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1H, 13C, 15N backbone resonance assignment of Escherichia coli adenylate kinase 大肠杆菌腺苷酸激酶的1H,13C,15N骨架共振定位
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2023-08-26 DOI: 10.1007/s12104-023-10147-1
Julia A. Brom, Sasiprapa Samsri, Ruta G. Petrikis, Stuart Parnham, Gary J. Pielak

Adenylate kinase reversibly catalyzes the conversion of ATP plus AMP to two ADPs. This essential catalyst is present in every cell, and the Escherichia coli protein is often employed as a model enzyme. Our aim is to use the E. coli enzyme to understand dry protein structure and protection. Here, we report the expression, purification, steady-state assay, NMR conditions and 1H, 13C, 15N backbone resonance NMR assignments of its C77S variant. These data will also help others utilize this prototypical enzyme.

腺苷酸激酶可逆地催化ATP加AMP转化为两个ADP。这种重要的催化剂存在于每个细胞中,大肠杆菌蛋白经常被用作模型酶。我们的目的是使用大肠杆菌酶来了解干蛋白的结构和保护作用。在此,我们报道了其C77S变体的表达、纯化、稳态测定、NMR条件和1H、13C、15N骨架共振NMR归属。这些数据也将帮助其他人利用这种原型酶。
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引用次数: 0
Backbone and sidechain NMR assignments of residues 1–81 from yeast Sis1 in complex with an Hsp70 C-terminal EEVD peptide 酵母Sis1与Hsp70 c端EEVD肽复合物中残基1-81的主链和侧链NMR定位。
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2023-08-17 DOI: 10.1007/s12104-023-10148-0
Carolina O. Matos, Glaucia M.S. Pinheiro, Carlos H. I. Ramos, Fabio C. L. Almeida

Molecular chaperones aid proteins to fold and assemble without modifying their final structure, requiring, in several folding processes, the interplay between members of the Hsp70 and Hsp40 families. Here, we report the NMR chemical shift assignments for 1 H, 15 N, and 13 C nuclei of the backbone and side chains of the J-domain of the class B Hsp40 from Saccharomyces cerevisiae, Sis1, complexed with the C-terminal EEVD motif of Hsp70. The data revealed information on the structure and backbone dynamics that add significantly to the understanding of the J-domain-Hsp70-EEVD mechanism of interaction.

分子伴侣有助于蛋白质折叠和组装,而不改变其最终结构,在几个折叠过程中,需要Hsp70和Hsp40家族成员之间的相互作用。在这里,我们报道了来自酿酒酵母Sis1的B类Hsp40的J结构域的主链和侧链的1H、15N和13C核与Hsp70的C末端EEVD基序复合的NMR化学位移分配。这些数据揭示了关于结构和骨架动力学的信息,这些信息大大增加了对J结构域-Hsp70-EEVD相互作用机制的理解。
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引用次数: 0
1H, 15N and 13C backbone and side chain solution NMR assignments of the TPM domain-containing protein of the thermophilic bacterium Rhodothermus marinus 嗜热细菌Rhodothermus marinus的含TPM结构域蛋白质的1H、15N和13C主链和侧链溶液NMR归属
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2023-08-05 DOI: 10.1007/s12104-023-10146-2
Leonardo Pellizza, Lila Ramis, Ignacio Argañaraz Araoz, Martín Aran

The InterPro family IPR007621 TPM_phosphatase is a widely conserved family of protein domains found in prokaryotes, plants and invertebrates. Despite similar predicted protein folding, members of this family are involved in different cellular processes. In recent years, the structural and biochemical characterization of evolutionarily divergent TPM domains has shown their ability to hydrolyze phosphate groups of different substrates. However, there are still inaccurate functional annotations and uncertain relationships between the structure and function of this domain family. We here report the 1H, 13C, and 15N backbone and sidechain resonances of the TPM domain of a predicted TPM domain-containing protein of the thermophilic bacterium Rhodothermus marinus. These data will lay the groundwork for future NMR-based investigations, contributing to a thorough comprehension of the intricate aspects governing the interplay between structure and function of TPM domains. Additionally, they will unlock opportunities to explore dynamic structural changes, providing valuable insights into the molecular mechanisms underlying the evolutionary adaptations to extreme environmental conditions within this protein family.

InterPro家族IPR007621 TPM_phosphate是一个广泛保守的蛋白质结构域家族,存在于原核生物、植物和无脊椎动物中。尽管预测的蛋白质折叠相似,但该家族的成员参与了不同的细胞过程。近年来,进化上不同的TPM结构域的结构和生化特征已经表明它们能够水解不同底物的磷酸基团。然而,该领域族的结构和功能之间仍然存在不准确的功能注释和不确定的关系。我们在此报道了嗜热细菌Rhodothermus marinus的预测的含TPM结构域蛋白质的TPM结构域的1H、13C和15N主链和侧链共振。这些数据将为未来基于NMR的研究奠定基础,有助于彻底理解TPM结构域的结构和功能之间相互作用的复杂方面。此外,它们将开启探索动态结构变化的机会,为该蛋白质家族中进化适应极端环境条件的分子机制提供有价值的见解。
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引用次数: 0
Backbone and side chain NMR assignments and secondary structure calculation of the pheromone binding protein3 of Ostrinia nubilalis, an agricultural pest 农业害虫nubilalis Ostrinia nubilalis信息素结合蛋白3的主侧链NMR定位和二级结构计算。
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2023-07-27 DOI: 10.1007/s12104-023-10145-3
Omar Al-Danoon, Smita Mohanty

Ostrinia nubilalis, also known as European Corn Borer (ECB), is a serious pest in Europe and North America, as well as in Central Asia and Northern Africa. It damages a variety of agricultural crops such as corn, oats, buckwheat, millet, and soybeans. causing annually at least one billion dollars in loss. The Ostrinia nubilalis pheromone-binding protein3 (OnubPBP3), preferentially expressed in the male moth antenna, has been implicated in the detection of the female-secreted pheromone blend during the mating process. Understanding the structure of and function of OnubPBP3, including the mechanism of pheromone binding and its release at the dendritic olfactory neuron (ORN), is essential if integrated pest management through sensory inhibition is to be achieved. We report here the backbone and side-chain resonance assignments of OnubPBP3 at pH 6.5 using various triple resonance NMR experiments on a 13C, 15N-labeled protein sample. The secondary structure of OnubPBP3 consists of six α-helices and an unstructured C-terminus based on backbone chemical shifts.

裸粒玉米螟,也称为欧洲玉米螟(ECB),是欧洲、北美、中亚和北非的一种严重害虫。它破坏了玉米、燕麦、荞麦、小米和大豆等多种农作物。每年造成至少10亿美元的损失。Ostrinia nubilalis信息素结合蛋白3(OnubPBP3)优先在雄蛾触角中表达,与交配过程中雌蛾分泌的信息素混合物的检测有关。了解OnubPBP3的结构和功能,包括信息素结合及其在树突嗅觉神经元(ORN)释放的机制,对于通过感官抑制实现害虫综合治理至关重要。我们在这里报道了OnubPBP3在pH 6.5下的主链和侧链共振归属,使用对13C,15N标记的蛋白质样品的各种三重共振NMR实验。OnubPBP3的二级结构由六个α-螺旋和一个基于骨架化学位移的非结构化C末端组成。
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引用次数: 0
1H, 13C and 15N backbone and side-chain resonance assignments of ∆∆BmSA1, the surface antigen of Babesia microti 微巴贝斯虫表面抗原∆∆BmSA1的1H、13C和15N主链和侧链共振分配
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2023-07-15 DOI: 10.1007/s12104-023-10144-4
Assia Mouhand, Joana Pissarra, Stéphane Delbecq, Christian Roumestand, Philippe Barthe

Human babesiosis is a vector-borne zoonotic infection caused mostly by the Apicomplexan parasite Babesia microti, distributed worldwide. The infection can result in severe symptoms such as hemolytic anemia, especially in immunodeficient patients. Also, asymptomatic patients continue transmission as unscreened blood donors, and represent a risk for Public Health. Early host-parasite interactions are mediated by BmSA1, the major surface antigen of Babesia microti, crucial for invasion and immune escape. Hence, a structural and functional characterization of the BmSA1 protein constitutes a first strategic milestone toward the development of innovative tools to control infection. Knowledge of the 3D structure of such an important antigen is crucial for the development of vaccines or new diagnostic tests. Here, we report the 1H, 15N and 13C NMR resonance assignment of ∆∆BmSA1, a truncated recombinant version of BmSA1 without the N-terminal signal peptide and the hydrophobic C-terminal GPI-anchor. Secondary structure prediction using CSI.3 and TALOS-N demonstrates a high content of alpha-helical structure. This preliminary study provides foundations for further structural characterization of BMSA1.

人类巴贝斯虫病是一种媒介传播的人畜共患传染病,主要由Apicocomplian寄生虫微小巴贝斯虫引起,分布在世界各地。感染可导致严重症状,如溶血性贫血,尤其是免疫缺陷患者。此外,无症状患者作为未经筛查的献血者继续传播,这对公共卫生构成了风险。早期的宿主-寄生虫相互作用是由BmSA1介导的,BmSA1是微小巴贝斯虫的主要表面抗原,对入侵和免疫逃逸至关重要。因此,BmSA1蛋白的结构和功能表征构成了开发控制感染的创新工具的第一个战略里程碑。了解这种重要抗原的3D结构对于开发疫苗或新的诊断测试至关重要。在这里,我们报道了∆∆BmSA1的1H、15N和13C NMR共振归属,这是BmSA1一种没有N端信号肽和疏水性C端GPI锚的截短重组版本。使用CSI.3和TALOS-N的二级结构预测显示了高含量的α螺旋结构。这项初步研究为BMSA1的进一步结构表征提供了基础。
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引用次数: 0
Backbone 1H, 13C and 15N assignments of the apo-acyl carrier protein (ACP1) of Pseudomonas aeruginosa 铜绿假单胞菌载脂蛋白载体蛋白(ACP1)骨架1H, 13C和15N的分配
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2023-07-08 DOI: 10.1007/s12104-023-10138-2
Madison Rizzo, Eric Baggs, Abu Sayeed Chowdhury, Rajesh Nagarajan, Lisa Rose Warner

The N-acyl-L-homoserine lactone (AHL) quorum sensing regulates virulence in the opportunistic pathogen, Pseudomonas aeruginosa. The LasI and RhlI AHL synthases use acyl carrier protein substrates to synthesize, respectively, the 3-oxododecanoyl-L-homoserine lactone (3-oxoC12-HSL) and butyryl-L-homoserine lactone (C4-HSL) QS signals for this bacterium. Although P. aeruginosa genome contains three open reading frames to encode three acyl carrier proteins, namely the ACP1, ACP2 and ACP3, microarray and gene replacement studies show that only the ACP1 carrier protein is under quorum sensing regulation. In this study, we isotopically enriched one of the acyl carrier proteins, ACP1 from P. aeruginosa and describe the backbone resonance assignments for this protein to delineate the structural and molecular basis of ACP1 recognition in P. aeruginosa AHL quorum sensing signal synthesis.

N-酰基-L-丝氨酸内酯(AHL)群体感应调节机会性病原体铜绿假单胞菌的毒力。LasI和RhlI-AHL合成酶使用酰基载体蛋白底物分别合成该细菌的3-氧代十二烷酰基-L-高丝氨酸内酯(3-氧代C12-HSL)和丁酰基-L-高丝氨酸内酯(C4-HSL)QS信号。尽管铜绿假单胞菌基因组包含三个开放阅读框来编码三种酰基载体蛋白,即ACP1、ACP2和ACP3,但微阵列和基因替换研究表明,只有ACP1载体蛋白处于群体感应调控之下。在本研究中,我们同位素富集了来自铜绿假单胞菌的酰基载体蛋白之一ACP1,并描述了该蛋白的骨架共振分配,以描述ACP1在铜绿假单胞杆菌AHL群体感应信号合成中识别的结构和分子基础。
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引用次数: 0
Chemical shift assignments of dsRBD1 and linker region of R2D2, a siRNA binding protein in the Drosophila RNAi pathway 果蝇RNAi通路中siRNA结合蛋白dsRBD1和R2D2连接区域的化学位移定位。
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2023-07-05 DOI: 10.1007/s12104-023-10143-5
Ramdas Aute, Mandar V. Deshmukh

In the model organism Drosophila melanogaster, one of the Dicer homologs, Dcr-2, initiates the RNA interference pathway by cleaving long double-stranded RNA into small interfering RNA (siRNA). The Dcr-2:R2D2 heterodimer subsequently binds to the 21-nucleotide siRNA to form the R2D2:Dcr-2 Initiator (RDI) complex, which is critical for initiating the assembly of the RNA-induced silencing complex containing guide siRNA strand. During RDI complex formation, R2D2 senses the stability of the 5′ end of the siRNA and a 5′-phosphate group, although the underlying mechanism of siRNA asymmetry sensing and 5′-phosphate recognition by R2D2 is elusive. In this study, we present nearly complete chemical shift assignments of the backbone and the side chain of a construct that comprises the N-terminus dsRBD1 and linker of R2D2 (~ 10.3 kDa; henceforth: R2D2D1L). Our study would further aid in the structural and functional characterization of R2D2.

在模型生物果蝇中,Dicer同源物之一Dcr-2通过将长双链RNA切割成小干扰RNA(siRNA)来启动RNA干扰途径。Dcr-2:R2D2异二聚体随后与21个核苷酸的siRNA结合以形成R2D2:Dcr-2启动子(RDI)复合物,其对于启动包含引导siRNA链的RNA诱导沉默复合物的组装至关重要。在RDI复合物形成过程中,R2D2感知siRNA的5’端和5’-磷酸基团的稳定性,尽管R2D2对siRNA不对称感知和5’–磷酸识别的潜在机制尚不清楚。在这项研究中,我们提出了一种构建体的主链和侧链几乎完全的化学位移分配,该构建体包括R2D2的N-末端dsRBD1和接头(~ 10.3kDa;以下简称R2D2D1L)。我们的研究将进一步有助于R2D2的结构和功能表征。
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引用次数: 0
Backbone 1H, 15N and 13C resonance assignments for dengue NS2B without the NS3 protease cofactor region in detergent micelles 洗涤剂胶束中不含NS3蛋白酶辅因子区的登革NS2B的主链1H、15N和13C共振分配
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2023-07-05 DOI: 10.1007/s12104-023-10142-6
Qingxin Li, Hui Qi Ng, Ying Ru Loh, CongBao Kang

Dengue virus is an important human pathogen affecting people especially in tropical and subtropical regions. Its genome encodes seven non-structural proteins that are important for viral assembly and replication. Dengue NS2B is a membrane protein containing four transmembrane helices and involved in protein-protein interactions. Its transmembrane helices are critical for location of NS2B on the cell membrane while one cytoplasmic region composed of approximately 40 amino acids serves as a cofactor of viral NS3 protease by forming a tight complex with the N-terminal region of NS3. Here, we report the backbone resonance assignments for a dengue NS2B construct referred to as mini-NS2B containing only the transmembrane regions without NS3 cofactor region in detergent micelles. Mini-NS2B exhibits well-dispersed cross-peaks in the 1H-15N-HSQC spectrum and contains four helices in solution. The available mini-NS2B and its assignment will be useful for determining the structure of NS2B and identifying small molecules binding to the transmembrane regions.

登革热病毒是一种重要的人类病原体,影响着热带和亚热带地区的人们。它的基因组编码七种对病毒组装和复制很重要的非结构蛋白。登革热NS2B是一种含有四个跨膜螺旋并参与蛋白质-蛋白质相互作用的膜蛋白。其跨膜螺旋对于NS2B在细胞膜上的定位至关重要,而由大约40个氨基酸组成的一个细胞质区域通过与NS3的N末端区域形成紧密复合物而充当病毒NS3蛋白酶的辅因子。在这里,我们报道了登革热NS2B构建体(称为mini-NS2B)的主链共振分配,该构建体在洗涤剂胶束中仅包含不含NS3辅因子区域的跨膜区域。Mini-NS2B在1H-15N-HSQC光谱中表现出良好分散的交叉峰,并且在溶液中含有四个螺旋。可用的mini-NS2B及其分配将有助于确定NS2B的结构和鉴定与跨膜区域结合的小分子。
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引用次数: 0
1H, 13C, and 15N resonance assignments of SarA monomer from Staphylococcus aureus in complex with DNA 金黄色葡萄球菌SarA单体与DNA复合物的1H、13C和15N共振归属
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2023-07-05 DOI: 10.1007/s12104-023-10140-8
Dihong Fu, Bo Duan, Xianzhi Dong, Bin Xia

SarA is a global transcription regulator in S. aureus which regulates the expression of over 120 genes related to quorum sensing, biofilm synthesis, drug resistance and many other important physiological processes during host infection. SarA can bind to the promoter region of agr and other target genes to activate or repress the transcription. The crystal structure of SarA uncovered a MarR protein-like conformation with two symmetrical winged helix domains, while its DNA binding mechanism is still unknown. We have constructed a monomeric DNA binding domain of SarA (SarAΔN19) for the study of the interaction between SarA and DNA with NMR spectroscopy. Here, we report the 1H, 13C and 15N NMR assignment of SarAΔN19/DNA complex which is the first step towards further structure and function analysis.

SarA是金黄色葡萄球菌的一种全局转录调节因子,在宿主感染期间调节120多个与群体感应、生物膜合成、耐药性和许多其他重要生理过程有关的基因的表达。SarA可以与agr和其他靶基因的启动子区结合,激活或抑制转录。SarA的晶体结构揭示了具有两个对称翼螺旋结构域的MarR蛋白样构象,而其DNA结合机制尚不清楚。我们构建了SarA的单体DNA结合结构域(SarAΔN19),用于NMR光谱研究SarA与DNA之间的相互作用。在此,我们报道了SarAΔN19/DNA复合物的1H、13C和15N NMR归属,这是进一步结构和功能分析的第一步。
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引用次数: 0
Resonance assignments of the PUB domain of the RNF31 protein RNF31蛋白PUB结构域的共振配位。
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2023-07-03 DOI: 10.1007/s12104-023-10139-1
Lanlan Song, Fumei Zhong, Xiaoming Tu, Jiahai Zhang

E3 ubiquitin protein ligase RNF31 is present in human proteins and is involved in linear ubiquitin chain assembly complex (LUBAC) activity and cell growth. RNF31 is involved in ubiquitination, which is the post-translational modification of proteins. Ubiquitin molecules connect with amino acid residues of target proteins under the action of ubiquitin-activating enzyme E1, ubiquitin binding enzyme E2 and ubiquitin ligase E3, so as to achieve certain physiological functions. The abnormal expression of ubiquitination promotes the formation of cancer. In studies of breast cancer, RNF31 mRNA levels were found to be higher in cancer cells than in other tissues. The PUB domain of RNF31 is the binding site of the ubiquitin thioesterase otulin. Here, we report the backbone and side-chain resonance assignments of the PUB domain of RNF31 and study the backbone relaxation of the domain. These studies will contribute to further understanding of the structural and functional relationship of RNF31 protein, which may also be a target for drug research.

E3泛素蛋白连接酶RNF31存在于人类蛋白质中,并参与线性泛素链组装复合体(LUBAC)活性和细胞生长。RNF31参与泛素化,泛素化是蛋白质的翻译后修饰。泛素分子在泛素激活酶E1、泛素结合酶E2和泛素连接酶E3的作用下与靶蛋白的氨基酸残基连接,从而实现一定的生理功能。泛素化的异常表达促进了癌症的形成。在对癌症的研究中,发现癌症细胞中RNF31mRNA水平高于其他组织。RNF31的PUB结构域是泛素硫酯酶otulin的结合位点。在这里,我们报道了RNF31的PUB结构域的主链和侧链共振分配,并研究了该结构域的骨架弛豫。这些研究将有助于进一步了解RNF31蛋白的结构和功能关系,这也可能是药物研究的目标。
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引用次数: 0
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Biomolecular NMR Assignments
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