Jayasinghe S, Hristova K, White S H
Department of Physiology and Biophysics and the Program in Macromolecular Structure, University of California at Irvine, Irvine, CA 92697-4560, USA.
J Mol Biol. 2001 Oct 5;312(5):927-34. doi: 10.1006/jmbi.2001.5008.
We show that the peptide backbone of an alpha-helix places a severe thermodynamic constraint on transmembrane (TM) stability. Neglect of this constraint by commonly used hydrophobicity scales underlies the notorious uncertainty of TM helix prediction by sliding-window hydropathy plots of membrane protein (MP) amino acid sequences. We find that an experiment-based whole-residue hydropathy scale (WW scale), which includes the backbone constraint, identifies TM helices of membrane proteins with an accuracy greater than 99 %. Furthermore, it correctly predicts the minimum hydrophobicity required for stable single-helix TM insertion observed in Escherichia coli. In order to improve membrane protein topology prediction further, we introduce the augmented WW (aWW) scale, which accounts for the energetics of salt-bridge formation. An important issue for genomic analysis is the ability of the hydropathy plot method to distinguish membrane from soluble proteins. We find that the method falsely predicts 17 to 43 % of a set of soluble proteins to be MPs, depending upon the hydropathy scale used.
我们发现，α-螺旋的肽主链对跨膜（TM）稳定性施加了严格的热力学限制。常用的疏水性标度忽略了这一限制，这是通过膜蛋白（MP）氨基酸序列的滑动窗口亲水性图谱预测TM螺旋时存在众所周知的不确定性的根本原因。我们发现，基于实验的全残基亲水性标度（WW标度），其中包括主链限制，能够以大于99%的准确率识别膜蛋白的TM螺旋。此外，它还能正确预测在大肠杆菌中观察到的稳定单螺旋TM插入所需的最小疏水性。为了进一步改进膜蛋白拓扑结构预测，我们引入了增强型WW（aWW）标度，该标度考虑了盐桥形成的能量学。基因组分析的一个重要问题是亲水性图谱方法区分膜蛋白和可溶性蛋白的能力。我们发现，根据所使用的亲水性标度，该方法会错误地将17%至43%的一组可溶性蛋白预测为MP。
