Zhang Liqun, Polyansky Anton, Buck Matthias
Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio, 44106, United States of America.
Max F. Perutz Laboratories, Department of Structural and Computational Biology, University of Vienna, Campus Vienna Biocenter 5, Vienna, AT-1030, Austria; M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
PLoS One. 2015 Apr 2;10(4):e0121513. doi: 10.1371/journal.pone.0121513. eCollection 2015.
Single-pass transmembrane (TM) receptors transmit signals across lipid bilayers by helix association or by configurational changes within preformed dimers. The structure determination for such TM regions is challenging and has mostly been accomplished by NMR spectroscopy. Recently, the computational prediction of TM dimer structures is becoming recognized for providing models, including alternate conformational states, which are important for receptor regulation. Here we pursued a strategy to predict helix oligomers that is based on packing considerations (using the PREDDIMER webserver) and is followed by a refinement of structures, utilizing microsecond all-atom molecular dynamics simulations. We applied this method to plexin TM receptors, a family of 9 human proteins, involved in the regulation of cell guidance and motility. The predicted models show that, overall, the preferences identified by PREDDIMER are preserved in the unrestrained simulations and that TM structures are likely to be diverse across the plexin family. Plexin-B1 and -B3 TM helices are regular and tend to associate, whereas plexin-A1, -A2, -A3, -A4, -C1 and -D1 contain sequence elements, such as poly-Glycine or aromatic residues that distort helix conformation and association. Plexin-B2 does not form stable dimers due to the presence of TM prolines. No experimental structural information on the TM region is available for these proteins, except for plexin-C1 dimeric and plexin-B1 - trimeric structures inferred from X-ray crystal structures of the intracellular regions. Plexin-B1 TM trimers utilize Ser and Thr sidechains for interhelical contacts. We also modeled the juxta-membrane (JM) region of plexin-C1 and plexin-B1 and show that it synergizes with the TM structures. The structure and dynamics of the JM region and TM-JM junction provide determinants for the distance and distribution of the intracellular domains, and for their binding partners relative to the membrane. The structures suggest experimental tests and will be useful for the interpretation of future studies.
单次跨膜（TM）受体通过螺旋缔合或预制二聚体内的构象变化在脂质双层中传递信号。此类TM区域的结构测定具有挑战性，大多通过核磁共振光谱法完成。最近，TM二聚体结构的计算预测因能提供包括交替构象状态在内的模型而受到认可，这些模型对受体调节很重要。在此，我们采用了一种基于堆积考虑（使用PREDDIMER网络服务器）来预测螺旋寡聚体的策略，随后利用微秒级全原子分子动力学模拟对结构进行优化。我们将此方法应用于丛状蛋白TM受体，这是一个由9种人类蛋白质组成的家族，参与细胞导向和运动的调节。预测模型表明，总体而言，PREDDIMER确定的偏好性在无约束模拟中得以保留，并且TM结构在丛状蛋白家族中可能各不相同。丛状蛋白-B1和-B3的TM螺旋规则且倾向于缔合，而丛状蛋白-A1、-A2、-A3、-A4、-C1和-D1含有诸如多聚甘氨酸或芳香族残基等序列元件，这些元件会扭曲螺旋构象和缔合。由于存在TM脯氨酸，丛状蛋白-B2不会形成稳定的二聚体。除了从细胞内区域的X射线晶体结构推断出的丛状蛋白-C1二聚体和丛状蛋白-B1三聚体结构外，这些蛋白质的TM区域没有可用的实验结构信息。丛状蛋白-B1的TM三聚体利用丝氨酸和苏氨酸侧链进行螺旋间接触。我们还对丛状蛋白-C1和丛状蛋白-B1的近膜（JM）区域进行了建模，结果表明它与TM结构协同作用。JM区域以及TM-JM连接的结构和动力学为细胞内结构域的距离和分布以及它们相对于膜的结合伴侣提供了决定因素。这些结构为实验测试提供了建议，将有助于解释未来的研究。
