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多结构域膜蛋白中跨膜螺旋方向的预测。

Prediction of transmembrane helix orientation in polytopic membrane proteins.

作者信息

Adamian Larisa, Liang Jie

机构信息

Department of Bioengineering, University of Illinois at Chicago, M/C 563, 835 S, Wolcott St, Chicago, IL 60612-7340, USA.

出版信息

BMC Struct Biol. 2006 Jun 22;6:13. doi: 10.1186/1472-6807-6-13.

DOI:10.1186/1472-6807-6-13
PMID:16792816
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1540425/
Abstract

BACKGROUND

Membrane proteins compose up to 30% of coding sequences within genomes. However, their structure determination is lagging behind compared with soluble proteins due to the experimental difficulties. Therefore, it is important to develop reliable computational methods to predict structures of membrane proteins.

RESULTS

We present a method for prediction of the TM helix orientation, which is an essential step in ab initio modeling of membrane proteins. Our method is based on a canonical model of the heptad repeat originally developed for coiled coils. We identify the helical surface patches that interface with lipid molecules at an accuracy of about 88% from the sequence information alone, using an empirical scoring function LIPS (LIPid-facing Surface), which combines lipophilicity and conservation of residues in the helix. We test and discuss results of prediction of helix-lipid interfaces on 162 transmembrane helices from 18 polytopic membrane proteins and present predicted orientations of TM helices in TRPV1 channel. We also apply our method to two structures of homologous cytochrome b6f complexes and find discrepancy in the assignment of TM helices from subunits PetG, PetN and PetL. The results of LIPS calculations and analysis of packing and H-bonding interactions support the helix assignment found in the cytochrome b6f structure from green alga but not the assignment of TM helices in the cyanobacterium b6f structure.

CONCLUSION

LIPS calculations can be used for the prediction of helix orientation in ab initio modeling of polytopic membrane proteins. We also show with the example of two cytochrome b6f structures that our method can identify questionable helix assignments in membrane proteins. The LIPS server is available online at http://gila.bioengr.uic.edu/lab/larisa/lips.html.

摘要

背景

膜蛋白在基因组编码序列中所占比例高达30%。然而，由于实验困难，与可溶性蛋白相比，其结构测定进展滞后。因此，开发可靠的计算方法来预测膜蛋白结构非常重要。

结果

我们提出了一种预测跨膜螺旋方向的方法，这是膜蛋白从头建模中的关键步骤。我们的方法基于最初为卷曲螺旋开发的七肽重复序列的规范模型。我们仅利用序列信息，使用结合了亲脂性和螺旋中残基保守性的经验评分函数LIPS（面向脂质的表面），以约88%的准确率识别与脂质分子相互作用的螺旋表面区域。我们测试并讨论了来自18种多结构域膜蛋白的162个跨膜螺旋的螺旋 - 脂质界面预测结果，并展示了TRPV1通道中跨膜螺旋的预测方向。我们还将我们的方法应用于同源细胞色素b6f复合物的两种结构，发现亚基PetG、PetN和PetL的跨膜螺旋归属存在差异。LIPS计算结果以及堆积和氢键相互作用分析支持绿藻细胞色素b6f结构中的螺旋归属，但不支持蓝细菌b6f结构中的跨膜螺旋归属。

结论

LIPS计算可用于多结构域膜蛋白从头建模中的螺旋方向预测。我们还通过两个细胞色素b6f结构的例子表明，我们的方法可以识别膜蛋白中可疑的螺旋归属。LIPS服务器可在线访问：http://gila.bioengr.uic.edu/lab/larisa/lips.html。

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