Mapping Protein Folding Energy Landscapes

How do proteins fold to their functional three-dimensional structures? A random search of all of the conformational degrees of freedom available to the polypeptide chain would require a time longer than the age of the universe, and yet proteins rapidly find their native structures, sometimes within microseconds. The answer lies in the energy landscape for protein folding, shown in the cartoon at right, which is thought to have a strong energy bias towards the native structure. We seek to map this energy landscape, in order to understand how proteins fold in detail, and what happens when they misfold with disastrous consequences as in Alzheimers and other misfolding diseases.

Our approach closely integrates experiment and simulation to answer these questions. We have designed experimental methods to quantitatively test the predictions of MD simulations of ultrafast folding proteins. In turn, we expect MD simulations to motivate new experiments, or help in the interpretation of experimental observables. We find such a close interplay between experiment and theory greatly benefits both, and ultimately improves our understanding of how proteins fold. Fundamentally new approaches to the rapid initiation and structure specific characterization of folding reactions are required to map the folding energy landscape. We have pioneered the development of such approaches in my laboratory, establishing the viability of laser-induced T-jump and pH-jump coupled with time-resolved spectroscopic methods. We emphasize time-resolved infrared and fluorescence techniques as well established, structure-specific probes of folding dynamics. We focus on small ultrafast folding proteins and peptide models to facilitate quantitative comparison of experiment with the predictions of folding theory and simulations.

Funding

NIH R01 GM53640-014, "Fast Events in Protein Folding," (Dyer, P.I.), 8/2008-4/2013

Recent Publications

“Dynamics of the gel to fluid phase transformation in unilamellar lipid bilayer vesicles,” S. Nagarajan, E. E. Schuler, K. Ma, J. T. Kindt and R. B Dyer, J. Phys. Chem. B 2012, 116 (46), pp 13749–13756. PMC3508262 (http://pubs.acs.org/doi/abs/10.1021/jp309832u)
“Temperature Dependence of Water Interactions with the Amide Carbonyls of α-Helices,” S. H. Brewer, S. Gnanakaran, Y. Tang, D. M. Vu, D. P. Raleigh, R. B. Dyer, Biochemistry 2012, 51 (26), pp 5293–5299. PMC3448027
“Raising the speed limit for β-Hairpin formation,” C. M. Davis, S. Xiao, D. P. Raleigh and R. B. Dyer, J. Am. Chem. Soc. 2012, 134 (35), 14476–14482. PMC3443077
“Early turn formation and chain collapse drive fast folding of the major cold shock protein CspA of E. coli,” D. M. Vu, S. H. Brewer, R. B. Dyer, Biochemistry 2012, 51 (45), pp 9104–9111. (http://pubs.acs.org/doi/abs/10.1021/bi301296y)
"Fast Events in Protein Folding," R. B. Dyer, D. M. Vu, Comprehensive Biophysics 3.3 Globular Proteins, Elsevier Press, E. Engelman, Editor, 2012 in press.
"Differential Ordering of the Protein Backbone and Side Chains during Protein Folding Revealed by Site-Specific Recombinant Infrared Probes S. Nagarajan, H. Taskent-Sezgin, D. Parul, I. Carrico, D. P. Raleigh, and R. B. Dyer, J. Am. Chem. Soc. 2011, 133, 20335–20340.
"Implementation of Time-Resolved Step-Scan Fourier Transform Infrared (FT-IR) Spectroscopy Using a kHz Repetition Rate Pump Laser", D. Magana, D. Parul, R. B. Dyer, A. P. Shreve, Appl. Spect. 2011, 65, 535-542.
"Azidohomoalanine: A Conformationally Sensitive IR Probe of Protein Folding, Protein Structure and Electrostatics," Humeyra Taskent-Sezgin, Juah Chung, Partha S. Banerjee, Sureshbabu Nagarajan, R. Brian Dyer, Isaac Carrico and Daniel P. Raleigh, Angewandte Chemie-International Edition 2010, 49, 7473–7475. (or Angewandte Chemie 122, 7635-7637)
"Laser-Induced Temperature Jump Infrared Measurements of RNA Folding," Dyer, RB; Brauns, EB, Methods in Enzymology: Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding, Pt B 2009, 469, 353-372.
T. L. Religa, C. M. Johnson, D. M. Vu, S. H. Brewer, R. B. Dyer, A. R. Fersht, Proc. Natl. Acad. Sci. USA 2007, 104, 9272-9277.
S. H. Brewer, B. Song, D. P. Raleigh, and R. B. Dyer, Biochemistry 2007, 46, 3279-3285.
"Ultrafast and Downhill Folding," R. B. Dyer, Curr. Opin. Struct. Biol. 2007, 17, 38-47.
J. H. Werner, R. Joggerst, R. Keller, R. B. Dyer, P. M. Goodwin, Proc. Natl. Acad. Sci. USA 2006, 103, 11130-11135
T. P. Causgrove and R. B. Dyer, Chem. Phys. 2006, 323, 2-10.
S. H. Brewer, D. M. Vu, Y. Tang, Y. Li, S. Franzen, D. P. Raleigh and R. B. Dyer, Proc. Natl. Acad. Sci. USA 2005, 102, 16662-16667.
R. M. Fesinmeyer, E. S. Peterson, R. B. Dyer and N. H. Andersen, Prot. Sci. 2005, 14, 2324-2332.
R. B. Dyer, S. J. Maness, S. Franzen, R. M. Fesinmeyer, K. A. Olsen, N. H. Andersen, Biochemistry 2005, 44, 10406 – 10415.