Anna Marie Pyle
Anna Marie Pyle is the William Edward Gilbert Professor of Molecular, Cellular and Developmental Biology and Professor of Chemistry at Yale University. Originally from New Mexico, she obtained her undergraduate degree in Chemistry from Princeton University and received her Ph.D. in Chemistry from Columbia University in 1990. During her graduate work with Professor Jacqueline K. Barton, Dr. Pyle developed transition-metal complexes for recognizing DNA microstructures and initiating site-specific redox chemistry. Dr. Pyle was a postdoctoral fellow in the laboratory of Thomas Cech, where she began her studies on molecular recognition of RNA. Specifically, she investigated the role of 2’-hydroxyl groups in the stabilization of RNA tertiary structure. Dr. Pyle formed her own research group in 1992 in the Department of Biochemistry and Molecular Biophysics at Columbia University Medical Center, where she initiated her studies on the structure and function of self-splicing group II introns and RNA remodeling proteins. In 2002, she moved to Yale University, where she is now a faculty member in the Biology and Chemistry departments. Dr. Pyle has received many awards, served in a leadership capacity at Yale and Columbia and is author of more than 130 publications.
The Pyle laboratory uses a diverse set of biochemical and biophysical techniques, including crystallography and chemical probing, to understand the structural complexity and plasticity of RNA architecture. The goal is to understand how specific three-dimensional RNA structures are formed, how their shapes are stabilized, and to define the constituent building blocks for RNA tertiary structure. Group II introns, which are among the largest ribozymes in nature, have provided a valuable model system for studying RNA tertiary structure and folding. These studies are now complemented by investigations on the tertiary structure of long noncoding RNAs that are involved in transcriptional activation and repression.
Just as RNA molecules must fold, they must also be disassembled during the dynamic process of cellular metabolism. Therefore, we also study how RNA structures are taken apart by cellular nanomachines such as RNA remodeling enzymes and helicases. These motor proteins are essential for all aspects of RNA metabolism, and yet we have only begun to understand the microscopic details of their behavior. More recently, we have begun to study how these machines function as surveillance proteins, binding viral RNA and protecting our cells from pathogens.
Experimental studies in the Pyle laboratory are complemented by computational investigations, as we develop new tools for solving, analyzing and predicting RNA tertiary structures. An integrated approach, involving experimental and computational science strategies, is providing useful new ways to conceptualize, study and utilize RNA molecules and their associated proteins.
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RNA Throws the Switch: RIG-I signaling and antiviral surveillance machinery.
One of the most abundant types of enzymes in our cells is a conserved family of RNA-dependent ATPases that play key roles in RNA metabolism. Upon binding RNA, these proteins hydrolyze ATP and undergo conformational changes that enable them to move along the RNA lattice, functioning as directional translocases, much like the cytoskeletal motor proteins. As these proteins travel along single-stranded RNA, they often function as helicases or protein displacement enzymes, displacing objects in their path. As a result of these activities, the enzyme family was originally named “Helicase Superfamily 2 (SF2)”, based on the phylogenetic conservation of ATPase motifs and RNA binding motifs that typify the proteins. We now know that most of these proteins are not actually helicases, but they all use RNA to activate ATP-dependent conformational changes that lead to important work in the cell. For example, a subgroup of SF2 proteins are essential players in our immune system, where they serve as cytoplasmic surveillance proteins that recognize viral RNAs and then activate antiviral signaling pathways in our cells. We have been studying the molecular basis for RNA recognition by family members Mda-5, DRH-3 and RIG-I, which hydrolyze ATP upon binding double-stranded RNA. These proteins distinguish viral RNA from human RNA in the cytoplasm, and the molecular basis for this discrimination is important for developing new antiviral strategies and therapeutics for autoimmune diseases. Our enzymological and crystallographic studies have demonstrated that the RIG-I family members recognize duplex RNA through a conserved molecular interface with three different protein domains, each of which plays a distinct role in viral RNA recognition. The C-terminal domain of the protein recognizes the 5’-triphosphate, while the helicase domain and a specialized insertion domain envelop the RNA backbone in a network of polar contacts (See crystal structure above, from Luo et al, Cell 2011). A V-shaped pincer motif connects the RNA binding interface to the ATPase domains, transmitting information about RNA binding to the catalytic and signaling domains of the protein. In this way, RNA acts as a switch that turns on the RIG-I motor and initiates a cascade of cellular responses to viral infection.