A simple protocol for identification of helical and mobile residues in membrane proteins.
A simple protocol for identification of helical and mobile residues in membrane proteins.
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用于识别膜蛋白中螺旋和移动残基的简单方案。
DOI：
10.1006/jmbi.1995.0561
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发表时间：
1995
期刊：
影响因子：
--
通讯作者：
Opella,SJ
中科院分区：
文献类型：
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作者：
Tobias,DJ;Gesell,J;Klein,ML;Opella,SJ
通过与实验核磁共振数据的比较。该方案包括在相对介电常数e= 2的介电连续体中对感兴趣的多肽序列进行几个独立的MD模拟。计算时间0和之后时间t时NH键矢量之间各个角度的时间历史，然后应用典型的50 ps高斯平滑。将平滑后的数据与原始数据相减，得到NH键向量的短时间波动，然后计算角度的均方根偏差，并与实验核磁共振结果进行比较。Pf1外壳蛋白和大肠杆菌F1F0 ATP合成酶的c亚基作为膜蛋白的例子。计算得到的nhh键rms波动与实验NMR数据在定性上一致，表明每一个蛋白质都有一个连接两个螺旋的移动片段，以及移动的N和c端区域。该MD模拟方案可以证明两亲和疏水螺旋的存在，而亲水性图只能检测到膜蛋白中存在的疏水螺旋。7 1995学术出版社有限公司
USA by comparisons with experimental NMR data. The protocol consists of performing several independent MD simulations on a polypeptide sequence of interest in a dielectric continuum with a relative permittivity e= 2. The time histories of the individual angles between NH bond vectors at time 0 and time t later are calculated, and then Gaussian smoothing of typically 50 ps is applied. The smoothed data are subtracted from the original data to yield the short time fluctuations of the NH bond vectors, and then the rms deviations of the angles are calculated and compared to experimental NMR results. Pf1 coat protein and the c subunit of the E. coli F1F0 ATP synthase are used as examples of membrane proteins. The calculated NH bond rms fluctuations are in qualitative agreement with experimental NMR data in showing that each of these proteins has a mobile segment connecting two helices, as well as mobile N and C-terminal regions. This MD simulations protocol can demonstrate the presence of both the amphipathic and hydrophobic helices while hydropathy plots are able to detect only the hydrophobic helices present in membrane proteins. 7 1995 Academic Press Limited