ChemBioChem最新文献_第2页

Engineering of a Malonyl-CoA Ligase for Production of Fluorinated Polyketide Extender Units. 工程化丙二酰-CoA 连接酶用于生产含氟多酮扩展单元。

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-04 Epub Date: 2024-09-09 DOI: 10.1002/cbic.202400532

Thaddeus Q Paulsel, Gavin J Williams

引用次数: 0

Sequence-Dependent Acylation of Peptide Lysine Residues by DNAzymes. DNA 酶对多肽赖氨酸的序列依赖性酰化作用

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-04 Epub Date: 2024-10-27 DOI: 10.1002/cbic.202400578

Prakriti K Das, Scott K Silverman

引用次数: 0

Isolation and Molecular Characterization of the LTA Precursor Molecule Glc₂-DAG, a Potential Target for Antibiotics. LTA前体分子Glc2-DAG的分离和分子特征，抗生素的潜在靶标。

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-04 Epub Date: 2024-10-21 DOI: 10.1002/cbic.202400543

Raj Kumar, Eefjan Breukink, Markus Weingarth

{"title":"Isolation and Molecular Characterization of the LTA Precursor Molecule Glc2-DAG, a Potential Target for Antibiotics.","authors":"Raj Kumar, Eefjan Breukink, Markus Weingarth","doi":"10.1002/cbic.202400543","DOIUrl":"10.1002/cbic.202400543","url":null,"abstract":"Bacterial infections present a major global health threat, often displaying resistance to various antibiotics. Lipoteichoic acid (LTA) is a vital component of bacterial cell envelopes of Gram-positive bacteria, crucial for cell integrity, cell division, and host inflammation. Due to its essential role for bacteria, LTA and its biosynthesis are also attractive drug targets, however, there is only scant molecular knowledge on LTA and its precursor molecules in membranes. Here, we report the isolation and molecular characterization of diglucosyldiacylglycerol (Glc2-DAG), the glycolipid precursor molecule that anchors LTA in the bacterial plasma-membrane. Using a tailored growth medium and purification protocols, we isolated 13C-isotope labelled Glc2-DAG from bacteria, which can then be used for high-resolution NMR studies. Using solution-state and solid-state NMR, we show an in-depth molecular characterization of Glc2-DAG, including in native-like membranes. Our approach may help to identify antibiotics that directly target LTA precursor molecules, and it offers a tool for future investigations into the role of Glc2-DAG in bacterial physiology.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141974573","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

Naphthalimide-Based, Single-Chromophore, Emission Ratiometric Fluorescent Sensor for Tracking Intracellular pH. 基于萘二甲酰亚胺的单色团发射比率荧光传感器，用于跟踪细胞内 pH 值。

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-04 Epub Date: 2024-10-16 DOI: 10.1002/cbic.202400538

Sujit Kumar Das, Smitaroopa Kahali, Sabnam Kar, Nandita Madhavan, Ankona Datta

引用次数: 0

Expanding the Repertoire of ceDAF-12 Ligands for Modulation of the Steroid Endocrine System in C. Elegans. 扩大ceDAF-12配体的范围，以调节秀丽隐杆线虫的类固醇内分泌系统。

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-04 Epub Date: 2024-10-23 DOI: 10.1002/cbic.202400018

Agustín Galilea, Vanessa J Santillán, Sofía L Acebedo, María Virginia Dansey, Lautaro D Álvarez, Gisela I Mazaira, Mario D Galigniana, Olga A Castro, Gabriel F Gola, Javier A Ramírez

{"title":"Expanding the Repertoire of ceDAF-12 Ligands for Modulation of the Steroid Endocrine System in C. Elegans.","authors":"Agustín Galilea, Vanessa J Santillán, Sofía L Acebedo, María Virginia Dansey, Lautaro D Álvarez, Gisela I Mazaira, Mario D Galigniana, Olga A Castro, Gabriel F Gola, Javier A Ramírez","doi":"10.1002/cbic.202400018","DOIUrl":"10.1002/cbic.202400018","url":null,"abstract":"Steroid hormones are essential for the biological processes of eukaryotic organisms. The steroid endocrine system of C. elegans, which includes dafachronic acids (DA) and the nuclear receptor ceDAF-12, provides a simple model for exploring the role of steroid hormone signaling pathways in animals. In this study, we show for the first time the feasibility of designing synthetic steroids that can modulate different physiological processes, such as development, reproduction and ageing, in relation to ceDAF-12. Our results not only confirm the conclusions derived from genetic studies linking these processes but also provide new chemical tools to selectively manipulate them, as we found that different compounds produce different phenotypic results. The structures of these compounds are much more diverse than those of endogenous hormones and analogues previously described by other researchers, allowing further development of the chemical modulation of the steroid endocrine system in C. elegans and related nematodes.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003186","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

Elucidating Evolutionary Mechanisms and Variants of the Hammerhead Ribozyme Using In Vitro Selection. 利用体外选择阐明锤头纹波酶的进化机制和变体

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-04 Epub Date: 2024-10-04 DOI: 10.1002/cbic.202400432

Jake Brill, Connor Nurmi, Yingfu Li

引用次数: 0

Comparative Study of Immobilized Biolipasa-R for Second Generation Biodiesel Production from an Acid Oil. 利用酸性油生产第二代生物柴油的固定化生物笠-R 比较研究

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-04 Epub Date: 2024-09-03 DOI: 10.1002/cbic.202400514

Androniki Spanou, Nektaria C Liakouli, Christina Fiotaki, Ioannis V Pavlidis

{"title":"Comparative Study of Immobilized Biolipasa-R for Second Generation Biodiesel Production from an Acid Oil.","authors":"Androniki Spanou, Nektaria C Liakouli, Christina Fiotaki, Ioannis V Pavlidis","doi":"10.1002/cbic.202400514","DOIUrl":"10.1002/cbic.202400514","url":null,"abstract":"The primary objective of this work is to develop a sustainable biocatalytic transesterification process for low-grade oils, aligning with EU green technology requirements for the shift to second generation biodiesel. Thus, we investigated the immobilization and subsequent application of the lipase Biolipasa-R on transesterification processes to produce fatty acid methyl esters (FAMEs) from both a sunflower oil and an acid oil which is a bioproduct of the biodiesel industry. The lipase was immobilized on biomaterials, such as diatomaceous earth, with a yield of 60 %, and commercial carriers such as methacrylic resins with a yield of 100 %. The enzyme demonstrated superior activity when immobilized on diatomaceous earth, particularly in reactions involving the acid oil, outperforming the benchmark enzyme Novozym® 435 (95.1 % and 35 % conversion respectively). This work highlights the potential of Biolipasa-R as a cost-effective and efficient biocatalyst for biodiesel production and emphasizes the environmental benefits of utilizing industrial byproducts and eco-friendly immobilization techniques. The findings suggest that Biolipasa-R is a promising candidate for industrial applications in biodiesel production, offering a sustainable solution for waste management and energy generation.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141615384","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

Bridging the Gap in the Structure-Function Paradigm of Enzymatic PET Degradation-Aromatic Residue Driven Balanced Interactions with Catalytic and Anchoring Subsite. 弥合酶促 PET 降解结构-功能范式中的差距--芳香族残基与催化和锚定亚基的平衡相互作用。

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-04 Epub Date: 2024-10-17 DOI: 10.1002/cbic.202400555

Anjima James, Anjitha Bhasi, Susmita De

{"title":"Bridging the Gap in the Structure-Function Paradigm of Enzymatic PET Degradation-Aromatic Residue Driven Balanced Interactions with Catalytic and Anchoring Subsite.","authors":"Anjima James, Anjitha Bhasi, Susmita De","doi":"10.1002/cbic.202400555","DOIUrl":"10.1002/cbic.202400555","url":null,"abstract":"Understanding all parameters contributing to enzyme activity is crucial in enzyme catalysis. For enzymatic PET degradation, this involves examining the formation of the enzyme-PET complex. In IsPETase (WT), a PET-degrading enzyme from Ideonella sakaiensis, mutating two non-catalytic residues (DM) significantly enhances activity. Such mutations, depending on their position in the tertiary structure, fine-tune enzyme function. However, detailed molecular insights into these mutations' structure-function relationship for PET degradation are lacking. This study characterizes IsPETase's catalytic ability compared to WT TfCut2 using molecular dynamics simulations and quantum mechanical methods. We explore the conformational landscape of the enzyme-PET complex and quantify residue-wise interaction energy. Notably, aromatic and hydrophobic residues Tyr, Trp, and Ile in the catalytic subsite S1, and aromatic Phe and polar Asn in the anchoring subsite S3, crucially optimize PET binding. These residues enhance PET specificity over non-aromatic plastics. Our findings suggest that the balance between binding at subsite S1 and subsite S3, which is influenced by cooperative mutations, underlies catalytic activity. This balance shows a positive correlation with experimentally obtained kcat/Km values: WT TfCut2<WT IsPETase≪DM IsPETase.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141986977","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

Zinc-Binding Oligonucleotide Backbone Modifications for Targeting a DNA-Processing Metalloenzyme. 针对 DNA 处理金属酶的锌结合寡核苷酸骨架修饰。

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-04 Epub Date: 2024-09-05 DOI: 10.1002/cbic.202400528

Mark Berney, Ellen M Fay, William Doherty, John J Deering, Eva-Maria Dürr, Steven Ferguson, Joanna F McGouran

{"title":"Zinc-Binding Oligonucleotide Backbone Modifications for Targeting a DNA-Processing Metalloenzyme.","authors":"Mark Berney, Ellen M Fay, William Doherty, John J Deering, Eva-Maria Dürr, Steven Ferguson, Joanna F McGouran","doi":"10.1002/cbic.202400528","DOIUrl":"10.1002/cbic.202400528","url":null,"abstract":"A series of chemically-modified oligonucleotides for targeting the DNA repair nuclease SNM1A have been designed and synthesised. Each oligonucleotide contains a modified internucleotide linkage designed to both mimic the native phosphodiester backbone and chelate to the catalytic zinc ion(s) in the SNM1A active site. Dinucleoside phosphoramidites containing urea, squaramide, sulfanylacetamide, and sulfinylacetamide linkages were prepared and employed successfully in solid-phase oligonucleotide synthesis. All the modified oligonucleotides were found to interact with SNM1A in a gel electrophoresis-based assay, demonstrating the first examples of inhibition of DNA damage repair enzymes for many of these groups in oligonucleotides. One strand containing a sulfinylacetamide-linkage was found to have the strongest interaction with SNM1A and was further tested in a real-time fluorescence assay. This allowed an IC50 value of 231 nM to be determined, significantly lower than previously reported substrate-mimics targeting this enzyme. It is expected that these modified oligonucleotides will serve as a scaffold for the future development of fluorescent or biotin-labelled probes for the in vivo study of DNA repair processes.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632098","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

Bio-electrocatalytic Alkene Reduction Using Ene-Reductases with Methyl Viologen as Electron Mediator. 以甲基紫精为电子媒介，利用烯还原酶进行生物电催化烯还原。

IF 2.6 4区生物学

ChemBioChem Pub Date : 2024-11-04 Epub Date: 2024-09-12 DOI: 10.1002/cbic.202400458

Zheng Wei, Tanja Knaus, Matteo Damian, Yuxin Liu, Cássia S Santana, Ning Yan, Gadi Rothenberg, Francesco G Mutti

{"title":"Bio-electrocatalytic Alkene Reduction Using Ene-Reductases with Methyl Viologen as Electron Mediator.","authors":"Zheng Wei, Tanja Knaus, Matteo Damian, Yuxin Liu, Cássia S Santana, Ning Yan, Gadi Rothenberg, Francesco G Mutti","doi":"10.1002/cbic.202400458","DOIUrl":"10.1002/cbic.202400458","url":null,"abstract":"Asymmetric hydrogenation of alkene moieties is important for the synthesis of chiral molecules, but achieving high stereoselectivity remains a challenge. Biocatalysis using ene-reductases (EReds) offers a viable solution. However, the need for NAD(P)H cofactors limits large-scale applications. Here, we explored an electrochemical alternative for recycling flavin-containing EReds using methyl viologen as a mediator. For this, we built a bio-electrocatalytic setup with an H-type glass reactor cell, proton exchange membrane, and carbon cloth electrode. Experimental results confirm the mediator's electrochemical reduction and enzymatic consumption. Optimization showed increased product concentration at longer reaction times with better reproducibility within 4-6 h. We tested two enzymes, Pentaerythritol Tetranitrate Reductase (PETNR) and the Thermostable Old Yellow Enzyme (TOYE), using different alkene substrates. TOYE showed higher productivity for the reduction of 2-cyclohexen-1-one (1.20 mM h-1), 2-methyl-2-cyclohexen-1-one (1.40 mM h-1) and 2-methyl-2-pentanal (0.40 mM h-1), with enantiomeric excesses ranging from 11 % to 99 %. PETNR outperformed TOYE in terms of enantioselectivity for the reduction of 2-methyl-2-pentanal (ee 59 % ± 7 % (S)). Notably, TOYE achieved promising results also in reducing ketoisophorone, a challenging substrate, with similar enantiomeric excess compared to published values using NADH.","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141746906","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