Stokeley Daniel, Bemporad Daniele, Gavaghan David, Sansom Mark S P
Department of Biochemistry, University of Oxford, UK.
Biochemistry. 2007 Nov 27;46(47):13573-80. doi: 10.1021/bi701320a. Epub 2007 Nov 6.
Saposin B is a water soluble alpha-helical protein which can bind to membranes and extract selected lipids, especially cerebroside sulfates. The X-ray structure of saposin B is homodimeric. There are two conformations of the dimer in the crystal-one with a closed central cavity (the AB dimer) and one (the CD dimer) with a more open cavity. We have conducted a series of short (5 ns) molecular dynamics simulations of saposin B, starting from both the AB and CD conformations and with/without bound lipid and/or water molecules within the central hydrophobic cavity. The more open (CD) dimer showed greater conformational drift than the AB dimer. The conformational drift was also somewhat higher in the absence of bound lipid. Two more extended (30 ns) simulations of AB and CD dimers were performed and analyzed in terms of changes in intersubunit packing within the dimers. The AB dimer remained largely unchanged in conformation over the duration of the extended simulation. In contrast, the CD dimer underwent a substantial conformational change corresponding to a 'scissor' motion of the two monomers so as to compress the central cavity to a more closed conformation than that seen in the AB dimer structure. A H-bond between the Q53 and Y54 side chains of the alpha3 helices of the two opposing monomers seems to hold the dimer in this 'scissor-closed' conformation. We suggest that a cycle of conformational changes, expanding and compressing the central cavity of the saposin B dimer, may play a key role in facilitating lipid extraction from bilayers.
鞘脂激活蛋白B是一种水溶性α-螺旋蛋白，它能够结合到细胞膜上并提取特定的脂质，尤其是脑硫脂。鞘脂激活蛋白B的X射线结构为同型二聚体。在晶体中有二聚体的两种构象——一种具有封闭的中央腔（AB二聚体），另一种（CD二聚体）具有更开放的腔。我们对鞘脂激活蛋白B进行了一系列短时间（5纳秒）的分子动力学模拟，从AB和CD两种构象开始，且中央疏水腔内有/无结合的脂质和/或水分子。更开放的（CD）二聚体比AB二聚体表现出更大的构象漂移。在没有结合脂质的情况下，构象漂移也略高一些。我们又对AB和CD二聚体进行了两次更长时间（30纳秒）的模拟，并根据二聚体内亚基间堆积的变化进行了分析。在长时间模拟过程中，AB二聚体的构象基本保持不变。相比之下，CD二聚体经历了显著的构象变化，对应于两个单体的“剪刀式”运动，从而将中央腔压缩到比AB二聚体结构中更封闭的构象。两个相对单体的α3螺旋的Q53和Y54侧链之间的氢键似乎使二聚体保持在这种“剪刀式闭合”构象。我们认为，鞘脂激活蛋白B二聚体中央腔的扩张和压缩的构象变化循环可能在促进从双层膜中提取脂质方面起关键作用。
