The FEBS journal最新文献_第9页

Corynebacterium glutamicum pyruvate:quinone oxidoreductase: an enigmatic metabolic enzyme with unusual structural features 谷氨酸棒杆菌丙酮酸：醌氧化还原酶：一种具有不寻常结构特征的神秘代谢酶。

The FEBS journal Pub Date : 2024-07-30 DOI: 10.1111/febs.17232

Cristiano da Silva Lameira, Sini Münßinger, Lu Yang, Bernhard J. Eikmanns, Marco Bellinzoni

{"title":"Corynebacterium glutamicum pyruvate:quinone oxidoreductase: an enigmatic metabolic enzyme with unusual structural features","authors":"Cristiano da Silva Lameira, Sini Münßinger, Lu Yang, Bernhard J. Eikmanns, Marco Bellinzoni","doi":"10.1111/febs.17232","DOIUrl":"10.1111/febs.17232","url":null,"abstract":"Pyruvate:quinone oxidoreductase (PQO) is a flavin-containing peripheral membrane enzyme catalyzing the decarboxylation of pyruvate to acetate and CO2 with quinone as an electron acceptor. Here, we investigate PQO activity in Corynebacterium glutamicum, examine purified PQO, and describe the crystal structure of the native enzyme and a truncated version. The specific PQO activity was highest in stationary phase cells grown in complex medium, lower in cells grown in complex medium containing glucose or acetate, and lowest in cells grown in minimal acetate-medium. A similar pattern with about 30-fold higher specific PQO activities was observed in C. glutamicum with plasmid-bound pqo expression under the control of the tac promoter, indicating that the differences in PQO activity are likely due to post-transcriptional control. Continuous cultivation of C. glutamicum at dilution rates between 0.05 and 0.4 h−1 revealed a negative correlation between PQO activity and growth rate. Kinetic analysis of PQO enzymes purified from cells grown in complex or in minimal acetate-medium revealed substantial differences in specific activity (72.3 vs. 11.9 U·mg protein−1) and turnover number (kcat: 440 vs. 78 s−1, respectively), suggesting post-translational modifications affecting PQO activity. Structural analysis of PQO revealed a homotetrameric arrangement very similar to the Escherichia coli pyruvate oxidase PoxB except for the C-terminal membrane binding domain, which exhibited a conformation markedly different from its PoxB counterpart. A truncated PQO variant lacking 17 C-terminal amino acids showed higher affinity to pyruvate and was independent of detergent activation, highlighting the importance of the C-terminus for enzyme activation and lipid binding.","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/febs.17232","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857524","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

Structures of BlEst2 from Bacillus licheniformis in its propeptide and mature forms reveal autoinhibitory effects of the C‐terminal domain 地衣芽孢杆菌 BlEst2 的前肽和成熟形式结构揭示了 C 端结构域的自动抑制作用

The FEBS journal Pub Date : 2024-07-27 DOI: 10.1111/febs.17229

Aline Minali Nakamura, Andre Schutzer Godoy, Marco Antônio Seiki Kadowaki, Lucas N. Trentin, Sinkler E. T. Gonzalez, Munir S. Skaf, Igor Polikarpov

{"title":"Structures of BlEst2 from Bacillus licheniformis in its propeptide and mature forms reveal autoinhibitory effects of the C‐terminal domain","authors":"Aline Minali Nakamura, Andre Schutzer Godoy, Marco Antônio Seiki Kadowaki, Lucas N. Trentin, Sinkler E. T. Gonzalez, Munir S. Skaf, Igor Polikarpov","doi":"10.1111/febs.17229","DOIUrl":"https://doi.org/10.1111/febs.17229","url":null,"abstract":"Carboxylesterases comprise a major class of α/β‐fold hydrolases responsible for the cleavage and formation of ester bonds. Found ubiquitously in nature, these enzymes are crucial for the metabolism of both endogenous and exogenous carboxyl esters in animals, plants and microorganisms. Beyond their essential physiological roles, carboxylesterases stand out as one of the important classes of biocatalysts for biotechnology. BlEst2, an enzyme previously classified as Bacillus licheniformis esterase, remains largely uncharacterized. In the present study, we elucidate the structural biology, molecular dynamics and biochemical features of BlEst2. Our findings reveal a canonical α/β‐hydrolase fold similar to the ESTHER block L of lipases, further augmented by two additional accessory C‐terminal domains. Notably, the catalytic domain demonstrates two insertions, which occupy conserved locations in α/β‐hydrolase proteins and commonly form the lid domain in lipase structures. Intriguingly, our in vitro cleavage of C‐terminal domains revealed the structure of the active form of BlEst2. Upon activation, BlEst2 showed a markedly elevated hydrolytic activity. This observation implies that the intramolecular C‐terminal domain serves as a regulatory intramolecular inhibitor. Interestingly, despite exhibiting esterase‐like activity, BlEst2 structural characteristics align more closely with lipases. This suggests that BlEst2 could potentially represent a previously unrecognized subgroup within the realm of carboxyl ester hydrolases.","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141780272","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

PACAP ameliorates obesity-induced insulin resistance through FAIM/Rictor/AKT axis PACAP通过FAIM/Rictor/AKT轴改善肥胖引起的胰岛素抵抗。

The FEBS journal Pub Date : 2024-07-23 DOI: 10.1111/febs.17228

Jia Feng, Wenhui Chen, Shanshan Li, Qianchen Fang, Xingwu Chen, Ge Bai, Meng Tian, Yongmei Huang, Pei Xu, Zixian Wang, Yi Ma

{"title":"PACAP ameliorates obesity-induced insulin resistance through FAIM/Rictor/AKT axis","authors":"Jia Feng, Wenhui Chen, Shanshan Li, Qianchen Fang, Xingwu Chen, Ge Bai, Meng Tian, Yongmei Huang, Pei Xu, Zixian Wang, Yi Ma","doi":"10.1111/febs.17228","DOIUrl":"10.1111/febs.17228","url":null,"abstract":"Obesity and obesity-related insulin resistance have been a research hotspot. Pituitary adenylate cyclase activating polypeptide (PACAP) has emerged as playing a significant role in energy metabolism, holding promising potential for attenuating insulin resistance. However, the precise mechanism is not fully understood. Palmitic acid and a high-fat diet (HFD) were used to establish insulin resistance model in Alpha mouse liver 12 cell line and C57BL/6 mice, respectively. Subsequently, we assessed the effects of PACAP both in vivo and in vitro. Lentivirus vectors were used to explore the signaling pathway through which PACAP may ameliorate insulin resistance. PACAP was found to selectively bind to the PACAP type I receptor receptor and ameliorate insulin resistance, which was characterized by increased glycogen synthesis and the suppression of gluconeogenesis in the insulin-resistant cell model and HFD-fed mice. These effects were linked to the activation of the Fas apoptotic inhibitory molecule/rapamycin-insensitive companion of mammalian target of rapamycin/RAC-alpha serine/threonine-protein kinase (FAIM/Rictor/AKT) axis. Furthermore, PACAP ameliorated insulin resistance by increasing solute carrier family 2, facilitated glucose transporter members 2/4 and inhibiting gluconeogenesis-related proteins glucose 6-phosphatase catalytic subunit 1 and phosphoenolpyruvate carboxykinase 2 expression. Meanwhile, the phosphorylation of hepatic AKT/glycogen synthase kinase 3β was promoted both in vivo and in vitro by PACAP. Additionally, PACAP treatment decreased body weight, food intake and blood glucose levels in obese mice. Our study shows that PACAP ameliorated insulin resistance through the FAIM/Rictor/AKT axis, presenting it as a promising drug candidate for the treatment of obesity-related insulin resistance.","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141750124","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

AXIN2 promotes degradation of AXIN1 through tankyrase in colorectal cancer cells. AXIN2通过tankyrase促进结直肠癌细胞中AXIN1的降解。

The FEBS journal Pub Date : 2024-07-18 DOI: 10.1111/febs.17226

Olivia Schmidt, Martina Brückner, Dominic B Bernkopf

{"title":"AXIN2 promotes degradation of AXIN1 through tankyrase in colorectal cancer cells.","authors":"Olivia Schmidt, Martina Brückner, Dominic B Bernkopf","doi":"10.1111/febs.17226","DOIUrl":"https://doi.org/10.1111/febs.17226","url":null,"abstract":"AXIN1 and AXIN2 are homologous proteins that inhibit the Wnt/β-catenin signaling pathway, which is frequently hyperactive in colorectal cancer. Stabilization of AXIN1 and AXIN2 by inhibiting their degradation through tankyrase (TNKS) allows the attenuation of Wnt signaling in cancer, attracting interest for potential targeted therapy. Here, we found that knockout or knockdown of AXIN2 in colorectal cancer cells increased the protein stability of AXIN1. The increase in AXIN1 overcompensated for the loss of AXIN2 with respect to protein levels; however, functionally it did not because loss of AXIN2 activated the pathway. Moreover, AXIN2 was highly essential in the context of TNKS inhibition because TNKS-targeting small-molecule inhibitors completely failed to inhibit Wnt signaling and to stabilize AXIN1 in AXIN2 knockout cells. The increased AXIN1 protein stability and the impaired stabilization by TNKS inhibitors indicated disrupted TNKS-AXIN1 regulation in AXIN2 knockout cells. Concordantly, mechanistic studies revealed that co-expression of AXIN2 recruited TNKS to AXIN1 and stimulated TNKS-mediated degradation of transiently expressed AXIN1 wild-type and AXIN1 mutants with impaired TNKS binding. Taken together, our data suggest that AXIN2 promotes degradation of AXIN1 through TNKS in colorectal cancer cells by directly linking the two proteins, and these findings may be relevant for TNKS inhibition-based colorectal cancer therapies.","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141636268","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

NFκB dynamics-dependent epigenetic changes modulate inflammatory gene expression and induce cellular senescence. 依赖于 NFκB 动态的表观遗传学变化可调节炎症基因表达并诱导细胞衰老。

The FEBS journal Pub Date : 2024-07-16 DOI: 10.1111/febs.17227

Sho Tabata, Keita Matsuda, Shou Soeda, Kenshiro Nagai, Yoshihiro Izumi, Masatomo Takahashi, Yasutaka Motomura, Ayaka Ichikawa Nagasato, Kazuyo Moro, Takeshi Bamba, Mariko Okada

{"title":"NFκB dynamics-dependent epigenetic changes modulate inflammatory gene expression and induce cellular senescence.","authors":"Sho Tabata, Keita Matsuda, Shou Soeda, Kenshiro Nagai, Yoshihiro Izumi, Masatomo Takahashi, Yasutaka Motomura, Ayaka Ichikawa Nagasato, Kazuyo Moro, Takeshi Bamba, Mariko Okada","doi":"10.1111/febs.17227","DOIUrl":"https://doi.org/10.1111/febs.17227","url":null,"abstract":"Upregulation of nuclear factor κB (NFκB) signaling is a hallmark of aging and a major cause of age-related chronic inflammation. However, its effect on cellular senescence remains unclear. Here, we show that alteration of NFκB nuclear dynamics from oscillatory to sustained by depleting a negative feedback regulator of NFκB pathway, NFκB inhibitor alpha (IκBα), in the presence of tumor necrosis factor α (TNFα) promotes cellular senescence. Sustained NFκB activity enhanced inflammatory gene expression through increased NFκB-DNA binding and slowed the cell cycle. IκBα protein was decreased under replicative or oxidative stress in vitro. Furthermore, a decrease in IκBα protein and an increase in DNA-NFκB binding at the transcription start sites of age-associated genes in aged mouse hearts suggested that nuclear NFκB dynamics may play a critical role in the progression of aging. Our study suggests that nuclear NFκB dynamics-dependent epigenetic changes regulated over time in a living system, possibly through a decrease in IκBα, enhance the expression of inflammatory genes to advance the cells to a senescent state.","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141622082","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

Structure–function analysis of nucleotide housekeeping protein HAM1 from human malaria parasite Plasmodium falciparum 恶性疟原虫核苷酸管家蛋白 HAM1 的结构功能分析。

The FEBS journal Pub Date : 2024-07-14 DOI: 10.1111/febs.17216

Debanjan Saha, Atanu Pramanik, Aline Freville, Asim Azhar Siddiqui, Uttam Pal, Chinmoy Banerjee, Shiladitya Nag, Subhashis Debsharma, Saikat Pramanik, Somnath Mazumder, Nakul C. Maiti, Saumen Datta, Christiaan van Ooij, Uday Bandyopadhyay

{"title":"Structure–function analysis of nucleotide housekeeping protein HAM1 from human malaria parasite Plasmodium falciparum","authors":"Debanjan Saha, Atanu Pramanik, Aline Freville, Asim Azhar Siddiqui, Uttam Pal, Chinmoy Banerjee, Shiladitya Nag, Subhashis Debsharma, Saikat Pramanik, Somnath Mazumder, Nakul C. Maiti, Saumen Datta, Christiaan van Ooij, Uday Bandyopadhyay","doi":"10.1111/febs.17216","DOIUrl":"10.1111/febs.17216","url":null,"abstract":"Non-canonical nucleotides, generated as oxidative metabolic by-products, significantly threaten the genome integrity of Plasmodium falciparum and thereby, their survival, owing to their mutagenic effects. PfHAM1, an evolutionarily conserved inosine/xanthosine triphosphate pyrophosphohydrolase, maintains nucleotide homeostasis in the malaria parasite by removing non-canonical nucleotides, although structure–function intricacies are hitherto poorly reported. Here, we report the X-ray crystal structure of PfHAM1, which revealed a homodimeric structure, additionally validated by size-exclusion chromatography–multi-angle light scattering analysis. The two monomeric units in the dimer were aligned in a parallel fashion, and critical residues associated with substrate and metal binding were identified, wherein a notable structural difference was observed in the β-sheet main frame compared to human inosine triphosphate pyrophosphatase. PfHAM1 exhibited Mg++-dependent pyrophosphohydrolase activity and the highest binding affinity to dITP compared to other non-canonical nucleotides as measured by isothermal titration calorimetry. Modifying the pfham1 genomic locus followed by live-cell imaging of expressed mNeonGreen-tagged PfHAM1 demonstrated its ubiquitous presence in the cytoplasm across erythrocytic stages with greater expression in trophozoites and schizonts. Interestingly, CRISPR-Cas9/DiCre recombinase-guided pfham1-null P. falciparum survived in culture under standard growth conditions, indicating its assistive role in non-canonical nucleotide clearance during intra-erythrocytic stages. This is the first comprehensive structural and functional report of PfHAM1, an atypical nucleotide-cleansing enzyme in P. falciparum.","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141604721","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

Decoy peptides that inhibit TNF signaling by disrupting the TNF homotrimeric oligomer 诱饵肽，通过破坏 TNF 同源三聚体寡聚体来抑制 TNF 信号传导。

The FEBS journal Pub Date : 2024-07-14 DOI: 10.1111/febs.17220

Nasir Javaid, Bilal Ahmad, Mahesh Chandra Patra, Sangdun Choi

{"title":"Decoy peptides that inhibit TNF signaling by disrupting the TNF homotrimeric oligomer","authors":"Nasir Javaid, Bilal Ahmad, Mahesh Chandra Patra, Sangdun Choi","doi":"10.1111/febs.17220","DOIUrl":"10.1111/febs.17220","url":null,"abstract":"Tumor necrosis factor (TNF) is a pro-inflammatory cytokine and its functional homotrimeric form interacts with the TNF receptor (TNFR) to activate downstream apoptotic, necroptotic, and inflammatory signaling pathways. Excessive activation of these pathways leads to various inflammatory diseases, which makes TNF a promising therapeutic target. Here, 12-mer peptides were selected from the interface of TNF-TNFR based upon their relative binding energies and were named ‘TNF-inhibiting decoys’ (TIDs). These decoy peptides inhibited TNF-mediated secretion of cytokines and cell death, as well as activation of downstream signaling effectors. Effective TIDs inhibited TNF signaling by disrupting the formation of TNF's functional homotrimeric form. Among derivatives of TIDs, TID3c showed slightly better efficacy in cell-based assays by disrupting TNF trimer formation. Moreover, TID3c oligomerized TNF to a high molecular weight configuration. In silico modeling and simulations revealed that TID3c and its parent peptide, TID3, form a stable complex with TNF through hydrogen bonds and electrostatic interactions, which makes them the promising lead to develop peptide-based anti-TNF therapeutics.","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141604720","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

6-Phosphogluconolactonase is critical for the efficient functioning of the pentose phosphate pathway 6- 磷酸葡萄糖酸内酯酶对磷酸戊糖途径的高效运作至关重要。

The FEBS journal Pub Date : 2024-07-10 DOI: 10.1111/febs.17221

Léa Phégnon, Julien Pérochon, Sandrine Uttenweiler-Joseph, Edern Cahoreau, Pierre Millard, Fabien Létisse

{"title":"6-Phosphogluconolactonase is critical for the efficient functioning of the pentose phosphate pathway","authors":"Léa Phégnon, Julien Pérochon, Sandrine Uttenweiler-Joseph, Edern Cahoreau, Pierre Millard, Fabien Létisse","doi":"10.1111/febs.17221","DOIUrl":"10.1111/febs.17221","url":null,"abstract":"The metabolic networks of microorganisms are remarkably robust to genetic and environmental perturbations. This robustness stems from redundancies such as gene duplications, isoenzymes, alternative metabolic pathways, and also from non-enzymatic reactions. In the oxidative branch of the pentose phosphate pathway (oxPPP), 6-phosphogluconolactone hydrolysis into 6-phosphogluconate is catalysed by 6-phosphogluconolactonase (Pgl) but in the absence of the latter, the oxPPP flux is thought to be maintained by spontaneous hydrolysis. However, in Δpgl Escherichia coli, an extracellular pathway can also contribute to pentose phosphate synthesis. This raises question as to whether the intracellular non-enzymatic reaction can compensate for the absence of 6-phosphogluconolactonase and, ultimately, on the role of 6-phosphogluconolactonase in central metabolism. Our results validate that the bypass pathway is active in the absence of Pgl, specifically involving the extracellular spontaneous hydrolysis of gluconolactones to gluconate. Under these conditions, metabolic flux analysis reveals that this bypass pathway accounts for the entire flux into the oxPPP. This alternative metabolic route—partially extracellular—sustains the flux through the oxPPP necessary for cell growth, albeit at a reduced rate in the absence of Pgl. Importantly, these findings imply that intracellular non-enzymatic hydrolysis of 6-phosphogluconolactone does not compensate for the absence of Pgl. This underscores the crucial role of Pgl in ensuring the efficient functioning of the oxPPP.","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/febs.17221","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141565492","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

Enhanced stabilisation and reduced fibril forming potential of an amyloidogenic light chain using a variable heavy domain to mimic the homodimer complex. 利用可变重结构域模拟同源二聚体复合物，增强淀粉样蛋白轻链的稳定性并降低其形成纤维的可能性。

The FEBS journal Pub Date : 2024-07-09 DOI: 10.1111/febs.17223

Alana Maerivoet, Rebecca Price, Cécile Galmiche, Anthony Scott-Tucker, Jeff Kennedy, Tom Crabbe, Svetlana Antonyuk, Jillian Madine

{"title":"Enhanced stabilisation and reduced fibril forming potential of an amyloidogenic light chain using a variable heavy domain to mimic the homodimer complex.","authors":"Alana Maerivoet, Rebecca Price, Cécile Galmiche, Anthony Scott-Tucker, Jeff Kennedy, Tom Crabbe, Svetlana Antonyuk, Jillian Madine","doi":"10.1111/febs.17223","DOIUrl":"https://doi.org/10.1111/febs.17223","url":null,"abstract":"Light chain amyloidosis (AL), is classified as a plasma cell dyscrasia, whereby a mutant plasma cell multiplies uncontrollably and secretes enormous amounts of immunoglobulin-free light chain (FLC) fragments. These FLCs undergo a process of misfolding and aggregation into amyloid fibrils, that can cause irreversible system-wide damage. Current treatments that focus on depleting the underlying plasma cell clone are often poorly tolerated, particularly in patients with severe cardiac involvement, meaning patient prognosis is poor. An alternative treatment approach currently being explored is the inhibition of FLC aggregation by stabilisation of the native conformer. Here, we aimed to identify and characterise antibody fragments that target FLC domains and promote their stabilisation. Using phage-display screening methods, we identified a variable heavy (VH) domain, termed VH1, targeted towards the FLC. Using differential scanning fluorimetry and surface plasmon resonance, VH1 was characterised to bind and kinetically stabilise an amyloidogenic FLC, whereby a > 5.5 °C increase in thermal stability was noted. This improved stability corresponded to the inhibition of fibril formation, where 10 : 1 LC : VH1 concentration reduced aggregation to baseline levels. X-ray crystallographic structures of the LC : VH1 complex at atomic resolution revealed binding in a 1 : 1 ratio, mimicking the dimeric antigen binding sites of the native immunoglobulin molecule and the native LC homodimer.","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141565493","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

MediatorWeb: a protein–protein interaction network database for the RNA polymerase II Mediator complex MediatorWeb：RNA 聚合酶 II Mediator 复合物的蛋白质-蛋白质相互作用网络数据库。

The FEBS journal Pub Date : 2024-07-08 DOI: 10.1111/febs.17225

Sourobh Maji, Mohd Waseem, Manish Kumar Sharma, Maninder Singh, Anamika Singh, Nidhi Dwivedi, Pallabi Thakur, David G. Cooper, Naveen C. Bisht, Jan S. Fassler, Naidu Subbarao, Jitendra P. Khurana, Neel Sarovar Bhavesh, Jitendra Kumar Thakur

{"title":"MediatorWeb: a protein–protein interaction network database for the RNA polymerase II Mediator complex","authors":"Sourobh Maji, Mohd Waseem, Manish Kumar Sharma, Maninder Singh, Anamika Singh, Nidhi Dwivedi, Pallabi Thakur, David G. Cooper, Naveen C. Bisht, Jan S. Fassler, Naidu Subbarao, Jitendra P. Khurana, Neel Sarovar Bhavesh, Jitendra Kumar Thakur","doi":"10.1111/febs.17225","DOIUrl":"10.1111/febs.17225","url":null,"abstract":"The protein–protein interaction (PPI) network of the Mediator complex is very tightly regulated and depends on different developmental and environmental cues. Here, we present an interactive platform for comparative analysis of the Mediator subunits from humans, baker's yeast Saccharomyces cerevisiae, and model plant Arabidopsis thaliana in a user-friendly web-interface database called MediatorWeb. MediatorWeb provides an interface to visualize and analyze the PPI network of Mediator subunits. The database facilitates downloading the untargeted and unweighted network of Mediator complex, its submodules, and individual Mediator subunits to better visualize the importance of individual Mediator subunits or their submodules. Further, MediatorWeb offers network visualization of the Mediator complex and interacting proteins that are functionally annotated. This feature provides clues to understand functions of Mediator subunits in different processes. In an additional tab, MediatorWeb provides quick access to secondary and tertiary structures, as well as residue–level contact information for Mediator subunits in each of the three model organisms. Another useful feature of MediatorWeb is detection of interologs based on orthologous analyses, which can provide clues to understand the functions of Mediator complex in less explored kingdoms. Thus, MediatorWeb and its features can help the user to understand the role of Mediator complex and its subunits in the transcription regulation of gene expression.","PeriodicalId":94226,"journal":{"name":"The FEBS journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141556243","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