February Monthly Meeting

Spectroscopy Society of Pittsburgh Monthly Meeting

TECHNOLOGY PROGRAM – 8:15PM
Dr. Angela Gronenborn, University of Pittsburgh School of Medicine

“Synergy between NMR, cryo-EM and large-scale MD simulations – Novel Findings for HIV Capsid Function”
Mature

HIV-1 particles contain a conical-shaped capsid that encloses the viral RNA genome and performs essential functions in the virus life cycle. Previous structural analysis of two- and three-dimensional arrays provided a molecular model of the capsid protein (CA) hexamer and revealed three interfaces in the lattice. Using the high-resolution NMR structure of the CA C-terminal domain (CTD) dimer and

in particular the unique interface identified, it was possible to reconstruct a model for a tubular assembly of CA protein that fit extremely well into the cryoEM density map. A novel CTD-CTD interface

at the local three-fold axis in the cryoEM map was confirmed by mutagenesis to be essential for function. More recently, the cryo-EM structure of the tube was solved at 8Å resolution and this cryo-EM structure allowed unambiguous modeling and refinement by large-scale molecular dynamics (MD) simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements of spheroidal capsids. Furthermore, the 3D structure of a native HIV-1 core was determined by cryo-electron tomography (Cryo-ET), which in combination with MD simulations permitted the construction of a realistic all-atom model for the entire capsid, based on the 3D authentic core structure.

TECHNICAL FORUM – 5:30 PM
Dr. Nathan Clark, University of Pittsburgh

“DNA Sequence Evolution: Resurrecting the Past to See the Future”
The wealth

of diversity between species provides us with a unique window on the forces that shaped the biological

world. By studying DNA sequences from these species we are able to reconstruct the relationships between them and reveal the functions of their genes. Here, we will review techniques of DNA sequence analysis and their application to pinpoint evolutionary adaptations that allow each species to survive in its environment. We will visit genetic adaptations that combat harmful pathogens and others that allow competition between them. Furthermore, analysis of Neanderthal and Denisovan DNA has revealed that evolutionary adaptations continued to occur relatively recently in our own evolutionary trajectory. In a separate application, our novel analysis technique, evolutionary rate covariation, allows us to computationally

predict relationships between genes so that we can piece together the genetic networks that compose all organisms. We demonstrate how rate covariation has been successfully employed to discover new genes in medical genetics, thereby revealing the genetic basis of disease.