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David Shortle Portrait

David Shortle
Professor of Biological Chemistry
Johns Hopkins University School of Medicine

725 N. Wolfe St.
513 Physiology
Baltimore, MD21205
Office Phone: 410-955-3738
Lab Phone: 410-955-3424
Fax: 410-955-5759
Email: shortle@jhmi.edu
Lab Web Site

Click Here for PDF of CV

Protein Folding; NMR characterization of unfolded proteins; protein structure prediction.

The principal research interest of the laboratory is protein folding and stability - how amino acid sequence encodes three-dimensional structure. On the experimental side, staphylococcal nuclease and eglin C are used as simple systems for characterizing the residual structure that persists in the ensemble of conformations known as the denatured states. Extensive use is made of 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. Paramagnetic relaxation enhancement is used to 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. Our current working assumption is that local side chain-backbone interactions, not long range hydrophobic contacts, are responsible for this structure.


Consequently, on the theoretical side, efforts to predict protein structure from sequence focus intensively on enforcing these local interactions in fragments built de novo, using short segments of chain taken from high resolution protein structures. Beginning with fragments of length 4 to 8 residues lacking side chain atoms beyond CG, larger fragments are assembled in a hierarchical fashion, using a variety of statistical potentials to enforce protein-like interactions between elements of secondary structure. In the final step, heavy atoms are added to form complete side chains, and several high resolution all atom potential, including one to quantify solvation, are used as fitness functions in a genetic algorithm-based conformational search.


The laboratory has participated in CASP’s 4, 5, and 6 in the new fold category and in CASP 6 in homology modeling. The upcoming CASP 7 challenge (May through August 2006) will provide us an opportunity to evaluate our new explicit side chain methods.

Recent Publications
Shortle D. (2009) One sequence plus one mutation equals two folds. Proc Natl Acad Sci USA 106: 21011-21012.
PubMed Reference

Shortle D. (2008) The Denatured States of Proteins: How Random Are They? In Unfolded Proteins, Trevor Creamer, editor. Nova Science Publishers, Inc., New York.

Gebel, E. and Shortle, D (2007) Characterization of denatured proteins using residual dipolar couplings. Methods in Molecular Biology, 350: 39-48.
PubMed Reference

Ohnishi S, Kamikubo H, Onitsuka M , Kataoka M, and Shortle D. (2006) Conformational preference of polyglycine in solution for elongated structures, submitted to J Am Chem Soc. 128:16338-16344.
PubMed Reference

Gebel, E. Ruan, K.; Tolman, J.R and Shortle, D. (2006) Multiple alignment tensors from a denatured protein. J. Am. Chem. Soc., 128: 9310-9311.
PubMed Reference

Gebel, E. and Shortle, D (2006) Characterization of denatured proteins using residual dipolar couplings. Methods in Molecular Biology, 350: 39-48.
PubMed Reference

Fang, Q and Shortle, D (2006) Protein refolding in silico with atom-based statistical potentials and conformational search using a simple genetic algorithm J. Mol. Biol. 359:1456-1467.
PubMed Reference

Fang, Q. and Shortle, D. (2005) Enhanced sampling near the native conformation using statistical potentials for local side-chain and backbone interactions. Proteins. 60: 97-102.
PubMed Reference

Fang Q. and Shortle, D. (2005) A consistent set of statistical potentials for quantifying local side-chain and backbone interactions. Proteins 60: 90-96.
PubMed Reference

Ohnishi, S., Lee, A.L., Edgell, M.H. and Shortle, D. (2004) Direct demonstration of structural similarity between native and denatured eglin C. Biochemistry 43: 4064-4070.
PubMed Reference

Ohnishi S. and Shortle, D. (2003) Effect of denaturants and substitutions of hydrophobic residues on backbone dynamics of denatured staphylococcal nuclease. Protein Science 12: 1530-1537.
PubMed Reference

Shortle, D. (2003) Propensities, probabilities, and the Boltzmann hypothesis. Protein Science 12: 1298-1302.
PubMed Reference

Fang, Q. and Shortle, D (2003) Prediction of Protein Structure by Emphasizing Local Side-Chain / Backbone Interactions in Ensembles of Turn Fragments Proteins: 53: 486-490.
PubMed Reference

Choy, W.-Y., Shortle, D. and Kay, L.E. (2003) Side chain dynamics in unfolded protein states: A 2H spin relaxation study of D131D. J. Amer. Chem. Soc., 125:1748-1758.
PubMed Reference

Ohnishi, S. and Shortle, D. (2003) Observation of residual dipolar couplings in short peptides. Proteins: 50: 546-51
PubMed Reference

Shortle, D. (2002) The Expanded Denatured State: An Ensemble of Conformations Trapped in a Locally Encoded Topological Space. Adv. Protein Chem. 62: 1-23.
PubMed Reference

Ackerman, M. S. and Shortle, D. (2002) Robustness of the long-range structure in denatured staphylococcal nuclease to changes in sequence. Biochemistry 41: 13791-13797.
PubMed Reference

Ackerman, M. S. and Shortle, D. (2002) Molecular Alignment of Denatured States of Staphylococcal Nuclease with Strained Polyacrylamide Gels and Alkyl-PEG Bicelles. Biochemistry 41: 3089-3095.
PubMed Reference

Shortle, D. (2002) Composites of Local Structural Propensities: Evidence for Local Encoding of Long Range Structure. Protein Science 11: 18-26.
PubMed Reference

Shortle, D. and Ackerman, M. S. (2001) Persistence of native-like topology in a denatured protein in 8 M urea. Science 293: 487-489.
PubMed Reference

Shortle, D. (2000) Prediction of protein structure (a primer). Current Biol. 10: R49-R51.
PubMed Reference


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