IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-18 DOI: 10.1002/cbic.202400801

Dan-Dan Xie, Xue-Lian Li, Li-Zhen Zeng, Xiaoxia Ren, Dan Zhang, Rong Yang, Feng Gao

引用次数: 0

Designer Helical Fibers and Tubes: Self-Assembling Hybrid Peptides via Leu/Ile-Phe Zipper. 设计螺旋状纤维和管材：通过Leu/Ile-Phe拉链自组装混合肽。

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-18 DOI: 10.1002/cbic.202400808

V Haridas, Souvik Dutta

引用次数: 0

Exploring Fluorinase Substrate Tolerance at C-2 of SAM. 探索 SAM C-2 的氟化酶底物耐受性。

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-17 DOI: 10.1002/cbic.202400861

Phillip T Lowe, Isabeau T Lüddecke, David O'Hagan

引用次数: 0

Protein-protein interaction and conformational change in the alpha-helical membrane transporter BtuCD-F in the native cellular envelope. α-螺旋膜转运体 BtuCD-F 在原生细胞包膜中的蛋白质相互作用和构象变化。

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-17 DOI: 10.1002/cbic.202400858

Benesh Joseph

{"title":"Protein-protein interaction and conformational change in the alpha-helical membrane transporter BtuCD-F in the native cellular envelope.","authors":"Benesh Joseph","doi":"10.1002/cbic.202400858","DOIUrl":"https://doi.org/10.1002/cbic.202400858","url":null,"abstract":"Alpha-helical membrane proteins perform numerous critical functions essential for the survival of living organisms. Traditionally, these proteins are extracted from membranes using detergent solubilization and reconstitution into liposomes or nanodiscs. However, these processes often obscure the effects of nanoconfinement and the native environment on the structure and conformational heterogeneity of the target protein. We demonstrate that pulsed dipolar electron spin resonance spectroscopy, combined with the Gd³⁺-nitroxide spin pair, enables the selective observation of the vitamin B12 importer BtuCD-F in its native cellular envelope. Despite the high levels of non-specific labeling in the envelope, this orthogonal approach combined with the long phase-memory time for the Gd³⁺ spin enables the observation of the target protein complex at a few micromolar concentrations with high resolution. In the native envelope, vitamin B12induces a distinct conformational shift at the BtuCD-BtuF interface, which is not observed in the micelles. This approach offers a general strategy for investigating protein-protein and protein-ligand/drug interactions and conformational changes of the alpha-helical membrane proteins in their native envelope context.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202400858"},"PeriodicalIF":2.6,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142646118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Impact of Antioxidants on Mechanical Properties and ROS levels of Neuronal Cells Exposed to β-amyloid peptide. 抗氧化剂对暴露于 β 淀粉样肽的神经元细胞的机械特性和 ROS 水平的影响

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-16 DOI: 10.1002/cbic.202400786

Alexander Vaneev, Petr Gorelkin, Eugene Barykin, Vasilii Kolmogorov, Roman Timoshenko, Vladimir Mitkevich, Irina Petrushanko, Ksenia Varshavskaya, Sergey Salikhov, Natalia Klyachko, Alexander Makarov, Alexander Erofeev

{"title":"Impact of Antioxidants on Mechanical Properties and ROS levels of Neuronal Cells Exposed to β-amyloid peptide.","authors":"Alexander Vaneev, Petr Gorelkin, Eugene Barykin, Vasilii Kolmogorov, Roman Timoshenko, Vladimir Mitkevich, Irina Petrushanko, Ksenia Varshavskaya, Sergey Salikhov, Natalia Klyachko, Alexander Makarov, Alexander Erofeev","doi":"10.1002/cbic.202400786","DOIUrl":"https://doi.org/10.1002/cbic.202400786","url":null,"abstract":"This study aims to investigate the potential role of antioxidants in oxidative stress and its consequent impact on the mechanical properties of neuronal cells, particularly the stress induced by amyloid-beta (1-42) (Aβ42) aggregates. A key aspect of our research involved using scanning ion-conductance microscopy (SICM) to assess the mechanical properties (Young's modulus) of neuronal cells under oxidative stress. Reactive oxygen species (ROS) level was measured in single-cell using the electrochemical method by low-invasive Pt nanoelectrode. We investigated the effects of the low molecular weight antioxidant N-acetylcysteine (NAC) and the antioxidant enzyme superoxide dismutase 1 (SOD1) on the physiological and mechanical properties of neuronal cells using SICM. Using electrochemical method and SICM, NAC effectively reduces oxidative stress and restores Young's Modulus in SH-SY5Y cells exposed to hydrogen peroxide and Aβ42 oligomers. Our study first examined the influence of SOD1 on intracellular ROS levels in the presence of Aβ oligomers. The investigation into the effects of SOD1 and its nanoparticle form SOD1 on SH-SY5Y cells reveals impacts on mechanical properties and oxidative stress. The combined use of SICM and electrochemical measurements provided a comprehensive understanding of how oxidative stress, including that triggered by the Aβ oligomers affects the mechanical properties of cells.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202400786"},"PeriodicalIF":2.6,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Chondroitin Sulfate-Coated Heteroduplex-Molecular Spherical Nucleic Acids. 硫酸软骨素包裹的异质双分子球形核酸。

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-15 DOI: 10.1002/cbic.202400908

Pasi Virta, Toni Laine, Prasannakumar Deshpande, Ville Tähtinen, Eleanor T Coffey

{"title":"Chondroitin Sulfate-Coated Heteroduplex-Molecular Spherical Nucleic Acids.","authors":"Pasi Virta, Toni Laine, Prasannakumar Deshpande, Ville Tähtinen, Eleanor T Coffey","doi":"10.1002/cbic.202400908","DOIUrl":"10.1002/cbic.202400908","url":null,"abstract":"Molecular Spherical Nucleic Acids (MSNAs) are atomically uniform dendritic nanostructures and potential delivery vehicles for oligonucleotides. The radial formulation combined with covalent conjugation may hide the oligonucleotide content and simultaneously enhance the role of appropriate conjugate groups on the outer sphere. The conjugate halo may be modulated to affect the delivery properties of the MSNAs. In the present study, [60]fullerene-based molecular spherical nucleic acids, consisting of a 2'-deoxyribonucleotide and a ribonucleotide sequence, were used as hybridization-mediated carriers (''DNA and RNA-carriers'') for an antisense oligonucleotide, suppressing Tau protein, (i.e. Tau-ASO) and its conjugates with chondroitin sulfate tetrasaccharides (CS) with different sulfation patterns. The impact of the MSNA carriers, CS-moieties on the conjugates and the CS-decorations on the MSNAs on cellular uptake and - activity (Tau-suppression) of the Tau-ASO was studied with hippocampal neurons in vitro. The formation and stability of these heteroduplex ASO-MSNAs were evaluated by UV melting profile analysis, polyacrylamide gel electrophoresis (PAGE), dynamic light scattering (DLS) and size exclusion chromatography equipped with a multi angle light scattering detector (SEC-MALS). The cellular uptake and - activity were studied by confocal microscopy and Western blot analysis, respectively.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202400908"},"PeriodicalIF":2.6,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Understanding the P-cluster of Vanadium Nitrogenase: an EPR and XAS study of the holo vs. apo forms of the enzyme. 了解钒氮酶的 P 簇：对酶的整体和非整体形式的 EPR 和 XAS 研究。

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-15 DOI: 10.1002/cbic.202400833

Serena DeBeer, Isis M Wahl, Kushal Sengupta, Maurice van Gastel, Laure Decamps

{"title":"Understanding the P-cluster of Vanadium Nitrogenase: an EPR and XAS study of the holo vs. apo forms of the enzyme.","authors":"Serena DeBeer, Isis M Wahl, Kushal Sengupta, Maurice van Gastel, Laure Decamps","doi":"10.1002/cbic.202400833","DOIUrl":"10.1002/cbic.202400833","url":null,"abstract":"The catalytic moiety of nitrogenases contains two complex metalloclusters: the M-cluster (also called cofactor), where the catalytic reduction of substrates takes place, and the [Fe8S7] P-cluster responsible for electron transfer. Due to discrepancies between crystallography and EPR spectroscopy, the exact structure of the P-cluster in the VFe protein remains a topic of debate. Herein, we use an apo-form of VFe (which retains the P-cluster but lacks the FeVco) to study the VFe P-cluster. SDS-PAGE and NativePAGE showed a heterogeneous composition of the VFe and the apo-VFe samples with presence of α1β2δ2 and α1β2 complexes. The parallel mode EPR measurements of IDS oxidized MoFe, apo-MoFe, and VFe samples reveal a signal at g = 12 associated with the two-electron oxidized state of the P-cluster (P2+) for all three samples, albeit with different intensities. In contrast, no P2+ was observed for IDS oxidized apo-VFe. Additionally, comparisons between apo-MoFe, apo-VFe and the model complex (NBu4)2[Fe4S4(SPh)4] via XAS and EXAFS measurements showed that apo-VFe does not contain a fully formed [Fe8S7] P-cluster, but rather is comprised of fragmented iron-sulfur clusters. Our results point to a possible variation on the structure of the P-cluster in the different forms of the nitrogenase.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202400833"},"PeriodicalIF":2.6,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Tailoring CotA Laccase Substrate Specificity by Rationally Reshaping Pocket Edge. 通过合理重塑口袋边缘来定制 CotA 漆酶底物特异性

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-15 DOI: 10.1002/cbic.202400660

Tian Xie, Jiakun Li, Ganggang Wang

{"title":"Tailoring CotA Laccase Substrate Specificity by Rationally Reshaping Pocket Edge.","authors":"Tian Xie, Jiakun Li, Ganggang Wang","doi":"10.1002/cbic.202400660","DOIUrl":"https://doi.org/10.1002/cbic.202400660","url":null,"abstract":"CotA is a bacterial multicopper oxidase, capable of oxidizing lots of substrates. In previous work, small size lignin phenol derivates were found to lay only in the partially covered part of pocket. However, big size substate would occupy the whole pocket to react. In this work, five residues sitting at the edge of the pocket were selected to study their roles in regulating activities against different size substrates. All mutants showed impaired activities against small size sinapic acid, however, A227E, G321F and G321P showed around 25% increase of activities against big size ditaurobilirubin compared to wild type (WT). T262F/G321F showed moderate increased activity to alazin red S. kcat/Kms against ditaurobilirubin of A227E, T262F and G321F are around 1.5, 3 and 1.5 folds of WT's. Unexpectedly, heterologous expression yields of T262F, T262F/G321F and T262F/G321P in Escherichia coli greatly increased by around 5, 7 and 21 folds compared to WT, respectively. It is speculated positive mutants would provide a beneficial orientation for big size substrates. Substituting semi-buried residue T262 by a hydrophobic amino acid might enhance expression yields mainly by increasing van der waals and hydrophobic interaction. This work exemplified rationally regulating specific activities of laccase and is valuable for industrial application.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202400660"},"PeriodicalIF":2.6,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Analysis and Prediction of Chymotrypsin Substrate Preferences through Large Data Acquisition with Target-Free mRNA Display. 通过无目标 mRNA 显示的大数据采集分析和预测糜蛋白酶底物偏好。

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-15 DOI: 10.1002/cbic.202400760

Dan Sindhikara, Sabrina E Iskandar, Lindsey Guan, Rumit Maini, Christopher J Hipolito, Congliang Sun, Lisa A Vasicek, Adam Weinglass, S Adrian Saldanha

{"title":"Analysis and Prediction of Chymotrypsin Substrate Preferences through Large Data Acquisition with Target-Free mRNA Display.","authors":"Dan Sindhikara, Sabrina E Iskandar, Lindsey Guan, Rumit Maini, Christopher J Hipolito, Congliang Sun, Lisa A Vasicek, Adam Weinglass, S Adrian Saldanha","doi":"10.1002/cbic.202400760","DOIUrl":"https://doi.org/10.1002/cbic.202400760","url":null,"abstract":"Oral delivery of peptide therapeutics is limited by degradation by gut proteases like chymotrypsin. Existing databases of peptidases are limited in size and do not enable systematic analyses of protease substrate preferences, especially for non-natural amino acids. Thus, stability optimization of hit compounds is time and resource intensive. To accelerate the stability optimization of peptide ligands, we generated large datasets of chymotrypsin-resistant peptides via mRNA display to create a predictive model for chymotrypsin-resistant sequences. Through analysis of enriched motifs, we recapitulate known chymotrypsin cleavage sites, reveal positionally dependent effects of monomers on peptide cleavage, and report previously unidentified protective and destabilizing residues. We then developed a machine-learning-based model predicting peptide resistance to chymotrypsin cleavage and validated both model performance and the NGS experimental data by measuring chymotrypsin half-lives for a subset of peptides. Finally, we simulated stability predictions on non-natural amino acids through a leucine hold-out model and observed robust performance. Overall, we demonstrate the utility of mRNA display as a tool for big data generation and show that pairing mRNA display with machine learning yields valuable predictions for chymotrypsin cleavage. Expansion of this workflow to additional proteases could provide complementary predictive models that focus future peptide drug discovery efforts.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202400760"},"PeriodicalIF":2.6,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142637957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Towards Bacterial Resistance via the Membrane Strategy: Enzymatic, Biophysical and Biomimetic Studies of the Lipid cis-trans Isomerase of Pseudomonas aeruginosa. 通过膜策略实现细菌抗药性：铜绿假单胞菌脂质顺反异构酶的酶学、生物物理和生物模拟研究。

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-14 DOI: 10.1002/cbic.202400844

Mickaël Mauger, Iryna Makarchuk, Yasmin Molter, Anna Sansone, Frédéric Melin, Philippe Chaignon, Philippe Schaeffer, Pierre Adam, Volker Schünemann, Petra Hellwig, Carla Ferreri, Chryssostomos Chatgilialoglu, Myriam Seemann

{"title":"Towards Bacterial Resistance via the Membrane Strategy: Enzymatic, Biophysical and Biomimetic Studies of the Lipid cis-trans Isomerase of Pseudomonas aeruginosa.","authors":"Mickaël Mauger, Iryna Makarchuk, Yasmin Molter, Anna Sansone, Frédéric Melin, Philippe Chaignon, Philippe Schaeffer, Pierre Adam, Volker Schünemann, Petra Hellwig, Carla Ferreri, Chryssostomos Chatgilialoglu, Myriam Seemann","doi":"10.1002/cbic.202400844","DOIUrl":"https://doi.org/10.1002/cbic.202400844","url":null,"abstract":"The lipid cis-trans isomerase (Cti) is a periplasmic heme-c enzyme found in several bacteria including Pseudomonas aeruginosa, a pathogen known for causing nosocomial infections. This metalloenzyme catalyzes the cis-trans isomerization of unsaturated fatty acids in order to rapidly modulate membrane fluidity in response to stresses that impede bacterial growth. As a consequence, breakthrough in the elucidation of the mechanism of this metalloenzyme might lead to new strategies to combat bacterial antibiotic resistance. We report the first comprehensive biochemical, electrochemical and spectroscopic characterization of a Cti enzyme. This has been possible by the successful purification of Cti from P. aeruginosa (Pa-Cti) in favorable yields with enzyme activity of 0.41 µmol/min/mg when tested with palmitoleic acid. Through a synergistic approach involving enzymology, site-directed mutagenesis, Raman spectroscopy, Mössbauer spectroscopy and electrochemistry, we identified the heme coordination and redox state, pinpointing Met163 as the sixth ligand of the FeII of heme-c in Pa-Cti. Significantly, the development of an innovative assay based on liposomes demonstrated for the first time that Cti catalyzes cis-trans isomerization directly using phospholipids as substrates without the need of protein partners, answering the important question about the substrate of Cti within the bacterial membrane.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":" ","pages":"e202400844"},"PeriodicalIF":2.6,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

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