For Alpay Dermenci, interacting with professors outside the classroom is the best part of research. “The most exciting part was eliciting solutions knowing that both the professors and I faced the same challenges.” He started working in the lab of Dr. A. J. Shaka in his freshman year, working in physical chemistry, organic chemistry, and structural biology. He looks forward to continuing his work in combining chemistry and biology beyond graduation, moving on to graduate school and eventually becoming a scientific research-er and professor. When he is away from his studies, Alpay enjoys reading, fishing, and spending time with his family.

For protein NMR, uniform isotopic labeling with 13C, 15N, and/or 2H has been used to aid structure determination. Proteins are usually expressed in bacteria like E. coli with isotopically labeled growth media, which leads to enrichment of the protein of interest. But such uniform labeling is not possible for carbohydrates because the samples are not obtained as simply as proteins. In addition, most sugars dissolve well only in polar solvents like water, which cause large residual solvent peaks, high viscosity with increased concentration, and other complicating factors. Therefore, we sought an alternative approach. We perderivatized the carbohydrate -OH groups, replacing the hydrogen with a small isotopically-enriched fragment called an isotag. The goals were to (a) improve the poor proton NMR spectral dispersion by creating electron-withdrawing inductive effects; (b) switch to organic solvents that are superior for NMR by capping the carbohydrate -OH groups with -OR groups, in which the R moiety changes the solubility; (c) apply powerful multidimensional heteronuclear protein methods to these systems by including 13C and 15N in the R group; and (d) see if the stereochemistry of the constituent sugar rings could be determined by analyzing the improved NMR spectra. Isotagging of carbohydrates avoids the time and expense of uniform labeling, improves chemical shift dispersion, and makes the sample soluble in organic solvents, such as CDCl3 or THF-d8.

Athan J. Shaka School of  Physical Sciences

Most biomolecular NMR spectroscopy focuses on proteins. There are a few groups working on DNA or RNA as well, but the effort in carbohydrates has been much less. The reason underlying this lopsided scientific resource allocation is not that carbohydrates are unimportant, or that we know the detailed structure of these molecules, especially as they are presented on cell surface membranes. Rather, it is that the NMR spectra of carbohydrates are much more difficult to resolve and assign than those from the other molecules. Alpay’s groundbreaking work, namely to introduce small isotopically-labeled protecting groups onto each hydroxyl group present in the sugar, will tip the balance in our favor, allowing spectra with excellent resolution and sensitivity to be obtained. This high-risk, high-reward project is a perfect example of how undergraduate research can really lead to a significant advance, even in a fairly mature field.