• Publications
  • Influence
From conversion to aggregation: protofibril formation of the prion protein.
  • M. DeMarco, V. Daggett
  • Biology, Chemistry
    Proceedings of the National Academy of Sciences…
  • 24 February 2004
TLDR
Molecular dynamics simulation produces a scrapie prion protein-like conformation enriched in beta-structure that is in good agreement with available experimental data and provides a non-branching aggregate with a 3(1) axis of symmetry that was derived from realistic simulation of the conversion process.
The molecular basis for the chemical denaturation of proteins by urea
  • B. Bennion, V. Daggett
  • Biology, Chemistry
    Proceedings of the National Academy of Sciences…
  • 17 April 2003
TLDR
These simulations suggest that urea denatures proteins via both direct and indirect mechanisms, and that through urea's weakening of water structure, water became free to compete with intraprotein interactions.
Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine–lysine distances
TLDR
The Dynameomics database is used, a repository of high‐quality molecular dynamics simulations of 807 proteins representative of diverse protein folds, to investigate the relationship between lysine–lysine distances in experimental starting structures and in simulation ensembles and concludes that for DSS/BS3, a distance constraint of 26–30 Å between Cα atoms is appropriate.
The complete folding pathway of a protein from nanoseconds to microseconds
TLDR
Molecular dynamics simulations give rate constants and structural details highly consistent with experiment, thereby completing the description of folding at atomic resolution.
Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution
The objective of this work is to obtain a water model for simulations of biological macromolecules in solution. A pragmatic approach is taken in which we use the same type of force field for the
Mapping the early steps in the pH-induced conformational conversion of the prion protein
TLDR
To investigate the effect of acidic pH on PrP conformation, 10-ns molecular dynamics simulations of PrPC in water at neutral and low pH show that the core of the protein is well maintained at neutral pH, but at low pH theprotein is more dynamic, and the sheet-like structure increases.
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