Summary Page
Folding@home project descriptions | ||||||||||||||||
| Project 10511 | ||||||||||||||||
Projects 10510-10516 consists of GPU simulations of the full-length NTL9 (56 residues) protein, with slightly different sequences (mutants), all starting from the native state. We are using these simulations to try and predict the effect of mutations on folding stability, folding rates, unfolded-state structure, and folding pathways.
Each project simulates the following sequence variants:
This work builds off of work recently published in JACS (Voelz et al.), showing that, for first time, we can simulate a protein that folds on the millisecond time scale. This was done for NTL9(1-39), a 39-residue truncation muatnt of NTL9. Since most of the experimental data for NTL9 is published for the full-length protein, we wanted to see if we could use the simulation data from the truncated sequence to "seed" simulations of the full length protein (56 residues) to achieve better sampling.  To do this, we used the Markov State Model (MSM) that was constructed in Voelz et al., describing the dynamics of protein folding in terms of transitions between metastable stables. Conformations from each of the 2000 macrostates of the MSM were used as templates on which we threaded the C-terminal sequence. This is an exciting use of MSMs as a multi-scale method for simulation that uses adaptive seeding, and later, adaptive sampling for a very thorough sampling of conformational space. If this approach works well, we hope to use it for even more slow-folding proteins. Points and deadlines: project 10510: 587 points, timeout 8 days, deadline 12 days project 10511: 587 points, timeout 8 days, deadline 12 days project 10512: 587 points, timeout 8 days, deadline 12 days project 10513: 587 points, timeout 8 days, deadline 12 days project 10514: 587 points, timeout 8 days, deadline 12 days project 10515: 587 points, timeout 8 days, deadline 12 days project 10516: 587 points, timeout 8 days, deadline 12 days (Note that these projects are identical to projects 10501-10504)
| ||||||||||||||||