TNF-α), interleukin-3 (IL-3), interleukin-8 (IL-8), and vascular endothelial growth factor (VEGF) that regulate processes that are involved in inflammation and in cancer initiation and progression. Our work is uncovering how an important class of proteins recognizes and binds to mRNA to promote its degradation.
2. C. elegans TZF proteins govern cell fate specification in early embryogenesis: In the early embryogenesis of C. elegans, the fates of all the founder cells are determined solely through the regulation of maternally supplied mRNA molecules, as zygotic transcription has not yet started: characterizing the mechanism of post-transcriptional mRNA regulation is fundamental, therefore, to a more complete understanding of embryogenesis. Several RNA binding proteins are necessary in this process, among them MEX-5, MEX-6, PIE-1, POS-1 and MEX-1 are all CCCH-type TZF proteins related to TTP. Mutations in the TZF domain of these proteins perturb the expression of several maternal genes, indicating that these proteins influence the stability and/or tune the translational efficiency of maternal mRNAs. It has been shown that these closely related proteins bind to RNA with different specificities, and that these differences have major implications for the biological activity of each protein. The origin of the different RNA-binding specificities is not yet understood. Our goal is to understand the factors that determine RNA-binding affinity and specificity and their role in embryogenesis.
3. The allosteric mechanism of Scapharca dimeric hemoglobin (HbI): Allosteric regulation is an essential function of many proteins that control a variety of different processes such as catalysis, signal transduction, and gene regulation. Structural rearrangements have historically been considered the main means of communication between different parts of a protein. Recent studies have highlighted the importance, however, of changes in protein flexibility as an effective way to mediate allosteric communication across a protein. We are characterizing the contributions of dynamics to allosteric function using a homodimeric hemoglobin that constitutes a unique system with which to probe these issues.
Rotation projects are available to address the following questions:
How does the lack of structure in the C-terminal zinc finger of TTP affect the activity of the protein in the cell?
In humans, there are three members in the TTP protein family: TTP, TIS11b and TIS11d. Structural studies performed by us and others have shown that while the TZF domain of TTP is partially unstructured in the free state and folds upon binding RNA, those of TIS11d and TIS11b are always folded. We have shown that the degree of structure of the TZF domain affects the activity of the protein in cells and indicates that the protein can modulate its activity through its dynamics. We want to determine whether structural disorder is directly linked to cellular stability or protein localization
How do mutations in the RNA-binding domain of TIS11d cause cancer?
Several point mutation in TTP and TIS11d have been linked to cancer. In particular, point mutations in the RNA-binding domain of TIS11d are found in leukemia patients. We are currently working on the characterization of the structure, dynamics and biological activity of these mutant proteins to understand their role in the pathogenesis of cancer.
How does HuR regulate the stability of its target mRNA?
HuR is another protein that, like TTP, binds to AU-rich elements (ARE) in mRNAs and regulate their stability. The detailed mechanisms that determine how HuR regulates transcripts stability are poorly understood. We are investigating how binding or HuR to the 3’UTR of an mRNA leads to its stabilization.