The Role of Thioamides in Natural and Designed Proteins

University Of Pennsylvania, Philadelphia PA

Investigators

Abstract

With the support of the Chemistry of Life Sciences (CLP) program in the Division of Chemistry, Professor E. James Petersson from the University of Pennsylvania is studying the effects of thioamides, oxygen-to-sulfur substitutions of the peptide bond found in proteins. The results of these studies will further the development of thioamides as tools for biophysical and medicinal chemistry by providing rules for the rational design of thioamide proteins with or without affecting stability, as desired. The work will also help to explain the evolutionary value of the thioamides found in certain natural proteins. The planned investigations of the fundamental properties of thioamides can impact areas as diverse as epigenetics, the biophysics of protein folding, the design of enzyme inhibitors, or even fluorescence-guided surgery using thioamide-stabilized peptides as tumor imaging agents. The broader impacts of this work include training undergraduate and graduate students in a multidisciplinary laboratory environment that makes use of organic synthesis and physical chemistry, as well as molecular and cellular biology, to investigate biological phenomena. In addition, Professor Petersson and his research group will participate in expositions both in-person, and virtual, to demonstrate their findings to K-12 groups and interested adults. They will also help to build the Penn Chemistry Summer Research Academy so that more students from groups under-represented in science have opportunities to experience science and participate in scientific research. Under this project, the physical properties and reactivity of thioamides will be studied as a function of amino acid sequence in model peptides. This will aid in the mechanistic understanding of environment-dependent properties such as pKa, and in benchmarking quantum mechanical (QM) calculations. For example, there is a need to better develop in molecular mechanics parameters for tripeptides or polypeptides, rather than use parameters based on small molecule values as has been done heretofore. Reactivity studies will be performed that have the potential to develop tools to identify new natural thioamide-containing proteins. Professor Petersson’s laboratory will also study thioamide effects on the secondary and tertiary structure of peptides, peptide/protein host-guest systems, and full-length proteins. Using data from model systems, novel PyRosetta programs will be developed in an effort to predict the effects of thioamides on protein stability. These predictions will be tested on thioamide-containing proteins, which will be characterized through X-ray crystallography and/or NMR as well as solution-phase stability measurements. Taken together, these experiments are expected to provide a better systematic understanding of the effects of thioamides on protein properties from local sequence-based effects, to effects on secondary, tertiary, and even quaternary structure. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.