Kalinina Olga V, Makeev Vsevolod J, Sutormin Roman A, Gelfand Mikhail S, Rakhmaninova Aleksandra B
State Scientific Center GosNIIGenetika, Moscow, Russia.
In Silico Biol. 2003;3(1-2):197-204.
Transmembrane transport is an essential component of the cell life. Many genes encoding known or putative transport proteins are found in bacterial genomes. In most cases their substrate specificity is not experimentally determined and only approximately predicted by comparative genomic analysis. Even less is known about the 3D structure of transporters. Nevertheless, the published experimental data demonstrate that channel-forming residues determine the substrate specificity of secondary transporters and analysis of these residues would provide better understanding of the transport mechanism. We developed a simple computational method for identification of channel-forming residues in transporter sequences. It is based on the analysis of amino acids frequencies in bacterial secondary transporters. We applied this method to a variety of transmembrane proteins with resolved 3D structure. The predictions are in sufficiently good agreement with the real protein structure.
跨膜运输是细胞生命活动的一个重要组成部分。细菌基因组中发现了许多编码已知或推测的转运蛋白的基因。在大多数情况下，它们的底物特异性并未通过实验确定，只是通过比较基因组分析进行大致预测。对于转运蛋白的三维结构，人们了解得更少。然而，已发表的实验数据表明，形成通道的残基决定了次级转运蛋白的底物特异性，对这些残基的分析将有助于更好地理解运输机制。我们开发了一种简单的计算方法来识别转运蛋白序列中形成通道的残基。该方法基于对细菌次级转运蛋白中氨基酸频率的分析。我们将此方法应用于多种具有解析三维结构的跨膜蛋白。预测结果与实际蛋白质结构充分吻合。
