Centro de Física da Matéria Condensada, Universidade de Lisboa, Lisboa, Portugal ; Departamento de Física, Universidade de Lisboa, Lisboa, Portugal.
PLoS One. 2013 Sep 4;8(9):e74755. doi: 10.1371/journal.pone.0074755. eCollection 2013.
This work explores the impact of knots, knot depth and motif of the threading terminus in protein folding properties (kinetics, thermodynamics and mechanism) via extensive Monte Carlo simulations of lattice models. A knotted backbone has no effect on protein thermodynamic stability but it may affect key aspects of folding kinetics. In this regard, we found clear evidence for a functional advantage of knots: knots enhance kinetic stability because a knotted protein unfolds at a distinctively slower rate than its unknotted counterpart. However, an increase in knot deepness does not necessarily lead to more effective changes in folding properties. In this regard, a terminus with a non-trivial conformation (e.g. hairpin) can have a more dramatic effect in enhancing kinetic stability than knot depth. Nevertheless, our results suggest that the probability of the denatured ensemble to keep knotted is higher for proteins with deeper knots, indicating that knot depth plays a role in determining the topology of the denatured state. Refolding simulations starting from denatured knotted conformations show that not every knot is able to nucleate folding and further indicate that the formation of the knotting loop is a key event in the folding of knotted trefoils. They also show that there are specific native contacts within the knotted core that are crucial to keep a native knotting loop in denatured conformations which otherwise have no detectable structure. The study of the knotting mechanism reveals that the threading of the knotting loop generally occurs towards late folding in conformations that exhibit a significant degree of structural consolidation.
这项工作通过对格子模型的广泛蒙特卡罗模拟，探索了蛋白质折叠性质（动力学、热力学和机制）中结、结深度和穿线末端图案的影响。打结的骨架对蛋白质热力学稳定性没有影响，但它可能会影响折叠动力学的关键方面。在这方面，我们发现了结的功能优势的明确证据：结增强了动力学稳定性，因为打结的蛋白质比未打结的蛋白质以明显更慢的速度展开。然而，结深度的增加不一定会导致折叠性质的更有效变化。在这方面，具有非平凡构象（例如发夹）的末端可以比结深度更显著地增强动力学稳定性。然而，我们的结果表明，对于具有更深结的蛋白质，变性集合体保持打结的概率更高，这表明结深度在确定变性状态的拓扑结构方面起着作用。从变性打结构象开始的重折叠模拟表明，并非每个结都能够引发折叠，进一步表明结环的形成是打结三叶形折叠的关键事件。它们还表明，在变性构象中，有特定的天然接触对于保持天然结环至关重要，否则这些构象没有可检测到的结构。结形成机制的研究表明，结环的穿线通常发生在具有显著结构整合度的折叠的后期。
