Glyakina Anna V, Likhachev Ilya V, Balabaev Nikolay K, Galzitskaya Oxana V
Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
Proteins. 2014 Jan;82(1):90-102. doi: 10.1002/prot.24373. Epub 2013 Sep 10.
Here, we study mechanical properties of eight 3-helix proteins (four right-handed and four left-handed ones), which are similar in size under stretching at a constant speed and at a constant force on the atomic level using molecular dynamics simulations. The analysis of 256 trajectories from molecular dynamics simulations with explicit water showed that the right-handed three-helix domains are more mechanically resistant than the left-handed domains. Such results are observed at different extension velocities studied (192 trajectories obtained at the following conditions: v = 0.1, 0.05, and 0.01 Å ps(-1) , T = 300 K) and under constant stretching force (64 trajectories, F = 800 pN, T = 300 K). We can explain this by the fact, at least in part, that the right-handed domains have a larger number of contacts per residue and the radius of cross section than the left-handed domains.
在此，我们使用分子动力学模拟，在原子水平上以恒定速度和恒定力拉伸的情况下，研究了八种三螺旋蛋白质（四种右手螺旋和四种左手螺旋）的力学性质，这些蛋白质在大小上相似。对含有明确水分子的分子动力学模拟得到的256条轨迹进行分析表明，右手三螺旋结构域比左手结构域具有更强的机械抗性。在研究的不同延伸速度下（在以下条件下获得192条轨迹：v = 0.1、0.05和0.01 Å ps(-1)，T = 300 K）以及在恒定拉伸力下（64条轨迹，F = 800 pN，T = 300 K）均观察到了这样的结果。我们至少可以部分地通过以下事实来解释这一点：右手结构域每个残基的接触数和横截面半径比左手结构域更大。
