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A cryptic allosteric pocket shapes isoform-selective inhibition of human malic enzymes. 一个隐变构口袋形状对人苹果酶的异构体选择性抑制。
IF 5.6 3区 生物学
Protein Science Pub Date : 2026-09-01 DOI: 10.1002/pro.70757
Ben A Krinkel, Yuliana Yosaatmadja, Mark D Slayton, Anita Krinkel, Jack Copping, Jin Heon Jeon, Joyce Eu, Kerslee Kohagen, Amir Ashoorzadeh, Jeff Smaill, Jack Flanagan, Christopher Walker, Sofia D Merajver, Kerry Loomes, Christopher J Squire
{"title":"A cryptic allosteric pocket shapes isoform-selective inhibition of human malic enzymes.","authors":"Ben A Krinkel, Yuliana Yosaatmadja, Mark D Slayton, Anita Krinkel, Jack Copping, Jin Heon Jeon, Joyce Eu, Kerslee Kohagen, Amir Ashoorzadeh, Jeff Smaill, Jack Flanagan, Christopher Walker, Sofia D Merajver, Kerry Loomes, Christopher J Squire","doi":"10.1002/pro.70757","DOIUrl":"10.1002/pro.70757","url":null,"abstract":"<p><p>Malic enzymes (ME) regulate central carbon metabolism and cellular redox balance, and the mitochondrial isoform ME2 is frequently upregulated in aggressive cancers to support metabolic flexibility and stress resistance. Isoform-selective inhibition has remained out of reach because the catalytic machinery is essentially invariant across the three human enzymes (ME1-3), suggesting that selectivity must arise elsewhere than the active site. Here, we define matched kinetic and regulatory profiles for all three isoforms, highlighting key differences in substrate and cofactor dependence and metabolic regulation. Our x-ray crystal structures show that the active-site inhibitor 3',6'-dihydroxy-4,4″-dimethoxy-[1,1':4',1″-terphenyl]-2',5'-dione (NPD-389) occupies a conserved, metal-coordinating pose in all three isoforms, explaining its non-selective inhibition observed in enzyme assays. We further identify a cryptic pocket adjacent to the active site that is engaged by our probe molecule, flavianic acid (FLA), and accessible only in the mitochondrial enzymes ME2 and ME3. FLA binding locks an open, inactive enzyme conformation in place, with kinetic studies revealing isoform-specific allosteric responses and suggesting that this pocket may be a native regulatory site sensitive to the mitochondrial metabolic state. Our cellular viability assays suggest that molecules exploiting this cryptic pocket reduce proliferation in cancer cell models with elevated ME2 expression. Conformational dynamics, rather than sequence divergence at the catalytic center, can therefore generate isoform-specific regulatory and inhibitory mechanisms within a conserved enzyme family.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 9","pages":"e70757"},"PeriodicalIF":5.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13461788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148713500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Buffer and salt dependent reassembly pathways of Myxococcus xanthus encapsulin. 黄粘球菌包封蛋白的缓冲和盐依赖性重组途径。
IF 5.6 3区 生物学
Protein Science Pub Date : 2026-09-01 DOI: 10.1002/pro.70756
Varnika Yadav, Tobias Beck
{"title":"Buffer and salt dependent reassembly pathways of Myxococcus xanthus encapsulin.","authors":"Varnika Yadav, Tobias Beck","doi":"10.1002/pro.70756","DOIUrl":"10.1002/pro.70756","url":null,"abstract":"<p><p>Protein cages that adopt multiple assembly states provide tractable systems for probing the mechanisms that govern icosahedral shell formation. The Myxococcus xanthus encapsulin shell protein assembles into either a T = 1 shell (60 subunits) or a T = 3 shell (180 subunits), making it an ideal model to investigate how solution conditions bias competing assembly pathways. Here, we examined the reassembly of M. xanthus encapsulin following complete urea-mediated disassembly, systematically varying buffer identity (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid [HEPES], Tris, or phosphate) and ionic strength (0-1M NaCl) at pH 7.5. Assembly products were analyzed by dynamic light scattering and size-exclusion chromatography, with selected fractions characterized by transmission electron microscopy. Buffer identity and salt concentration reproducibly determined the T = 1 versus T = 3 distribution: phosphate buffer strongly favored T = 1 under all conditions, Tris at low ionic strength promoted T = 3 formation, and increasing NaCl progressively shifted outcomes toward T = 1 or unassembled subunits depending on the buffer. Assembled populations remained fixed upon shell closure and did not interconvert upon buffer exchange, demonstrating kinetic trapping. Interface analysis of both assembly states reveals that T = 3 formation requires reversible sampling of multiple weak contacts following formation of one dominant interface, whereas T = 1 relies on repeated formation of a single hydrophobic interface. Together, these results show that M. xanthus encapsulin assembly proceeds through competing kinetic pathways, with the outcome determined by how solution conditions modulate the reversibility and selectivity of early subunit encounters.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 9","pages":"e70756"},"PeriodicalIF":5.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13468902/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148723563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Catalytic architecture and cyclase-mediated dimerization of a newly identified class III-c lanthipeptide synthetase. 新发现的III-c类硫肽合成酶的催化结构和环化酶介导的二聚化。
IF 5.6 3区 生物学
Protein Science Pub Date : 2026-09-01 DOI: 10.1002/pro.70776
Haojie Zhang, Yifan Li, Yi Shi, Jian Shi, Bochu Wang, Min Luo
{"title":"Catalytic architecture and cyclase-mediated dimerization of a newly identified class III-c lanthipeptide synthetase.","authors":"Haojie Zhang, Yifan Li, Yi Shi, Jian Shi, Bochu Wang, Min Luo","doi":"10.1002/pro.70776","DOIUrl":"10.1002/pro.70776","url":null,"abstract":"<p><p>Lanthipeptide synthetases catalyze dehydration and cyclization reactions that generate structurally complex ribosomally synthesized and post-translationally modified peptides. Class III LanKC enzymes are distinguished by their tri-functional kinase, lyase, and cyclase architecture, yet their mechanistic diversity remains incompletely understood due to limited structural and biochemical characterization. Here, we identify a previously unrecognized subgroup of Class III LanKC enzymes, designated Class III-c, through phylogenetic analysis and conserved substrate peptide features. Using cryo-electron microscopy, we determined the structure of a representative Class III-c enzyme, TherKC, in complex with its peptide substrate. We performed a systematic structural and functional characterization of TherKC, encompassing peptide substrate binding, oligomerization, and catalysis, providing a comprehensive mechanistic framework for this new LanKC class. TherKC assembles as a homodimer mediated exclusively by cyclase-cyclase interactions, a mode of oligomerization distinct from all previously characterized LanKC enzymes. Structural analysis identifies Arg685 as a conserved cyclase-domain hotspot that anchors dimer formation through symmetric electrostatic interactions. Disruption of this interface abolishes dimerization and reduces enzyme stability, while preserving substrate binding and catalytic competence. Structure-guided mutagenesis and mass spectrometric analyses further define conserved cyclase residues essential for efficient dehydration-cyclization coupling, provide insight into the formation of the conserved labionin-forming motif, revealing a noncanonical yet conserved catalytic framework. Together, these findings establish Class III-c LanKC enzymes as a mechanistically coherent subgroup and provide a comprehensive structural and functional understanding of this newly identified class, including its substrate-recognition, oligomerization, and cyclization mechanisms, thereby expanding the current landscape of lanthipeptide biosynthesis.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 9","pages":"e70776"},"PeriodicalIF":5.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13504147/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148813927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Conformational diversity in poly-HAMP arrays and its implications for signal transduction. poly-HAMP阵列的构象多样性及其对信号转导的影响。
IF 5.6 3区 生物学
Protein Science Pub Date : 2026-09-01 DOI: 10.1002/pro.70743
Murray Coles, Carolin P Ewers, Reinhard Albrecht, Mikel Martinez-Goikoetxea, Malgorzata Orlowska, Jörg Martin, Andrei N Lupas, Marcus D Hartmann, Stanislaw Dunin-Horkawicz
{"title":"Conformational diversity in poly-HAMP arrays and its implications for signal transduction.","authors":"Murray Coles, Carolin P Ewers, Reinhard Albrecht, Mikel Martinez-Goikoetxea, Malgorzata Orlowska, Jörg Martin, Andrei N Lupas, Marcus D Hartmann, Stanislaw Dunin-Horkawicz","doi":"10.1002/pro.70743","DOIUrl":"10.1002/pro.70743","url":null,"abstract":"<p><p>Prokaryotic transmembrane receptors are built around a helical coiled-coil backbone, with sensory, modulatory, and effector domains arranged along its length. The modulatory HAMP domain forms a parallel four-helix coiled coil integrated into this backbone, typically connecting transmembrane segments with downstream cytosolic domains. In many systems, HAMP domains transduce signals through axial rotation of their helices; however, it is not clear how broadly applicable this mechanism is. Here, we describe two families of soluble chemoreceptors and sensory kinases that contain long arrays of concatenated HAMP domains, which we term poly-HAMP. Although these poly-HAMP arrays evolved independently, both families share sequence features consistent with convergence on a similar functional system. We determined the crystal structures of 4-HAMP and 6-HAMP segments from the poly-HAMP array of histidine kinase AskA of Myxococcus xanthus, revealing unusually close packing between adjacent domains and conformational patterns compatible with the rotational signaling model. To define the broader conformational landscape, we computed AlphaFold2 models for over 200 chemoreceptor- and kinase-associated arrays. The models were consistent with the AskA structures, yet revealed distinct preferences: chemoreceptor arrays were predicted to adopt stable conformations, whereas kinase arrays more frequently adopted potentially less favorable conformations. When modeled in isolation from neighboring domains, HAMP domains from kinase arrays adopted alternative conformations related to their array-embedded forms by axial helix rotation. Taken together, our results suggest that, despite their independent origins, HAMP-containing systems including poly-HAMP arrays and canonical single-HAMP receptors may share a conserved mode of conformational plasticity involving axial helix rotation.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 9","pages":"e70743"},"PeriodicalIF":5.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13446029/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148679784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Evolutionary insights into bilin biosynthesis: Functional characterization of pre-PcyA enzymes. 胆囊蛋白生物合成的进化见解:pcya前酶的功能表征。
IF 5.6 3区 生物学
Protein Science Pub Date : 2026-09-01 DOI: 10.1002/pro.70748
Federica Frascogna, Nathan C Rockwell, Gunhild Layer, Nicole Frankenberg-Dinkel
{"title":"Evolutionary insights into bilin biosynthesis: Functional characterization of pre-PcyA enzymes.","authors":"Federica Frascogna, Nathan C Rockwell, Gunhild Layer, Nicole Frankenberg-Dinkel","doi":"10.1002/pro.70748","DOIUrl":"10.1002/pro.70748","url":null,"abstract":"<p><p>Biosynthesis of the linear tetrapyrrole phycocyanobilin (PCB) by the ferredoxin-dependent bilin reductase (FDBR) PcyA is essential for light-harvesting and regulatory processes in diverse photosynthetic organisms, yet its evolutionary origins are not fully understood. PcyA evolved from pre-PcyA proteins found in diverse bacteria. Three lineages of pre-PcyA proteins were previously identified: Pre-1, Pre-2, and Pre-3. Using an in vivo co-expression assay, in this work, Pre-2 and Pre-3 proteins were shown to be active FDBRs that did not synthesize PCB, whereas Pre-1 activity was apparently low. In refining these results, we noted a discrepancy between phycoerythrobilin populations generated by Pre-3 and by the distantly related FDBR PebS. We therefore examined the properties of pre-PcyA enzymes in vitro, using an updated pre-PcyA phylogeny to select an alternative pre-1 target. Biochemical analyses revealed that Pre-1 and Pre-2 catalyze the two-electron reduction of biliverdin (BV) to 3E-phytochromobilin (3E-PФB), in contrast to the known synthesis of 3Z-phytobilins by other FDBRs. Pre-3 can also carry out an additional two-electron reduction to yield 3E-phycoerythrobilin (3E-PEB), again distinct from the 3Z-PEB produced by PebS. We then used comparative sequence and structure analysis to target candidate catalytic residues for site-directed mutagenesis. Variant Pre-1 exhibited altered product stereochemistry, but no effects on Pre-2 were observed, and Pre-3 variants unexpectedly gained the ability to bind cyclic tetrapyrroles. These findings underscore the plasticity and promiscuity of this enzyme family. Together, this work illustrates how the flexible catalytic potential of ancestral enzymes shaped the evolution and diversification of bilin biosynthetic pathways.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 9","pages":"e70748"},"PeriodicalIF":5.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13446030/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148679799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Identification of a key water molecule involved in the macrophage migration inhibitory factor-catalyzed tautomerization of para-hydroxyphenylpyruvate using neutron crystallography. 利用中子晶体学鉴定参与巨噬细胞迁移抑制因子催化对羟基苯基丙酮酸重异构化的关键水分子。
IF 5.6 3区 生物学
Protein Science Pub Date : 2026-09-01 DOI: 10.1002/pro.70666
Gabriela C Schröder, Gregg V Crichlow, Ewelina Jablonowski, Georgios Pantouris, Jay Nix, Naomi Chayen, Flora Meilleur, Elias J Lolis
{"title":"Identification of a key water molecule involved in the macrophage migration inhibitory factor-catalyzed tautomerization of para-hydroxyphenylpyruvate using neutron crystallography.","authors":"Gabriela C Schröder, Gregg V Crichlow, Ewelina Jablonowski, Georgios Pantouris, Jay Nix, Naomi Chayen, Flora Meilleur, Elias J Lolis","doi":"10.1002/pro.70666","DOIUrl":"10.1002/pro.70666","url":null,"abstract":"<p><p>Neutron crystallography was used to determine a 2.5-Å resolution all-atom structure of macrophage migration inhibitory factor (MIF) interacting with 3-(4-hydroxyphenyl)-pyruvate (HPP). MIF is a pro-inflammatory, pro-tumorigenic protein that may be an attractive therapeutic target. MIF catalyzes the interconversion of the keto and enol forms of HPP by a tautomerase reaction. Although HPP is evidently not a physiological substrate of MIF, many compounds that inhibit this activity in enzymatic assays have been found also to inhibit physiological activities of MIF. Therefore, the MIF-catalyzed HPP tautomerization reaction is used in initial screening of compounds in the search for inhibitors of MIF physiological activity. The neutron diffraction-derived crystal structure reveals the position of a water molecule involved in the tautomerization reaction, and also confirms the charged state of lysine-32 in the active site. The structure confirms the previously proposed catalytic mechanism of MIF, with the N-terminal Pro-1 abstracting a proton to generate an HPP enolate intermediate which is subsequently protonated. The structure reported herein reveals that this proton is supplied by a neighboring water molecule. Along with the neutron structure, a room-temperature synchrotron x-ray crystal structure reveals a covalent adduct between HPP and MIF. While this adduct is a result of radiation-induced chemistry, its formation confirms the catalytic role of the active site residue because a covalent complex could only form if the reactive carbon of the substrate is correctly positioned by the enzyme.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 9","pages":"e70666"},"PeriodicalIF":5.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13451966/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148689742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
The modular evolution of multiheme cytochromes c bucks the general trend observed in most proteins. 多血红素细胞色素c的模块化进化与大多数蛋白质中观察到的一般趋势相反。
IF 5.6 3区 生物学
Protein Science Pub Date : 2026-09-01 DOI: 10.1002/pro.70737
Ricardo Soares, Catarina M Paquete, Ricardo O Louro
{"title":"The modular evolution of multiheme cytochromes c bucks the general trend observed in most proteins.","authors":"Ricardo Soares, Catarina M Paquete, Ricardo O Louro","doi":"10.1002/pro.70737","DOIUrl":"10.1002/pro.70737","url":null,"abstract":"<p><p>Multiheme cytochromes c are versatile enzymes which contribute to key steps in diverse biogeochemical cycles of chemical elements such as nitrogen, iron, and sulfur, and are also key players in microbial electrochemical technologies. Understanding how they evolved offers a blueprint on how nature tuned their sequence and heme c cofactors to accomplish this versatile chemistry. We previously focused our attention on the largest group of homologous multiheme cytochrome c and showed that these enzymes evolve by fusion and fission of cytochrome c modules. Here, we extended our analysis to all characterized multiheme cytochromes and found that, in general, the evolution of multiheme cytochromes is governed by the same principles of fusion and fission. In addition, here we show that fusion can also involve the incorporation of domains of other protein families and small peptide sequences that affect the heme coordination environment. We found that loss of heme-binding motifs is more prevalent than gain. The addition of hemes to multiheme cytochromes c occurs exclusively by integrating heme-binding peptides and not by gradual accumulation of mutations and is equally probable along the protein sequence. By contrast, heme loss occurs by the loss of heme-binding peptides and the accumulation of point mutations. Notably, heme-binding motif loss is disproportionately more prevalent at the position nearer to the N-terminus. This observation contrasts with the general trend observed in proteins, which are usually more conserved at the N-terminus, and likely reflects the way in which multiheme cytochromes c are assembled.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 9","pages":"e70737"},"PeriodicalIF":5.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13449693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148685515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Pro4S: Prediction of protein solubility by fusing sequence, structure, and surface. Pro4S:通过融合序列、结构和表面来预测蛋白质的溶解度。
IF 5.6 3区 生物学
Protein Science Pub Date : 2026-09-01 DOI: 10.1002/pro.70749
Jie Qian, Lin Yang, Renxiao Wang, Yifei Qi
{"title":"Pro4S: Prediction of protein solubility by fusing sequence, structure, and surface.","authors":"Jie Qian, Lin Yang, Renxiao Wang, Yifei Qi","doi":"10.1002/pro.70749","DOIUrl":"10.1002/pro.70749","url":null,"abstract":"<p><p>Protein solubility is a critical physicochemical property influencing protein stability, therapeutic efficacy, and overall developability in drug discovery. However, traditional experimental methods for assessing solubility are often resource-intensive and time-consuming. To address these limitations, computational approaches leveraging artificial intelligence have emerged. However, few existing frameworks are designed to effectively support both qualitative classification and quantitative regression tasks, which predominantly rely on sequence-based information. Although several recent methods have incorporated structural features, protein surface characteristics remain relatively underexplored and are not yet systematically integrated with sequence and structural representations. Here, we introduce Pro4S, a novel multimodal Protein Solubility predictive model that integrates Sequence feature, Structural feature, and Surface descriptors using advanced contrastive learning techniques. Our framework achieves significant improvements in prediction accuracy, robustness, and generalizability for both qualitative and quantitative solubility assessments. Benchmark comparisons demonstrate that Pro4S consistently outperforms existing state-of-the-art predictors across diverse datasets. Furthermore, by applying Pro4S to the emerging area of de novo protein design, we validated a strong correlation between predicted solubility and experimental expression levels, reducing the proportion of non-expressed proteins by 52.7% while retaining 96.7% of highly expressed proteins. This highlights Pro4S's potential to serve as a reliable upfront screening tool for increasing expression success rates and accelerating rational protein engineering.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 9","pages":"e70749"},"PeriodicalIF":5.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13463320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148713530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
AVIDbase: A biologically accurate structural dataset of nanobody-antigen complexes. AVIDbase:纳米体抗原复合物的生物学精确结构数据集。
IF 5.6 3区 生物学
Protein Science Pub Date : 2026-09-01 DOI: 10.1002/pro.70773
Tadej Medved, Jurij Lah, Goran Miličić, San Hadži
{"title":"AVIDbase: A biologically accurate structural dataset of nanobody-antigen complexes.","authors":"Tadej Medved, Jurij Lah, Goran Miličić, San Hadži","doi":"10.1002/pro.70773","DOIUrl":"10.1002/pro.70773","url":null,"abstract":"<p><p>Accurate structural data in a standardized format is one of the key factors behind the success of machine learning (ML)-based methods for protein design and structure prediction. However, their application to nanobody-antigen complexes has lower success rates compared to globular protein complexes, partly due to the limited amount of high-quality structural data. While several dedicated databases already exist, automated assembly pipelines frequently overlook various artifacts, which act as additional noise and limit the effectiveness of ML applications. Common issues include incorrectly defined antigen assemblies, redundancy bias, inclusion of crystal contacts, strained geometry due to crystal packing, as well as missing density or post-translational modifications near the interface. To address these issues, we present Antigen-VHH Interface Database (AVIDbase), a highly curated dataset of nanobody-antigen structures. In addition to correcting structural artifacts, the dataset provides a nonredundant set of structures with standardized chain identifiers, harmonized metadata, and cleaned atomic coordinates in a ready-to-use format for ML applications. AVIDbase is available on GitHub (github.com/Novartis/AVIDbase) and Zenodo (doi.org/10.5281/zenodo.20488703).</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 9","pages":"e70773"},"PeriodicalIF":5.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13501898/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148808988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Adaptation of OXPHOS biogenesis to cellular requirements. OXPHOS生物发生对细胞需求的适应。
IF 5.6 3区 生物学
Protein Science Pub Date : 2026-09-01 DOI: 10.1002/pro.70763
Sven Dennerlein, Peter Rehling
{"title":"Adaptation of OXPHOS biogenesis to cellular requirements.","authors":"Sven Dennerlein, Peter Rehling","doi":"10.1002/pro.70763","DOIUrl":"10.1002/pro.70763","url":null,"abstract":"<p><p>Metabolic cues regulate the formation of the mitochondrial OXPHOS machinery. These regulatory processes are tightly linked to mitochondrial translation, proteolytic degradation of unassembled subunits, and the formation of supercomplexes, creating checkpoints at which nutrient availability, oxygen tension, and signaling pathways remodel OXPHOS content and activity. In particular, the cytochrome c oxidase (COX) assembly pathway is regulated at multiple steps of its biogenesis in response to cellular demands. COX consists of mitochondrially encoded catalytic core subunits and nuclear-encoded accessory subunits whose coordinated expression, cofactor insertion, and incorporation into the COX enzyme result in optimized electron transport capacity. Consequently, COX assembly depends on numerous dedicated factors and protein isoforms, many of which are expressed in a tissue-specific manner. Through these metabolically regulated processes, cells tune oxidative phosphorylation efficiency, limit reactive oxygen species production, and support context-specific metabolic programs in development, adaptation, and disease.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 9","pages":"e70763"},"PeriodicalIF":5.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13476344/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148761599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
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