Wojciechowski Michał, Gómez-Sicilia Àngel, Carrión-Vázquez Mariano, Cieplak Marek
Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668 Warsaw, Poland.
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.
Mol Biosyst. 2016 Aug 16;12(9):2700-12. doi: 10.1039/c6mb00214e.
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.
蛋白质中的结被认为可以抵抗蛋白酶体降解。大量证据将蛋白酶体降解与神经退行性变联系起来。一种有趣的可能性是，确实打结的构象会使这种机制停滞，从而导致毒性。然而，尽管已知蛋白酶体通过机械方式展开其底物，但目前尚无实验方法来模拟这种特定的牵引几何形状。在这里，我们考虑了几种蛋白酶体的动力学模型，其中复合物由具有附加拉力的有效势表示。该力旨在诱导蛋白质或多肽进入催化腔。该力要么是恒定的，要么是周期性施加的。易位的蛋白质以粗粒度方式建模。我们对几种打结的球状蛋白质以及单独的长度为60的瞬时打结的聚谷氨酰胺片段进行了比较分析，这些片段融合在亨廷顿蛋白的外显子1中。亨廷顿蛋白与亨廷顿舞蹈病有关，这是一种著名的由基因决定的神经退行性疾病。我们表明，结的存在会阻碍甚至有时会阻止易位。我们证明这样做的概率取决于蛋白质、蛋白酶体模型、拉力大小以及被拉动末端的选择。在任何情况下，净效应都会是细胞中蛋白酶体降解过程的阻碍。这将通过两种不同机制产生毒性：一种是通过有毒单体损害降解，另一种是通过形成有毒寡聚体。我们的工作为蛋白酶体对打结结构的机械展开及其与毒性和疾病的关系的机制研究铺平了道路。
