Sutormin Roman A, Rakhmaninova Aleksandra B, Gelfand Mikhail S
State Scientific Center GosNIIGenetica, Moscow, Russia.
Proteins. 2003 Apr 1;51(1):85-95. doi: 10.1002/prot.10308.
Aligned amino acid sequences of three functionally independent samples of transmembrane (TM) transport proteins have been analyzed. The concept of TM-kernel is proposed as the most probable transmembrane region of a sequence. The average amino acid composition of TM-kernels differs from the published amino acid composition of transmembrane segments. TM-kernels contain more alanines, glycines, and less polar, charged, and aromatic residues in contrast to non-TM-proteins. There are also differences between TM-kernels of bacterial and eukaryotic proteins. We have constructed amino acid substitution matrices for bacterial TM-kernels, named the BATMAS (BActerial Transmembrane MAtrix of Substitutions) series. In TM-kernels, polar and charged residues, as well as proline and tyrosine, are highly conserved, whereas there are more substitutions within the group of hydrophobic residues, in contrast to non-TM-proteins that have fewer, relatively more conserved, hydrophobic residues. These results demonstrate that alignment of transmembrane proteins should be based on at least two amino acid substitution matrices, one for loops (e.g., the BLOSUM series) and one for TM-segments (the BATMAS series), and the choice of the TM-matrix should be different for eukaryotic and bacterial proteins.
对三个功能独立的跨膜（TM）转运蛋白样本的氨基酸序列进行了比对分析。提出了TM核的概念，作为序列中最可能的跨膜区域。TM核的平均氨基酸组成与已发表的跨膜片段的氨基酸组成不同。与非TM蛋白相比，TM核含有更多的丙氨酸、甘氨酸，以及更少的极性、带电荷和芳香族残基。细菌蛋白和真核蛋白的TM核之间也存在差异。我们构建了细菌TM核的氨基酸替换矩阵，命名为BATMAS（细菌跨膜替换矩阵）系列。在TM核中，极性和带电荷的残基，以及脯氨酸和酪氨酸高度保守，而与非TM蛋白相比，疏水残基组内的替换更多，非TM蛋白的疏水残基较少且相对更保守。这些结果表明，跨膜蛋白的比对应基于至少两个氨基酸替换矩阵，一个用于环（例如BLOSUM系列），一个用于TM片段（BATMAS系列），并且对于真核蛋白和细菌蛋白，TM矩阵的选择应该不同。
