Forrest L R, Tieleman D P, Sansom M S
Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, England.
Biophys J. 1999 Apr;76(4):1886-96. doi: 10.1016/s0006-3495(99)77347-9.
Integral membrane proteins containing at least one transmembrane (TM) alpha-helix are believed to account for between 20% and 30% of most genomes. There are several algorithms that accurately predict the number and position of TM helices within a membrane protein sequence. However, these methods tend to disagree over the beginning and end residues of TM helices, posing problems for subsequent modeling and simulation studies. Molecular dynamics (MD) simulations in an explicit lipid and water environment are used to help define the TM helix of the M2 protein from influenza A virus. Based on a comparison of the results of five different secondary structure prediction algorithms, three different helix lengths (an 18mer, a 26mer, and a 34mer) were simulated. Each simulation system contained 127 POPC molecules plus approximately 3500-4700 waters, giving a total of approximately 18,000-21,000 atoms. Two simulations, each of 2 ns duration, were run for the 18mer and 26mer, and five separate simulations were run for the 34mer, using different starting models generated by restrained in vacuo MD simulations. The total simulation time amounted to 11 ns. Analysis of the time-dependent secondary structure of the TM segments was used to define the regions that adopted a stable alpha-helical conformation throughout the simulation. This analysis indicates a core TM region of approximately 20 residues (from residue 22 to residue 43) that remained in an alpha-helical conformation. Analysis of atomic density profiles suggested that the 18mer helix revealed a local perturbation of the lipid bilayer. Polar side chains on either side of this region form relatively long-lived H-bonds to lipid headgroups and water molecules.
含有至少一个跨膜（TM）α-螺旋的整合膜蛋白据信占大多数基因组的20%至30%。有几种算法可以准确预测膜蛋白序列中TM螺旋的数量和位置。然而，这些方法在TM螺旋的起始和终止残基上往往存在分歧，给后续的建模和模拟研究带来了问题。在明确的脂质和水环境中进行分子动力学（MD）模拟，以帮助确定甲型流感病毒M2蛋白的TM螺旋。基于对五种不同二级结构预测算法结果的比较，模拟了三种不同的螺旋长度（18聚体、26聚体和34聚体）。每个模拟系统包含127个POPC分子以及大约3500 - 4700个水分子，总共约18000 - 21000个原子。对18聚体和26聚体进行了两个时长为2 ns的模拟，对34聚体进行了五个独立的模拟，使用由真空中受限MD模拟生成的不同起始模型。总模拟时间达11 ns。对TM片段随时间变化的二级结构进行分析，以确定在整个模拟过程中采用稳定α-螺旋构象的区域。该分析表明，大约20个残基（从第22位残基到第43位残基）的核心TM区域保持α-螺旋构象。原子密度分布分析表明，18聚体螺旋揭示了脂质双层的局部扰动。该区域两侧的极性侧链与脂质头部基团和水分子形成相对持久的氢键。
