A novel, non-statistical method for predicting breaks in transmembrane helices.
A novel, non-statistical method for predicting breaks in transmembrane helices.
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一种预测跨膜螺旋断裂的新颖的非统计方法。
DOI：
10.1093/protein/11.4.279
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发表时间：
1998
期刊：
影响因子：
--
通讯作者：
Nikiforovich,GV
中科院分区：
文献类型：
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作者：
Nikiforovich,GV
我们开发了一种新的、非统计的程序，用于基于能量计算来预测跨膜螺旋可能的断裂。该程序包括由几个可用的预测程序的一致结果确定的“核心”螺旋片段的逐步延长。在每一步中，我们计算了由两个侧翼残基E(α)拉长的“核心”片段的规则“冻结”螺旋构象对应的构象能，以及通过改变侧翼残基的构象Ei使片段进入或离开螺旋的几个选项的构象能。Ei-E(α)，β(K)的最小值可以看作是相对能量的分布，其中，每个最小值的β(K)都是启动或停止跨膜螺旋的信号。我们认为，跨膜螺旋的边界将由Delta(K)剖面中最接近核心序列的信号决定。我们的程序被应用于绿色红假单胞菌光合作用反应中心的45个跨膜螺旋、细菌视紫质和脱氮副球藻细胞色素C氧化酶的N-末端和C-末端的预测。结果清楚地表明，我们的方法比三种不同的统计方法获得+/-2残基误差范围内的预测精度的可能性要大得多。
We have developed a novel, non-statistical procedure for predicting possible breaks in transmembrane helices based on energy calculations. The procedure consists of stepwise elongation of the 'core' helical fragment determined by consensus results of several available prediction procedures. At each step, we calculate the conformational energies corresponding to the regular 'frozen' helical conformer of the 'core' fragment elongated by two flanking residues, E(alpha), as well as those to several options for the fragment to enter or exit the helix by changing conformations of the flanking residues, Ei. The minimal values out of Ei - E(alpha), delta(k), can be viewed as a profile of relative energies, where each minimum of delta(k) is a signal to start or to stop transmembrane helix. We suggest that boundaries of the transmembrane helix would be determined by the signals closest to the 'core' sequence in the delta(k) profiles. Our procedure was applied to prediction of the N- and C-termini for 45 transmembrane helices from the photosynthetic reaction center from Rhodopseudomonas viridis, bacteriorhodopsin and the cytochrome c oxidase from Paracoccus denitrificans. The results clearly showed that it is significantly more probable that a prediction accuracy within an error of +/- 2 residues will be obtained by our procedure than by three different statistical approaches.