Current Research in Structural Biology最新文献_第9页

Mutations in human SARS-CoV-2 spike proteins, potential drug binding and epitope sites for COVID-19 therapeutics development 人类SARS-CoV-2刺突蛋白的突变，潜在的药物结合和表位位点，用于COVID-19治疗开发

IF 2.8

Current Research in Structural Biology Pub Date : 2022-01-01 Epub Date: 2022-02-09 DOI: 10.1016/j.crstbi.2022.01.002

Kunchur Guruprasad

{"title":"Mutations in human SARS-CoV-2 spike proteins, potential drug binding and epitope sites for COVID-19 therapeutics development","authors":"Kunchur Guruprasad","doi":"10.1016/j.crstbi.2022.01.002","DOIUrl":"10.1016/j.crstbi.2022.01.002","url":null,"abstract":"<div><p>The comparison of 303,250 human SARS-CoV-2 spike protein sequences with the reference protein sequence Wuhan-Hu-1, showed ∼96.5% of the spike protein sequence has undergone the mutations till date, since outbreak of the COVID-19 pandemic disease that was first reported in December 2019. A total of 1,269,629 mutations were detected corresponding to 1,229 distinct mutation sites in the spike proteins comprising 1,273 amino acid residues. Thereby, ∼3.5% of the human SARS-CoV-2 spike protein sequence has remained invariant in the past two years. Considering different mutations occur at the same mutation site, a total of 4,729 distinct mutations were observed and are catalogued in the present work. The WHO/CDC, U.S.A., classification and definitions for the current variants being monitored (VBM) and variant of concern (VOC) are assigned to the SARS-CoV-2 spike protein mutations identified in the present work along with a list of other amino acid substitutions observed for the variants. All 195 amino acid residues in receptor binding domain (Thr333-Pro527) were associated with mutations in SARS-CoV-2 spike protein sequence including Lys417, Tyr449, Tyr453, Ala475, Asn487, Thr500, Asn501 and Gly502 that make interactions with the ACE-2 receptor ≤3.2 Å distance as observed in the crystal structure complex available in the Protein Data Bank (PDB code:<span>6LZG</span><svg><path></path></svg>). However, not all these residues were mutated in the same spike protein. Especially, Gly502 mutated only in two spike protein sequences and Tyr449 mutated only in seven spike protein sequences among the spike protein sequences analysed constitute potential sites for the design of suitable inhibitors/drugs. Further, forty-four invariant residues were observed that correspond to ten domains/regions in the SARS-CoV-2 spike protein and some of the residues exposed to the protein surface amongst these may serve as epitope targets to develop monoclonal antibodies.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 41-50"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/16/87/main.PMC8824715.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39622806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 21

Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins 电喷雾和水合噬菌体MS2病毒外壳蛋白的稳定性和构象记忆

IF 2.8

Current Research in Structural Biology Pub Date : 2022-01-01 Epub Date: 2022-11-04 DOI: 10.1016/j.crstbi.2022.10.001

Maxim N. Brodmerkel , Emiliano De Santis , Charlotte Uetrecht , Carl Caleman , Erik G. Marklund

{"title":"Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins","authors":"Maxim N. Brodmerkel , Emiliano De Santis , Charlotte Uetrecht , Carl Caleman , Erik G. Marklund","doi":"10.1016/j.crstbi.2022.10.001","DOIUrl":"10.1016/j.crstbi.2022.10.001","url":null,"abstract":"<div><p>Proteins are innately dynamic, which is important for their functions, but which also poses significant challenges when studying their structures. Gas-phase techniques can utilise separation and a range of sample manipulations to transcend some of the limitations of conventional techniques for structural biology in crystalline or solution phase, and isolate different states for separate interrogation. However, the transfer from solution to the gas phase risks affecting the structures, and it is unclear to what extent different conformations remain distinct in the gas phase, and if resolution <em>in silico</em> can recover the native conformations and their differences. Here, we use extensive molecular dynamics simulations to study the two distinct conformations of dimeric capsid protein of the MS2 bacteriophage. The protein undergoes notable restructuring of its peripheral parts in the gas phase, but subsequent simulation in solvent largely recovers the native structure. Our results suggest that despite some structural loss due to the experimental conditions, gas-phase structural biology techniques provide meaningful data that inform not only about the structures but also conformational dynamics of proteins.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 338-348"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9685359/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40515049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Putting on molecular weight: Enabling cryo-EM structure determination of sub-100-kDa proteins 增加分子量:使低温电镜结构测定低于100 kda的蛋白质

IF 2.8

Current Research in Structural Biology Pub Date : 2022-01-01 Epub Date: 2022-10-02 DOI: 10.1016/j.crstbi.2022.09.005

Koen Wentinck , Christos Gogou , Dimphna H. Meijer

引用次数: 5

Amyloid management by chaperones: The mystery underlying protein oligomers’ dual functions 淀粉样蛋白的伴侣管理:神秘的潜在的蛋白质低聚物的双重功能

IF 2.8

Current Research in Structural Biology Pub Date : 2022-01-01 Epub Date: 2022-12-07 DOI: 10.1016/j.crstbi.2022.11.002

Payam Arghavani, Mitra Pirhaghi, Faezeh Moosavi-Movahedi, Fatemeh Mamashli, Elnaz Hosseini, Ali Akbar Moosavi-Movahedi

{"title":"Amyloid management by chaperones: The mystery underlying protein oligomers’ dual functions","authors":"Payam Arghavani, Mitra Pirhaghi, Faezeh Moosavi-Movahedi, Fatemeh Mamashli, Elnaz Hosseini, Ali Akbar Moosavi-Movahedi","doi":"10.1016/j.crstbi.2022.11.002","DOIUrl":"10.1016/j.crstbi.2022.11.002","url":null,"abstract":"<div><p>Protein oligomerization has two notable aspects: it is crucial for the performing cellular and molecular processes accurately, and it produces amyloid fibril precursors. Although a clear explanation for amyloidosis as a whole is lacking, most studies have emphasized the importance of protein misfolding followed by formation of cytotoxic oligomer structures, which are responsible for disorders as diverse as neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases, and metabolic disorders, such as type 2 diabetes. Constant surveillance by oligomeric protein structures known as molecular chaperones enables cells to overcome the challenge of misfolded proteins and their harmful assemblies. These molecular chaperones encounter proteins in cells, and benefit cell survival as long as they perform correctly. Thus, this review highlights the roles of structural aspects of chaperone protein oligomers in determining cell fate—either succumbing to amyloid oligomers or survival—as well as experimental approaches used to investigate these entities.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 356-364"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9747510/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10713287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Regulation of the interactions between human eIF5 and eIF1A by the CK2 kinase CK2激酶调控人类eIF5和eIF1A之间的相互作用

IF 2.8

Current Research in Structural Biology Pub Date : 2022-01-01 Epub Date: 2022-09-13 DOI: 10.1016/j.crstbi.2022.09.003

Nathan Gamble, Eleanor Elise Paul, Bibin Anand, Assen Marintchev

{"title":"Regulation of the interactions between human eIF5 and eIF1A by the CK2 kinase","authors":"Nathan Gamble, Eleanor Elise Paul, Bibin Anand, Assen Marintchev","doi":"10.1016/j.crstbi.2022.09.003","DOIUrl":"10.1016/j.crstbi.2022.09.003","url":null,"abstract":"<div><p>Translation initiation in eukaryotes relies on a complex network of interactions that are continuously reorganized throughout the process. As more information becomes available about the structure of the ribosomal preinitiation complex (PIC) at various points in translation initiation, new questions arise about which interactions occur when, their roles, and regulation. The eukaryotic translation factor (eIF) 5 is the GTPase-activating protein (GAP) for the GTPase eIF2, which brings the initiator Met-tRNA<sub>i</sub> to the PIC. eIF5 also plays a central role in PIC assembly and remodeling through interactions with other proteins, including eIFs 1, 1A, and 3c. Phosphorylation by casein kinase 2 (CK2) significantly increases the eIF5 affinity for eIF2. The interaction between eIF5 and eIF1A was reported to be mediated by the eIF5 C-terminal domain (CTD) and the eIF1A N-terminal tail. Here, we report a new contact interface, between eIF5-CTD and the oligonucleotide/oligosaccharide-binding fold (OB) domain of eIF1A, which contributes to the overall affinity between the two proteins. We also show that the interaction is modulated by dynamic intramolecular interactions within both eIF5 and eIF1A. CK2 phosphorylation of eIF5 increases its affinity for eIF1A, offering new insights into the mechanisms by which CK2 stimulates protein synthesis and cell proliferation.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 308-319"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/79/5b/main.PMC9508154.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9578516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural biology - Painting the mechanistic landscape of biomolecules 结构生物学-描绘生物分子的机械景观

IF 2.8

Current Research in Structural Biology Pub Date : 2022-01-01 Epub Date: 2022-05-21 DOI: 10.1016/j.crstbi.2022.05.004

Tom L. Blundell, Peter E. Wright

引用次数: 1

Biochemical and structural analysis of a cytosolic sulfotransferase of the malaria vector Anopheles gambiae overexpressed in the reproductive tissues 冈比亚按蚊生殖组织中过表达胞质硫转移酶的生化和结构分析

IF 2.8

Current Research in Structural Biology Pub Date : 2022-01-01 Epub Date: 2022-07-21 DOI: 10.1016/j.crstbi.2022.07.001

Arianna Esposito Verza , Riccardo Miggiano , Fabrizio Lombardo , Carmine Fiorillo , Bruno Arcà , Beatrice Purghé , Erika Del Grosso , Ubaldina Galli , Menico Rizzi , Franca Rossi

{"title":"Biochemical and structural analysis of a cytosolic sulfotransferase of the malaria vector Anopheles gambiae overexpressed in the reproductive tissues","authors":"Arianna Esposito Verza , Riccardo Miggiano , Fabrizio Lombardo , Carmine Fiorillo , Bruno Arcà , Beatrice Purghé , Erika Del Grosso , Ubaldina Galli , Menico Rizzi , Franca Rossi","doi":"10.1016/j.crstbi.2022.07.001","DOIUrl":"10.1016/j.crstbi.2022.07.001","url":null,"abstract":"<div><p>The temporary or permanent chemical modification of biomolecules is a crucial aspect in the physiology of all living species. However, while some modules are well characterised also in insects, others did not receive the same attention. This holds true for sulfo-conjugation that is catalysed by cytosolic sulfotransferases (SULT), a central component of the metabolism of endogenous low molecular weight molecules and xenobiotics. In particular, limited information is available about the functional roles of the mosquito predicted enzymes annotated as SULTs in genomic databases. The herein described research is the first example of a biochemical and structural study of a SULT of a mosquito species, in general, and of the malaria vector <em>Anopheles gambiae</em> in particular. We confirmed that the AGAP001425 transcript displays a peculiar expression pattern that is suggestive of a possible involvement in modulating the mosquito reproductive tissues physiology, a fact that could raise attention on the enzyme as a potential target for insect-containment strategies. The crystal structures of the enzyme in alternative ligand-bound states revealed elements distinguishing <em>Ag</em>SULT-001425 from other characterized SULTs, including a peculiar conformational plasticity of a discrete region that shields the catalytic cleft and that could play a main role in the dynamics of the reaction and in the substrate selectivity of the enzyme. Along with further <em>in vitro</em> biochemical studies, our structural investigations could provide a framework for the discovery of small-molecule inhibitors to assess the effect of interfering with <em>Ag</em>SULT-001425-mediated catalysis at the organismal level.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 246-255"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/e8/73/main.PMC9356239.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40704012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

FOXO transcription factors differ in their dynamics and intra/intermolecular interactions FOXO转录因子在动力学和分子内/分子间相互作用方面有所不同

IF 2.8

Current Research in Structural Biology Pub Date : 2022-01-01 Epub Date: 2022-04-27 DOI: 10.1016/j.crstbi.2022.04.001

Emil Spreitzer , T. Reid Alderson , Benjamin Bourgeois , Loretta Eggenreich , Hermann Habacher , Greta Bramerdorfer , Iva Pritišanac , Pedro A. Sánchez-Murcia , Tobias Madl

{"title":"FOXO transcription factors differ in their dynamics and intra/intermolecular interactions","authors":"Emil Spreitzer , T. Reid Alderson , Benjamin Bourgeois , Loretta Eggenreich , Hermann Habacher , Greta Bramerdorfer , Iva Pritišanac , Pedro A. Sánchez-Murcia , Tobias Madl","doi":"10.1016/j.crstbi.2022.04.001","DOIUrl":"10.1016/j.crstbi.2022.04.001","url":null,"abstract":"<div><p>Transcription factors play key roles in orchestrating a plethora of cellular mechanisms and controlling cellular homeostasis. Transcription factors share distinct DNA binding domains, which allows to group them into protein families. Among them, the Forkhead box O (FOXO) family contains transcription factors crucial for cellular homeostasis, longevity and response to stress. The dysregulation of FOXO signaling is linked to drug resistance in cancer therapy or cellular senescence, however, selective drugs targeting FOXOs are limited, thus knowledge about structure and dynamics of FOXO proteins is essential. Here, we provide an extensive study of structure and dynamics of all FOXO family members. We identify residues accounting for different dynamic and structural features. Furthermore, we show that the auto-inhibition of FOXO proteins by their C-terminal trans-activation domain is conserved throughout the family and that these interactions are not only possible intra-, but also inter-molecularly. This indicates a model in which FOXO transcription factors would modulate their activities by interacting mutually.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 118-133"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665928X22000095/pdfft?md5=2c2ec2f297b19f624c1eda55d104f5c9&pid=1-s2.0-S2665928X22000095-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47295491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Integrative structural studies of the SARS-CoV-2 spike protein during the fusion process (2022) SARS-CoV-2刺突蛋白在融合过程中的整合结构研究(2022)

IF 2.8

Current Research in Structural Biology Pub Date : 2022-01-01 Epub Date: 2022-06-23 DOI: 10.1016/j.crstbi.2022.06.004

Jacob C. Miner , Paul W. Fenimore , William M. Fischer , Benjamin H. McMahon , Karissa Y. Sanbonmatsu , Chang-Shung Tung

{"title":"Integrative structural studies of the SARS-CoV-2 spike protein during the fusion process (2022)","authors":"Jacob C. Miner , Paul W. Fenimore , William M. Fischer , Benjamin H. McMahon , Karissa Y. Sanbonmatsu , Chang-Shung Tung","doi":"10.1016/j.crstbi.2022.06.004","DOIUrl":"10.1016/j.crstbi.2022.06.004","url":null,"abstract":"<div><p>SARS-CoV-2 is the virus responsible for the COVID-19 pandemic and catastrophic, worldwide health and economic impacts. The spike protein on the viral surface is responsible for viral entry into the host cell<del>.</del> The binding of spike protein to the host cell receptor ACE2 is the first step leading to fusion of the host and viral membranes. Despite the vast amount of structure data that has been generated for the spike protein of SARS-CoV-2, many of the detailed structures of the spike protein in different stages of the fusion pathway are unknown, leaving a wealth of potential drug-target space unexplored. The atomic-scale structure of the complete S2 segment, as well as the complete fusion intermediate are also unknown and represent major gaps in our knowledge of the infectious pathway of SAR-CoV-2. The conformational changes of the spike protein during this process are similarly not well understood. Here we present structures of the spike protein at different stages of the fusion process. With the transitions being a necessary step before the receptor binding, we propose sites along the transition pathways as potential targets for drug development.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 220-230"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/20/50/main.PMC9221923.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40407521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Transactivation domain of Adenovirus Early Region 1A (E1A): Investigating folding dynamics and aggregation 腺病毒早期1A区(E1A)的转激活结构域:研究折叠动力学和聚集

IF 2.8

Current Research in Structural Biology Pub Date : 2022-01-01 Epub Date: 2022-01-13 DOI: 10.1016/j.crstbi.2022.01.001

Nitin Sharma , Kundlik Gadhave , Prateek Kumar , Rajanish Giri

{"title":"Transactivation domain of Adenovirus Early Region 1A (E1A): Investigating folding dynamics and aggregation","authors":"Nitin Sharma , Kundlik Gadhave , Prateek Kumar , Rajanish Giri","doi":"10.1016/j.crstbi.2022.01.001","DOIUrl":"10.1016/j.crstbi.2022.01.001","url":null,"abstract":"<div><p>Transactivation domain of Adenovirus Early region 1A (E1A) oncoprotein is an intrinsically disordered molecular hub protein. It is involved in binding to different domains of human cell transcriptional co-activators such as retinoblastoma (pRb), CREB-binding protein (CBP), and its paralogue p300. The conserved region 1 (TAD) of E1A is known to undergo structural transitions and folds upon interaction with transcriptional adaptor zinc finger 2 (TAZ2). Previous reports on Taz2-E1A studies have suggested the formation of helical conformations of E1A-TAD. However, the folding behavior of the TAD region in isolation has not been studied in detail. Here, we have elucidated the folding behavior of E1A peptide at varied temperatures and solution conditions. Further, we have studied the effects of macromolecular crowding on E1A-TAD peptide. Additionally, we have also predicted the molecular recognition features of E1A using MoRF predictors. The predicted MoRFs are consistent with its structural transitions observed during TAZ2 interactions for transcriptional regulation in literature. Also, as a general rule of MoRFs, E1A undergoes helical transitions in alcohol and osmolyte solution. Finally, we studied the aggregation behavior of E1A, where we observed that the E1A could form amyloid-like aggregates that are cytotoxic to mammalian cells.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 29-40"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/da/77/main.PMC8801969.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39908538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1