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含序列差异的三螺旋束中变性状态构象偏向定位于转角和螺旋帽残基附近。

Denatured State Conformational Biases in Three-Helix Bundles Containing Divergent Sequences Localize near Turns and Helix Capping Residues.

机构信息

Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States.

Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States.

出版信息

Biochemistry. 2021 Oct 19;60(41):3071-3085. doi: 10.1021/acs.biochem.1c00400. Epub 2021 Oct 4.

Abstract

cytochrome ', a four-helix bundle, and the second ubiquitin-associated domain, UBA(2), a three-helix bundle from the human homologue of yeast Rad23, HHR23A, deviate from random coil behavior under denaturing conditions in a fold-specific manner. The random coil deviations in each of these folds occur near interhelical turns and loops in their tertiary structures. Here, we examine an additional three-helix bundle with an identical fold to UBA(2), but a highly divergent sequence, the first ubiquitin-associated domain, UBA(1), of HHR23A. We use histidine-heme loop formation methods, employing eight single histidine variants, to probe for denatured state conformational bias of a UBA(1) domain fused to the N-terminus of iso-1-cytochrome (iso-1-Cyt). Guanidine hydrochloride (GuHCl) denaturation shows that the iso-1-Cyt domain unfolds first, followed by the UBA(1) domain. Denatured state (4 and 6 M GuHCl) histidine-heme loop formation studies show that as the size of the histidine-heme loop increases, loop stability decreases, as expected for the Jacobson-Stockmayer relationship. However, loops formed with His35, His31, and His15, of UBA(1), are 0.6-1.1 kcal/mol more stable than expected from the Jacobson-Stockmayer relationship, confirming the importance of deviations of the denatured state from random coil behavior near interhelical turns of helical domains for facilitating folding to the correct topology. For UBA(1) and UBA(2), hydrophobic clusters on either side of the turns partially explain deviations from random coil behavior; however, helix capping also appears to be important.

摘要

细胞色素 ',一个四螺旋束,和第二个泛素相关结构域,UBA(2),来自酵母 Rad23 同源物的人 HHR23A 的三个螺旋束,在变性条件下以特定于折叠的方式偏离无规卷曲行为。这些折叠中的每一个的无规卷曲偏差发生在它们的三级结构的螺旋间转弯和环附近。在这里,我们检查了另外一个具有与 UBA(2)相同折叠的三螺旋束,但序列高度不同,即 HHR23A 的第一个泛素相关结构域,UBA(1)。我们使用组氨酸血红素环形成方法,使用八个单一组氨酸变体,来探测与异源-1-细胞色素(iso-1-Cyt)的 N 端融合的 UBA(1)结构域的变性状态构象偏向。盐酸胍(GuHCl)变性表明,iso-1-Cyt 结构域首先展开,然后是 UBA(1)结构域。变性状态(4 和 6 M GuHCl)组氨酸血红素环形成研究表明,随着组氨酸血红素环的大小增加,环稳定性降低,这与 Jacobson-Stockmayer 关系一致。然而,UBA(1)中的 His35、His31 和 His15 形成的环比 Jacobson-Stockmayer 关系预期的稳定 0.6-1.1 kcal/mol,这证实了在螺旋结构域的螺旋间转弯附近偏离无规卷曲行为的变性状态的偏差对于促进正确拓扑结构的折叠的重要性。对于 UBA(1)和 UBA(2),转弯两侧的疏水区簇部分解释了偏离无规卷曲行为的原因;然而,螺旋帽也似乎很重要。

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本文引用的文献

1
ProteinTools: a toolkit to analyze protein structures.
Nucleic Acids Res. 2021 Jul 2;49(W1):W559-W566. doi: 10.1093/nar/gkab375.
2
Properties of protein unfolded states suggest broad selection for expanded conformational ensembles.
Proc Natl Acad Sci U S A. 2020 Sep 22;117(38):23356-23364. doi: 10.1073/pnas.2003773117. Epub 2020 Sep 2.
3
Half a century of amyloids: past, present and future.
Chem Soc Rev. 2020 Aug 7;49(15):5473-5509. doi: 10.1039/c9cs00199a. Epub 2020 Jul 7.
4
Water as a Good Solvent for Unfolded Proteins: Folding and Collapse are Fundamentally Different.
J Mol Biol. 2020 Apr 17;432(9):2882-2889. doi: 10.1016/j.jmb.2020.01.031. Epub 2020 Feb 7.
5
Emerging consensus on the collapse of unfolded and intrinsically disordered proteins in water.
Curr Opin Struct Biol. 2020 Feb;60:27-38. doi: 10.1016/j.sbi.2019.10.009. Epub 2019 Dec 2.
6
Unfolded states under folding conditions accommodate sequence-specific conformational preferences with random coil-like dimensions.
Proc Natl Acad Sci U S A. 2019 Jun 18;116(25):12301-12310. doi: 10.1073/pnas.1818206116. Epub 2019 Jun 5.
10
Probing Denatured State Conformational Bias in a Three-Helix Bundle, UBA(2), Using a Cytochrome c Fusion Protein.
Biochemistry. 2018 Mar 20;57(11):1711-1721. doi: 10.1021/acs.biochem.8b00015. Epub 2018 Mar 7.

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