The Use of Vibrational Spectroscopy to Probe the Conformational Propensities of Amino Acid Residues in Unfolded Peptides

Drexel University, Philadelphia PA

Investigators

Abstract

In this project funded by the Experimental Physical Chemistry Program in the Chemistry Division, Professor Reinhard Schweitzer-Stenner and his students will employ a battery of spectroscopic techniques to investigate the structure of unfolded peptides in water. For a long time, it was assumed that the biologically active ("native") form of most proteins involves one of the well known folded states, such as the alpha helix or beta sheet. In recent years, the discovery of native unfolded proteins has challenged the physical chemistry discipline to develop approaches to determine and understand their structure. While "unfolded," these protein systems are not completely random, but have local order or "propensities" that can, in principle, be determined with spectroscopic techniques. The first aim of the research will be to determine the intrinsic propensity of individual amino acids. Different amino acids will be inserted into a host glycine peptide chain, and examined using conventional infrared, Raman, and two dimensional nuclear magnetic resonance (2D NMR) spectroscopies, and also advanced techniques such as vibrational circular dichroism (VDC) and Raman Optical Activity (ROA) spectroscopies. In collaboration with Professor Minghaeng Cho at Korea University, the infrared, Raman and NMR spectra will be modeled using quantum mechanical and molecular dynamics simulations. The second aim is to explore the dependence of amino acid conformational propensities on the structure and charge of adjacent amino acids in the peptide chain. For example, what happens to the conformational tendencies of a given amino acid if the next acid in the chain is the branched species alanine? The third part of the project is aimed at exploring the structure of unfolded alanine based peptides. While conclusive evidence now suggests that alanine has a high preference for polyproline II like conformations, it is yet unclear whether extended conformations are maintained in longer peptides which contain between 6 and 12 amino acid residues. Finally, energy transfer experiments will be performed on specifically labeled peptides to measure end to end distance distributions. Taken together, the expected results will substantially enhance the understanding of the properties of the unfolded state of peptides and proteins. The combination of experiment and theory will enable us (and others) to judge the validity of coil libraries for models of unfolded peptides and proteins, as well as assist computationally oriented researchers in constructing molecular dynamics force fields suitable for unfolded states. Graduate and undergraduate students, as well as high school students will be trained at the interface of chemistry, biochemistry, and molecular biology. They will learn quantum mechanics, the theory and practice of Raman, optical absorption and CD spectroscopy, protein biochemistry, and different aspects of the relationship between structure and function of proteins. Students from underrepresented groups will be involved in the project.