Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule"
Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule"
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DOI：
10.1186/s12915-017-0404-4
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发表时间：
2017-07-24
期刊：
影响因子：
5.4
通讯作者：
Eisenhaber, Frank
中科院分区：
文献类型：
--
作者：
Baker, James Alexander;Wong, Wing-Cheong;Eisenhaber, Frank
背景：跨膜螺旋(TMHs)经常出现在蛋白质结构中，作为蛋白质附着或嵌入生物膜的手段。物理限制，如膜的疏水性和静电势，对TMH及其侧翼区域提出了统一的要求；结果：根据大量蛋白质序列的统计数据，我们证明，除了细胞质内部的正电荷偏好(正-内规则)，负电荷残基优先出现在非细胞质侧翼，或者至少，它们在细胞质侧翼被抑制(负-不-内/负-外(NNI/NO)规则)。由于TMH中或附近的阴性残留物通常很少，统计意义对于TMH比对和残基频率归一化的细节以及数据集的大小都很敏感；因此，这一趋势在以前的工作中被掩盖了。我们观察到不同分类群之间以及分泌途径上细胞器的变化。与具有多个TMH(多位蛋白)的TMH相比，单通道跨膜TMH的这种影响最为明显。结论：带电残基侧翼偏向只是TMH序列特征之一，在锚定机制中起作用，其他特征明显是亮氨酸螺旋内倾向向胞质侧倾斜，色氨酸侧翼以及半胱氨酸和酪氨酸的偏爱。这些观察结果将激发从序列中预测TMHs和蛋白质拓扑结构的新方法，以及人造膜蛋白的新工程设计。
Background: Transmembrane helices (TMHs) frequently occur amongst protein architectures as means for proteins to attach to or embed into biological membranes. Physical constraints such as the membrane's hydrophobicity and electrostatic potential apply uniform requirements to TMHs and their flanking regions; consequently, they are mirrored in their sequence patterns (in addition to TMHs being a span of generally hydrophobic residues) on top of variations enforced by the specific protein's biological functions.Results: With statistics derived from a large body of protein sequences, we demonstrate that, in addition to the positive charge preference at the cytoplasmic inside (positive-inside rule), negatively charged residues preferentially occur or are even enriched at the non-cytoplasmic flank or, at least, they are suppressed at the cytoplasmic flank (negative-not-inside/ negative-outside (NNI/NO) rule). As negative residues are generally rare within or near TMHs, the statistical significance is sensitive with regard to details of TMH alignment and residue frequency normalisation and also to dataset size; therefore, this trend was obscured in previous work. We observe variations amongst taxa as well as for organelles along the secretory pathway. The effect is most pronounced for TMHs from single-pass transmembrane (bitopic) proteins compared to those with multiple TMHs (polytopic proteins) and especially for the class of simple TMHs that evolved for the sole role as membrane anchors.Conclusions: The charged-residue flank bias is only one of the TMH sequence features with a role in the anchorage mechanisms, others apparently being the leucine intra-helix propensity skew towards the cytoplasmic side, tryptophan flanking as well as the cysteine and tyrosine inside preference. These observations will stimulate new prediction methods for TMHs and protein topology from a sequence as well as new engineering designs for artificial membrane proteins.