Biochemistry, Structural Biology
Dr. Pyle is also William Edward Gilbert Professor of Molecular, Cellular and Developmental Biology and a professor of chemistry at Yale University.
RNA Tertiary Structure and Recognition by Proteins
Inside the cell, RNA is a molecular bag of tricks. This close chemical cousin of DNA, best known for carrying the genetic instructions to build proteins, also folds into elaborate shapes, allowing it to bind to other molecules and speed up chemical reactions. Anna Marie Pyle explores how RNA folds and organizes itself into different three-dimensional shapes that catalyze reactions essential for turning on genes. She also studies the molecular motor proteins that unwind RNA, a crucial step in the metabolic function of all organisms, and particularly in the life cycle of viruses such as hepatitis C. Understanding the way these proteins work will help scientists design drugs to stop certain viruses from reproducing.
Pyle became a chemistry devotee at an early age. Her father, a cardiologist and medical researcher, often told his daughter about his own aspirations to do basic chemistry research. As a young boy, he raided an abandoned military base for chemicals to stock his bedroom laboratory. "From the time I was a very little kid, he would regale me with stories about the incendiary experiments he did as a child," Pyle explained. "There was no question that I wanted to be a scientist, even from a young age."
Initially, Pyle set her sights on the pursuit of "pure" chemistry—inorganic chemistry with a focus on metals and metal complexes—never bothering to take a biology or biochemistry course. But as a graduate student at Columbia in the 1980s, Pyle began synthesizing metal probes that recognize and bind to DNA, with the goal of understanding how proteins that service the genome find their targets within DNA's complex double-helical structure. About the same time, Thomas Cech, former HHMI president, made a surprising discovery—for which he earned a Nobel Prize in Chemistry in 1989—demonstrating that RNA can catalyze chemical reactions, a job previously thought to be the exclusive domain of proteins. Cech's work indicated that catalytic RNAs would have to fold into unusual structures and their way of recognizing other molecules would be highly complex. Pyle decided that if she were really interested in how nucleic acids interact with other molecules, she should work with RNA. She joined Cech's University of Colorado laboratory as a postdoctoral fellow, investigating the molecular interactions that stabilize the folding of catalytic RNA.
In her laboratory at Yale University, Pyle now studies the structures of exceptionally large RNA molecules, focusing on a family of catalytic RNAs called group II introns. Many scientists believe that these sections of RNA are the evolutionary ancestors of about a third of the DNA in the human body. Group II introns continue to affect the structure and organization of many modern genomes, facilitating evolutionary change over time. By solving the first crystal structures of group II introns, which are among the largest RNA molecules ever glimpsed, Pyle enabled us to visualize the machinery of pre-mRNA splicing at high resolution. While this work revealed the architectural organization and active-site structure of an RNA splicing machine. Pyle continues to believe that structure is only part of the story: "Although there are an increasing number of static RNA structures, we have a lot more to learn about how RNA achieves the folded state, what the molecular interactions look like, and more importantly, how it is all stabilized," she says.
Pyle also investigates a family of molecular motor proteins that bind RNA and carry out work in the cell. Some of them create single strands that can be copied or used as templates for building proteins. The family of helicases she studies is essential for the replication of hepatitis C and for the transcription of pox viruses. "It is our feeling that if you don't understand how these critical proteins work, you can't design good inhibitors for them," she says. Pyle's research shows that helicases skitter along single-stranded RNA, moving with regular, periodic steps and kicking off any proteins or other molecules impeding their movement. She has also shown that certain family members (such as the human innate immune receptor RIG-I) function as switches, rather than directional motors, and that they utilize RNA binding and ATP hydrolysis to send signals in the cell.
Pyle's investigations demonstrate firsthand the value of laboratory research. "You can make an impact on medicine and biology by doing very basic work on biomolecules," she explains. "I try to encourage people to realize that it is great to do extremely basic molecular research. In the end, it provides critical pieces of the larger puzzle."