Jensen Morten Ø, Jensen Torben R, Kjaer Kristian, Bjørnholm Thomas, Mouritsen Ole G, Peters Günther H
Center for Biomembrane Physics (MEMPHYS), Department of Chemistry, Technical University of Denmark, DK-2800 Lyngby, Denmark.
Biophys J. 2002 Jul;83(1):98-111. doi: 10.1016/S0006-3495(02)75152-7.
Electron density profiles calculated from molecular dynamics trajectories are used to deduce the orientation and conformation of Thermomyces lanuginosa lipase and a mutant adsorbed at an air-water interface. It is demonstrated that the profiles display distinct fine structures, which uniquely characterize enzyme orientation and conformation. The density profiles are, on the nanosecond timescale, determined by the average enzyme conformation. We outline a computational scheme that from a single molecular dynamics trajectory allows for extraction of electron density profiles referring to different orientations of the lipase relative to an implicit interface. Profiles calculated for the inactive and active conformations of the lipase are compared with experimental electron density profiles measured by x-ray reflectivity for the lipase adsorbed at an air-water interface. The experimental profiles contain less fine structural information than the calculated profiles because the resolution of the experiment is limited by the intrinsic surface roughness of water. Least squares fits of the calculated profiles to the experimental profiles provide areas per adsorbed enzyme and suggest that Thermomyces lanuginosa lipase adsorbs to the air-water interface in a semiopen conformation with the lid oriented away from the interface.
从分子动力学轨迹计算得到的电子密度分布用于推断嗜热栖热菌脂肪酶及其吸附在气-水界面的突变体的取向和构象。结果表明，这些分布呈现出独特的精细结构，这些结构独特地表征了酶的取向和构象。在纳秒时间尺度上，密度分布由平均酶构象决定。我们概述了一种计算方案，该方案从单个分子动力学轨迹出发，能够提取与脂肪酶相对于隐式界面的不同取向相关的电子密度分布。将脂肪酶的无活性和活性构象计算得到的分布与通过X射线反射率测量的吸附在气-水界面的脂肪酶的实验电子密度分布进行比较。由于实验分辨率受水的固有表面粗糙度限制，实验分布包含的精细结构信息比计算分布少。将计算分布与实验分布进行最小二乘拟合，得到每个吸附酶的面积，并表明嗜热栖热菌脂肪酶以半开放构象吸附在气-水界面，盖子远离界面。
