Biomolecular NMR Assignments最新文献_第10页

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

Biomolecular NMR Assignments 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

{"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, Periklis Charalampous, Aikaterini C. Tsika, Konstantina P. Kravvariti, Christos Sideras-Bisdekis, Angelo Gallo, Georgios A. Spyroulias","doi":"10.1007/s12104-022-10110-6","DOIUrl":"10.1007/s12104-022-10110-6","url":null,"abstract":"<div>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.</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

Biomolecular NMR Assignments 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

{"title":"Assignment of IVL-Methyl side chain of the ligand-free monomeric human MALT1 paracaspase-IgL3 domain in solution","authors":"Xiao Han, Maria Levkovets, Dmitry Lesovoy, Renhua Sun, Johan Wallerstein, Tatyana Sandalova, Tatiana Agback, Adnane Achour, Peter Agback, Vladislav Yu. Orekhov","doi":"10.1007/s12104-022-10105-3","DOIUrl":"10.1007/s12104-022-10105-3","url":null,"abstract":"<div>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).</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

Biomolecular NMR Assignments Pub Date : 2022-09-09 DOI: 10.1007/s12104-022-10109-z

Houman Ghasriani, Sara Ahmadi, Derek J. Hodgson, Yves Aubin

{"title":"Backbone and side-chain resonance assignments of the NISTmAb-scFv and antigen-binding study","authors":"Houman Ghasriani, Sara Ahmadi, Derek J. Hodgson, Yves Aubin","doi":"10.1007/s12104-022-10109-z","DOIUrl":"10.1007/s12104-022-10109-z","url":null,"abstract":"<div>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.</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

Backbone and side chain NMR assignments for the ribosome maturation factor P (RimP) from Staphylococcus aureus 金黄色葡萄球菌核糖体成熟因子P (RimP)的主链和侧链核磁共振鉴定

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2022-09-07 DOI: 10.1007/s12104-022-10106-2

Natalia S. Garaeva, Aydar G. Bikmullin, Bulat F. Fatkhullin, Shamil Z. Validov, Bruno Keiffer, Marat M. Yusupov, Konstantin S. Usachev

{"title":"Backbone and side chain NMR assignments for the ribosome maturation factor P (RimP) from Staphylococcus aureus","authors":"Natalia S. Garaeva, Aydar G. Bikmullin, Bulat F. Fatkhullin, Shamil Z. Validov, Bruno Keiffer, Marat M. Yusupov, Konstantin S. Usachev","doi":"10.1007/s12104-022-10106-2","DOIUrl":"10.1007/s12104-022-10106-2","url":null,"abstract":"<div>The ribosomal maturation factor (RimP) is a 17.7 kDa protein and is the assembly factor of the 30S subunit. RimP is essential for efficient processing of 16S rRNA and maturation (assembly) of the 30S ribosome. It was suggested that RimP takes part in stabilization of the central pseudoknot at the early stages of the 30S subunit maturation, and this \u0000process may occur before the head domain assembly and later stages of the 30S assembly, but the mechanism of this interaction is still not fully understood. Here we report the assignment of the 1H, 13C and 15N chemical shift in the backbone and side chains of RimP from Staphylococcus aureus. Analysis of chemical shifts of the main chain using TALOS + suggests that the RimP contains eight β-strands and three α-helices with the topology α1-β1-β2-α2- β3- α3- β4- β5- β6- β7- β8. Structural studies of RimP and its complex with the ribosome by integrated structural biology approaches (NMR spectroscopy, X-ray diffraction analysis and cryoelectron microscopy) will allow further screening of highly selective inhibitors of the translation of S. aureus.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"16 2","pages":"373 - 377"},"PeriodicalIF":0.9,"publicationDate":"2022-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-022-10106-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4323308","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: 1

Backbone and side chain NMR assignment of the heme-nitric oxide/oxygen binding (H-NOX) domain from Nostoc punctiforme Nostoc punctiformme血红素-一氧化氮/氧结合(H-NOX)结构域的主链和侧链核磁共振分配

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2022-09-06 DOI: 10.1007/s12104-022-10107-1

Styliani A. Chasapi, Aikaterini I. Argyriou, Georgios A. Spyroulias

{"title":"Backbone and side chain NMR assignment of the heme-nitric oxide/oxygen binding (H-NOX) domain from Nostoc punctiforme","authors":"Styliani A. Chasapi, Aikaterini I. Argyriou, Georgios A. Spyroulias","doi":"10.1007/s12104-022-10107-1","DOIUrl":"10.1007/s12104-022-10107-1","url":null,"abstract":"<div>Soluble guanylate cyclase (sGC) is considered as the primary NO receptor across several known eukaryotes. The main interest regarding the biological role and its function, focuses on the H-NOX domain of the β1 subunit. This domain in its active form bears a ferrous b type heme as prosthetic group, which facilitates the binding of NO and other diatomic gases. The key point that still needs to be answered is how the protein selectively binds the NO and how the redox state of heme and coordination determines H-NOX active state upon binding of diatomic gases. H-NOX domain is present in the genomes of both prokaryotes and eukaryotes, either as a stand-alone protein domain or as a partner of a larger polypeptide. The biological functions of these signaling modules for a wide range of genomes, diverge considerably along with their ligand binding properties. In this direction, we examine the prokaryotic H-NOX protein domain from Nostoc punctiforme (Npun H-NOX). Herein, we first report the almost complete NMR backbone and side-chain resonance assignment (1H, 13C, 15 N) of Npun H-NOX domain together with the NMR chemical shift-based prediction of the domain’s secondary structure elements.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"16 2","pages":"379 - 384"},"PeriodicalIF":0.9,"publicationDate":"2022-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-022-10107-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4282202","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

Chemical shift assignments of the C-terminal domain of CaBP1 bound to the IQ-motif of voltage-gated Ca2+ channel (CaV1.2) 电压门控Ca2+通道iq基序结合的CaBP1 c端结构域的化学位移赋值(CaV1.2)

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2022-09-05 DOI: 10.1007/s12104-022-10108-0

Ian Salveson, James B. Ames

引用次数: 0

NMR resonance assignment of the N-terminal GTPase domain of human Miro2 Bound to GTP 人类与GTP结合的Miro2的n端GTPase结构域的核磁共振分配

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2022-09-01 DOI: 10.1007/s12104-022-10103-5

Cassandra E. Smith, David N. M. Jones

{"title":"NMR resonance assignment of the N-terminal GTPase domain of human Miro2 Bound to GTP","authors":"Cassandra E. Smith, David N. M. Jones","doi":"10.1007/s12104-022-10103-5","DOIUrl":"10.1007/s12104-022-10103-5","url":null,"abstract":"<div>Miro2 and Miro1 are mitochondrial-associated proteins critical for regulating mitochondrial movement within the cell. Both Miro1 and Miro2 have roles in promoting neuron function, but recently Miro2 has been shown to have additional roles in response to nutrient starvation in tumor cells. Miro1 and 2 consist of two small GTPase domains flanking a pair of EF-hands. The N-terminal GTPase (nGTPase) domain is responsible for initiating mitochondrial trafficking and interactions with GCN1 in prostate cancer. The crystal structure of Miro1 nGTPase bound to GTP has been solved. However, no structural data is available for the nGTPase domain of Miro2. To better understand the similarities and differences in the functions of Miro1 and Miro2, we have initiated structural studies of Miro2. Here we report the backbone NMR chemical shift assignments of a 22 KDa construct of the nGTPase domain of Miro2 bound to GTP that includes residues 1–180 of the full-length protein. We affirm that the overall secondary structure of this complex closely resembles that of Miro1 nGTPase bound to GTP. Minor variations in the overall structures can be attributed to crystal packing interactions in the structure of Miro1. These NMR studies will form the foundation for future work identifying the specific interaction sites between Miro2 and its cellular binding partners.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"16 2","pages":"349 - 355"},"PeriodicalIF":0.9,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-022-10103-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4063009","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

Chemical shift assignments of a fusion protein comprising the C-terminal-deleted hepatitis B virus X protein BH3-like motif peptide and Bcl-xL 包含c端缺失的乙型肝炎病毒X蛋白bh3样基序肽和Bcl-xL的融合蛋白的化学位移定位

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2022-08-31 DOI: 10.1007/s12104-022-10104-4

Hideki Kusunoki, Isao Hamaguchi, Naohiro Kobayashi, Takashi Nagata

{"title":"Chemical shift assignments of a fusion protein comprising the C-terminal-deleted hepatitis B virus X protein BH3-like motif peptide and Bcl-xL","authors":"Hideki Kusunoki, Isao Hamaguchi, Naohiro Kobayashi, Takashi Nagata","doi":"10.1007/s12104-022-10104-4","DOIUrl":"10.1007/s12104-022-10104-4","url":null,"abstract":"<div>Chronic hepatitis B virus (HBV) infection is a major risk factor for the development of liver diseases including fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). HBV has the multifunctional protein, HBV X protein (HBx, 154 residues), which plays key roles in HBV replication and liver disease development. Interaction of HBx through its BH3-like motif with the anti-apoptotic protein Bcl-xL leads to HBV replication and induction of apoptosis, resulting in HCC development. Our previous nuclear magnetic resonance (NMR) study revealed that the HBx BH3-like motif peptide (residues 101–136) binds to the common BH3-binding groove of Bcl-xL. Importantly, a C-terminal-truncated HBx, e.g., residues 1–120 of HBx, is strongly associated with the increased risk of HBV-related HCC development. However, the interaction mode between the C-terminal-truncated HBx and Bcl-xL remains unclear. To elucidate this interaction mode, the C-terminal-deleted HBx BH3-like motif peptide (residues 101–120) was used as a model peptide in this study. To facilitate the NMR analysis, we prepared a fusion protein of HBx (101–120) and Bcl-xL connected with five repeats of the glycine-serine dipeptide as a linker. Here, we report the 1H, 13C, and 15N resonance assignments of the fusion protein. This is the first step for the elucidation of the pathogenesis of liver diseases caused by the interaction between the C-terminal-truncated HBx and Bcl-xL.</div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"16 2","pages":"357 - 361"},"PeriodicalIF":0.9,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-022-10104-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4046843","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 resonance assignment of the enzyme KdgF from Bacteroides eggerthii 蛋拟杆菌KdgF酶的1H, 13C, 15N共振分配

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2022-08-30 DOI: 10.1007/s12104-022-10102-6

Agnes Beenfeldt Petersen, Idd Andrea Christensen, Mette E. Rønne, Emil G. P. Stender, David Teze, Birte Svensson, Finn Lillelund Aachmann

引用次数: 0

Resonance assignments of the ORC2-WH domain of the human ORC protein 人ORC蛋白ORC2-WH结构域的共振配位

IF 0.9 4区生物学

Biomolecular NMR Assignments Pub Date : 2022-08-11 DOI: 10.1007/s12104-022-10100-8

Lanlan Song, Xiaoming Tu, Jiahai Zhang

引用次数: 0