Daggett Research Group | Amanda Jonsson
Amanda Jonsson
Postdoctoral FellowDepartment of Bioengineering
University of Washington
Ph.D. Biochemistry
Biomolecular Structure and Design Program
University of Washington
B.S. Chemistry
Loyola University Chicago
ajonsson(at)u.washington.edu
Research | top
Dynameomics is an effort to simulate representative proteins from each known protein folds to study native state dynamics and the unfolding pathway. To date we have simulated representative proteins from over 800 protein folds. Native state simulations of proteins in the most populated folds are available at dynameomics.org. In particular, I am interested in the identification and characterization of the transition state ensemble from high temperature unfolding simulations. We have identified the transition state ensembles from simulations of 183 proteins in 176 structurally diverse folds.
Unfolding Pathways of β-Proteins
WW domains are small proteins that act as a model system for the folding of β-hairpins. Our unfolding simulations of FBP28 WW domain reveal that formation of the first hairpin is not nucleated by the precise structure of the first β-turn but instead the turn acts as a kink in the backbone allowing inter-strand contacts to form between residues in the first two strands. We are extending this work to study the unfolding pathways of larger β-proteins with conventional hydrophobic cores to see if the same pathway is observed for β-hairpin formation.
Publications | top
- Jonsson A.L., Scott K.A., and Daggett V. Dynameomics: A consensus view of the protein unfolding/folding transition state ensemble across a diverse set of protein folds. Biophysical Journal, In Press, 2009.
- Beck D.A.C., Jonsson A.L., Schaeffer R.D., Scott K.A., Day R., Toofanny R.D., Alonso D.O.V., and Daggett V. Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations. Protein Engineering Design & Selection 21: 353-368, 2008. [DOI]
- Sharpe T., Jonsson A.L., Rutherford T.J., Daggett V., and Fersht A.R. The role of the turn in β-hairpin formation during WW domain folding. Protein Science 16: 2233-2239, 2007. [DOI]
- Petrovich M., Jonsson A.L., Ferguson N., Daggett V., and Fersht A.R. Φ-Analysis at the Experimental Limits: Mechanism of β-Hairpin Formation. Journal of Molecular Biology 360: 865-881, 2006. [DOI]
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Daggett Group
Department of Bioengineering
University of Washington
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