Structure最新文献_第8页

Systematic characterization of indel variants using a yeast-based protein folding sensor 利用酵母蛋白折叠传感器系统表征indel变异

IF 5.7 2区生物学

Structure Pub Date : 2024-12-19 DOI: 10.1016/j.str.2024.11.017

Sven Larsen-Ledet, Søren Lindemose, Aleksandra Panfilova, Sarah Gersing, Caroline H. Suhr, Aitana Victoria Genzor, Heleen Lanters, Sofie V. Nielsen, Kresten Lindorff-Larsen, Jakob R. Winther, Amelie Stein, Rasmus Hartmann-Petersen

{"title":"Systematic characterization of indel variants using a yeast-based protein folding sensor","authors":"Sven Larsen-Ledet, Søren Lindemose, Aleksandra Panfilova, Sarah Gersing, Caroline H. Suhr, Aitana Victoria Genzor, Heleen Lanters, Sofie V. Nielsen, Kresten Lindorff-Larsen, Jakob R. Winther, Amelie Stein, Rasmus Hartmann-Petersen","doi":"10.1016/j.str.2024.11.017","DOIUrl":"https://doi.org/10.1016/j.str.2024.11.017","url":null,"abstract":"Gene variants resulting in insertions or deletions of amino acid residues (indels) have important consequences for evolution and are often linked to disease, yet, compared to missense variants, the effects of indels are poorly understood and predicted. We developed a sensitive protein folding sensor based on the complementation of uracil auxotrophy in yeast by circular permutated orotate phosphoribosyltransferase (CPOP). The sensor reports on the folding of disease-linked missense variants and de-novo-designed proteins. Applying the folding sensor to a saturated library of single-residue indels in human dihydrofolate reductase (DHFR) revealed that most regions that tolerate indels are confined to internal loops, the termini, and a central α helix. Several indels are temperature sensitive, and folding is rescued upon binding to methotrexate. Rosetta and AlphaFold2 predictions correlate with the observed effects, suggesting that most indels destabilize the native fold and that these computational tools are useful for the classification of indels observed in population sequencing.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"87 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142849500","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

Conformational response of αIIbβ3 and αVβ3 integrins to force αⅡbβ3和αVβ3整合素对力的构象反应

IF 5.7 2区生物学

Structure Pub Date : 2024-12-19 DOI: 10.1016/j.str.2024.11.016

Reza Kolasangiani, Khashayar Farzanian, Yunfeng Chen, Martin A. Schwartz, Tamara C. Bidone

{"title":"Conformational response of αIIbβ3 and αVβ3 integrins to force","authors":"Reza Kolasangiani, Khashayar Farzanian, Yunfeng Chen, Martin A. Schwartz, Tamara C. Bidone","doi":"10.1016/j.str.2024.11.016","DOIUrl":"https://doi.org/10.1016/j.str.2024.11.016","url":null,"abstract":"As major adhesion receptors, integrins transmit biochemical and mechanical signals across the plasma membrane. These functions are regulated by transitions between bent and extended conformations and modulated by force. To understand how force on integrins mediates cellular mechanosensing, we compared two highly homologous integrins, αIIbβ3 and αVβ3. These integrins, expressed in circulating platelets vs. solid tissues, respectively, share the β3 subunit, bind similar ligands and have similar bent and extended conformations. Here, we report that in cells expressing equivalent levels of each integrin, αIIbβ3 mediates spreading on softer substrates than αVβ3. These effects correlate with differences in structural dynamics of the two integrins under force. All-atom simulations show that αIIbβ3 is more flexible than αVβ3 due to correlated residue motions within the α subunit domains. Single molecule measurements confirm that αIIbβ3 extends faster than αVβ3. These results reveal a fundamental relationship between protein function and structural dynamics in cell mechanosensing.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"23 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142849503","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

Near-atomic cryo-EM structure of the light-harvesting complex LH2 from the sulfur purple bacterium Ectothiorhodospira haloalkaliphila 紫色硫杆菌中的采光复合物 LH2 的近原子低温电子显微镜结构

IF 5.7 2区生物学

Structure Pub Date : 2024-12-17 DOI: 10.1016/j.str.2024.11.015

Anna D. Burtseva, Timur N. Baymukhametov, Maxim A. Bolshakov, Zoya К. Makhneva, Andrey V. Mardanov, Andrey M. Tsedilin, Huawei Zhang, Vladimir.O. Popov, Aleksandr A. Ashikhmin, Konstantin M. Boyko

{"title":"Near-atomic cryo-EM structure of the light-harvesting complex LH2 from the sulfur purple bacterium Ectothiorhodospira haloalkaliphila","authors":"Anna D. Burtseva, Timur N. Baymukhametov, Maxim A. Bolshakov, Zoya К. Makhneva, Andrey V. Mardanov, Andrey M. Tsedilin, Huawei Zhang, Vladimir.O. Popov, Aleksandr A. Ashikhmin, Konstantin M. Boyko","doi":"10.1016/j.str.2024.11.015","DOIUrl":"https://doi.org/10.1016/j.str.2024.11.015","url":null,"abstract":"Bacteria with the simplest system for solar energy absorption and conversion use various types of light-harvesting complexes for these purposes. Light-harvesting complex 2 (LH2), an important component of the bacterial photosynthetic apparatus, has been structurally well characterized among purple non-sulfur bacteria. In contrast, so far only one high-resolution LH2 structure from sulfur bacteria is known. Here, we report the near-atomic resolution cryoelectron microscopy (cryo-EM) structure of the LH2 complex from the purple sulfur bacterium Ectothiorhodospira haloalkaliphila, which allowed us to determine the predominant polypeptide composition of this complex and the identification of the most probable type of its carotenoid. Comparison of our structure with the only known LH2 complex from a sulfur bacterium revealed severe differences in the overall ring-like organization. Expanding the architectural universe of bacterial light-harvesting complexes, our results demonstrate that, as observed for non-sulfur bacteria, the LH2 complexes of sulfur bacteria may also exhibit various types of spatial organization.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"48 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142832784","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 insights into subunit-dependent functional regulation in epithelial sodium channels 上皮钠通道中亚基依赖性功能调节的结构见解

IF 5.7 2区生物学

Structure Pub Date : 2024-12-11 DOI: 10.1016/j.str.2024.11.013

Alexandra Houser, Isabelle Baconguis

引用次数: 0

Automated fibril structure calculations in Xplor-NIH 自动纤维结构计算在explore - nih

IF 5.7 2区生物学

Structure Pub Date : 2024-12-10 DOI: 10.1016/j.str.2024.11.011

Alexander M. Barclay, Moses H. Milchberg, Owen A. Warmuth, Marcus D. Tuttle, Christopher J. Dennis, Charles D. Schwieters, Chad M. Rienstra

引用次数: 0

Ion coupling and inhibitory mechanisms of the human presynaptic high-affinity choline transporter CHT1 人突触前高亲和胆碱转运体CHT1的离子偶联及抑制机制

IF 5.7 2区生物学

Structure Pub Date : 2024-12-09 DOI: 10.1016/j.str.2024.11.009

Yunlong Qiu, Yiwei Gao, Qinru Bai, Yan Zhao

引用次数: 0

Assembly of the Xrn2/Rat1–Rai1–Rtt103 termination complexes in mesophilic and thermophilic organisms 中温和亲热生物中Xrn2/ Rat1-Rai1-Rtt103末端复合物的组装

IF 5.7 2区生物学

Structure Pub Date : 2024-12-09 DOI: 10.1016/j.str.2024.11.010

Alzbeta Dikunova, Nikola Noskova, Jan H. Overbeck, Martin Polak, David Stelzig, David Zapletal, Karel Kubicek, Jiri Novacek, Remco Sprangers, Richard Stefl

{"title":"Assembly of the Xrn2/Rat1–Rai1–Rtt103 termination complexes in mesophilic and thermophilic organisms","authors":"Alzbeta Dikunova, Nikola Noskova, Jan H. Overbeck, Martin Polak, David Stelzig, David Zapletal, Karel Kubicek, Jiri Novacek, Remco Sprangers, Richard Stefl","doi":"10.1016/j.str.2024.11.010","DOIUrl":"https://doi.org/10.1016/j.str.2024.11.010","url":null,"abstract":"The 5′–3′ exoribonuclease Xrn2, known as Rat1 in yeasts, terminates mRNA transcription by RNA polymerase II (RNAPII). In the torpedo model of termination, the activity of Xrn2/Rat1 is enhanced by Rai1, which is recruited to the termination site by Rtt103, an adaptor protein binding to the RNAPII C-terminal domain (CTD). The overall architecture of the Xrn2/Rat1-Rai1-Rtt103 complex remains unknown. We combined structural biology methods to characterize the torpedo complex from Saccharomyces cerevisiae and Chaetomium thermophilum. Comparison of the structures from these organisms revealed a conserved protein core fold of the subunits, but significant variability in their interaction interfaces. We found that in the mesophile, Rtt103 utilizes an unstructured region to augment a Rai1 β-sheet, while in the thermophile Rtt103 binds to a C-terminal helix of Rai1 via its CTD-interacting domain with an α-helical fold. These different torpedo complex assemblies reflect adaptations to the environment and impact complex recruitment to RNAPII.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"34 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142793552","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

Cost-benefit analysis of cryogenic electron tomography subtomogram averaging of chaperonin MmCpn at near atomic resolution 近原子分辨率下伴侣蛋白MmCpn的低温电子断层亚断层平均的成本效益分析

IF 5.7 2区生物学

Structure Pub Date : 2024-12-06 DOI: 10.1016/j.str.2024.11.008

Yanyan Zhao, Michael F. Schmid, Wah Chiu

引用次数: 0

Trace_y: Software algorithms for structural analysis of individual helical filaments by three-dimensional contact point reconstruction atomic force microscopy 用三维接触点重建原子力显微镜对单个螺旋细丝进行结构分析的软件算法

IF 5.7 2区生物学

Structure Pub Date : 2024-12-05 DOI: 10.1016/j.str.2024.11.007

Wei-Feng Xue

引用次数: 0

The universal Rhs shell structure accommodates various toxins inside and different functional decorations on the outside 通用的Rhs外壳结构内部容纳各种毒素，外部容纳不同的功能装饰