Daggett Research Group 

Denatured barnase solvated by water and urea Multiple members of the ubiquitin-like fold
R. Dustin Schaeffer
Valerie Daggett Research Group
Biochemistry Department
Biomolecular Structure and Design Program
University of Washington


Selected projects:
  • Dynameomics - Large-scale native state and unfolding molecular dynamics simulations of proteins
    • Analysis of denatured states
      • Criteria for identifcation of denatured states in molecular dynamics simulations of experimentally uncharacterized proteins
      • Common elements among residual structure from different protein fold families
    • Target selection and preparation
      • Select representative targets from a fold family that are tractable to simulation
      • Minimize and solvate protein targets in preparation for simulation
      • Incorporate the changes in protein space as new proteins are discovered
    • Visualization of multi-dimensional structural information
      • Derivation and validation of pairwise contact potentials for protein transition and unfolded states
      • Divergence and convergence of protein trajectories in non-metric structural dissimilarity space
  • EBD - A small thermophillic fast-folding protein
    • Study of solvation effects from isosteric mutations (valine to threonine)
  • The Fundamental Hypothesis of Dynameomics - To what extent are single protein dynamics representative of a fold family?
    • Mass simulation of protein folds from three well-characterized proteins
      • SH3 domains
      • Ubiquitin-like proteins
      • Three-helix bundle DNA-binding domains
      • Testing of dissimilarity measures for the comparison of homologous protein dynamics
        • CONGENEAL
        • DALI Dissimilarity score
        • and others...
  • Chemical denaturant quenches of thermally-denatured barnase structures

    Selected publications:
    • Beck, D.A.C., Jonsson, A.L., Schaeffer, R.D., Scott, K.A., Day, R., Alonso, D.O.V. and V. Daggett, Dynameomics: Mass annotation of protein dynamics and folding by all-atom molecular dynamics simulations, To be submitted
    • Ferguson, N.F., Schaeffer, R.D., Daggett V., and A. Fersht, Solvation effects in the transition state of a small fast-folding protein probed by isosteric mutants, To be submitted
    • Schaeffer, R.D., and V. Daggett, Focusing in on the denatured state, To be submitted

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rschaeff@u.washington.edu