Le T, Tseng T T, Saier M H
Department of Biology, University of California at San Diego, La Jolla 92093-0116, USA.
Mol Membr Biol. 1999 Apr-Jun;16(2):173-9. doi: 10.1080/096876899294634.
Simple flexible programs (TREEMOMENT and PILEUPMOMENT) are described for depicting the average amphipathicity (hydrophobic moment) along multiply aligned sequences of a family of evolutionarily related proteins. The programs are applicable to any number of aligned sequences and can be set for any desired angle corresponding to a residue repeat unit in a protein secondary structural element such as 100 degrees per residue for an alpha-helix or 180 degrees per residue for a beta-strand. These programs can be used to identify amphipathic regions common to the members of a protein family. The use of these programs is exemplified by showing that some families of integral membrane transport proteins (i.e. permeases of the bacterial phosphotransferase system (PTS) and the anion exchangers of animals) exhibit strikingly amphipathic alpha-helical structures immediately preceding the first hydrophobic transmembrane segment of their membrane-embedded domain(s). Other families, such as the major facilitator superfamily of uniporters, symporters and antiporters, do not exhibit this structural feature. The amphipathic structures in PTS permeases have been implicated in membrane insertion during biogenesis.
描述了简单灵活的程序（TREEMOMENT和PILEUPMOMENT），用于描绘进化相关蛋白质家族多重比对序列上的平均两亲性（疏水矩）。这些程序适用于任意数量的比对序列，并且可以针对蛋白质二级结构元件中与残基重复单元对应的任意所需角度进行设置，例如α螺旋每个残基100度或β链每个残基180度。这些程序可用于识别蛋白质家族成员共有的两亲区域。通过显示一些整合膜转运蛋白家族（即细菌磷酸转移酶系统（PTS）的通透酶和动物的阴离子交换器）在其膜嵌入结构域的第一个疏水跨膜片段之前立即呈现出显著的两亲性α螺旋结构，举例说明了这些程序的用途。其他家族，如单向转运体、同向转运体和反向转运体的主要促进剂超家族，则不具有这种结构特征。PTS通透酶中的两亲结构与生物发生过程中的膜插入有关。
