Haglund Ellinor, Sulkowska Joanna I, Noel Jeffrey K, Lammert Heiko, Onuchic José N, Jennings Patricia A
Center for Theoretical Biological Physics (CTBP) and Department of Physics, University of California at San Diego (UCSD), La Jolla, California, United States of America; Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America.
Laboratory of Theory of Biopolymers, University of Warsaw, Warsaw, Poland.
PLoS Comput Biol. 2014 Jun 19;10(6):e1003613. doi: 10.1371/journal.pcbi.1003613. eCollection 2014 Jun.
A four-helix bundle is a well-characterized motif often used as a target for designed pharmaceutical therapeutics and nutritional supplements. Recently, we discovered a new structural complexity within this motif created by a disulphide bridge in the long-chain helical bundle cytokine leptin. When oxidized, leptin contains a disulphide bridge creating a covalent-loop through which part of the polypeptide chain is threaded (as seen in knotted proteins). We explored whether other proteins contain a similar intriguing knot-like structure as in leptin and discovered 11 structurally homologous proteins in the PDB. We call this new helical family class the Pierced Lasso Bundle (PLB) and the knot-like threaded structural motif a Pierced Lasso (PL). In the current study, we use structure-based simulation to investigate the threading/folding mechanisms for all the PLBs along with three unthreaded homologs as the covalent loop (or lasso) in leptin is important in folding dynamics and activity. We find that the presence of a small covalent loop leads to a mechanism where structural elements slipknot to thread through the covalent loop. Larger loops use a piercing mechanism where the free terminal plugs through the covalent loop. Remarkably, the position of the loop as well as its size influences the native state dynamics, which can impact receptor binding and biological activity. This previously unrecognized complexity of knot-like proteins within the helical bundle family comprises a completely new class within the knot family, and the hidden complexity we unraveled in the PLBs is expected to be found in other protein structures outside the four-helix bundles. The insights gained here provide critical new elements for future investigation of this emerging class of proteins, where function and the energetic landscape can be controlled by hidden topology, and should be take into account in ab initio predictions of newly identified protein targets.
四螺旋束是一种特征明确的基序，常被用作设计药物治疗剂和营养补充剂的靶点。最近，我们在长链螺旋束细胞因子瘦素中发现了由二硫键产生的该基序内的一种新结构复杂性。氧化时，瘦素含有一个二硫键，形成一个共价环，部分多肽链穿过该环（如在纽结蛋白中所见）。我们探究了其他蛋白质是否含有与瘦素中类似的有趣的纽结样结构，并在蛋白质数据银行（PDB）中发现了11种结构同源的蛋白质。我们将这个新的螺旋家族类别称为穿孔套索束（PLB），将纽结样穿线结构基序称为穿孔套索（PL）。在当前研究中，我们使用基于结构的模拟来研究所有PLB的穿线/折叠机制，同时以三个未穿线的同源物作为对照，因为瘦素中的共价环（或套索）在折叠动力学和活性中很重要。我们发现，小共价环的存在导致一种机制，即结构元件通过滑结穿过共价环。较大的环则使用一种穿孔机制，即自由末端穿过共价环。值得注意的是，环的位置及其大小会影响天然态动力学，这可能会影响受体结合和生物活性。螺旋束家族中这种以前未被认识到的纽结样蛋白质的复杂性在纽结家族中构成了一个全新的类别，我们在PLB中揭示的隐藏复杂性预计也会在四螺旋束之外的其他蛋白质结构中发现。这里获得的见解为未来对这类新兴蛋白质的研究提供了关键的新元素，在这类蛋白质中，功能和能量景观可以由隐藏的拓扑结构控制，并且在新鉴定的蛋白质靶点的从头预测中应该予以考虑。
