Nature structural & molecular biology最新文献

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Mechanistic basis for PYROXD1-mediated protection of the human tRNA ligase complex against oxidative inactivation pyroxd1介导的人类tRNA连接酶复合物抗氧化失活的机制基础
Nature structural & molecular biology Pub Date : 2025-03-11 DOI: 10.1038/s41594-025-01516-6
Luuk Loeff, Alena Kroupova, Igor Asanović, Franziska M. Boneberg, Moritz M. Pfleiderer, Luca Riermeier, Alexander Leitner, Andrè Ferdigg, Fabian Ackle, Javier Martinez, Martin Jinek
{"title":"Mechanistic basis for PYROXD1-mediated protection of the human tRNA ligase complex against oxidative inactivation","authors":"Luuk Loeff, Alena Kroupova, Igor Asanović, Franziska M. Boneberg, Moritz M. Pfleiderer, Luca Riermeier, Alexander Leitner, Andrè Ferdigg, Fabian Ackle, Javier Martinez, Martin Jinek","doi":"10.1038/s41594-025-01516-6","DOIUrl":"https://doi.org/10.1038/s41594-025-01516-6","url":null,"abstract":"<p>The metazoan tRNA ligase complex (tRNA-LC) has essential roles in tRNA biogenesis and unfolded protein response. Its catalytic subunit RTCB contains a conserved active-site cysteine that is susceptible to metal ion-induced oxidative inactivation. The flavin-containing oxidoreductase PYROXD1 preserves the activity of human tRNA-LC in a NAD(P)H-dependent manner, but its protective mechanism remains elusive. Here, we report a cryogenic electron microscopic structure of the human RTCB–PYROXD1 complex, revealing that PYROXD1 directly interacts with the catalytic center of RTCB through its carboxy-terminal tail. NAD(P)H binding and FAD reduction allosterically control PYROXD1 activity and RTCB recruitment, while reoxidation of PYROXD1 enables timed release of RTCB. PYROXD1 interaction is mutually exclusive with Archease-mediated RTCB guanylylation, and guanylylated RTCB is intrinsically protected from oxidative inactivation. Together, these findings provide a mechanistic framework for the protective function of PYROXD1 that maintains the activity of the tRNA-LC under aerobic conditions.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143589618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Condensation of ZFP207 and U1 snRNP promotes spliceosome assembly ZFP207和U1 snRNP的缩合促进剪接体的组装
Nature structural & molecular biology Pub Date : 2025-03-06 DOI: 10.1038/s41594-025-01501-z
Yuenan Zhou, Chong Tong, Zuokun Shi, Yan Zhang, Xushen Xiong, Xiaohua Shen, Xiaoyu Li, Yafei Yin
{"title":"Condensation of ZFP207 and U1 snRNP promotes spliceosome assembly","authors":"Yuenan Zhou, Chong Tong, Zuokun Shi, Yan Zhang, Xushen Xiong, Xiaohua Shen, Xiaoyu Li, Yafei Yin","doi":"10.1038/s41594-025-01501-z","DOIUrl":"https://doi.org/10.1038/s41594-025-01501-z","url":null,"abstract":"<p>The U1 small nuclear ribonucleoprotein (snRNP) has an essential role in initiating spliceosome assembly, yet the mechanism underlying its synergy with other splicing regulators for efficient spliceosome assembly remains elusive. Here we identify zinc finger protein 207 (ZFP207) as a key regulator of U1 snRNP function that substantially promotes spliceosome assembly. Acute depletion of ZFP207 results in a series of molecular phenotypes indicative of U1 snRNP dysregulation. Mechanistically, the N-terminal zinc finger domains of ZFP207 directly bind to stem-loop 3 of U1 snRNA, while its C-terminal intrinsically disordered regions undergo phase separation to form biomolecular condensates with U1 snRNP. These condensates create a crowded molecular environment that increases the local concentration of splicing snRNPs and regulators, thereby accelerating the speed of spliceosome assembly by facilitating interactions between U1 snRNP and other snRNPs. Collectively, our study demonstrates the critical role of phase separation in ensuring effective U1 snRNP function and promoting efficient spliceosome assembly.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Tau filaments with the Alzheimer fold in human MAPT mutants V337M and R406W 人类MAPT突变体V337M和R406W中Tau丝与阿尔茨海默病折叠的关系
Nature structural & molecular biology Pub Date : 2025-03-05 DOI: 10.1038/s41594-025-01498-5
Chao Qi, Sofia Lövestam, Alexey G. Murzin, Sew Peak-Chew, Catarina Franco, Marika Bogdani, Caitlin Latimer, Jill R. Murrell, Patrick W. Cullinane, Zane Jaunmuktane, Thomas D. Bird, Bernardino Ghetti, Sjors H. W. Scheres, Michel Goedert
{"title":"Tau filaments with the Alzheimer fold in human MAPT mutants V337M and R406W","authors":"Chao Qi, Sofia Lövestam, Alexey G. Murzin, Sew Peak-Chew, Catarina Franco, Marika Bogdani, Caitlin Latimer, Jill R. Murrell, Patrick W. Cullinane, Zane Jaunmuktane, Thomas D. Bird, Bernardino Ghetti, Sjors H. W. Scheres, Michel Goedert","doi":"10.1038/s41594-025-01498-5","DOIUrl":"https://doi.org/10.1038/s41594-025-01498-5","url":null,"abstract":"<p>Frontotemporal dementia (FTD) and Alzheimer’s disease (AD) are the most common forms of early-onset dementia. Unlike AD, FTD begins with behavioral changes before the development of cognitive impairment. Dominantly inherited mutations in <i>MAPT</i>, the microtubule-associated protein tau gene, give rise to cases of FTD and parkinsonism linked to chromosome 17. These individuals develop abundant filamentous tau inclusions in brain cells in the absence of β-amyloid deposits. Here, we used cryo-electron microscopy to determine the structures of tau filaments from the brains of human <i>MAPT</i> mutants V337M and R406W. Both amino acid substitutions gave rise to tau filaments with the Alzheimer fold, which consisted of paired helical filaments in all V337M and R406W cases and of straight filaments in two V337M cases. We also identified another assembly of the Alzheimer fold into triple tau filaments in a V337M case. Filaments assembled from recombinant tau (297–391) with substitution V337M had the Alzheimer fold and showed an increased rate of assembly.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143546602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D 利用Dip3D从嘈杂的Pore-C数据重建二倍体高阶人类三维基因组相互作用
Nature structural & molecular biology Pub Date : 2025-03-04 DOI: 10.1038/s41594-025-01512-w
Ying Chen, Zhuo-Bin Lin, Shao-Kai Wang, Bo Wu, Longjian Niu, Jia-Yong Zhong, Yi-Meng Sun, Zhenxian Zheng, Xin Bai, Luo-Ran Liu, Wei Xie, Wei Chi, Titantian Ye, Ruibang Luo, Chunhui Hou, Feng Luo, Chuan-Le Xiao
{"title":"Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D","authors":"Ying Chen, Zhuo-Bin Lin, Shao-Kai Wang, Bo Wu, Longjian Niu, Jia-Yong Zhong, Yi-Meng Sun, Zhenxian Zheng, Xin Bai, Luo-Ran Liu, Wei Xie, Wei Chi, Titantian Ye, Ruibang Luo, Chunhui Hou, Feng Luo, Chuan-Le Xiao","doi":"10.1038/s41594-025-01512-w","DOIUrl":"https://doi.org/10.1038/s41594-025-01512-w","url":null,"abstract":"<p>Differential high-order chromatin interactions between homologous chromosomes affect many biological processes. Traditional chromatin conformation capture genome analysis methods mainly identify two-way interactions and cannot provide comprehensive haplotype information, especially for low-heterozygosity organisms such as human. Here, we present a pipeline of methods to delineate diploid high-order chromatin interactions from noisy Pore-C outputs. We trained a previously published single-nucleotide variant (SNV)-calling deep learning model, Clair3, on Pore-C data to achieve superior SNV calling, applied a filtering strategy to tag reads for haplotypes and established a haplotype imputation strategy for high-order concatemers. Learning the haplotype characteristics of high-order concatemers from high-heterozygosity mouse allowed us to devise a progressive haplotype imputation strategy, which improved the haplotype-informative Pore-C contact rate 14.1-fold to 76% in the HG001 cell line. Overall, the diploid three-dimensional (3D) genome interactions we derived using Dip3D surpassed conventional methods in noise reduction and contact distribution uniformity, with better haplotype-informative contact density and genomic coverage rates. Dip3D identified previously unresolved haplotype high-order interactions, in addition to an understanding of their relationship with allele-specific expression, such as in X-chromosome inactivation. These results lead us to conclude that Dip3D is a robust pipeline for the high-quality reconstruction of diploid high-order 3D genome interactions.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143539115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ZBTB16/PLZF regulates juvenile spermatogonial stem cell development through an extensive transcription factor poising network ZBTB16/PLZF通过广泛的转录因子调控网络调控幼代精原干细胞的发育
Nature structural & molecular biology Pub Date : 2025-03-03 DOI: 10.1038/s41594-025-01509-5
Chongil Yi, Yuka Kitamura, So Maezawa, Satoshi H. Namekawa, Bradley R. Cairns
{"title":"ZBTB16/PLZF regulates juvenile spermatogonial stem cell development through an extensive transcription factor poising network","authors":"Chongil Yi, Yuka Kitamura, So Maezawa, Satoshi H. Namekawa, Bradley R. Cairns","doi":"10.1038/s41594-025-01509-5","DOIUrl":"https://doi.org/10.1038/s41594-025-01509-5","url":null,"abstract":"<p>Spermatogonial stem cells balance self-renewal with differentiation and spermatogenesis to ensure continuous sperm production. Here, we identify roles for the transcription factor zinc finger and BTB domain-containing protein 16 (ZBTB16; also known as promyelocytic leukemia zinc finger (PLZF)) in juvenile mouse undifferentiated spermatogonia (uSPG) in promoting self-renewal and cell-cycle progression to maintain uSPG and transit-amplifying states. Notably, ZBTB16, Spalt-like transcription factor 4 (SALL4) and SRY-box transcription factor 3 (SOX3) colocalize at over 12,000 promoters regulating uSPG and meiosis. These regions largely share broad histone 3 methylation and acetylation (H3K4me3 and H3K27ac), DNA hypomethylation, RNA polymerase II (RNAPol2) and often CCCTC-binding factor (CTCF). Hi-C analyses show robust three-dimensional physical interactions among these cobound promoters, suggesting the existence of a transcription factor and higher-order active chromatin interaction network within uSPG that poises meiotic promoters for subsequent activation. Conversely, these factors do not notably occupy germline-specific promoters driving spermiogenesis, which instead lack promoter–promoter physical interactions and bear DNA hypermethylation, even when active. Overall, ZBTB16 promotes uSPG cell-cycle progression and colocalizes with SALL4, SOX3, CTCF and RNAPol2 to help establish an extensive and interactive chromatin poising network.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"66 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143532510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
CTCF-mediated 3D chromatin sets up the gene expression program in the male germline ctcf介导的三维染色质在雄性种系中建立了基因表达程序
Nature structural & molecular biology Pub Date : 2025-03-03 DOI: 10.1038/s41594-025-01482-z
Yuka Kitamura, Kazuki Takahashi, So Maezawa, Yasuhisa Munakata, Akihiko Sakashita, Shawna P. Katz, Noam Kaplan, Satoshi H. Namekawa
{"title":"CTCF-mediated 3D chromatin sets up the gene expression program in the male germline","authors":"Yuka Kitamura, Kazuki Takahashi, So Maezawa, Yasuhisa Munakata, Akihiko Sakashita, Shawna P. Katz, Noam Kaplan, Satoshi H. Namekawa","doi":"10.1038/s41594-025-01482-z","DOIUrl":"https://doi.org/10.1038/s41594-025-01482-z","url":null,"abstract":"<p>Spermatogenesis is a unidirectional differentiation process that generates haploid sperm, but how the gene expression program that directs this process is established is largely unknown. Here we determine the high-resolution three-dimensional (3D) chromatin architecture of mouse male germ cells during spermatogenesis and show that CTCF-mediated 3D chromatin dictates the gene expression program required for spermatogenesis. In undifferentiated spermatogonia, CTCF-mediated chromatin interactions between meiosis-specific super-enhancers (SEs) and their target genes precede activation of these SEs on autosomes. These meiotic SEs recruit the master transcription factor A-MYB (MYBL1) in meiotic spermatocytes, which strengthens their 3D contacts and instructs a burst of meiotic gene expression. We also find that at the mitosis-to-meiosis transition, the germline-specific Polycomb protein SCML2 facilitates the resolution of chromatin loops that are specific to mitotic spermatogonia. Moreover, SCML2 and A-MYB help shape the unique 3D chromatin organization of sex chromosomes during meiotic sex chromosome inactivation. We propose that CTCF-mediated 3D chromatin organization regulates epigenetic priming that directs unidirectional differentiation, thereby determining the cellular identity of the male germline.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143532506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Human polymerase θ helicase positions DNA microhomologies for double-strand break repair 人类聚合酶θ解旋酶定位DNA微同源,用于双链断裂修复
Nature structural & molecular biology Pub Date : 2025-02-28 DOI: 10.1038/s41594-025-01514-8
Christopher J. Zerio, Yonghong Bai, Brian A. Sosa-Alvarado, Timothy Guzi, Gabriel C. Lander
{"title":"Human polymerase θ helicase positions DNA microhomologies for double-strand break repair","authors":"Christopher J. Zerio, Yonghong Bai, Brian A. Sosa-Alvarado, Timothy Guzi, Gabriel C. Lander","doi":"10.1038/s41594-025-01514-8","DOIUrl":"https://doi.org/10.1038/s41594-025-01514-8","url":null,"abstract":"<p>DNA double-strand breaks occur daily in all human cells and must be repaired with high fidelity to minimize genomic instability. Deficiencies in high-fidelity DNA repair by homologous recombination lead to dependence on DNA polymerase θ, which identifies DNA microhomologies in 3′ single-stranded DNA overhangs and anneals them to initiate error-prone double-strand break repair. The resulting genomic instability is associated with numerous cancers, thereby making this polymerase an attractive therapeutic target. However, despite the biomedical importance of polymerase θ, the molecular details of how it initiates DNA break repair remain unclear. Here, we present cryo-electron microscopy structures of the polymerase θ helicase domain bound to microhomology-containing DNA, revealing DNA-induced rearrangements of the helicase that enable DNA repair. Our structures show that DNA-bound helicase dimers facilitate a microhomology search that positions 3′ single-stranded DNA ends in proximity to align complementary bases and anneal DNA microhomology. We characterize the molecular determinants that enable the helicase domain of polymerase θ to identify and pair DNA microhomologies to initiate mutagenic DNA repair, thereby providing insight into potentially targetable interactions for therapeutic interventions.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143518646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structures of a natural circularly permuted group II intron reveal mechanisms of branching and backsplicing 自然循环排列的II族内含子的结构揭示了分支和反向剪接的机制
Nature structural & molecular biology Pub Date : 2025-02-27 DOI: 10.1038/s41594-025-01489-6
Xiaobin Ling, Yuqi Yao, Jinbiao Ma
{"title":"Structures of a natural circularly permuted group II intron reveal mechanisms of branching and backsplicing","authors":"Xiaobin Ling, Yuqi Yao, Jinbiao Ma","doi":"10.1038/s41594-025-01489-6","DOIUrl":"https://doi.org/10.1038/s41594-025-01489-6","url":null,"abstract":"<p>Circularly permuted (CP) group II introns, identified in various bacteria phyla, swap domains D5 and D6 near the 5′ end and have reversed splice sites (SSs), leading to backsplicing and circular RNA formation. In this study, we present multiple high-resolution cryo-electron microscopy structures of a natural CP group II intron from <i>Comamonas testosteroni</i> KF-1 (<i>Cte</i> 1), elucidating the molecular mechanisms of branching and backsplicing. During branching, the 5′ SS is positioned by an auxiliary sequence (AUX)-enhanced interaction between the exon-binding site and intron-binding site (IBS) and stacks on the branch-site adenosine within D6, allowing the attacking 2′-OH group to coordinate with a metal ion in the active center. In backsplicing, the 3′ SS is aligned with the branching step, leaving IBS in the active center, stabilized by base pairing with the AUX, which enables the free 3′-end hydroxyl group to directly attack the scissile phosphate of 3′ SS. Furthermore, a groove in <i>Cte</i> 1 may stabilize the circular RNA. These findings highlight a conserved catalytic mechanism for canonical group II introns, albeit facilitated by the versatile AUX, opening avenues for designing potent ribozymes producing circular RNAs.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143506861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A PAR6–aPKC–LGL structure reveals how LGL antagonizes aPKC PAR6-aPKC-LGL结构揭示了LGL如何拮抗aPKC
Nature structural & molecular biology Pub Date : 2025-02-27 DOI: 10.1038/s41594-025-01506-8
Daniel St Johnston
{"title":"A PAR6–aPKC–LGL structure reveals how LGL antagonizes aPKC","authors":"Daniel St Johnston","doi":"10.1038/s41594-025-01506-8","DOIUrl":"https://doi.org/10.1038/s41594-025-01506-8","url":null,"abstract":"The apical–basal polarity of epithelial cells depends on mutual antagonism between the apical aPKC and lateral LGL proteins. Until now, it has been unclear how LGL can be both a substrate and inhibitor of aPKC. Now, a cryo-electron microscopy (cryo-EM) structure of a stalled PAR6–aPKC–LGL complex addresses this conundrum.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143507259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Local structural flexibility drives oligomorphism in computationally designed protein assemblies 局部结构灵活性驱动寡胚性在计算设计的蛋白质组装
Nature structural & molecular biology Pub Date : 2025-02-26 DOI: 10.1038/s41594-025-01490-z
Alena Khmelinskaia, Neville P. Bethel, Farzad Fatehi, Bhoomika Basu Mallik, Aleksandar Antanasijevic, Andrew J. Borst, Szu-Hsueh Lai, Ho Yeung Chim, Jing Yang ‘John’ Wang, Marcos C. Miranda, Andrew M. Watkins, Cassandra Ogohara, Shane Caldwell, Mengyu Wu, Albert J. R. Heck, David Veesler, Andrew B. Ward, David Baker, Reidun Twarock, Neil P. King
{"title":"Local structural flexibility drives oligomorphism in computationally designed protein assemblies","authors":"Alena Khmelinskaia, Neville P. Bethel, Farzad Fatehi, Bhoomika Basu Mallik, Aleksandar Antanasijevic, Andrew J. Borst, Szu-Hsueh Lai, Ho Yeung Chim, Jing Yang ‘John’ Wang, Marcos C. Miranda, Andrew M. Watkins, Cassandra Ogohara, Shane Caldwell, Mengyu Wu, Albert J. R. Heck, David Veesler, Andrew B. Ward, David Baker, Reidun Twarock, Neil P. King","doi":"10.1038/s41594-025-01490-z","DOIUrl":"https://doi.org/10.1038/s41594-025-01490-z","url":null,"abstract":"<p>Many naturally occurring protein assemblies have dynamic structures that allow them to perform specialized functions. Although computational methods for designing novel self-assembling proteins have advanced substantially over the past decade, they primarily focus on designing static structures. Here we characterize three distinct computationally designed protein assemblies that exhibit unanticipated structural diversity arising from flexibility in their subunits. Cryo-EM single-particle reconstructions and native mass spectrometry reveal two distinct architectures for two assemblies, while six cryo-EM reconstructions for the third likely represent a subset of its solution-phase structures. Structural modeling and molecular dynamics simulations indicate that constrained flexibility within the subunits of each assembly promotes a defined range of architectures rather than nonspecific aggregation. Redesigning the flexible region in one building block rescues the intended monomorphic assembly. These findings highlight structural flexibility as a powerful design principle, enabling exploration of new structural and functional spaces in protein assembly design.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143495264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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