Journal of structural biology最新文献_第2页

Common structural features in some of the sequentially distant neurotransmitter transporters N-termini 一些相距较远的神经递质转运体 N 端的共同结构特征。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2024-10-18 DOI: 10.1016/j.jsb.2024.108137

Martina Baliova, Frantisek Jursky

The N-terminal regions of SLC6 transporters are sequentially unrelated, and the majority of such transporters contain only relatively short peptide N-terminal extensions. Currently, it is not clear if a diversity of N-terminal sequences represents diverse functions among the transporters or if there are common functions hidden behind similar, as yet unidentified, structures. Using alignment of amino acid sequences with the hydropathy plot, disorder prediction, and calpain recognition sites, we show that common structural features among the N-termini of some transporters might exist. We previously showed that polymeric neurotransmitter transporter N-termini exhibit very similar profiles of dynamic, time-dependent 465-595-350-750 nm absorbance metachromasia in the Bradford assay. Here we report that under certain mild denaturing conditions, filamentous aggregation of glutathione S-transferase (GST) protein results in similar near-infrared metachromasia. This effect was eliminated by further GST protein denaturation and solubilization. The results suggest that aggregation of partially denatured GST stabilizes Coomassie dye docking sites, producing a near-infrared absorbance shift similar to that observed in the polymeric unstructured N-termini of transporters.

SLC6 转运体的 N 端区域在序列上互不关联，大多数此类转运体只包含相对较短的肽 N 端延伸。目前还不清楚 N 端序列的多样性是代表了转运体的不同功能，还是在相似但尚未确定的结构背后隐藏着共同的功能。我们以前曾发现，在布拉德福德测定法中，聚合神经递质转运体 N 端表现出非常相似的动态、随时间变化的 465 nm-595 nm-750 nm 吸光度变色曲线。我们在此报告，在某些轻度变性条件下，谷胱甘肽 S-转移酶（GST）蛋白的丝状聚集会导致类似的近红外变色。进一步变性和增溶谷胱甘肽 S 转移酶蛋白后，这种效应就会消失。研究结果表明，部分变性的 GST 聚合会稳定库马西染料对接位点，产生类似于在转运体聚合非结构 N 端观察到的近红外吸光度偏移。

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引用次数: 0

3D distribution of biomineral and chitin matrix in the stomatopod dactyl club by high energy XRD-CT 通过高能 XRD-CT 观察口足类双足俱乐部中生物矿物质和甲壳素基质的三维分布。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2024-10-09 DOI: 10.1016/j.jsb.2024.108136

Thorbjørn Erik Køppen Christensen , Maja Østergaard , Olof Gutowski , Ann-Christin Dippel , Henrik Birkedal

Stomatopods are ferocious hunters that use weaponized appendages to strike down their pray. The clubs of species such as Odontodactylus scyllarus undergo tremendous forces, and in consequence they have intricate structures, consisting of hydroxyapatite, chitin, amorphous calcium phosphate and carbonate, and occasionally calcite. These materials are distributed differently across the four major zones of the dactyl club: the impact, periodic lateral and medial, and striated regions. While stomatopod clubs and their structure have been studied for a long time, studies have thus far been constrained to 2D mapping experiments with moderate resolution due to difficulties in preparing whole club thin sections, and absorption tomography that gives information on densities but not molecular length scales. To address this problem, and shed light on the structure of entire clubs, we herein used X-ray powder diffraction computed tomography (XRD-CT) using high energy X-rays at the P07 beamline of PETRA-III to allow penetrating the large samples whilst still obtaining high resolution information. This allowed mapping the 3D distribution of diffraction phases including the biomineral apatite and the semi-crystal chitin matrix. This showed that hydroxyapatite forms an envelope around the club, and that chitin forms 2D sheets in the periodic region of the club.

节肢动物是凶猛的猎手，它们使用武器化的附肢来击倒它们的猎物。齿龙（Odontodactylus scyllarus）等物种的棍棒承受着巨大的力量，因此具有复杂的结构，由羟基磷灰石、甲壳素、无定形磷酸钙和碳酸钙组成，偶尔还有方解石。这些物质以不同的方式分布在双齿龙骨的四个主要区域：冲击区、周期性外侧区、内侧区和横纹区。虽然对口足类俱乐部及其结构的研究由来已久，但由于难以制备整个俱乐部的薄切片，以及吸收层析技术只能提供密度信息而无法提供分子长度尺度信息，因此迄今为止的研究仅限于分辨率适中的二维绘图实验。为了解决这个问题，并揭示整个球杆的结构，我们在 PETRA-III 的 P07 光束线使用高能 X 射线粉末衍射计算机断层扫描（XRD-CT），以便在获得高分辨率信息的同时穿透大型样品。这样就可以绘制衍射相的三维分布图，包括生物矿物磷灰石和半晶体甲壳素基质。结果表明，羟基磷灰石在球杆周围形成一个包层，甲壳素在球杆的周期性区域形成二维薄片。

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引用次数: 0

The intricacies of tooth enamel: Embryonic origin, development and human genetics 牙釉质的复杂性：胚胎起源、发育和人类遗传学。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2024-10-09 DOI: 10.1016/j.jsb.2024.108135

Olivier Duverger, Janice S. Lee

Tooth enamel is a fascinating tissue with exceptional biomechanical properties that allow it to last for a lifetime. In this mini review, we discuss the unique embryonic origin of this highly mineralized tissue, the complex differentiation process that leads to its “construction” (amelogenesis), and the various genetic conditions that lead to impaired enamel development in humans (amelogenesis imperfecta). Tremendous progress was made in the last 30 years in understanding the molecular and cellular mechanism that leads to normal and pathologic enamel development. However, several aspects of amelogenesis remain to be elucidated and the function of many genes associated with amelogenesis imperfecta still needs to be decoded.

牙釉质是一种令人着迷的组织，它具有特殊的生物力学特性，可以终生使用。在这篇微型综述中，我们将讨论这种高度矿化组织的独特胚胎起源、导致其 "生成"（釉质生成）的复杂分化过程，以及导致人类釉质发育受损（釉质发育不全）的各种遗传条件。在过去的 30 年中，人们在了解导致正常和病理性釉质发育的分子和细胞机制方面取得了巨大进步。然而，釉质发育的几个方面仍有待阐明，许多与釉质发育不全症相关的基因的功能仍有待解码。

引用次数: 0

Arabidopsis thaliana argininosuccinate lyase structure uncovers the role of serine as the catalytic base 拟南芥精琥珀酸裂解酶的结构揭示了丝氨酸作为催化基的作用。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2024-10-09 DOI: 10.1016/j.jsb.2024.108130

Maciej Nielipinski, Dominika Nielipinska, Agnieszka J. Pietrzyk-Brzezinska, Bartosz Sekula

Arginine is an important amino acid in plants, as it not only plays a structural role and serves as nitrogen storage but is also a precursor for various molecules, including polyamines and proline. Arginine is produced by argininosuccinate lyase (ASL) which catalyzes the cleavage of argininosuccinate to arginine and fumarate. ASL belongs to the fumarate lyase family and while many members of this family were well-characterized, little is known about plant ASLs. Here we present the first crystal structures of ASL from the model plant, Arabidopsis thaliana (AtASL). One of the structures represents the unliganded form of the AtASL homotetramer. The other structure, obtained from a crystal soaked in argininosuccinate, accommodates the substrate or the reaction products in one of four active sites of the AtASL tetramer. Each active site is located at the interface of three neighboring protomers. The AtASL structure with ligands allowed us to analyze the enzyme-substrate and the enzyme-product interactions in detail. Furthermore, based on our analyses, we describe residues of AtASL crucial for catalysis. The structure of AtASL gives the rationale for the open-to-close transition of the GSS mobile loop and indicates the importance of serine 333 from this loop for the enzymatic action of the enzyme. Finally, we supplemented the structural data with the identification of sequence motifs characteristic for ASLs.

精氨酸是植物体内的一种重要氨基酸，因为它不仅起着结构作用和储氮作用，还是多胺和脯氨酸等多种分子的前体。精氨酸由精琥珀酸裂解酶（ASL）生成，该酶催化精琥珀酸裂解为精氨酸和富马酸。ASL 属于富马酸裂解酶家族，尽管该家族中的许多成员都已被很好地描述，但人们对植物 ASL 却知之甚少。在这里，我们首次展示了来自模式植物拟南芥（Arabidopsis thaliana，AtASL）的 ASL 晶体结构。其中一个结构代表了 AtASL 同源四聚体的非连接形式。另一个结构是从浸泡在精琥珀酸中的晶体中获得的，它将底物或反应产物容纳在 AtASL 四聚体的四个活性位点之一。每个活性位点都位于三个相邻原体的界面上。带有配体的 AtASL 结构使我们能够详细分析酶与底物和酶与产物之间的相互作用。此外，根据我们的分析，我们描述了AtASL中对催化作用至关重要的残基。AtASL 的结构给出了 GSS 移动环从打开到关闭转变的基本原理，并指出了该环中的丝氨酸 333 对该酶的酶促作用的重要性。最后，我们通过鉴定 ASL 的特征序列图案对结构数据进行了补充。

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引用次数: 0

Transcriptome profiling of DPP stimulated DPSCs identifies the role of autophagy in odontogenic differentiation DPP 刺激的 DPSCs 转录组图谱确定了自噬在牙本质分化中的作用。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2024-10-09 DOI: 10.1016/j.jsb.2024.108134

Yinghua Chen, Cassandra Villani, Amudha Ganapathy, Anne George

Dentin phosphophoryn (DPP), synthesized and processed predominantly by the odontoblasts, serves both a structural and signaling role in dentin. In the ECM, DPP functions as an avid calcium and collagen binding protein and it also plays a crucial role as a scaffold for cell attachment and survival. The signaling function of DPP was demonstrated when undifferentiated mesenchymal cells stimulated with DPP, mediated calcium signaling through release of intracellular Ca²⁺. The objective of this study was to identify potentially novel signaling mechanisms that mediate odontoblast differentiation. Therefore, transcriptomes of DPSCs (dental pulp stem cells) with or without DPP stimulation were compared by bulk RNA-seq. Analysis of the unbiased RNA-seq data were subjected to functional enrichment analysis using Gene Ontology (GO) and KEGG pathways. Results identified several upregulated genes which were associated with autophagy, that were subsequently validated by RT-PCR. Western blotting analysis confirmed the up regulation of several autophagy markers such as ATG5, BECN1 and LC3A/B at specific time points. Autophagosome formation was also observed with DPP treatment. Additionally, autophagy supported a role for odontoblast differentiation of DPSCs. These findings suggest that DPP mediated autophagy might be a potential mechanism for the survival and terminal differentiation of DPSCs.

牙本质磷脂（Dentin phosphophoryn，DPP）主要由牙本质母细胞合成和加工，在牙本质中发挥着结构和信号作用。在 ECM 中，DPP 发挥着钙和胶原蛋白结合蛋白的作用，同时也是细胞附着和存活的重要支架。当未分化的间充质细胞受到 DPP 刺激时，DPP 通过释放细胞内 Ca2+ 介导钙信号传导，这证明了 DPP 的信号传导功能。本研究的目的是找出介导颌骨母细胞分化的潜在新型信号机制。因此，通过批量 RNA-seq 比较了有无 DPP 刺激的 DPSCs（牙髓干细胞）转录组。利用基因本体（GO）和 KEGG 通路对无偏 RNA-seq 数据进行了功能富集分析。结果发现了几个与自噬相关的上调基因，并随后通过 RT-PCR 进行了验证。Western 印迹分析证实了几个自噬标记物（如 ATG5、BECN1 和 LC3A/B）在特定时间点的上调。DPP 处理还观察到了自噬体的形成。此外，自噬还支持 DPSCs 在趾骨母细胞分化过程中发挥作用。这些研究结果表明，DPP 介导的自噬可能是 DPSCs 存活和终端分化的潜在机制。

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引用次数: 0

Role of DMP1-mediated GRP78 activation in osteoimmunomodulation of periodontal ligament stem cells DMP1 介导的 GRP78 激活在牙周韧带干细胞骨免疫调节中的作用

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2024-10-09 DOI: 10.1016/j.jsb.2024.108133

Cassandra Villani, Yinghua Chen, Anne George

The oral microbiome dysbiosis that causes periodontal disease leads to disruption of various signaling pathways that can result in alveolar bone degradation and subsequent tooth loss. Previous studies have demonstrated the potential of stem cell-based therapies in regeneration of the lost periodontium for the preservation of natural dentition. Periodontal ligament stem cells (PDLSCs) have osteoblast differentiation potential and their proximity to bone makes them an ideal candidate for regenerative therapies. Dentin matrix protein 1 (DMP1), a non-collagenous extracellular matrix protein, is integral to mineralized tissue formation due to its dual roles as an extracellular mediator of hydroxyapatite deposition and intracellular regulator of osteoblastogenesis. Heat shock protein 5A (GRP78) is a master regulator of the endoplasmic reticulum stress response and previous studies in our laboratory have also demonstrated its function as a membrane receptor for DMP1. Bulk RNA sequencing analysis of PDLSCs and PDLSCs overexpressing GRP78 (PDLSCs GRP78) with or without treatment with DMP1 was conducted to evaluate alterations to the differentially expressed gene profiles. This study aims to elucidate pathways in PDLSCs that are altered upon treatment with DMP1 to further characterize its relationship with GRP78 and cell stress signaling cascades. Pathway enrichment analysis of each transcriptomic profile demonstrated enrichment of osteogenic and immune response pathways upon DMP1 stimulation. Results from this study indicate a novel role for DMP1 and GRP78 in modulating immune signaling cascades in PDLSCs.

引起牙周病的口腔微生物群失调会导致各种信号通路的破坏，从而导致牙槽骨退化和随后的牙齿脱落。以往的研究表明，干细胞疗法在牙周再生以保护天然牙齿方面具有潜力。牙周韧带干细胞（PDLSCs）具有成骨细胞分化潜能，而且接近牙槽骨，是再生疗法的理想候选者。牙本质基质蛋白1（Dentin matrix protein 1，DMP1）是一种非胶原性细胞外基质蛋白，具有双重作用，既是羟磷灰石沉积的细胞外介质，又是成骨细胞生成的细胞内调节剂，是矿化组织形成不可或缺的成分。热休克蛋白 5A (GRP78) 是内质网应激反应的主调节因子，我们实验室以前的研究也证明了它作为 DMP1 膜受体的功能。我们对使用或不使用 DMP1 处理的 PDLSCs 和过表达 GRP78 的 PDLSCs（PDLSCs GRP78）进行了大量 RNA 测序分析，以评估差异表达基因谱的变化。本研究旨在阐明 DMP1 处理后 PDLSCs 中发生改变的通路，从而进一步确定其与 GRP78 和细胞应激信号级联的关系。对每个转录组图谱进行的通路富集分析表明，DMP1刺激后，成骨和免疫反应通路发生了富集。这项研究的结果表明，DMP1 和 GRP78 在调节 PDLSCs 的免疫信号级联方面发挥了新的作用。

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引用次数: 0

The role of bone sialoprotein in bone healing 骨唾液蛋白在骨愈合中的作用

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2024-10-05 DOI: 10.1016/j.jsb.2024.108132

B.L. Foster

Bone sialoprotein (BSP) is a multi-functional extracellular matrix (ECM) protein associated with mineralized tissues, particularly bone and cementum. The amino acid sequence of BSP includes three evolutionarily conserved sequences which contribute to functions of the protein: an N-terminal collagen-binding domain, polyglutamic acid (polyE) sequences involved in hydroxyapatite nucleation and crystal growth, and a C-terminal arginine-glycine-aspartic acid (RGD) integrin-binding domain. BSP promotes attachment and differentiation of osteogenic and osteoclastic cells. Genetic ablation of BSP in mice results in skeletal and dental developmental defects and impaired bone healing in both appendicular bone and alveolar bone of the jaw.

Several studies demonstrated positive effects of BSP on bone healing in rodent models, though other experiments show negligible results. Native (harvested from rat bones) BSP cross-linked to collagen induced slight improvements in calvarial bone healing in rats. Recombinant BSP and collagen delivered in a polylactide (PLA) cylinder improved bone defect healing in rat femurs. Both native and recombinant BSP delivered in a collagen gel improved alveolar bone healing in wild-type and BSP-deficient mice. These advances suggest BSP is a new player in bone healing that has potential to be an alternative or complimentary to other bioactive factors. Future studies are necessary to understand mechanisms of how BSP influences bone healing and optimize delivery and dose in different types of bone defects and injuries.

骨硅蛋白（BSP）是一种与矿化组织（尤其是骨和骨水泥）相关的多功能细胞外基质（ECM）蛋白。BSP 的氨基酸序列包括三个进化保守的功能域，这些功能域有助于发挥该蛋白的功能：N 端胶原结合域、参与羟基磷灰石成核和晶体生长的多谷氨酸（polyE）序列以及 C 端精氨酸-甘氨酸-天冬氨酸（RGD）整合素结合域。BSP 可促进成骨细胞和破骨细胞的附着和分化。对小鼠进行 BSP 基因消减会导致骨骼和牙齿发育缺陷以及颌骨附骨和牙槽骨的骨愈合受损。有几项研究表明，BSP 对啮齿动物模型的骨愈合有积极作用，但其他实验的结果却微乎其微。与胶原交联的原生（从大鼠骨骼中提取）BSP 能使大鼠腓骨愈合略有改善。用聚乳酸（PLA）圆筒输送重组 BSP 和胶原蛋白可改善大鼠股骨的骨缺损愈合。在胶原凝胶中输送的原生和重组 BSP 均能改善野生型和 BSP 缺陷小鼠的牙槽骨愈合。这些进展表明，BSP 是骨愈合中的新角色，有可能成为其他生物活性因子的替代品或补充品。未来的研究有必要了解 BSP 如何影响骨愈合的机制，并优化不同类型骨缺损和骨损伤的给药方式和剂量。

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引用次数: 0

SAXS of murine amelogenin identifies a persistent dimeric species from pH 5.0 to 8.0 小鼠淀粉样蛋白的 SAXS 发现了一种在 pH 值 5.0 到 8.0 之间持续存在的二聚体物种。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2024-10-04 DOI: 10.1016/j.jsb.2024.108131

Sebastian T. Mergelsberg , Hoshin Kim , Garry W. Buchko , Bojana Ginovska

Amelogenin is an intrinsically disordered protein essential to tooth enamel formation in mammals. Using advanced small angle X-ray scattering (SAXS) capabilities at synchrotrons and computational models, we revisited measuring the quaternary structure of murine amelogenin as a function of pH and phosphorylation at serine-16. The SAXS data shows that at the pH extremes, amelogenin exists as an extended monomer at pH 3.0 (R_g = 38.4 Å) and nanospheres at pH 8.0 (R_g = 84.0 Å), consistent with multiple previous observations. At pH 5.0 and above there was no evidence for a significant population of monomeric species. Instead, at pH 5.0, ∼80 % of the population is a heterogenous dimeric species that increases to ∼100 % at pH 5.5. The dimer population was observed at all pH > 5 conditions in dynamic equilibrium with a species in the pentamer range at pH < 6.5 and nanospheres at pH 8.0. At pH 8.0, ∼40 % of the amelogenin remained in the dimeric state. In general, serine-16 phosphorylation of amelogenin appears to modestly stabilize the population of the dimeric species.

amelogenin是哺乳动物牙釉质形成所必需的一种内在无序蛋白。利用同步加速器上最新、最先进的小角 X 射线散射（SAXS）功能和计算模型，我们重新研究了鼠淀粉样蛋白的四元结构随 pH 值和 Ser-16 处磷酸化的变化。SAXS 数据显示，在极端 pH 值下，淀粉样球蛋白在 pH 值为 3.0 时为扩展单体（Rg = 38.4 Å），在 pH 值为 8.0 时为纳米球（Rg = 84.0 Å），这与之前的多次观察结果一致。在 pH 值为 5.0 及以上时，没有证据表明存在大量单体物种。相反，在 pH 值为 5.0 时，80% 的单体是异源二聚体，而在 pH 值为 5.5 时，这一比例增加到 100%。在所有 pH > 5 的条件下，都能观察到二聚物群与 pH < 6.5 时的五聚物群和 pH 8.0 时的纳米球处于动态平衡状态。在 pH 值为 8.0 时，40% 的淀粉样蛋白仍处于二聚体状态。总的来说，丝氨酸-16 磷酸化似乎能适度稳定二聚体物种的数量。

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引用次数: 0

On the abundance and importance of AXXXA sequence motifs in globular proteins and their involvement in CβCβ interaction 论球蛋白中 AXXXA 序列基序的丰度和重要性及其在 CβCβ 相互作用中的参与。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2024-09-27 DOI: 10.1016/j.jsb.2024.108129

Surbhi Vilas Tajane , Abhilasha Thakur , Srijita Acharya , Pinak Chakrabarti , Sucharita Dey

The AXXXA and GXXXG motifs are frequently observed in helices, especially in membrane proteins. The motif GXXXG is known to stabilize helix-helix association in membrane proteins via C_αHO bonding. AXXXA sequence motif additionally stabilizes the folded state of proteins. We found 27,000 and 18,000 occurrences of AXXXA and GXXXG motifs in a non-redundant set of 6000 obligate homodimeric (OD) complexes. Interestingly, this is less pronounced in transient homodimers (TD) and heterodimers (HetD). On average each obligate homodimer contains four AXXXA motifs, it is 2 and 3.5 for HetD and TD, respectively. Focusing on the binding surface it is seen that 27 % of the ODs contain at least one AXXXA motif at the interface, whereas it is 17 % and 15 % for HetD and TD respectively. AXXXA predominantly stabilizes the OD quaternary structure via the side chain C_βC_β interactions. This interaction is energetically favorable and is found to be a major driving force for OD quaternary structure stability. C_β-C_β interactions are observed ∼6 times higher than the known C_αHO interaction for helix-helix stabilization. Two additional new interactions of C_βO and OO are observed at the AXXXA containing interface regions. The occurrence of the motif gets drastically reduced if any of the terminal Ala residues are replaced by Gly. Our findings show the importance of AXXXA in providing stability to the quaternary structure through specific hydrophobic interactions and the specificity of the Ala residue at motif termini. The knowledge gained can be used for designing synthetic proteins of improved stability and for designing peptide-based therapeutics.

AXXXA 和 GXXXG 主题经常在螺旋中出现，尤其是在膜蛋白中。已知 GXXXG 主题通过 CHO 键稳定膜蛋白中的螺旋-螺旋结合。此外，AXXXA 序列主题还能稳定蛋白质的折叠状态。我们发现，在一组非冗余的 6000 个强制性同源二聚体（OD）复合物中，AXXXA 和 GXXXG 主题分别出现了 27,000 和 18,000 次。有趣的是，这种情况在瞬时同源二聚体（TD）和异源二聚体（HetD）中并不明显。每个同源二聚体平均含有四个 AXXXA 矩阵，HetD 和 TD 分别为 2 个和 3.5 个。从结合表面可以看出，27%的 OD 在界面上至少含有一个 AXXXA 基序，而 HetD 和 TD 的这一比例分别为 17% 和 15%。AXXXA 主要通过侧链 CβCβ 相互作用来稳定 OD 的四元结构。这种相互作用在能量上是有利的，是 OD 四元结构稳定性的主要驱动力。观察到的 Cβ-Cβ 相互作用比已知的用于稳定螺旋-螺旋的 CHO 相互作用高出 6 倍。在含有 AXXXA 的界面区域还观察到 CβO 和 OO 的两种新的相互作用。如果任何一个末端的 Ala 残基被 Gly 取代，则该图案的出现率会急剧下降。我们的研究结果表明了 AXXXA 在通过特异性疏水相互作用为四元结构提供稳定性方面的重要性，以及图案末端 Ala 残基的特异性。所获得的知识可用于设计稳定性更好的合成蛋白质和设计基于肽的疗法。

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引用次数: 0

Selective signal enhancement in Fourier space as a tool for discovering ultrastructural organization of macromolecules from in situ TEM 傅立叶空间的选择性信号增强，作为从原位 TEM 发现大分子超微结构组织的工具。

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology

Pub Date : 2024-09-14 DOI: 10.1016/j.jsb.2024.108128

Nadejda B. Matsko , Martin Schorb , Yannick Schwab

We present a Fourier transform (FT) based analytical method that allows to obtain of ultrastructural details from TEM images at sub-nanometer scale applying a selective filtering for singular macromolecule electron microscopy density information. It can be applied to high-pressure frozen, frozen hydrated and epoxy freeze substituted and embedded biological species. Both 2D projections and orthoslices from reconstructed tomograms can be used as a source of structural information. The key to the method is to select the macromolecule or organelle of interest with an accuracy of ≥ 7 – 3 nm (depending on pixel size of initial tilt series or singular image acquisition) and explore both the central low frequency FT intensity and diffraction regions to obtain the spatial structural organization and its dimensional characteristics, respectively. We also introduce a structure-specific selective mask FT filtering approach that can significantly improve image information even in poorly contrasted TEM of resin sections without heavy metal been used. The described method elucidates chromatin architecture without the need of averaging. A zigzag symmetry of 30 nm diameter chromatin fibers which in general is a controversial topic of research has been identified for C. elegans cells in vivo with sub-nanometer details being preserved in the images.

我们提出了一种基于傅立叶变换（FT）的分析方法，通过对奇异的大分子电子显微镜密度信息进行选择性过滤，可以从亚纳米尺度的 TEM 图像中获得超微结构细节。它适用于高压冷冻、冷冻水合和环氧树脂冷冻替代和嵌入的生物物种。二维投影和来自重建断层扫描的正切片都可用作结构信息的来源。该方法的关键在于选择感兴趣的大分子或细胞器，精确度≥ 7 - 3 nm（取决于初始倾斜序列或奇异图像采集的像素大小），并探索中心低频 FT 强度和衍射区域，以分别获得空间结构组织及其尺寸特征。我们还介绍了一种针对特定结构的选择性掩膜 FT 滤波方法，即使在对比度较差的树脂切片 TEM 中也能显著改善图像信息，而无需使用重金属。所述方法无需平均值即可阐明染色质结构。研究人员在体内发现了直径为 30 nm 的染色质纤维呈人字形对称，而这种染色质纤维在图像中保留了亚纳米级的细节。

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引用次数: 0