David Shortle

Research output

Research output per year 1970 1989 1990 1992 1993 1994 1995 1996 1997 1999 2002 2003 2009

• 82 Article
• 6 Review article
• 3 Comment/debate
• 2 Editorial
• 2 More
  • 2 Short survey

Research output per year

Research output per year

Search results

• 2009

  One sequence plus one mutation equals two folds

  Shortle, D., Dec 15 2009, In: Proceedings of the National Academy of Sciences of the United States of America. 106, 50, p. 21011-21012 2 p.

  Research output: Contribution to journal › Comment/debate › peer-review
  7 Scopus citations
• 2007

  Characterization of denatured proteins using residual dipolar couplings.

  Gebel, E. B. & Shortle, D., 2007, In: Methods in molecular biology (Clifton, N.J.). 350, p. 39-48 10 p.

  Research output: Contribution to journal › Article › peer-review

  • Magnetic Resonance Spectroscopy 100%
  • Proteins 72%
  • polyacrylamide gels 47%
  • Urea 37%
  • Observation 28%
  3 Scopus citations
• 2006

  Conformational preference of polyglycine in solution to elongated structure

  Ohnishi, S., Kamikubo, H., Onitsuka, M., Kataoka, M. & Shortle, D., Dec 20 2006, In: Journal of the American Chemical Society. 128, 50, p. 16338-16344 7 p.

  Research output: Contribution to journal › Article › peer-review

  • polyglycine 100%
  • Amino acids 62%
  • Tripeptide 57%
  • Glycine 53%
  • Peptides 51%
  56 Scopus citations

• Multiple alignment tensors from a denatured protein

  Gebel, E. B., Ruan, K., Tolman, J. R. & Shortle, D., Jul 26 2006, In: Journal of the American Chemical Society. 128, 29, p. 9310-9311 2 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Tensors 100%
  • Proteins 92%
  • Datasets 80%
  • Amides 30%
  • Polyacrylates 26%
  6 Scopus citations

• Protein Refolding in Silico with Atom-based Statistical Potentials and Conformational Search Using a Simple Genetic Algorithm

  Fang, Q. & Shortle, D., Jun 23 2006, In: Journal of molecular biology. 359, 5, p. 1456-1467 12 p.

  Research output: Contribution to journal › Article › peer-review

  • Protein Refolding 100%
  • Computer Simulation 62%
  • Hydrogen Bonding 40%
  • Proteins 24%
  • Amino Acids 23%
  12 Scopus citations
• 2005

  A consistent set of statistical potentials for quantifying local side-chain and backbone interactions

  Fang, Q. & Shortle, D., Jun 15 2005, In: Proteins: Structure, Function and Genetics. 60, 1, p. 90-96 7 p.

  Research output: Contribution to journal › Article › peer-review

  • Peptides 100%
  • Energy 73%
  • Amides 61%
  • Solution Structure 54%
  • Protons 53%
  34 Scopus citations

• Enhanced sampling near the native conformation using statistical potentials for local side-chain and backbone interactions

  Fang, Q. & Shortle, D., Jun 15 2005, In: Proteins: Structure, Function and Genetics. 60, 1, p. 97-102 6 p.

  Research output: Contribution to journal › Article › peer-review

  • Sampling 100%
  • Energy 56%
  • Protein Structure 47%
  • Proteins 44%
  • Protein Conformation 40%
  8 Scopus citations
• 2004

  Direct Demonstration of Structural Similarity between Native and Denatured Eglin C

  Ohnishi, S., Lee, A. L., Edgell, M. H. & Shortle, D., Apr 13 2004, In: Biochemistry. 43, 14, p. 4064-4070 7 p.

  Research output: Contribution to journal › Article › peer-review

  • eglin proteinase inhibitors 100%
  • Micrococcal Nuclease 39%
  • Amyloid 25%
  • Urea 25%
  • Computer Simulation 25%
  59 Scopus citations
• 2003

  Effects of denaturants and substitutions of hydrophobic residues on backbone dynamics of denatured staphylococcal nuclease

  Ohnishi, S. & Shortle, D., Jul 1 2003, In: Protein Science. 12, 7, p. 1530-1537 8 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Micrococcal Nuclease 100%
  • Urea 48%
  • Substitution Reaction 43%
  • pH Value 28%
  • Compound Mobility 13%
  17 Scopus citations

• Observation of residual dipolar couplings in short peptides

  Ohnishi, S. & Shortle, D., Mar 1 2003, In: Proteins: Structure, Function and Genetics. 50, 4, p. 546-551 6 p.

  Research output: Contribution to journal › Article › peer-review

  • Observation 100%
  • Peptides 89%
  • Length 66%
  • Gel 52%
  • Gels 38%
  35 Scopus citations

• Prediction of Protein Structure by Emphasizing Local Side-Chain/Backbone Interactions in Ensembles of Turn Fragments

  Fang, Q. & Shortle, D., 2003, In: Proteins: Structure, Function and Genetics. 53, SUPPL. 6, p. 486-490 5 p.

  Research output: Contribution to journal › Article › peer-review

  • Statistical Ensemble 100%
  • Protein Structure 98%
  • Amino Acids 70%
  • Genetic Recombination 64%
  • Pair Potential 48%
  27 Scopus citations

• Propensities, probabilities, and the Boltzmann hypothesis

  Shortle, D., Jun 1 2003, In: Protein Science. 12, 6, p. 1298-1302 5 p.

  Research output: Contribution to journal › Article › peer-review

  • Protein Structure 100%
  • Gibbs Free Energy 76%
  • Protein Conformation 68%
  • Protein Stability 60%
  • Helical Structure 56%
  45 Scopus citations

• Side chain dynamics in unfolded protein states: An NMR based ²H spin relaxation study of Δ131Δ

  Choy, W. Y., Shortle, D. & Kay, L. E., Feb 15 2003, In: Journal of the American Chemical Society. 125, 7, p. 1748-1758 11 p.

  Research output: Contribution to journal › Article › peer-review

  • Protein Unfolding 100%
  • Nuclear magnetic resonance 87%
  • Relaxation 68%
  • Proteins 67%
  • Micrococcal Nuclease 35%
  38 Scopus citations
• 2002

  Composites of local structure propensities: Evidence for local encoding of long-range structure

  Shortle, D., 2002, In: Protein Science. 11, 1, p. 18-26 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Length 100%
  • Rotamer 98%
  • Statistical Ensemble 83%
  • Composite Material 83%
  • Protein 69%
  70 Scopus citations

• Molecular alignment of denatured states of staphylococcal nuclease with strained polyacrylamide gels and surfactant liquid crystalline phases

  Ackerman, M. S. & Shortle, D., Mar 5 2002, In: Biochemistry. 41, 9, p. 3089-3095 7 p.

  Research output: Contribution to journal › Article › peer-review

  • Micrococcal Nuclease 100%
  • polyacrylamide gels 82%
  • Surface-Active Agents 71%
  • Surfactant 46%
  • Urea 43%
  37 Scopus citations

• Robustness of the long-range structure in denatured staphylococcal nuclease to changes in amino acid sequence

  Ackerman, M. S. & Shortle, D., Nov 19 2002, In: Biochemistry. 41, 46, p. 13791-13797 7 p.

  Research output: Contribution to journal › Article › peer-review

  • Micrococcal Nuclease 100%
  • Urea 65%
  • Amino Acid Sequence 63%
  • methionine sulfoxide 57%
  • Valine Residue 52%
  48 Scopus citations

• The expanded denatured state: An ensemble of conformations trapped in a locally encoded topological space

  Shortle, D., Jan 1 2002, In: Advances in Protein Chemistry. 62, p. 1-23 23 p.

  Research output: Contribution to journal › Review article › peer-review
  71 Scopus citations
• 2001

  Persistence of native-like topology in a denatured protein in 8 M urea

  Shortle, D. & Ackerman, M. S., Jul 20 2001, In: Science. 293, 5529, p. 487-489 3 p.

  Research output: Contribution to journal › Article › peer-review

  • Protein Folding 100%
  • Urea 80%
  • Micrococcal Nuclease 61%
  • Protein Unfolding 57%
  • polyacrylamide gels 51%
  535 Scopus citations
• 2000

  Correlation between changes in nuclear magnetic resonance order parameters and conformational entropy: Molecular dynamics simulations of native and denatured staphylococcal nuclease

  Wrabl, J. O., Shortle, D. & Woolf, T. B., Feb 1 2000, In: Proteins: Structure, Function and Genetics. 38, 2, p. 123-133 11 p.

  Research output: Contribution to journal › Article › peer-review

  • Micrococcal Nuclease 100%
  • Entropy 82%
  • Order Parameter 81%
  • Molecular Dynamics Simulation 76%
  • Magnetic Resonance Spectroscopy 57%
  45 Scopus citations

• Prediction of protein structure

  Shortle, D., Jan 1 2000, In: Current Biology. 10, 2, p. R49-R51

  Research output: Contribution to journal › Short survey › peer-review

  Open Access
  13 Scopus citations
• 1999

  A model of the changes in denatured state structure underlying m value effects in staphylococcal nuclease

  Wrabl, J. & Shortle, D., 1999, In: Nature Structural Biology. 6, 9, p. 876-883 8 p.

  Research output: Contribution to journal › Article › peer-review

  • Barrel Shaped Crystal 100%
  • Micrococcal Nuclease 84%
  • Guanidine 74%
  • Hydrogen 67%
  • Hydrochloride 52%
  63 Scopus citations

• Analysis of long-range interactions in a model denatured state of staphylococcal nuclease based on correlated changes in backbone dynamics

  Sinclair, J. F. & Shortle, D., 1999, In: Protein Science. 8, 5, p. 991-1000 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Micrococcal Nuclease 100%
  • Sodium Perchlorate 89%
  • 15N NMR Spectroscopy 83%
  • beta-Strand Protein Conformation 81%
  • Statistical Ensemble 68%
  24 Scopus citations

• Protein folding as seen from water's perspective

  Shortle, D., 1999, In: Nature Structural Biology. 6, 3, p. 203-205 3 p.

  Research output: Contribution to journal › Short survey › peer-review

  • Magnetic Relaxation 100%
  • Protein Folding 93%
  • Water 52%
  • Protein 32%
  • Proteins 29%
  14 Scopus citations

• Structure prediction: The state of the art

  Shortle, D., Mar 25 1999, In: Current Biology. 9, 6, p. R205-R209

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • prediction 100%
  • Protein Structure 71%
  • Proteins 54%
  • protein structure 50%
  • methodology 13%
  13 Scopus citations
• 1998

  Clustering of low-energy conformations near the native structures of small proteins

  Shortle, D., Simons, K. T. & Baker, D., Sep 15 1998, In: Proceedings of the National Academy of Sciences of the United States of America. 95, 19, p. 11158-11162 5 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Cluster Analysis 100%
  • Proteins 41%
  • Amino Acid Sequence 25%
  236 Scopus citations
• 1997

  Characterization of long-range structure in the denatured state of staphylococcal nuclease. I. Paramagnetic relaxation enhancement by nitroxide spin labels

  Gillespie, J. R. & Shortle, D., Apr 25 1997, In: Journal of molecular biology. 268, 1, p. 158-169 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Spin Labels 100%
  • Micrococcal Nuclease 92%
  • Protons 51%
  • Amides 44%
  • Cysteine 23%
  266 Scopus citations

• Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures

  Gillespie, J. R. & Shortle, D., Apr 25 1997, In: Journal of molecular biology. 268, 1, p. 170-184 15 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Spin Labels 100%
  • Micrococcal Nuclease 92%
  • Amides 74%
  • Protons 64%
  • Hydrogen Bonding 38%
  259 Scopus citations

• Comprehensive NOE characterization of a partially folded large fragment of staphylococcal nuclease Δ131Δ, using NMR methods with improved resolution

  Zhang, O., Kay, L. E., Shortle, D. & Forman-Kay, J. D., Sep 12 1997, In: Journal of molecular biology. 272, 1, p. 9-20 12 p.

  Research output: Contribution to journal › Editorial › peer-review

  Open Access

  • Micrococcal Nuclease 100%
  • Protein Unfolding 93%
  • src Homology Domains 83%
  • Amides 81%
  • Peptides 43%
  56 Scopus citations

• Measurement of water-amide proton exchange rates in the denatured state of staphylococcal nuclease by a magnetization transfer technique

  Mori, S., Van Zijl, P. C. M. & Shortle, D., 1997, In: Proteins: Structure, Function and Genetics. 28, 3, p. 325-332 8 p.

  Research output: Contribution to journal › Article › peer-review

  • Micrococcal Nuclease 100%
  • Amides 81%
  • Protons 70%
  • Viperidae 46%
  • Water 45%
  36 Scopus citations

• Residual helical and turn structure in the denatured state of staphylococcal nuclease: Analysis of peptide fragments

  Wang, Y. & Shortle, D., 1997, In: Folding and Design. 2, 2, p. 93-100 8 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Micrococcal Nuclease 100%
  • Peptide Fragments 91%
  • Helical Structure 76%
  • Secondary Structure 48%
  • Peptides 43%
  39 Scopus citations

• Structure prediction: Folding proteins by pattern recognition

  Shortle, D., 1997, In: Current Biology. 7, 3, p. R151-R154

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Pattern Recognition 100%
  • Protein Folding 99%
  • protein folding 99%
  • protein structure 87%
  • Protein Structure 82%
  13 Scopus citations

• Triple-resonance NOESY-based experiments with improved spectral resolution: Applications to structural characterization of unfolded, partially folded and folded proteins

  Zhang, O., Forman-Kay, J. D., Shortle, D. & Kay, L. E., 1997, In: Journal of Biomolecular NMR. 9, 2, p. 181-200 20 p.

  Research output: Contribution to journal › Article › peer-review

  • Micrococcal Nuclease 100%
  • thymidine 3',5'-diphosphate 81%
  • Protons 70%
  • Chemical Shift 55%
  • Nuclear Overhauser Effect 54%
  82 Scopus citations
• 1996

  A dynamic bundle of four adjacent hydrophobic segments in the denatured state of staphylococcal nuclease

  Wang, Y. & Shortle, D., Sep 1996, In: Protein Science. 5, 9, p. 1898-1906 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Micrococcal Nuclease 100%
  • beta-Strand Protein Conformation 81%
  • Resonance 54%
  • Urea 54%
  • Antiparallel Beta-Sheet 44%
  47 Scopus citations

• Contributions of the ionizable amino acids to the stability of staphylococcal nuclease

  Meeker, A. K., Garcia-Moreno E., B. & Shortle, D., May 21 1996, In: Biochemistry. 35, 20, p. 6443-6449 7 p.

  Research output: Contribution to journal › Article › peer-review

  • Micrococcal Nuclease 100%
  • Guanidine 88%
  • Static Electricity 80%
  • Alanine 69%
  • Hydrochloride 62%
  88 Scopus citations

• Perturbations of the denatured state ensemble: Modeling their effects on protein stability and folding kinetics

  Wrabl, J. O. & Shortle, D., Nov 1996, In: Protein Science. 5, 11, p. 2343-2352 10 p.

  Research output: Contribution to journal › Article › peer-review

  • Protein Stability 100%
  • Protein Folding 99%
  • Statistical Ensemble 83%
  • Mutation 71%
  • Kinetics 61%
  20 Scopus citations

• Protein folding for realists: A timeless phenomenon

  Shortle, D., Wang, Y., Gillespie, J. R. & Wrabl, J. O., Jun 1996, In: Protein Science. 5, 6, p. 991-1000 10 p.

  Research output: Contribution to journal › Review article › peer-review

  • Protein Folding 100%
  • Protein 35%
  • Proteins 31%
  • Micrococcal Nuclease 30%
  • Statistical Ensemble 21%
  45 Scopus citations

• Structural analysis of non-native states of proteins by NMR methods

  Shortle, D. R., Feb 1996, In: Current Opinion in Structural Biology. 6, 1, p. 24-30 7 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Protein Folding 100%
  • Proteins 93%
  • Protons 86%
  197 Scopus citations

• The denatured state (the other half of the folding equation) and its role in protein stability

  Shortle, D., Jan 1996, In: FASEB Journal. 10, 1, p. 27-34 8 p.

  Research output: Contribution to journal › Review article › peer-review

  • Protein Stability 100%
  • Protein 34%
  • Protein Structure 33%
  • Proteins 31%
  • Protein Unfolding 28%
  356 Scopus citations
• 1995

  Initial studies of the equilibrium folding pathway of staphylococcal nuclease

  Wang, Y., Alexandrescu, A. T. & Shortle, D., Apr 1 1995, In: Philosophical Transactions of the Royal Society B: Biological Sciences. 348, 1323, p. 27-34 8 p.

  Research output: Contribution to journal › Article › peer-review

  • Micrococcal Nuclease 100%
  • micrococcal nuclease 91%
  • beta-Strand Protein Conformation 81%
  • Glycerol 58%
  • glycerol 56%
  20 Scopus citations

• NMR Structure of a Stable "OB-fold" Sub-domain Isolated from Staphylococcal Nuclease

  Alexandrescu, A. T., Gittis, A. G., Abeygunawardana, C. & Shortle, D., Jul 7 1995, In: Journal of molecular biology. 250, 2, p. 134-143 10 p.

  Research output: Contribution to journal › Editorial › peer-review

  Open Access

  • Micrococcal Nuclease 100%
  • Protein Unfolding 31%
  • Mutation 25%
  • Oligosaccharides 25%
  • Proteins 25%
  44 Scopus citations

• Protein fold recognition

  Shortle, D., Feb 1995, In: Nature Structural Biology. 2, 2, p. 91-93 3 p.

  Research output: Contribution to journal › Article › peer-review

  • Protein Tertiary Structure 100%
  • Proteins 28%
  26 Scopus citations

• Staphylococcal Nuclease: A Showcase of m-Value Effects

  Shortle, D., Jan 1 1995, In: Advances in Protein Chemistry. 46, C, p. 217-247 31 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Micrococcal Nuclease 100%
  • Mutation 58%
  • Gibbs Free Energy 34%
  • Entropy 27%
  • Heat Capacity 23%
  155 Scopus citations

• The emerging role of insertions and deletions in protein engineering

  Shortle, D. & Sondek, J., 1995, In: Current Opinion in Biotechnology. 6, 4, p. 387-393 7 p.

  Research output: Contribution to journal › Article › peer-review

  • Protein Engineering 100%
  • Proteins 66%
  • Substitution reactions 48%
  • Substitution Reaction 45%
  • Protein Stability 43%
  37 Scopus citations

• The Equilibrium Folding Pathway of Staphylococcal Nuclease: Identification of the Most Stable Chain-Chain Interactions by NMR and CD Spectroscopy

  Wang, Y. & Shortle, D., Dec 1995, In: Biochemistry. 34, 49, p. 15895-15905 11 p.

  Research output: Contribution to journal › Article › peer-review

  • Micrococcal Nuclease 100%
  • Spectrum Analysis 67%
  • Urea 65%
  • Magnetic Resonance Spectroscopy 57%
  • NMR Spectroscopy 45%
  104 Scopus citations
• 1994

  Assignment of Amino Acid Type in ¹H-¹⁵N Correlation Spectra by Labeling with ¹⁴N-Amino Acids

  Shortle, D., 1994, In: Journal of Magnetic Resonance, Series B. 105, 1, p. 88-90 3 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access
  34 Scopus citations

• Backbone dynamics of a highly disordered 131 residue fragment of staphylococcal nuclease

  Alexandrescu, A. T. & Shortle, D., Sep 29 1994, In: Journal of molecular biology. 242, 4, p. 527-546 20 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Micrococcal Nuclease 100%
  • Hydrophobic and Hydrophilic Interactions 37%
  • Population 6%
  • Proteins 6%
  125 Scopus citations

• Electrophoretic characterization of the denatured states of staphylococcal nuclease

  Creighton, T. E. & Shortle, D., Oct 6 1994, In: Journal of molecular biology. 242, 5, p. 670-682 13 p.

  Research output: Contribution to journal › Article › peer-review

  • Micrococcal Nuclease 100%
  • Urea 65%
  • Hydrodynamics 39%
  • Mutation 38%
  • Ligands 36%
  35 Scopus citations

• Evidence for strained interactions between side-chains and the polypeptide backbone

  Stites, W. E., Meeker, A. K. & Shortle, D., Jan 7 1994, In: Journal of molecular biology. 235, 1, p. 27-32 6 p.

  Research output: Contribution to journal › Article › peer-review

  • Glycine 100%
  • Peptides 83%
  • Alanine 66%
  • Proteins 48%
  • Micrococcal Nuclease 47%
  55 Scopus citations

• Structure and Dynamics of a Denatured 131-Residue Fragment of Staphylococcal Nuclease: A Heteronuclear NMR Study

  Alexandrescu, A. T., Abeygunawardana, C. & Shortle, D., Feb 1 1994, In: Biochemistry. 33, 5, p. 1063-1072 10 p.

  Research output: Contribution to journal › Article › peer-review

  • Biomolecular Nuclear Magnetic Resonance 100%
  • Micrococcal Nuclease 86%
  • Triple Resonance Spectroscopy 33%
  • Chemical Shift 31%
  • Protein 24%
  171 Scopus citations
• 1993

  Alpha helix propensity of amino acids

  Shortle, D., Clarke, N., Blaber, M., Zhang, X. J. & Matthews, B. W., 1993, In: Science. 262, 5135, p. 917-918 2 p.

  Research output: Contribution to journal › Comment/debate › peer-review
  6 Scopus citations