NMR

We utilize NMR spectroscopy for studying the structures, dynamics, and interactions of proteins and nucleic acids. NMR is essential technique for understanding protein-ligand interactions, protein-protein interactions, and conformational changes. NMR is also uniquely capable to elucidate structures and conformational dynamics of RNA, RNA-protein and RNA-small molecule interactions. Obtaining insights into complex interactions, characterizing biomolecular dynamics, and determining pathways for conformational exchange not only reveals insights into biological function, but provides molecular blueprints to develop new therapeutics.

Shared facility

https://www.med.upenn.edu/jf/bsbcore/index.html

The biomolecular NMR facility allows studies of proteins, RNA and other important biomolecules in a physiologically relevant, aqueous environment. Our facility is equipped with 600 MHz and 800 MHz Avance Neo NMR systems with 5mm 1H-optimized triple resonance cryoprobe designed for 1H or 19F observation with 13C/15N decoupling, and 13C observation with 1H decoupling due to superior sensitivity on 13C. These capabilities are utilized in structure determination, studies of intrinsically disordered proteins, ligand binding and fragment-based drug discovery applications which serve the broader structural biology community at Penn and CHOP.

Researchers

Nikolaos Sgourakis, Ph.D

The Sgourakis lab sheds light on the dynamic molecular processes which determine immune recognition, signaling and the formation of long-term memory against viral, tumor and autoimmune targets. To address these questions, we integrate cutting-edge structural biology tools from (NMR) Nuclear Magnetic Resonance Spectroscopy, X-ray crystallography with complementary biophysical and biochemical techniques, computational modeling and functional assays.

NMR NMR cryoEM

James E. Petersson, Ph.D

Protein folding and protein interactions underlie both proper function and disease in biological systems. Many receptor proteins signal through complex interactions and rearrangements, and some proteins, such as the Parkinson’s Disease protein α-synuclein, misfold into toxic conformations. Studying these protein motions not only aids our understanding of diverse biological phenomena, it also contributes to an important fundamental problem in biochemistry: understanding how proteins fold and change shape. The Petersson laboratory is developing tools to address questions of how peptides and proteins mediate cellular communication and how the cellular environment catalyzes protein misfolding, from detailed in vitrofolding studies to imaging in live animals. These tools include novel chromophores, which we synthesize and incorporate into proteins through unnatural amino acid mutagenesis and synthetic protein ligation. We apply these tools to several key disease areas through collaborations in the Perelman School of Medicine: preventing the acquisition of antibiotic resistance by bacteria, Parkinson’s Disease, and fluorescence-guided cancer surgery. In many cases, the balance between health and disease is governed by post-translational modifications, for which we study the enzymes that install them, both to understand their biological roles and to utilize them in synthetic protein modification. Finally, an area of particular interest in the Petersson laboratory is the introduction of thioamide modifications to the peptide backbone, which can serve as protein folding probes, or stabilizers for improved therapeutic peptides or in vivoimaging reagents.

NMR cryoEM

Blanton S. Tolbert, Ph.D

The Tolbert lab research focuses on the biochemical mechanisms by which RNA viruses replicate within the cellular environment. Specifically, they use NMR spectroscopy and other biophysical methods to characterize complexes formed between host proteins and viral RNA elements. The group leverages their understanding of the foundational principles of these interactions to identify novel targets for therapeutic intervention.