Producción CyT
Sociedad de Bioquímica y Biología Molecular de Chile - Effects of knots in protein degradation by ATP-dependent proteases using GFPMJ0366 fusion protein constructs
Congreso
Fecha:
2023Editorial y Lugar de Edición:
Sociedad de Bioquímica y Biología Molecular de ChileResumen *
ATP-dependent proteases translocate proteins through a narrow pore for their con- trolleddegradation. However, how a protein containing a knotted topology affects this processremains unknown at a molecular level. Our experimental data suggest that a substrate-fusedshallow 31 knot (GFP-MJ0366 construct) could impair protein translocation at standardprote- olysis mediated by archetypal AAA+ ClpXP protease. The degradation could lead tothe release of partially processed products that may be harmful for the cell or possess newbiological ac- tivities. This knot gives some kind of protective degree that may be related tothe length of the fusion linker (San Martín A et al., 2017). In this work we implemented a Cαcoarse-grained pro- tein simulations to account for the above translocation process based onan open source project named OpenMM, coded in pure Python in a Jupyter Notebook. Inaddition to the simulation algorithm, we developed two extra modules: an implicit pore tostudy the protein translocation and a constant-force pulling potentials to make the protein gothrough the pore. We simulated GFP-MJ0366 fusion proteins with different linkers sizesranging from 17 to 117 amino acids. Early results would confirm the experimental behavior,where linkers of more than 36 residues between the MJ0366´s knot core and GFP would allowthe complete unfolding and degradation of the substrate. Nevertheless, it is still necessary toanalyze the effect of all linker sizes, in- crease the number of replicas and better tune the porepotential in the dynamics. Información suministrada por el agente en SIGEVAPalabras Clave
degradationknotssimulationatp