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University of Washington - Department of Bioengineering

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Paper of the Month

Side-chain dynamics are critical for water permeation through aquaporin-1

Smolin N., Li B., Beck D.A.C., and Daggett V.
Biophysical Journal (2008) In Press

Molecular dynamics simulations of aquaporin-1 embedded in a solvated lipid bilayer were performed to investigate the mechanism of water permeation. The 2.2 Â resolution crystal structure of the bovine protein was used for five independent trajectories, lasting between 4 and 10 ns. more...


Goals: Realistic simulation of protein dynamics, unfolding/folding, conformational transitions linked to disease, and the design of biomaterials

News

  • Microsoft featured the Group's integration of Windows software in a Case Study in June of 2008. High-performance computing clusters running Windows Compute Cluster Server are used to run the lab's molecular dynamics software with better performace than the optimized Linux version, and Microsoft SQL Server powers the 14-terabyte Dynameomics Database. The group's application of Microsoft's software was also featured in a Press Release later that month.
  • Bleeding Edge Biotech, a blog hosted by Carnegie Mellon computational biologist Adam Kraut, highlighted the Dynameomics Project in April of 2008.
  • The Daggett Lab was awarded 10 million processor hours for 2008 on the Department of Energy's supercomputers! The National Energy Research Scientific Computing Center (NERSC), located in Berkeley, CA, is one of the largest computing facilities in the world for basic scientific research.
  • The Benjamin Hall Interdisciplinary Research Building, one of only 11 Gold-level green buildings in the US, is the new home of the Daggett Lab.
  • The Daggett Group's work on prion protein was referenced in the September 2007 issue of Wellcome Trust's Big Pictures Series on Epidemics. [PDF]
  • The work on prion protein was again cited in the August 2007 Issue of Chemical and Engineering News.
  • The Dynameomics project and potential startup company was featured in the Biomedical Computation Review article "Biocomputation Startups: Where Does Value Lie?" by Katharine Miller. [PDF]
  • The Department of Energy awarded the Daggett group 2 million processor hours in 2005 through an Innovative and Novel Computational Impact on Theory and Experiment Award (INCITE), one of 3 awards in the country, for the Molecular Dynameomics project. [DOE press release]
    • Update: The NERSC Annual Report feature, "Proteins in Motion," details the Daggett group's Dynameomics Project.
    • Update: The Department of Energy has awarded the Daggett group an additional 5 million processor hours at NERSC for 2006 and 2007!
  • Now you can download Powerpoint slides of our prion conversion trajectory. If you want to know how your experimental data compare with our model or you want specific figures or analyses email us.
  • The Dynameomics project was the subject of a recent article in The Scientist, "Unraveling Protein Folding" by Melissa Lee Phillips. [PDF]
  • The Daggett Group's work on amyloid disease was the subject of recent editorials in Science by Orla Smith [PDF] and in Nature by Christopher Surridge. [PDF]

Daggett Group
Department of Bioengineering
University of Washington
Foege Building N310B, Box 355061
1705 NE Pacific Street
Seattle, WA 98195-5061

616 NE Northlake Place, Suite 300H
Seattle, WA 98105

daglab@u.washington.edu