Dr. Shortle’s principal research interest is protein folding and stability: how amino acid sequence information encodes three-dimensional structure. The Shortle Lab combines experimental and computational approaches to study this longstanding puzzle of fundamental biochemistry. Several small proteins are being used as simple systems for characterizing the structure that persists in the unfolded (denatured) state, the starting point for folding both in the cell and in the test tube. In addition, the laboratory is working to predict protein structure from sequence in ways that make the underlying physical chemistry transparent and the relative contributions of different interactions quantifiable.
On the experimental side, the Shortle Lab uses staphylococcal nuclease and eglin C as simple systems for characterizing the residual structure that persists in the ensemble of conformations known as the denatured states. The lab uses several multi-dimensional NMR spectra collected on 15N and 13C labeled protein to assign all backbone resonances and identify protein segments that retain partial helix, strand, or turn structure. Through paramagnetic relaxation enhancement, the lab can define the three-dimensional topology of the denatured state and residual dipolar couplings are tracked as a function of solution conditions to monitor the change in this topology. The most important conclusion reached to date is that a native-like topology persists for both proteins, even at high concentrations of urea. This has led to a current working assumption that local side chain-backbone interactions, not long-range hydrophobic contacts, are responsible for this structure.
Shortle D. “One sequence plus one mutation equals two folds.” Proc Natl Acad Sci USA. 2009. 106: 21011-21012.
Shortle D. “The Denatured States of Proteins: How Random Are They?” In Unfolded Proteins, Trevor Creamer, editor. Nova Science Publishers, Inc., New York. 2008.
Gebel, E. and Shortle, D. “Characterization of denatured proteins using residual dipolar couplings.” Methods in Molecular Biology. 2007. 350: 39-48.
Ohnishi S, Kamikubo H, Onitsuka M , Kataoka M, and Shortle D. “Conformational preference of polyglycine in solution for elongated structures.” Submitted to J Am Chem Soc. 2006. 128:16338-16344.
Gebel, E. Ruan, K.; Tolman, J.R and Shortle, D. “Multiple alignment tensors from a denatured protein.” J. Am. Chem. Soc. 2006. 128: 9310-9311.