对 NowGFP 的两种晶体多态性进行比较,发现了一种被晶体堆积困住的新构象状态。

IF 2.6 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-09-01 Epub Date: 2024-09-02 DOI:10.1107/S2059798324008246
Jin Kyun Kim, Hannah Jeong, Jeongwoo Seo, Seoyoon Kim, Kyung Hyun Kim, Duyoung Min, Chae Un Kim
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引用次数: 0

摘要

晶体多态性是研究蛋白质构象灵活性的一种策略。然而,蛋白质晶体结构与蛋白质构象之间的关系往往仍然难以捉摸。本研究比较了一种绿色荧光蛋白变体 NowGFP 的两种不同晶体形态:一种是以前发现的单斜晶体形态(空间群 C2),另一种是新发现的正菱形晶体形态(空间群 P212121)。比较分析表明,这两种晶体形态都显示出几乎相同的 NowGFP 分子线性组合,它们通过类似的晶体接触相互连接。然而,一个显著的区别在于这些组装体的堆叠方式:单斜晶体的堆叠方式是平行的,而正方晶体的堆叠方式是垂直的。这种不同的堆叠模式导致了不同的晶体接触,并引起了正方晶型不对称单元中两个分子之一的结构变化。正方晶堆积捕捉到的这种新构象状态表现出两个独特的特征:β-桶支架的构象转移和限制关键残基 Lys61 的 pH 依赖性转移,而 Lys61 对这种蛋白质的 pH 依赖性光谱转移至关重要。这些发现证明了晶体包装与蛋白质的替代构象状态之间的明确联系,为我们深入了解结构变化如何影响荧光蛋白的功能提供了启示。
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Comparison of two crystal polymorphs of NowGFP reveals a new conformational state trapped by crystal packing.

Crystal polymorphism serves as a strategy to study the conformational flexibility of proteins. However, the relationship between protein crystal packing and protein conformation often remains elusive. In this study, two distinct crystal forms of a green fluorescent protein variant, NowGFP, are compared: a previously identified monoclinic form (space group C2) and a newly discovered orthorhombic form (space group P212121). Comparative analysis reveals that both crystal forms exhibit nearly identical linear assemblies of NowGFP molecules interconnected through similar crystal contacts. However, a notable difference lies in the stacking of these assemblies: parallel in the monoclinic form and perpendicular in the orthorhombic form. This distinct mode of stacking leads to different crystal contacts and induces structural alteration in one of the two molecules within the asymmetric unit of the orthorhombic crystal form. This new conformational state captured by orthorhombic crystal packing exhibits two unique features: a conformational shift of the β-barrel scaffold and a restriction of pH-dependent shifts of the key residue Lys61, which is crucial for the pH-dependent spectral shift of this protein. These findings demonstrate a clear connection between crystal packing and alternative conformational states of proteins, providing insights into how structural variations influence the function of fluorescent proteins.

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来源期刊
Acta Crystallographica. Section D, Structural Biology
Acta Crystallographica. Section D, Structural Biology BIOCHEMICAL RESEARCH METHODSBIOCHEMISTRY &-BIOCHEMISTRY & MOLECULAR BIOLOGY
CiteScore
4.50
自引率
13.60%
发文量
216
期刊介绍: Acta Crystallographica Section D welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules or the methods used to determine them. Reports on new structures of biological importance may address the smallest macromolecules to the largest complex molecular machines. These structures may have been determined using any structural biology technique including crystallography, NMR, cryoEM and/or other techniques. The key criterion is that such articles must present significant new insights into biological, chemical or medical sciences. The inclusion of complementary data that support the conclusions drawn from the structural studies (such as binding studies, mass spectrometry, enzyme assays, or analysis of mutants or other modified forms of biological macromolecule) is encouraged. Methods articles may include new approaches to any aspect of biological structure determination or structure analysis but will only be accepted where they focus on new methods that are demonstrated to be of general applicability and importance to structural biology. Articles describing particularly difficult problems in structural biology are also welcomed, if the analysis would provide useful insights to others facing similar problems.
期刊最新文献
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