title: Unfolding knots by proteasome-like systems: simulations of the behaviour of folded and neurotoxic proteins.
abstract: Knots in proteins have been proposed to resist proteasomal degradation. Ample evidence associates proteasomal degradation with neurodegeneration. One interesting possibility is that indeed knotted conformers stall this machinery leading to toxicity. However, although the proteasome is known to unfold mechanically its substrates, at present there are no experimental methods to emulate this particular traction geometry. Here, we consider several dynamical models of the proteasome in which the complex is represented by an effective potential with an added pulling force. This force is meant to induce the translocation of a protein or a polypeptide into the catalytic chamber. The force is either constant or applied periodically. The translocated proteins are modelled in a coarse-grained fashion. We do comparative analysis of several knotted globular proteins and the transiently knotted polyglutamine tracts of length 60 alone and fused in exon 1 of the huntingtin protein. Huntingtin is associated with Huntington's disease, a well-known genetically determined neurodegenerative disease. We show that the presence of a knot hinders and sometimes even jams translocation. We demonstrate that the probability to do so depends on the protein, the model of the proteasome, the magnitude of the pulling force, and the choice of the pulled terminus. In any case, the net effect would be a hindrance in the proteasomal degradation process in the cell. This would then yield toxicity via two different mechanisms: one through toxic monomers compromising degradation and another by the formation of toxic oligomers. Our work paves the way for the mechanistic investigation of the mechanical unfolding of knotted structures by the proteasome and its relation to toxicity and disease.
authors.affiliation: Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668 Warsaw, Poland. mc@ifpan.edu.pl.
authors.forename: Michał
authors.initials: M
authors.lastname: Wojciechowski
authors.affiliation: Instituto Cajal, Consejo Superior de Investigaciones Científicas, (CSIC), Av. Doctor Arce, 37, 28002 Madrid, Spain and Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), C/ Faraday 9, 28049 Cantoblanco, Madrid, Spain.
authors.forename: Àngel
authors.initials: À
authors.lastname: Gómez-Sicilia
authors.affiliation: Instituto Cajal, Consejo Superior de Investigaciones Científicas, (CSIC), Av. Doctor Arce, 37, 28002 Madrid, Spain and Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), C/ Faraday 9, 28049 Cantoblanco, Madrid, Spain.
authors.forename: Mariano
authors.initials: M
authors.lastname: Carrión-Vázquez
authors.affiliation: Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668 Warsaw, Poland. mc@ifpan.edu.pl.
authors.forename: Marek
authors.initials: M
authors.lastname: Cieplak
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008958:Models, Molecular; D009498:Neurotoxins / Q000737:chemistry / Q000378:metabolism; D046988:Proteasome Endopeptidase Complex / Q000737:chemistry* / Q000378:metabolism*; D011487:Protein Conformation; D017510:Protein Folding; D055550:Protein Stability; D021381:Protein Transport; D058767:Protein Unfolding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D009498:Neurotoxins; D011506:Proteins; D046988:Proteasome Endopeptidase Complex