发布求助
文献互助 智能选刊 最新文献

Structure最新文献

筛选
英文 中文
The human touch: Utilizing AlphaFold 3 to analyze structures of endogenous metabolons
IF 5.7 2区 生物学
Structure Pub Date : 2024-09-19 DOI: 10.1016/j.str.2024.08.018
Toni K. Träger, Christian Tüting, Panagiotis L. Kastritis
{"title":"The human touch: Utilizing AlphaFold 3 to analyze structures of endogenous metabolons","authors":"Toni K. Träger, Christian Tüting, Panagiotis L. Kastritis","doi":"10.1016/j.str.2024.08.018","DOIUrl":"https://doi.org/10.1016/j.str.2024.08.018","url":null,"abstract":"<p>Computational structural biology aims to accurately predict biomolecular complexes with AlphaFold 3 spearheading the field. However, challenges loom for structural analysis, especially when complex assemblies such as the pyruvate dehydrogenase complex (PDHc), which catalyzes the link reaction in cellular respiration, are studied. PDHc subcomplexes are challenging to predict, particularly interactions involving weaker, lower-affinity subcomplexes. Supervised modeling, i.e., integrative structural biology, will continue to play a role in fine-tuning this type of prediction (e.g., removing clashes, rebuilding loops/disordered regions, and redocking interfaces). 3D analysis of endogenous metabolic complexes continues to require, in addition to AI, precise and multi-faceted interrogation methods.</p>","PeriodicalId":22168,"journal":{"name":"Structure","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142246054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
AlphaFold with conformational sampling reveals the structural landscape of homorepeats 带有构象取样功能的 AlphaFold 揭示了同源重复序列的结构景观
IF 5.7 2区 生物学
Structure Pub Date : 2024-09-18 DOI: 10.1016/j.str.2024.08.016
David Fernandez Bonet, Shahrayar Ranyai, Luay Aswad, David P. Lane, Marie Arsenian-Henriksson, Michael Landreh, Dilraj Lama
{"title":"AlphaFold with conformational sampling reveals the structural landscape of homorepeats","authors":"David Fernandez Bonet, Shahrayar Ranyai, Luay Aswad, David P. Lane, Marie Arsenian-Henriksson, Michael Landreh, Dilraj Lama","doi":"10.1016/j.str.2024.08.016","DOIUrl":"https://doi.org/10.1016/j.str.2024.08.016","url":null,"abstract":"<p>Homorepeats are motifs with reiterations of the same amino acid. They are prevalent in proteins associated with diverse physiological functions but also linked to several pathologies. Structural characterization of homorepeats has remained largely elusive, primarily because they generally occur in the disordered regions or proteins. Here, we address this subject by combining structures derived from machine learning with conformational sampling through physics-based simulations. We find that hydrophobic homorepeats have a tendency to fold into structured secondary conformations, while hydrophilic ones predominantly exist in unstructured states. Our data show that the flexibility rendered by disorder is a critical component besides the chemical feature that drives homorepeats composition toward hydrophilicity. The formation of regular secondary structures also influences their solubility, as pathologically relevant homorepeats display a direct correlation between repeat expansion, induction of helicity, and self-assembly. Our study provides critical insights into the conformational landscape of protein homorepeats and their structure-activity relationship.</p>","PeriodicalId":22168,"journal":{"name":"Structure","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142237024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Lys716 in the transmembrane domain of yeast mitofusin Fzo1 modulates anchoring and fusion 酵母丝裂蛋白Fzo1跨膜结构域中的Lys716调节锚定和融合
IF 5.7 2区 生物学
Structure Pub Date : 2024-09-18 DOI: 10.1016/j.str.2024.08.017
Raphaëlle Versini, Marc Baaden, Laetitia Cavellini, Mickaël M. Cohen, Antoine Taly, Patrick F.J. Fuchs
{"title":"Lys716 in the transmembrane domain of yeast mitofusin Fzo1 modulates anchoring and fusion","authors":"Raphaëlle Versini, Marc Baaden, Laetitia Cavellini, Mickaël M. Cohen, Antoine Taly, Patrick F.J. Fuchs","doi":"10.1016/j.str.2024.08.017","DOIUrl":"https://doi.org/10.1016/j.str.2024.08.017","url":null,"abstract":"<p>Outer mitochondrial membrane fusion, a vital cellular process, is mediated by mitofusins. However, the underlying molecular mechanism remains elusive. We have performed extensive multiscale molecular dynamics simulations to predict a model of the transmembrane (TM) domain of the yeast mitofusin Fzo1. Coarse-grained simulations of the two TM domain helices, TM1 and TM2, reveal a stable interface, which is controlled by the charge status of residue Lys716. Atomistic replica-exchange simulations further tune our model, which is confirmed by a remarkable agreement with an independent AlphaFold2 (AF2) prediction of Fzo1 in complex with its fusion partner Ugo1. Furthermore, the presence of the TM domain destabilizes the membrane, even more if Lys716 is charged, which can be an asset for initiating fusion. The functional role of Lys716 was confirmed with yeast experiments, which show that mutating Lys716 to a hydrophobic residue prevents mitochondrial fusion.</p>","PeriodicalId":22168,"journal":{"name":"Structure","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142237065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The future of integrated structural biology 综合结构生物学的未来
IF 5.7 2区 生物学
Structure Pub Date : 2024-09-17 DOI: 10.1016/j.str.2024.08.014
Harald Schwalbe, Pauline Audergon, Natalie Haley, Claudia Alen Amaro, Jon Agirre, Marc Baldus, Lucia Banci, Wolfgang Baumeister, Martin Blackledge, Jose Maria Carazo, Kristina Djinovic Carugo, Patrick Celie, Isabella Felli, Darren J. Hart, Thomas Hauß, Lari Lehtiö, Kresten Lindorff-Larsen, José Márquez, André Matagne, Roberta Pierattelli, Matthias Wilmanns
{"title":"The future of integrated structural biology","authors":"Harald Schwalbe, Pauline Audergon, Natalie Haley, Claudia Alen Amaro, Jon Agirre, Marc Baldus, Lucia Banci, Wolfgang Baumeister, Martin Blackledge, Jose Maria Carazo, Kristina Djinovic Carugo, Patrick Celie, Isabella Felli, Darren J. Hart, Thomas Hauß, Lari Lehtiö, Kresten Lindorff-Larsen, José Márquez, André Matagne, Roberta Pierattelli, Matthias Wilmanns","doi":"10.1016/j.str.2024.08.014","DOIUrl":"https://doi.org/10.1016/j.str.2024.08.014","url":null,"abstract":"<p>Instruct-ERIC, “the European Research Infrastructure Consortium for Structural biology research,” is a pan-European distributed research infrastructure making high-end technologies and methods in structural biology available to users. Here, we describe the current state-of-the-art of integrated structural biology and discuss potential future scientific developments as an impulse for the scientific community, many of which are located in Europe and are associated with Instruct. We reflect on where to focus scientific and technological initiatives within the distributed Instruct research infrastructure. This review does not intend to make recommendations on funding requirements or initiatives directly, neither at the national nor the European level. However, it addresses future challenges and opportunities for the field, and foresees the need for a stronger coordination within the European and international research field of integrated structural biology to be able to respond timely to thematic topics that are often prioritized by calls for funding addressing societal needs.</p>","PeriodicalId":22168,"journal":{"name":"Structure","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structural characterization of the POTRA domains from A. baumannii reveals new conformations in BamA 鲍曼不动杆菌 POTRA 结构域的结构表征揭示了 BamA 的新构象
IF 5.7 2区 生物学
Structure Pub Date : 2024-09-17 DOI: 10.1016/j.str.2024.08.013
Claire Overly Cottom, Robert Stephenson, Dante Ricci, Lixinhao Yang, James C. Gumbart, Nicholas Noinaj
{"title":"Structural characterization of the POTRA domains from A. baumannii reveals new conformations in BamA","authors":"Claire Overly Cottom, Robert Stephenson, Dante Ricci, Lixinhao Yang, James C. Gumbart, Nicholas Noinaj","doi":"10.1016/j.str.2024.08.013","DOIUrl":"https://doi.org/10.1016/j.str.2024.08.013","url":null,"abstract":"<p>Recent studies have demonstrated BamA, the central component of the β-barrel assembly machinery (BAM), as an important therapeutic target to combat infections caused by <em>Acinetobacter baumannii</em> and other Gram-negative pathogens. Homology modeling indicates BamA in <em>A. baumannii</em> consists of five polypeptide transport-associated (POTRA) domains and a β-barrel membrane domain. We characterized the POTRA domains of BamA from <em>A. baumannii</em> in solution using size-exclusion chromatography small angle X-ray scattering (SEC-SAXS) analysis and determined crystal structures in two conformational states that are drastically different than those previously observed in BamA from other bacteria, indicating that the POTRA domains are even more conformationally dynamic than has been observed previously. Molecular dynamics simulations of the POTRA domains from <em>A. baumannii</em> and <em>Escherichia coli</em> allowed us to identify key structural features that contribute to the observed novel states. Together, these studies expand on our current understanding of the conformational plasticity within BamA across differing bacterial species.</p>","PeriodicalId":22168,"journal":{"name":"Structure","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rewiring protein binding specificity in paralogous DRG/DFRP complexes 重构同类 DRG/DFRP 复合物中的蛋白质结合特异性
IF 5.7 2区 生物学
Structure Pub Date : 2024-09-13 DOI: 10.1016/j.str.2024.08.012
Christian A.E. Westrip, Stephen J. Smerdon, Mathew L. Coleman
{"title":"Rewiring protein binding specificity in paralogous DRG/DFRP complexes","authors":"Christian A.E. Westrip, Stephen J. Smerdon, Mathew L. Coleman","doi":"10.1016/j.str.2024.08.012","DOIUrl":"https://doi.org/10.1016/j.str.2024.08.012","url":null,"abstract":"<p>Eukaryotes have two paralogous developmentally regulated GTP-binding (DRG) proteins: DRG1 and DRG2, both of which have a conserved binding partner called DRG family regulatory protein 1 and 2 (DFRP1 and DFRP2), respectively. DFRPs are important for the function of DRGs and interact with their respective DRG via a conserved region called the DFRP domain. Despite being highly similar, DRG1 and DRG2 have strict binding specificity for their respective DFRP. Using AlphaFold generated structure models of the human DRG/DFRP complexes, we have biochemically characterized their interactions and identified interface residues involved in determining specificity. This analysis revealed that as few as five mutations in DRG1 can switch binding from DFRP1 to DFRP2. Moreover, while DFRP1 binding confers increased stability and GTPase activity to DRG1, DFRP2 binding only supports increased stability. Overall, this work provides new insight into the structural determinants responsible for the binding specificities of the DRG/DFRP complexes.</p>","PeriodicalId":22168,"journal":{"name":"Structure","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142202321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structural organization of pyruvate: ferredoxin oxidoreductase from the methanogenic archaeon Methanosarcina acetivorans 产甲烷古菌 Methanosarcina acetivorans 的丙酮酸铁氧还蛋白氧化还原酶的结构组织
IF 5.7 2区 生物学
Structure Pub Date : 2024-09-11 DOI: 10.1016/j.str.2024.08.011
Matteo Cossu, Daniel Catlin, Sean J. Elliott, William W. Metcalf, Satish K. Nair
{"title":"Structural organization of pyruvate: ferredoxin oxidoreductase from the methanogenic archaeon Methanosarcina acetivorans","authors":"Matteo Cossu, Daniel Catlin, Sean J. Elliott, William W. Metcalf, Satish K. Nair","doi":"10.1016/j.str.2024.08.011","DOIUrl":"https://doi.org/10.1016/j.str.2024.08.011","url":null,"abstract":"<p>Enzymes of the 2-oxoacid:ferredoxin oxidoreductase (OFOR) superfamily catalyze the reversible oxidation of 2-oxoacids to acyl-coenzyme A esters and carbon dioxide (CO<sub>2</sub>)using ferredoxin or flavodoxin as the redox partner. Although members of the family share primary sequence identity, a variety of domain and subunit arrangements are known. Here, we characterize the structure of a four-subunit family member: the pyruvate:ferredoxin oxidoreductase (PFOR) from the methane producing archaeon <em>Methanosarcina acetivorans</em> (<em>Ma</em>PFOR). The 1.92 Å resolution crystal structure of <em>Ma</em>PFOR shows a protein fold like those of single- or two-subunit PFORs that function in 2-oxoacid oxidation, including the location of the requisite thiamine pyrophosphate (TPP), and three [4Fe-4S] clusters. Of note, <em>Ma</em>PFOR typically functions in the CO<sub>2</sub> reductive direction, and structural comparisons to the pyruvate oxidizing PFORs show subtle differences in several regions of catalytical relevance. These studies provide a framework that may shed light on the biochemical mechanisms used to facilitate reductive pyruvate synthesis.</p>","PeriodicalId":22168,"journal":{"name":"Structure","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142166296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Ping, pong, and freeze: Structural insights into the inhibition of ceramide synthase by Fumonisin B1 乒乓球和冷冻：伏马菌素 B1 对神经酰胺合成酶抑制作用的结构性启示
IF 5.7 2区 生物学
Structure Pub Date : 2024-09-05 DOI: 10.1016/j.str.2024.08.010
Kexin Hu, Yu Cao
{"title":"Ping, pong, and freeze: Structural insights into the inhibition of ceramide synthase by Fumonisin B1","authors":"Kexin Hu, Yu Cao","doi":"10.1016/j.str.2024.08.010","DOIUrl":"https://doi.org/10.1016/j.str.2024.08.010","url":null,"abstract":"<p>Fumonisin B1 (FB1) targets sphingolipid biosynthesis, inhibiting ceramide synthases. In this issue of <em>Structure</em>, Zhang et al.<span><span><sup>1</sup></span></span> determined the cryoelectron microscopic structures of yeast ceramide synthase in complex with FB1 and its acylated derivative, acyl-FB1, revealing a two-step “ping-pong” mechanism for the N-acylation of FB1 and how it inhibits ceramide synthase.</p>","PeriodicalId":22168,"journal":{"name":"Structure","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142138207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Expanding the insect defensin landscape 扩大昆虫防御素范围
IF 5.7 2区 生物学
Structure Pub Date : 2024-09-05 DOI: 10.1016/j.str.2024.08.009
Krishnakoli Adhikary, Sébastien F. Poget
{"title":"Expanding the insect defensin landscape","authors":"Krishnakoli Adhikary, Sébastien F. Poget","doi":"10.1016/j.str.2024.08.009","DOIUrl":"https://doi.org/10.1016/j.str.2024.08.009","url":null,"abstract":"<p>In this issue of <em>Structure</em>, Walker et al.<span><span><sup>1</sup></span></span> determined the NMR structure of a recently discovered defensin, Pp19, from the venom of an assassin bug. This peptide adopts an α-defensin-like structure, which had not been observed in insects before. Unlike mammalian α-defensins, which are generally antimicrobial, Pp19 has insecticidal activity.</p>","PeriodicalId":22168,"journal":{"name":"Structure","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142138212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Ordering the disordered 为无序者排序
IF 5.7 2区 生物学
Structure Pub Date : 2024-09-05 DOI: 10.1016/j.str.2024.08.004
Sarah Shammas, Gabriella Heller, Alaji Bah, Emmanouela Filippidi, Alex Holehouse, Miao Yu, Janin Lautenschläger
{"title":"Ordering the disordered","authors":"Sarah Shammas, Gabriella Heller, Alaji Bah, Emmanouela Filippidi, Alex Holehouse, Miao Yu, Janin Lautenschläger","doi":"10.1016/j.str.2024.08.004","DOIUrl":"https://doi.org/10.1016/j.str.2024.08.004","url":null,"abstract":"<p>In this Voices article, we introduce seven impressive young group leaders that presented their work at the recent Gordon Research Conference “Biophysics and biology of intrinsically disordered proteins” in Les Diablerets, Switzerland. We asked them to tell us more about their careers and their fascinating research on proteins that do not adopt a single-folded structure.</p>","PeriodicalId":22168,"journal":{"name":"Structure","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142138214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
下一页 尾页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们：info@booksci.cn Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：481959085
Book学术官方微信