Chemistry Weekly Seminar - Dr. Jean Duhamel, University of Waterloo

Title

Structure and Dynamics of Synthetic and Biological Macromolecules Characterized in Solution by Pyrene Excimer Fluorescence (PEF)

Abstract

Pyrene excimer fluorescence or PEF is a powerful but massively underutilized analytical tool to characterize the structure of synthetic and biological macromolecules in solution. The PEF-based procedure works by randomly labeling a macromolecule with a pyrene derivative. Upon absorption of a UV photon, an excited pyrene can form an excimer upon encounter with a ground-state pyrene covalently attached to the same macromolecule. Recognizing that the macromolecule is essentially immobile on the time scale of pyrene fluorescence (~ 1 us), an excited pyrene can only probe a subdomain of the macromolecular volume that we describe as a blob. Application of the fluorescence blob model (FBM) to describe the PEF kinetics yields N_blob which represents the maximum number of structural units separating two pyrene labels inside a blob and still allowing PEF. Molecular mechanics optimizations (MMOs) are then conducted to search for the macromolecular conformation (helical, random coil, or array of helices …) that would satisfy the N_blob value determined experimentally. The procedure takes advantage of the ability of the FBM to deal with polydisperse macromolecules and at polymer concentrations that are 2 – 3 orders of magnitude lower than most other techniques. This presentation will review the applicability of the combination of PEF, FBM, and MMOs to the characterization of structured polysaccharides and polypeptides in solution as well as unstructured polypeptides with implications to protein folding.

Date:       Friday, October 9, 2020

Time:      1:30 p.m.

Via Zoom video conference (link available by request to chem.dept@usask.ca)