ChemBioChemPub Date : 2024-10-02DOI: 10.1002/cbic.202400674
Guoxia Yu, Shijun Zou, Ji-Shen Zheng
{"title":"Biomimetic Folding Strategies for Chemical Synthesis of Disulfide-Bonded Peptides and Proteins.","authors":"Guoxia Yu, Shijun Zou, Ji-Shen Zheng","doi":"10.1002/cbic.202400674","DOIUrl":"10.1002/cbic.202400674","url":null,"abstract":"<p><p>Disulfide-bonded peptides and proteins, including hormones, toxins, growth factors, and others, are abundant in living organisms. These molecules play crucial physiological roles such as regulating cell and organism growth, development, and metabolism. They have also found widespread applications as drugs or tool molecules in biomedical and pharmaceutical research. However, the chemical synthesis of disulfide-bonded proteins is complicated by the challenges associated with their folding. This review focuses on the latest advancements in disulfide-bonded peptide and protein folding technologies. Particularly, it highlights biomimetic folding strategies that emulate the naturally occurring oxidative folding processes in nature. These strategies include chaperone-assisted folding, glycosylation-assisted folding, and organic-based oxidative folding methods. The review also anticipates future directions in folding technology. Such research offers innovative approaches for the chemical synthesis of complex proteins that are otherwise difficult to fold.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142360829","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}
ChemBioChemPub Date : 2024-10-01DOI: 10.1002/cbic.202481902
Yanjun Chen, Miriam Gavriliuc, Yi Zeng, Shoujun Xu, Yuhong Wang
{"title":"Cover Feature: Allosteric Effects of EF-G Domain I Mutations Inducing Ribosome Frameshifting Revealed by Multiplexed Force Spectroscopy (ChemBioChem 19/2024)","authors":"Yanjun Chen, Miriam Gavriliuc, Yi Zeng, Shoujun Xu, Yuhong Wang","doi":"10.1002/cbic.202481902","DOIUrl":"https://doi.org/10.1002/cbic.202481902","url":null,"abstract":"<p>Ribosomal translocation, catalyzed by elongation factor G (EF-G), is a critical step in protein synthesis during which the ribosome typically moves three nucleotides along the mRNA per cycle. Using a new technique of multiplexed super-resolution force spectroscopy, it is shown that two engineered EF-G mutants, with mutated residues located approximately 80 Angstroms away from the EF-G pivot point, induce the ribosome to translocate by only two nucleotides, resulting in “-1” frameshifting. The article 10.1002/cbic.202400130 by Shoujun Xu, Yuhong Wang, and provides unique insights into EF-G-catalyzed ribosomal motion with single-nucleotide resolution from both ends of the mRNA.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure>\u0000 </p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cbic.202481902","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142404182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Optimizing Transfection Efficiency of Spermine Polar Head Cholesterol-Based Cationic Lipids with Amino Acid Linker.","authors":"Chopaka Thongbamrer, Nawapol Kunkeaw, Wang Nguitragool, Wanlapa Roobsoong, Jetsumon Sattabongkot, Praneet Opanasopit, Boon-Ek Yingyongnarongkul","doi":"10.1002/cbic.202400490","DOIUrl":"10.1002/cbic.202400490","url":null,"abstract":"<p><p>In this work, a series of spermine polar head cholesterol-based cationic lipids with various amino acid spacers were synthesized and evaluated as non-viral gene delivery systems. The physicochemical properties of the resulting lipoplexes, formed from these lipids and DOPE, were assessed, including zeta-potential, DNA binding and DNA protection from serum. Transfection efficiency and cytotoxicity were examined under serum-free and 10-40 % serum-containing conditions. The results showed that the physicochemical properties of cationic lipids, both with and without amino acid spacers, were not significantly different. Cationic liposomes composed of lipid Sper-Ahx-Chol, which has a 6-aminohexanoic acid spacer, and DOPE exhibited greater transfection efficiency in HeLa cells compared to Lipofectamine3000, both in the absence and presence of 10-40 % serum. Additionally, lipid Sper-His-Chol with a histidine spacer and Sper-Ahx-Chol showed higher efficiency than Lipofectamine3000 against HEK293T under 40 % serum conditions. These results suggest that the incorporation of amino acids into the cationic lipids can significantly enhance their DNA delivery efficiency. Specifically, certain amino acid modifications improved transfection efficiency while maintaining low cytotoxicity. Our findings highlight the potential of amino acid-tailored cationic lipids as promising vectors for enhanced DNA delivery.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363577","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}
ChemBioChemPub Date : 2024-10-01DOI: 10.1002/cbic.202481901
Minako Narita, Dr. Ai Kohata, Taiichi Kageyama, Honoka Watanabe, Dr. Kohsuke Aikawa, Prof. Dr. Daisuke Kawaguchi, Dr. Kunihiko Morihiro, Prof. Dr. Akimitsu Okamoto, Dr. Takashi Okazoe
{"title":"Front Cover: Fluorocarbon-DNA Conjugates for Enhanced Cellular Delivery: Formation of a Densely Packed DNA Nano-Assembly (ChemBioChem 19/2024)","authors":"Minako Narita, Dr. Ai Kohata, Taiichi Kageyama, Honoka Watanabe, Dr. Kohsuke Aikawa, Prof. Dr. Daisuke Kawaguchi, Dr. Kunihiko Morihiro, Prof. Dr. Akimitsu Okamoto, Dr. Takashi Okazoe","doi":"10.1002/cbic.202481901","DOIUrl":"https://doi.org/10.1002/cbic.202481901","url":null,"abstract":"<p>Several RF-DNA conjugates are synthesized, and the relationship between the uptake efficiency and the physicochemical properties is systematically investigated. RF-DNA conjugates carrying two C8F17 groups at the terminus of a DNA strand form a nano-assembly with the highest DNA content, leading to the greatest cellular uptake via scavenger receptors. More details can be found in article 10.1002/cbic.202400436 by Ai Kohata, Kohsuke Aikawa, and co-workers.<figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure>\u0000 </p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cbic.202481901","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142404181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ChemBioChemPub Date : 2024-10-01DOI: 10.1002/cbic.202400441
Laurent Devel, Carole Malgorn, Regis-William Tohon, Marie Launay, Konstantinos Patiniotis, Mylene Sejalon-Cipolla, Fabrice Beau, Robert Thai, Pierrick Bruyat, Annabelle Bonino, Sarah Bregant, Gilles Subra, Sonia Cantel, Dimitris Georgiadis
{"title":"Covalent Labeling of Matrix Metalloproteases with Affinity-Based Probes Containing Tuned Reactive N-Acyl-N-Alkyl Sulfonamide Cleavable Linkers.","authors":"Laurent Devel, Carole Malgorn, Regis-William Tohon, Marie Launay, Konstantinos Patiniotis, Mylene Sejalon-Cipolla, Fabrice Beau, Robert Thai, Pierrick Bruyat, Annabelle Bonino, Sarah Bregant, Gilles Subra, Sonia Cantel, Dimitris Georgiadis","doi":"10.1002/cbic.202400441","DOIUrl":"10.1002/cbic.202400441","url":null,"abstract":"<p><p>Original covalent probes with an N-acyl-N-alkyl sulfonamide cleavable linker were developed to target a broad set of human Matrix Metalloproteases (MMPs). The electrophilicity of this cleavable linker was modulated to improve the selectivity of the probes as well as reduce their unspecific reactivity in complex biological matrices. We first demonstrated that targeting the S<sub>3</sub> subsite of MMPs enables access to broad-spectrum affinity-based probes that exclusively react with the active version of these proteases. The probes were further assessed in proteomes of varying complexity, where human MMP-13 was artificially introduced at known concentration and the resulting labeled MMP was imaged by in-gel fluorescence imaging. We showed that the less reactive probe was still able to covalently modify MMP-13 while exhibiting reduced off-target unspecific reactivity. This study clearly demonstrated the importance of finely controlling the reactivity of the NASA warhead to improve the selectivity of covalent probes in complex biological systems.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363576","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}
ChemBioChemPub Date : 2024-09-30DOI: 10.1002/cbic.202400500
Tian Zeng, Jie Liu, Cham Wah Cheung, Youzhi Li, Han Jia, Edmund Chun Ming Tse, Ying Li
{"title":"Manganese Complex-Gold Nanoparticle Hybrid for Biofilm Inhibition and Eradication.","authors":"Tian Zeng, Jie Liu, Cham Wah Cheung, Youzhi Li, Han Jia, Edmund Chun Ming Tse, Ying Li","doi":"10.1002/cbic.202400500","DOIUrl":"10.1002/cbic.202400500","url":null,"abstract":"<p><p>Biofilms, which are resistant to conventional antimicrobial treatments, pose significant challenges in medical and industrial environments. This study introduces manganese complex-gold nanoparticles (Mn-DPA-AuNPs) as a hybrid strategy for biofilm inhibition and eradication. Upon exposure to green light, these nanoparticles significantly enhance the generation of reactive oxygen species (ROS), including hydrogen peroxide and superoxide. This activity substantially reduces the regrowth potential of the surviving bacteria within the biofilm, with marked efficacy noted in Pseudomonas aeruginosa PAO1. This study highlights the potential of integrating manganese complexes with gold nanoparticles to develop advanced antimicrobial agents against resistant biofilms, offering a promising approach to enhance microbial control in diverse settings.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337759","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}
{"title":"One-Pot Enzymatic Cascade for Toxicant Degradation and Sugar Acid Production.","authors":"Vinutsada Pongsupasa, Pangrum Punthong, Pimchai Chaiyen, Thanyaporn Wongnate","doi":"10.1002/cbic.202400281","DOIUrl":"10.1002/cbic.202400281","url":null,"abstract":"<p><p>This study introduces a novel one-pot enzymatic cascade approach for converting toxicants and continuously generating an electron acceptor for production of sugar acids. This method offers a promising solution to concerns about pesticide toxicity and environmental contamination by transforming hazardous substances into a useful electron acceptor. This acceptor is then utilized to produce valuable chemicals with broad industrial applications, particularly in the food and pharmaceutical sectors. The cascade reaction employs organophosphate hydrolase (OPD) to convert pesticides into 4-nitrophenol (4-NP), which is subsequently transformed into 1,4-benzoquinone by HadA monooxygenase (HadA). 1,4-benzoquinone serves as an electron acceptor in the catalysis of sugar acid formation via pyranose dehydrogenase (PDH). The results indicate that this cascade reaction effectively converts lactose to lactobionic acid and xylose to 2-keto-xylonic acid. The latter can be further processed into xylonic acid through NaBH<sub>4</sub> reduction. Notably, the one-pot reaction yields up to 10 % higher compared to the direct addition of 1,4-benzoquinone. The synthesized xylonic acid exhibits exceptional water uptake properties in hydrogels, and the synthesized lactobionic acid shows antioxidant activity comparable to well-established antioxidants. These findings demonstrate the technological viability of these reaction cascades for various applications.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337762","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}
ChemBioChemPub Date : 2024-09-27DOI: 10.1002/cbic.202400535
Tobias W Giessen
{"title":"The Structural Diversity of Encapsulin Protein Shells.","authors":"Tobias W Giessen","doi":"10.1002/cbic.202400535","DOIUrl":"10.1002/cbic.202400535","url":null,"abstract":"<p><p>Subcellular compartmentalization is a universal feature of all cells. Spatially distinct compartments, be they lipid- or protein-based, enable cells to optimize local reaction environments, store nutrients, and sequester toxic processes. Prokaryotes generally lack intracellular membrane systems and usually rely on protein-based compartments and organelles to regulate and optimize their metabolism. Encapsulins are one of the most diverse and widespread classes of prokaryotic protein compartments. They self-assemble into icosahedral protein shells and are able to specifically internalize dedicated cargo enzymes. This review discusses the structural diversity of encapsulin protein shells, focusing on shell assembly, symmetry, and dynamics. The properties and functions of pores found within encapsulin shells will also be discussed. In addition, fusion and insertion domains embedded within encapsulin shell protomers will be highlighted. Finally, future research directions for basic encapsulin biology, with a focus on the structural understand of encapsulins, are briefly outlined.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337766","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}
ChemBioChemPub Date : 2024-09-27DOI: 10.1002/cbic.202400643
Jagandeep S Saraya, Scott R Sammons, Derek K O'Flaherty
{"title":"Aqueous Compatible Post-Synthetic On-Column Conjugation of Nucleic Acids Using Amino-Modifiers.","authors":"Jagandeep S Saraya, Scott R Sammons, Derek K O'Flaherty","doi":"10.1002/cbic.202400643","DOIUrl":"10.1002/cbic.202400643","url":null,"abstract":"<p><p>Nucleic acid conjugation methodologies involve linking the nucleic acid sequence to other (bio)molecules covalently. This typically allows for nucleic acid property enhancement whether it be for therapeutic purposes, biosensing, etc. Here, we report a streamlined, aqueous compatible, on-column conjugation methodology using nucleic acids containing a site-specific amino-modifier. Both monophosphates and carboxylates were amenable to the conjugation strategy, allowing for the introduction of a variety of useful handles including azide, aryl, and hydrophobic groups in DNA. We find that an on-column approach is superior to post-synthetic template-directed synthesis, mainly with respect to product purification and recovery.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337758","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}
ChemBioChemPub Date : 2024-09-26DOI: 10.1002/cbic.202400521
Laura M Jansen, Veronique C A Hendriks, Herman Bentlage, Adeline Ranoux, Harry W C Raaijmakers, Thomas Jan Boltje
{"title":"The industrial application potential of sugar beet pulp derived monosaccharides d-Galacturonic acid and l-Arabinose.","authors":"Laura M Jansen, Veronique C A Hendriks, Herman Bentlage, Adeline Ranoux, Harry W C Raaijmakers, Thomas Jan Boltje","doi":"10.1002/cbic.202400521","DOIUrl":"https://doi.org/10.1002/cbic.202400521","url":null,"abstract":"<p><p>This review provides a perspective on the industrial application potential of sugar beet pulp (SBP) derived monosaccharides. The broad application of these monosaccharides could contribute to bio-based alternatives and sustainable practices, essential for the transition towards a more circular economy. This review focuses on the utilization and application of two SBP monosaccharides, d-galacturonic acid (d-GalA) and l-arabinose (l-Ara), derived from pectin and hemicellulose. These polysaccharides are major components of sugar beet pulp, an important side stream of sucrose production. d-GalA and l-Ara are therefore abundant in biomass and offer unique molecular structures amenable to selective chemical or enzymatic modifications. We review their application in various industrial applications such as the development and production of bioactive compounds, home and personal care products, and other industries.</p>","PeriodicalId":140,"journal":{"name":"ChemBioChem","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337765","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}