Dhar Rik, Feehan Ryan, Slusky Joanna S G
Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States.
Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, United States.
J Phys Chem B. 2021 Apr 15;125(14):3622-3628. doi: 10.1021/acs.jpcb.1c00878. Epub 2021 Apr 2.
Up-and-down β-barrel topology exists in both the membrane and soluble environment. By comparing features of these structurally similar proteins, we can determine what features are particular to the environment rather than the fold. Here we compare structures of membrane β-barrels to soluble β-barrels and evaluate their relative size, shape, amino acid composition, hydrophobicity, and periodicity. We find that membrane β-barrels are generally larger than soluble β-barrels, with more strands per barrel and more amino acids per strand, making them wider and taller. We also find that membrane β-barrels are inside-out soluble β-barrels. The inward region of membrane β-barrels has similar hydrophobicity to the outward region of soluble β-barrels, and the outward region of membrane β-barrels has similar hydrophobicity to the inward region of the soluble β-barrels. Moreover, even though both types of β-barrel have been assumed to have strands with amino acids that alternate in direction and hydrophobicity, we find that the membrane β-barrels have more regular alternation than soluble β-barrels. These features give insight into how membrane barrels maintain their fold and function in the membrane.
上下β桶拓扑结构同时存在于膜环境和可溶性环境中。通过比较这些结构相似的蛋白质的特征，我们可以确定哪些特征是特定于环境而非折叠结构的。在这里，我们将膜β桶的结构与可溶性β桶的结构进行比较，并评估它们的相对大小、形状、氨基酸组成、疏水性和周期性。我们发现，膜β桶通常比可溶性β桶更大，每个桶有更多的链，每条链有更多的氨基酸，使其更宽更高。我们还发现膜β桶是内翻的可溶性β桶。膜β桶的内部区域与可溶性β桶的外部区域具有相似的疏水性，膜β桶的外部区域与可溶性β桶的内部区域具有相似的疏水性。此外，尽管两种类型的β桶都被认为具有氨基酸方向和疏水性交替的链，但我们发现膜β桶比可溶性β桶具有更规则的交替。这些特征有助于深入了解膜桶如何在膜中维持其折叠结构和功能。
