Dr. David Boehr
Professor
Department: Chemistry
College: Eberly College of Science
Address: 107 Chemistry Building
Phone: 814-863-8605
E-mail: ddb12@psu.edu
Website: http://sites.psu.edu/boehrlab/
Enzymes important for virus replication
“Some of the most important new and (re)emerging pathogens are positive-strand RNA viruses, including coronavirus and picornaviruses Enterovirus D68, Enterovirus A71 and even poliovirus. These viruses directly use their RNA genome to guide the synthesis of a large polyprotein, which must then be proteolyzed into its component parts, including the capsid proteins and enzymes important for genome replication and encapsidation. Virus RNA genomes are rather small, and so these viruses have evolved strategies to essentially expand their functional proteomes. Many of these proteins have multiple functions and precursor proteins may have different or emergent functions compared to their fully proteolyzed counterparts. Our group studies key enzymes involved in enterovirus replication, including the 3D RNA-dependent RNA polymerase, the 3C protease, the 3CD polyprotein with 3C and 3D domains but with unique functions, and most recently, the 2C RNA helicase. The 2C, 3C and 3D enzymes are all highly conserved among enteroviruses and other RNA viruses, and so have been identified as important anti-viral drug targets.
Our research group is interested in understanding the three-dimensional structure and conformational dynamics of these proteins, as we believe this information can be leveraged towards anti-viral strategies. We especially use nuclear magnetic resonance (NMR) spectroscopy, but also take advantage of a number of other biophysical methods, including calorimetry, analytical ultracentrifugation and small angle X-ray scattering (SAXS). This work is complemented with enzyme kinetic assays and we have collaborators who have the potential to take our biochemical/biophysical observations and test them with viruses in cells and model organisms. Students in the lab also learn basic microbiology methods and protein purification techniques.
Current projects include:
1. Investigating lipid membrane interactions with 3C, 3D and 3CD. Infection with viruses causes host cells to break apart their internal membranes so the material can be used to make so-called replication organelles, within which viruses are “”safe”” to replicate. We are trying to understand the molecular determinants of virus protein binding to these membrane systems.
2. Investigating RNA interactions with 3C and 3CD. The 3C(D) protease also interacts with RNA sequences within the virus genome, which helps to coordinate RNA processing events like replication and translation. Most recently, we discovered that 3C-RNA interactions leads to liquid-liquid phase separation (LLPS), which may have functional consequences within the infected cell.
3. Understanding functional differences between 3C, 3D and 3CD. The 3CD polyprotein contains both 3C and 3D domains, which are almost structurally identical to the 3C and 3D proteins. However, there are important functional differences between 3CD and the free 3C and 3D proteins. We propose that the internal motions of 3CD are different than that of 3C and 3D, which translates into functional differences. This adds a new dimension to structure-function relationships (bio)chemists generally consider.
4. Investigating anti-viral drug interactions with 2C. The 2C helicase has been proposed as an anti-viral drug target. However, only recently have groups been able to purifiy/isolate 2C. Our group was the first to confirm experimentally that the anti-viral drug “”hydantoin”” directly binds to 2C. We are now in the process of building a model of that interaction, which can be important for future drug design.”