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1H, 15N and 13C resonance assignments of a minimal CPSF73-CPSF100 C-terminal heterodimer 最小CPSF73-CPSF100 c端异二聚体的1H, 15N和13C共振分配
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2023-02-01 DOI: 10.1007/s12104-023-10118-6
Stéphane Thore, Sébastien Fribourg, Cameron D. Mackereth

The initial pre-mRNA transcript in eukaryotes is processed by a large multi-protein complex in order to correctly cleave the 3’ end, and to subsequently add the polyadenosine tail. This cleavage and polyadenylation specificity factor (CPSF) is composed of separate subunits, with structural information available for both isolated subunits and also larger assembled complexes. Nevertheless, certain key components of CPSF still lack high-resolution atomic data. One such region is the heterodimer formed between the first and second C-terminal domains of the endonuclease CPSF73, with those from the catalytically inactive CPSF100. Here we report the backbone and sidechain resonance assignments of a minimal C-terminal heterodimer of CPSF73–CPSF100 derived from the parasite Encephalitozoon cuniculi. The assignment process used several amino-acid specific labeling strategies, and the chemical shift values allow for secondary structure prediction.

真核生物中最初的pre-mRNA转录物由一个大的多蛋白复合物加工,以正确地切割3 '端,并随后添加聚腺苷尾部。这种切割和聚腺苷酸化特异性因子(CPSF)由独立的亚基组成,其结构信息可用于分离的亚基和更大的组装复合物。然而,CPSF的某些关键组件仍然缺乏高分辨率的原子数据。其中一个区域是在内切酶CPSF73的第一和第二c端结构域之间形成的异二聚体,这些区域来自催化活性不强的CPSF100。在这里,我们报道了CPSF73-CPSF100的最小c端异二聚体的主链和侧链共振分配。分配过程使用了几种氨基酸特异性标记策略,化学位移值允许二级结构预测。
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引用次数: 1
The 1H, 15N and 13C resonance assignments of dengue virus capsid protein with the deletion of the intrinsically disordered N-terminal region 登革病毒衣壳蛋白内在无序n端缺失的1H、15N和13C共振配位
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2023-02-01 DOI: 10.1007/s12104-022-10115-1
Glauce M. Barbosa, Maria A. Morando, Andrea T. Da Poian, Fabio C. L. Almeida

Dengue virus belongs to the Flaviviridae family, being responsible for an endemic arboviral disease in humans. It is an enveloped virus, whose genome is a positive-stranded RNA packaged by the capsid protein. Dengue virus capsid protein (DENVC) forms homodimers in solution organized in 4 α-helices and an intrinsically disordered N-terminal region. The N-terminal region is involved in the binding of membranous structures in host cells and in the recognition of nucleotides. Here we report the 1H, 15N and 13C resonance assignments of the DENVC with the deletion of the first 19 intrinsically disordered residues. The backbone chemical shift perturbations suggest changes in the α1 and α2 helices between full length and the truncated proteins.

登革热病毒属于黄病毒科,是造成人类地方病的一种虫媒病毒性疾病。它是一种包膜病毒,其基因组是由衣壳蛋白包装的正链RNA。登革病毒衣壳蛋白(DENVC)在4 α-螺旋和内在无序的n端区中形成同型二聚体。n端区域参与宿主细胞膜结构的结合和核苷酸的识别。在这里,我们报道了DENVC的1H, 15N和13C共振分配,删除了前19个本质无序残基。主链化学位移扰动表明全长和截断的蛋白之间α1和α2螺旋发生了变化。
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引用次数: 0
1H, 15N, 13C backbone and sidechain resonance assignments and secondary structure of mouse NOTCH1 EGF27 小鼠NOTCH1 EGF27的1H, 15N, 13C骨干和侧链共振分配和二级结构
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2022-12-24 DOI: 10.1007/s12104-022-10116-0
Justin A. Grennell, Kendra D. Jenkins, Kelvin B. Luther, John Glushka, Robert S. Haltiwanger, Megan A. Macnaughtan

NOTCH1 is a transmembrane receptor in metazoans that is linked to a variety of disorders. The receptor contains an extracellular domain (ECD) with 36 tandem epidermal growth factor-like (EGF) repeats. The ECD is responsible for intercellular signaling via protein–ligand interactions with neighboring cells. Each EGF repeat consists of approximately 40 amino acids and 3 conserved disulfide bonds. The Abruptex region (EGF24-29) is critical for NOTCH1 signaling and is known for its missense mutations. Certain EGF repeats are modified with the addition of O-linked glycans and many have calcium binding sites, which give each EGF repeat a unique function. It has been shown that the loss of the O-fucose site of EGF27 alters NOTCH1 activity. To investigate the role of glycosylation in the NOTCH1 signaling pathway, nuclear magnetic resonance spectroscopy has been employed to study the structures of EGF27 and its glycoforms. Here, we report the backbone and sidechain 1H, 15N, and 13C-resonance assignments of the unmodified EGF27 protein and the predicted secondary structure derived from the assigned chemical shifts.

NOTCH1是后生动物中的一种跨膜受体,与多种疾病有关。该受体包含一个细胞外结构域(ECD),具有36个串联表皮生长因子样(EGF)重复序列。ECD通过与邻近细胞的蛋白质配体相互作用负责细胞间信号传导。每个EGF重复序列由大约40个氨基酸和3个保守的二硫键组成。Abruptex区域(EGF24-29)对NOTCH1信号传导至关重要,并以其错义突变而闻名。某些EGF重复序列通过添加o链聚糖进行修饰,并且许多具有钙结合位点,这使每个EGF重复序列具有独特的功能。研究表明,EGF27 O-聚焦位点的缺失会改变NOTCH1的活性。为了研究糖基化在NOTCH1信号通路中的作用,我们利用核磁共振波谱技术研究了EGF27及其糖型的结构。在这里,我们报告了未修饰的EGF27蛋白的主链和侧链1H, 15N和13c共振分配以及由分配的化学位移得出的预测二级结构。
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引用次数: 0
1H, 13C, and 15N assignments of the mRNA binding protein hnRNP A18 mRNA结合蛋白hnRNP A18的1H, 13C和15N分配
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2022-12-21 DOI: 10.1007/s12104-022-10117-z
Katherine M. Coburn, Braden Roth, Kristen M. Varney, France Carrier, David J. Weber

Heterogeneous ribonuclear protein A18 (hnRNP A18) is an RNA binding protein (RBP) involved in the hypoxic cellular stress response and regulation of cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) expression in melanoma, breast cancer, prostate cancer, and colon cancer solid tumors. hnRNP A18 is comprised of an N-terminal structured RNA recognition motif (RMM) and a C-terminal intrinsically disordered domain (IDD). Upon cellar stressors, such as UV and hypoxia, hnRNP A18 is phosphorylated by casein kinase 2 (CK2) and glycogen synthase kinase 3β (GSK-3β). After phosphorylation, hnRNP A18 translocates from the nucleus to the cytosol where it interacts with pro-survival mRNA transcripts for proteins such as hypoxia inducible factor 1α and CTLA-4. Both the hypoxic cellular response and modulation of immune checkpoints by cancer cells promote chemoradiation resistance and metastasis. In this study, the 1 H, 13 C, and 15 N backbone and sidechain resonances of the 172 amino acid hnRNP A18 were assigned sequence-specifically and provide a framework for future NMR-based drug discovery studies toward targeting hnRNP A18. These data will also enable the investigation of the dynamic structural changes within the IDD of hnRNP A18 upon phosphorylation by CK2 and GSK-3β to provide critical insight into the structure and function of IDDs.

异质核糖核蛋白A18 (hnRNP A18)是一种RNA结合蛋白(RBP),在黑色素瘤、乳腺癌、前列腺癌和结肠癌实体瘤中参与缺氧细胞应激反应和细胞毒性t淋巴细胞相关蛋白4 (CTLA-4)表达的调节。hnRNP A18由一个n端结构化RNA识别基序(RMM)和一个c端内在无序结构域(IDD)组成。在低温胁迫条件下,如紫外线和缺氧,hnRNP A18被酪蛋白激酶2 (CK2)和糖原合成酶激酶3β (GSK-3β)磷酸化。磷酸化后,hnRNP A18从细胞核转运到细胞质,在那里它与促存活mRNA转录物相互作用,如缺氧诱导因子1α和CTLA-4。低氧细胞反应和癌细胞免疫检查点的调节都促进了放化疗抵抗和转移。在这项研究中,172个氨基酸hnRNP A18的1 H、13 C和15 N的主链和侧链共振被指定为序列特异性,并为未来针对hnRNP A18的基于nmr的药物发现研究提供了框架。这些数据也将使研究hnRNP A18被CK2和GSK-3β磷酸化后IDD内的动态结构变化成为可能,从而为IDD的结构和功能提供关键的见解。
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引用次数: 1
1H, 13C and 15N assignment of the human mitochondrial paramagnetic iron–sulfur protein CISD3 人线粒体顺磁铁硫蛋白CISD3的1H, 13C和15N分配
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2022-12-15 DOI: 10.1007/s12104-022-10113-3
José Malanho Silva, Deborah Grifagni, Francesca Cantini, Mario Piccioli

CISD3 is a mitochondrial protein that contains two [2Fe–2S] clusters. This protein is overexpressed in some types of cancer, so it has emerged as a potential drug target. A detailed characterization of this protein is crucial to understand how CISD3 is involved in these physiopathologies. In this study, isotopically labeled human CISD3 was expressed in Escherichia coli. A set of double and triple resonance experiments performed with standard parameters/datasets provided the assignment of 40% of the HN resonances, 47% of Cα, and 46% of C′ resonances. Tailored paramagnetic HSQC, CON and CACO experiments extended up to 59% for HN, 70% for Cα and 69% for C′. The 1H, 13C and 15N NMR chemical shift assignment of human CISD3 is reported here.

CISD3是一种线粒体蛋白,包含两个[2Fe-2S]簇。这种蛋白在某些类型的癌症中过度表达,因此它已成为潜在的药物靶点。该蛋白的详细表征对于理解CISD3如何参与这些生理病理至关重要。在这项研究中,同位素标记的人CISD3在大肠杆菌中表达。使用标准参数/数据集进行的一组双共振和三共振实验提供了40%的HN共振,47%的Cα和46%的C '共振的分配。定制顺磁HSQC, CON和CACO实验扩展到HN的59%,Cα的70%和C '的69%。本文报道了人CISD3的1H、13C和15N核磁共振化学位移分配。
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引用次数: 1
1H, 15N and 13C backbone resonance assignments of the acidic domain of the human MDM2 protein 人MDM2蛋白酸性结构域的1H, 15N和13C骨干共振分配
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2022-10-29 DOI: 10.1007/s12104-022-10112-4
Qinyan Song, Xiang-Qin Liu, Jan K. Rainey

The human MDM2 protein regulates the tumor suppressor protein p53 by restricting its transcriptional activity and by promoting p53 degradation. MDM2 is ubiquitously expressed, with its overexpression implicated in many forms of cancer. The inhibitory effects of MDM2 on p53 have been shown to involve its N-terminal p53-binding domain and its C-terminal RING domain. The presence of an intact central acidic domain of MDM2 has also been shown to regulate p53 ubiquitination, with this domain shown to directly interact with the p53 DNA-binding domain to regulate the DNA binding activity of p53. To date, little structural information has been obtained for the MDM2 acidic domain. Thus, to gain insight into the structure and function relationship of this region, we have applied solution-state NMR spectroscopy to characterize the segment of MDM2 spanning residues 215–300. These boundaries for the acidic domain were determined on the basis of consensus observed in multiple sequence alignment. Here, we report the 1H, 15N and 13C backbone and 13Cβ chemical shift assignments and steady-state {1H}-15N heteronuclear NOE enhancement factors as a function of residue for the acidic domain of MDM2. We show that this domain exhibits the hallmarks of being a disordered protein, on the basis both of assigned chemical shifts and residue-level backbone dynamics, with localized variation in secondary structure propensity inferred from chemical shift analysis.

人MDM2蛋白通过限制肿瘤抑制蛋白p53的转录活性和促进p53的降解来调节肿瘤抑制蛋白p53。MDM2普遍表达,其过表达与多种形式的癌症有关。MDM2对p53的抑制作用涉及其n端p53结合域和c端RING结构域。完整的MDM2中心酸性结构域的存在也被证明可以调节p53的泛素化,该结构域被证明可以直接与p53的DNA结合结构域相互作用,从而调节p53的DNA结合活性。迄今为止,关于MDM2酸性结构域的结构信息很少。因此,为了深入了解该区域的结构和功能关系,我们应用溶液态核磁共振光谱对MDM2跨越残基215-300的片段进行了表征。这些酸性区域的边界是根据在多个序列比对中观察到的一致性确定的。本文报道了MDM2酸性结构域残基的1H、15N和13C主链和13Cβ化学位移赋值以及稳态{1H}-15N异核NOE增强因子的变化。我们表明,该结构域显示出无序蛋白的特征,基于指定的化学位移和残基水平的骨干动力学,以及从化学位移分析推断的二级结构倾向的局部变化。
{"title":"1H, 15N and 13C backbone resonance assignments of the acidic domain of the human MDM2 protein","authors":"Qinyan Song,&nbsp;Xiang-Qin Liu,&nbsp;Jan K. Rainey","doi":"10.1007/s12104-022-10112-4","DOIUrl":"10.1007/s12104-022-10112-4","url":null,"abstract":"<div><p>The human MDM2 protein regulates the tumor suppressor protein p53 by restricting its transcriptional activity and by promoting p53 degradation. MDM2 is ubiquitously expressed, with its overexpression implicated in many forms of cancer. The inhibitory effects of MDM2 on p53 have been shown to involve its N-terminal p53-binding domain and its C-terminal RING domain. The presence of an intact central acidic domain of MDM2 has also been shown to regulate p53 ubiquitination, with this domain shown to directly interact with the p53 DNA-binding domain to regulate the DNA binding activity of p53. To date, little structural information has been obtained for the MDM2 acidic domain. Thus, to gain insight into the structure and function relationship of this region, we have applied solution-state NMR spectroscopy to characterize the segment of MDM2 spanning residues 215–300. These boundaries for the acidic domain were determined on the basis of consensus observed in multiple sequence alignment. Here, we report the <sup>1</sup>H, <sup>15</sup>N and <sup>13</sup>C backbone and <sup>13</sup>C<sub>β</sub> chemical shift assignments and steady-state {<sup>1</sup>H}-<sup>15</sup>N heteronuclear NOE enhancement factors as a function of residue for the acidic domain of MDM2. We show that this domain exhibits the hallmarks of being a disordered protein, on the basis both of assigned chemical shifts and residue-level backbone dynamics, with localized variation in secondary structure propensity inferred from chemical shift analysis.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 1","pages":"9 - 16"},"PeriodicalIF":0.9,"publicationDate":"2022-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-022-10112-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5132648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
1H, 13C, 15N backbone resonance assignment of apo and ADP-ribose bound forms of the macro domain of Hepatitis E virus through solution NMR spectroscopy 戊型肝炎病毒大结构域载脂蛋白和adp核糖结合形式的1H, 13C, 15N骨干共振分配
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2022-10-22 DOI: 10.1007/s12104-022-10111-5
Maria D. Politi, Angelo Gallo, Georgios Bouras, Maria Birkou, Bruno Canard, Bruno Coutard, Georgios A. Spyroulias

The genome of Hepatitis E virus (HEV) is 7.2 kilobases long and has three open reading frames. The largest one is ORF1, encoding a non-structural protein involved in the replication process, and whose processing is ill-defined. The ORF1 protein is a multi-modular protein which includes a macro domain (MD). MDs are evolutionarily conserved structures throughout all kingdoms of life. MDs participate in the recognition and removal of ADP-ribosylation, and specifically viral MDs have been identified as erasers of ADP-ribose moieties interpreting them as important players at escaping the early stages of host-immune response. A detailed structural analysis of the apo and bound to ADP-ribose state of the native HEV MD would provide the structural information to understand how HEV MD is implicated in virus-host interplay and how it interacts with its intracellular partner during viral replication. In the present study we present the high yield expression of the native macro domain of HEV and its analysis by solution NMR spectroscopy. The HEV MD is folded in solution and we present a nearly complete backbone and sidechains assignment for apo and bound states. In addition, a secondary structure prediction by TALOS + analysis was performed. The results indicated that HEV MD has a α/β/α topology very similar to that of most viral macro domains.

戊型肝炎病毒(HEV)的基因组长7.2千碱基,有三个开放阅读框。最大的一个是ORF1,它编码一种参与复制过程的非结构蛋白,其加工过程不明确。ORF1蛋白是一种包含宏结构域(MD)的多模块蛋白。MDs是所有生物王国中进化上保守的结构。MDs参与adp核糖基化的识别和去除,特别是病毒MDs被鉴定为adp核糖片段的擦除者,这解释了它们在逃避宿主免疫反应的早期阶段是重要的参与者。对天然HEV MD的载脂蛋白和adp核糖结合状态的详细结构分析将提供结构信息,以了解HEV MD如何参与病毒-宿主相互作用以及在病毒复制过程中它如何与细胞内伙伴相互作用。本文报道了HEV原生宏结构域的高产表达及其溶液核磁共振光谱分析。HEV MD在溶液中折叠,我们给出了载脂蛋白和结合态的几乎完整的主链和侧链分配。此外,利用TALOS +分析进行了二级结构预测。结果表明,HEV MD具有与大多数病毒宏结构域非常相似的α/β/α拓扑结构。
{"title":"1H, 13C, 15N backbone resonance assignment of apo and ADP-ribose bound forms of the macro domain of Hepatitis E virus through solution NMR spectroscopy","authors":"Maria D. Politi,&nbsp;Angelo Gallo,&nbsp;Georgios Bouras,&nbsp;Maria Birkou,&nbsp;Bruno Canard,&nbsp;Bruno Coutard,&nbsp;Georgios A. Spyroulias","doi":"10.1007/s12104-022-10111-5","DOIUrl":"10.1007/s12104-022-10111-5","url":null,"abstract":"<div><p>The genome of Hepatitis E virus (HEV) is 7.2 kilobases long and has three open reading frames. The largest one is ORF1, encoding a non-structural protein involved in the replication process, and whose processing is ill-defined. The ORF1 protein is a multi-modular protein which includes a macro domain (MD). MDs are evolutionarily conserved structures throughout all kingdoms of life. MDs participate in the recognition and removal of ADP-ribosylation, and specifically viral MDs have been identified as erasers of ADP-ribose moieties interpreting them as important players at escaping the early stages of host-immune response. A detailed structural analysis of the <i>apo</i> and bound to ADP-ribose state of the native HEV MD would provide the structural information to understand how HEV MD is implicated in virus-host interplay and how it interacts with its intracellular partner during viral replication. In the present study we present the high yield expression of the native macro domain of HEV and its analysis by solution NMR spectroscopy. The HEV MD is folded in solution and we present a nearly complete backbone and sidechains assignment for <i>apo</i> and bound states. In addition, a secondary structure prediction by TALOS + analysis was performed. The results indicated that HEV MD has a <i>α/β/α</i> topology very similar to that of most viral macro domains.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 1","pages":"1 - 8"},"PeriodicalIF":0.9,"publicationDate":"2022-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-022-10111-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4880695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
NMR study of human macroPARPs domains: 1H, 15N and 13C resonance assignment of hPARP14 macro domain 2 in the free and the ADPr bound state 人类macroPARPs结构域的NMR研究:hPARP14宏观结构域2在自由和ADPr结合状态下的1H, 15N和13C共振分配
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2022-09-15 DOI: 10.1007/s12104-022-10110-6
Nikolaos K. Fourkiotis, Periklis Charalampous, Aikaterini C. Tsika, Konstantina P. Kravvariti, Christos Sideras-Bisdekis, Angelo Gallo, Georgios A. Spyroulias

hPARP14 is a human ADP-ribosyl-transferase (ART) that belongs to the macroPARPs family, together with hPARP9 and hPARP15. It contains a tandem of three macro domains (MD) while each of them has different properties. The first one, namely MD1, has not been reported to exhibit a high binding affinity for ADP-ribose (ADPr) in contrast to the following two (MD2 and MD3). All three MDs exhibit an α/β/α sandwich-like fold as reported by the deposited crystallographic structures. MD2 and MD3 recognize mono-ADP-ribosylated (MARylated) but not poly-ADP-ribosylated (PARylated) substrates and thus they allow hPARP14 to bind its targets, which can be potentially MARylated by its catalytic domain (CD). hPARP14 participates in DNA damage repair process and immune response against viruses like SARS-CoV-2, which also harbors an MD fold. Furthermore, hPARP14 like the other two macroPARPs (hPARP9 and hPARP15), is implicated in numerous types of cancer, such as B-aggressive lymphoma and sarcoma, rendering its MDs as potential important drug targets. Herein, we report the complete NMR backbone and side chain assignment (1H, 13C, 15N) of hPARP14 MD2 in the free and ADPr bound states and the NMR chemical shift-based prediction of its secondary structure elements. This is the first reported NMR study of a hPARP macro domain, paving the way to screen by NMR chemical compounds which may alter the ability of hPARP14 to interact with its substrates affecting its function.

hPARP14是一种人类adp -核糖基转移酶(ART),与hPARP9和hPARP15一起属于macroPARPs家族。它包含三个宏域(MD)的串联,而每个宏域具有不同的性质。第一个,即MD1,与后面两个(MD2和MD3)相比,没有报道显示出对adp核糖(ADPr)的高结合亲和力。三种MDs均表现出α/β/α三明治状褶皱。MD2和MD3识别单adp核糖基化(MARylated)底物,但不识别多adp核糖基化(PARylated)底物,因此它们允许hPARP14结合其靶标,这些靶标可能通过其催化结构域(CD)被MARylated。hPARP14参与DNA损伤修复过程和针对SARS-CoV-2等病毒的免疫反应,SARS-CoV-2也含有MD折叠。此外,hPARP14与其他两个macroPARPs (hPARP9和hPARP15)一样,与许多类型的癌症(如b侵袭性淋巴瘤和肉瘤)有关,使其MDs成为潜在的重要药物靶点。本文报道了hPARP14 MD2在自由和ADPr结合状态下完整的核磁共振主链和侧链分配(1H, 13C, 15N),以及基于核磁共振化学位移的二级结构元素预测。这是首次报道的hPARP宏观结构域的核磁共振研究,为通过核磁共振筛选可能改变hPARP14与其底物相互作用影响其功能的化合物铺平了道路。
{"title":"NMR study of human macroPARPs domains: 1H, 15N and 13C resonance assignment of hPARP14 macro domain 2 in the free and the ADPr bound state","authors":"Nikolaos K. Fourkiotis,&nbsp;Periklis Charalampous,&nbsp;Aikaterini C. Tsika,&nbsp;Konstantina P. Kravvariti,&nbsp;Christos Sideras-Bisdekis,&nbsp;Angelo Gallo,&nbsp;Georgios A. Spyroulias","doi":"10.1007/s12104-022-10110-6","DOIUrl":"10.1007/s12104-022-10110-6","url":null,"abstract":"<div><p>hPARP14 is a human ADP-ribosyl-transferase (ART) that belongs to the macroPARPs family, together with hPARP9 and hPARP15. It contains a tandem of three macro domains (MD) while each of them has different properties. The first one, namely MD1, has not been reported to exhibit a high binding affinity for ADP-ribose (ADPr) in contrast to the following two (MD2 and MD3). All three MDs exhibit an α/β/α sandwich-like fold as reported by the deposited crystallographic structures. MD2 and MD3 recognize mono-ADP-ribosylated (MARylated) but not poly-ADP-ribosylated (PARylated) substrates and thus they allow hPARP14 to bind its targets, which can be potentially MARylated by its catalytic domain (CD). hPARP14 participates in DNA damage repair process and immune response against viruses like SARS-CoV-2, which also harbors an MD fold. Furthermore, hPARP14 like the other two macroPARPs (hPARP9 and hPARP15), is implicated in numerous types of cancer, such as B-aggressive lymphoma and sarcoma, rendering its MDs as potential important drug targets. Herein, we report the complete NMR backbone and side chain assignment (<sup>1</sup>H, <sup>13</sup>C, <sup>15</sup>N) of hPARP14 MD2 in the free and ADPr bound states and the NMR chemical shift-based prediction of its secondary structure elements. This is the first reported NMR study of a hPARP macro domain, paving the way to screen by NMR chemical compounds which may alter the ability of hPARP14 to interact with its substrates affecting its function.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"16 2","pages":"399 - 406"},"PeriodicalIF":0.9,"publicationDate":"2022-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-022-10110-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4635275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Assignment of IVL-Methyl side chain of the ligand-free monomeric human MALT1 paracaspase-IgL3 domain in solution 溶液中无配体单体人MALT1副半乳糖酶- igl3结构域的ivl -甲基侧链的定位
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2022-09-12 DOI: 10.1007/s12104-022-10105-3
Xiao Han, Maria Levkovets, Dmitry Lesovoy, Renhua Sun, Johan Wallerstein, Tatyana Sandalova, Tatiana Agback, Adnane Achour, Peter Agback, Vladislav Yu. Orekhov

Mucosa-associated lymphoid tissue protein 1 (MALT1) plays a key role in adaptive immune responses by modulating specific intracellular signalling pathways that control the development and proliferation of both T and B cells. Dysfunction of these pathways is coupled to the progress of highly aggressive lymphoma as well as to potential development of an array of different immune disorders. In contrast to other signalling mediators, MALT1 is not only activated through the formation of the CBM complex together with the proteins CARMA1 and Bcl10, but also by acting as a protease that cleaves multiple substrates to promote lymphocyte proliferation and survival via the NF-κB signalling pathway. Herein, we present the partial 1H, 13C Ile/Val/Leu-Methyl resonance assignment of the monomeric apo form of the paracaspase-IgL3 domain of human MALT1. Our results provide a solid ground for future elucidation of both the three-dimensional structure and the dynamics of MALT1, key for adequate development of inhibitors, and a thorough molecular understanding of its function(s).

粘膜相关淋巴组织蛋白1 (MALT1)通过调节控制T细胞和B细胞发育和增殖的特异性细胞内信号通路,在适应性免疫应答中发挥关键作用。这些途径的功能障碍与高度侵袭性淋巴瘤的进展以及一系列不同免疫疾病的潜在发展有关。与其他信号介质不同的是,MALT1不仅通过与CARMA1和Bcl10蛋白形成CBM复合物而被激活,而且还作为蛋白酶裂解多种底物,通过NF-κB信号通路促进淋巴细胞增殖和存活。在此,我们提出了部分1H, 13C Ile/Val/ leu -甲基共振分配的人MALT1的paracaspase-IgL3结构域的单体载子形式。我们的研究结果为未来阐明MALT1的三维结构和动力学提供了坚实的基础,这是充分开发抑制剂的关键,并对其功能进行彻底的分子理解。
{"title":"Assignment of IVL-Methyl side chain of the ligand-free monomeric human MALT1 paracaspase-IgL3 domain in solution","authors":"Xiao Han,&nbsp;Maria Levkovets,&nbsp;Dmitry Lesovoy,&nbsp;Renhua Sun,&nbsp;Johan Wallerstein,&nbsp;Tatyana Sandalova,&nbsp;Tatiana Agback,&nbsp;Adnane Achour,&nbsp;Peter Agback,&nbsp;Vladislav Yu. Orekhov","doi":"10.1007/s12104-022-10105-3","DOIUrl":"10.1007/s12104-022-10105-3","url":null,"abstract":"<div><p>Mucosa-associated lymphoid tissue protein 1 (MALT1) plays a key role in adaptive immune responses by modulating specific intracellular signalling pathways that control the development and proliferation of both T and B cells. Dysfunction of these pathways is coupled to the progress of highly aggressive lymphoma as well as to potential development of an array of different immune disorders. In contrast to other signalling mediators, MALT1 is not only activated through the formation of the CBM complex together with the proteins CARMA1 and Bcl10, but also by acting as a protease that cleaves multiple substrates to promote lymphocyte proliferation and survival via the NF-κB signalling pathway. Herein, we present the partial <sup>1</sup>H, <sup>13</sup>C Ile/Val/Leu-Methyl resonance assignment of the monomeric apo form of the paracaspase-IgL<sub>3</sub> domain of human MALT1. Our results provide a solid ground for future elucidation of both the three-dimensional structure and the dynamics of MALT1, key for adequate development of inhibitors, and a thorough molecular understanding of its function(s).</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"16 2","pages":"363 - 371"},"PeriodicalIF":0.9,"publicationDate":"2022-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-022-10105-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4521118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Backbone and side-chain resonance assignments of the NISTmAb-scFv and antigen-binding study NISTmAb-scFv的主链和侧链共振配位和抗原结合研究
IF 0.9 4区 生物学 Q4 BIOPHYSICS Pub Date : 2022-09-09 DOI: 10.1007/s12104-022-10109-z
Houman Ghasriani, Sara Ahmadi, Derek J. Hodgson, Yves Aubin

Monoclonal antibodies (mAbs) therapeutics are the largest and fastest growing class of biologic drugs, amongst which, the vast majority are immunoglobulin G1 (IgG1). Their antigen binding abilities are used for the treatment of immunologic diseases, cancer therapy, reversal of drug effects, and targeting viruses and bacteria. The high importance of therapeutic mAbs and their derivatives has called for the generation of well-characterized standards for method development and calibration. One such standard, the NISTmAb RM 8621 based on the antibody motavizumab, has been developed by the National Institute of Standards and Technologies (NIST) in the US. Here, we present the resonance assignment of the single chain variable fragment, NISTmAb-scFv, that was engineered by linking the variable domains of the heavy and light chains of the NISTmAb. Also, addition of a peptide, corresponding to the target antigen of motavizumab, to samples of NISTmAb-scFv has induced chemical shift perturbations on residues lining the antigen binding interface thereby indicating proper folding of the NISTmAb-scFv.

单克隆抗体(Monoclonal antibodies, mab)是目前发展最快、规模最大的一类生物药物,其中绝大多数是免疫球蛋白G1 (immunoglobulin G1, IgG1)。它们的抗原结合能力被用于治疗免疫疾病、癌症治疗、逆转药物作用以及靶向病毒和细菌。治疗性单克隆抗体及其衍生物的高度重要性要求为方法开发和校准制定具有良好特征的标准。基于motavizumab抗体的NISTmAb RM 8621已由美国国家标准与技术研究所(NIST)开发。在这里,我们提出了单链可变片段NISTmAb- scfv的共振分配,该片段是通过连接NISTmAb重链和轻链的可变结构域而设计的。此外,在NISTmAb-scFv样品中添加与motavizumab靶抗原相对应的肽,可以诱导抗原结合界面衬里残基的化学位移扰动,从而表明NISTmAb-scFv的适当折叠。
{"title":"Backbone and side-chain resonance assignments of the NISTmAb-scFv and antigen-binding study","authors":"Houman Ghasriani,&nbsp;Sara Ahmadi,&nbsp;Derek J. Hodgson,&nbsp;Yves Aubin","doi":"10.1007/s12104-022-10109-z","DOIUrl":"10.1007/s12104-022-10109-z","url":null,"abstract":"<div><p>Monoclonal antibodies (mAbs) therapeutics are the largest and fastest growing class of biologic drugs, amongst which, the vast majority are immunoglobulin G1 (IgG1). Their antigen binding abilities are used for the treatment of immunologic diseases, cancer therapy, reversal of drug effects, and targeting viruses and bacteria. The high importance of therapeutic mAbs and their derivatives has called for the generation of well-characterized standards for method development and calibration. One such standard, the NISTmAb RM 8621 based on the antibody motavizumab, has been developed by the National Institute of Standards and Technologies (NIST) in the US. Here, we present the resonance assignment of the single chain variable fragment, NISTmAb-scFv, that was engineered by linking the variable domains of the heavy and light chains of the NISTmAb. Also, addition of a peptide, corresponding to the target antigen of motavizumab, to samples of NISTmAb-scFv has induced chemical shift perturbations on residues lining the antigen binding interface thereby indicating proper folding of the NISTmAb-scFv.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"16 2","pages":"391 - 398"},"PeriodicalIF":0.9,"publicationDate":"2022-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-022-10109-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4408120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
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Biomolecular NMR Assignments
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