Now showing items 1-6 of 6

    • Altered Backbone and Side-Chain Interactions Result in Route Heterogeneity during the Folding of Interleukin-1b (IL-1b) 

      Capraro, Dominique T.; Lammert, Heiko; Heidary, David K.; Roy, Melinda; Gross, Larry A.; Onuchic, José N.; Jennings, Patricia A. (2013-08)
      Deletion of the b-bulge trigger-loop results in both a switch in the preferred folding route, from the functional loop packing folding route to barrel closure, as well as conversion of the agonist activity of IL-1b into ...
    • Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures 

      Lammert, Heiko; Noel, Jeffrey K.; Haglund, Ellinor; Schug, Alexander; Onuchic, José N. (2015)
      The diversity in a set of protein nuclear magnetic resonance (NMR) structures provides an estimate of native state fluctuations that can be used to refine and enrich structure-based protein models (SBMs). Dynamics are an ...
    • The Dominant Folding Route Minimizes Backbone Distortion in SH3 

      Lammert, Heiko; Noel, Jeffrey K.; Onuchic, Jose´ N. (2012)
      Energetic frustration in protein folding is minimized by evolution to create a smooth and robust energy landscape. As a result the geometry of the native structure provides key constraints that shape protein folding ...
    • A magnesium-induced triplex pre-organizes the SAM-II riboswitch 

      Roy, Susmita; Lammert, Heiko; Hayes, Ryan L.; Chen, Bin; LeBlanc, Regan; Dayie, T. Kwaku; Onuchic, José N.; Sanbonmatsu, Karissa Y. (2017)
      Our 13C- and 1H-chemical exchange saturation transfer (CEST) experiments previously revealed a dynamic exchange between partially closed and open conformations of the SAM-II riboswitch in the absence of ligand. Here, ...
    • Pierced Lasso Bundles Are a New Class of Knot-like Motifs 

      Haglund, Ellinor; Sulkowska, Joanna I.; Noel, Jeffrey K.; Lammert, Heiko; Onuchic, José N.; Jennings, Patricia A. (2014)
      A four-helix bundle is a well-characterized motif often used as a target for designed pharmaceutical therapeutics and nutritional supplements. Recently, we discovered a new structural complexity within this motif created ...
    • SMOG 2: A Versatile Software Package for Generating Structure-Based Models 

      Noel, Jeffrey K.; Levi, Mariana; Raghunathan, Mohit; Lammert, Heiko; Hayes, Ryan L.; Onuchic, José N.; Whitford, Paul C. (2016)
      Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. ...