@article{Coarse-Grained:2274,
      recid = {2274},
      author = {Jarin, Zachary},
      title = {Coarse-Grained Approaches to Membrane Remodeling and I-BAR  Domain Self-Assembly},
      publisher = {University of Chicago},
      school = {Ph.D.},
      address = {2020-06},
      pages = {110},
      abstract = {I-BAR proteins are located at the plasma membrane to sense  and generate local membrane curvature. Prior to inducing  membrane shape changes larger than a single protein, I-BAR  domains are believed to aggregate and assemble. To discern  how I-BAR domains organize and collectively stabilize  membrane deformation, I developed two distinct  coarse-grained membrane-protein models: one is a bottom-up  model parameterized from all-atom simulations to capture  low bound protein density behavior of the I-BAR domain of  IRSp53 and the other is a tunable, lower resolution model  used to assess the effects of various characteristics of  the I-BAR family (e.g., intrinsic protein curvature). The  separate approaches highlight the strengths of various  coarse-graining approaches while providing key insights  into I-BAR domain assembly. Together, I elucidate the role  of attractive membrane-mediated forces in I-BAR domain  assembly and the interplay between protein and membrane  curvatures.

After using both bottom-up and top-down  methodologies to understand I-BAR domain self-assembly, I  assess how coarse-grained representation affects the  estimation of the membrane bending modulus and the  temperature-dependence in the popular top-down model,  MARTINI. Issues of transferability and representability  have been identified in the bottom-up coarse-grained  models, but a computational demonstration of these effects  in top-down coarse-grained models does not exist. I use  MARTINI as a test case to understand how the coarse-grained  representation affects cholesterol and amphipathic helix  association in bilayers. The correctness of MARTINI in  capturing these various effects is of growing interest as  coarse-grained simulations are applied outside of  parametrization data.},
      url = {http://knowledge.uchicago.edu/record/2274},
      doi = {https://doi.org/10.6082/uchicago.2274},
}