@article{18934,
  abstract     = {The assembly of biomolecular condensate in eukaryotic cells and the accumulation of amyloid deposits in neurons are processes involving the nucleation and growth (NAG) of new protein phases. To therapeutically target protein phase separation, drug candidates are tested in in vitro assays that monitor the increase in the mass or size of the new phase. Limited mechanistic insight is, however, provided if empirical or untestable kinetic models are fitted to these progress curves. Here we present the web server NAGPKin that quantifies NAG rates using mass-based or size-based progress curves as the input data. A report is generated containing the fitted NAG parameters and elucidating the phase separation mechanisms at play. The NAG parameters can be used to predict particle size distributions of, for example, protein droplets formed by liquid-liquid phase separation (LLPS) or amyloid fibrils formed by protein aggregation. Because minimal intervention is required from the user, NAGPKin is a good platform for standardized reporting of LLPS and protein self-assembly data. NAGPKin is useful for drug discovery as well as for fundamental studies on protein phase separation. NAGPKin is freely available (no login required) at https://nagpkin.i3s.up.pt .},
  author       = {Sárkány, Zsuzsa and Figueiredo, Francisco and Macedo-Ribeiro, Sandra and Martins, Pedro M.},
  issn         = {1939-4586},
  journal      = {Molecular Biology of the Cell},
  number       = {3},
  publisher    = {American Society for Cell Biology},
  title        = {{NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation}},
  doi          = {10.1091/mbc.e23-07-0289},
  volume       = {35},
  year         = {2024},
}

@article{9414,
  abstract     = {Microtubule plus-end depolymerization rate is a potentially important target of physiological regulation, but it has been challenging to measure, so its role in spatial organization is poorly understood. Here we apply a method for tracking plus ends based on time difference imaging to measure depolymerization rates in large interphase asters growing in Xenopus egg extract. We observed strong spatial regulation of depolymerization rates, which were higher in the aster interior compared with the periphery, and much less regulation of polymerization or catastrophe rates. We interpret these data in terms of a limiting component model, where aster growth results in lower levels of soluble tubulin and microtubule-associated proteins (MAPs) in the interior cytosol compared with that at the periphery. The steady-state polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the aster interior. We propose that the limiting component for microtubule assembly is a MAP that inhibits depolymerization, and that egg asters are tuned to low microtubule density.},
  author       = {Ishihara, Keisuke and Decker, Franziska and Dos Santos Caldas, Paulo R and Pelletier, James F. and Loose, Martin and Brugués, Jan and Mitchison, Timothy J.},
  issn         = {1939-4586},
  journal      = {Molecular Biology of the Cell},
  number       = {9},
  pages        = {869--879},
  publisher    = {American Society for Cell Biology},
  title        = {{Spatial variation of microtubule depolymerization in large asters}},
  doi          = {10.1091/MBC.E20-11-0723},
  volume       = {32},
  year         = {2021},
}

@article{5992,
  abstract     = {Lamellipodia are flat membrane protrusions formed during mesenchymal motion. Polymerization at the leading edge assembles the actin filament network and generates protrusion force. How this force is supported by the network and how the assembly rate is shared between protrusion and network retrograde flow determines the protrusion rate. We use mathematical modeling to understand experiments changing the F-actin density in lamellipodia of B16-F1 melanoma cells by modulation of Arp2/3 complex activity or knockout of the formins FMNL2 and FMNL3. Cells respond to a reduction of density with a decrease of protrusion velocity, an increase in the ratio of force to filament number, but constant network assembly rate. The relation between protrusion force and tension gradient in the F-actin network and the density dependency of friction, elasticity, and viscosity of the network explain the experimental observations. The formins act as filament nucleators and elongators with differential rates. Modulation of their activity suggests an effect on network assembly rate. Contrary to these expectations, the effect of changes in elongator composition is much weaker than the consequences of the density change. We conclude that the force acting on the leading edge membrane is the force required to drive F-actin network retrograde flow.},
  author       = {Dolati, Setareh and Kage, Frieda and Mueller, Jan and Müsken, Mathias and Kirchner, Marieluise and Dittmar, Gunnar and Sixt, Michael K and Rottner, Klemens and Falcke, Martin},
  issn         = {1939-4586},
  journal      = {Molecular Biology of the Cell},
  number       = {22},
  pages        = {2674--2686},
  publisher    = {American Society for Cell Biology },
  title        = {{On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility}},
  doi          = {10.1091/mbc.e18-02-0082},
  volume       = {29},
  year         = {2018},
}