Article
Medicine, Research & Experimental
Kweku K. Amponsah-Efah, Borries Demeler, Raj Suryanarayanan
Summary: This study presents a new approach using AUC to characterize drug-polymer interactions in aqueous media. The sedimentation profiles of drug-polymer mixtures differ from those of the neat drug and polymer, indicating the presence of interactions between the two components.
MOLECULAR PHARMACEUTICS
(2021)
Review
Biotechnology & Applied Microbiology
Joshua C. Corpuz, Javier O. Sanlley, Michael D. Burkart
Summary: This review compiles recent efforts in structural biology to shed light on the protein-protein interfaces formed between the peptidyl carrier protein (PCP) and its partner enzymes in non-ribosomal peptide synthetases (NRPSs). Integrating our understanding of how the PCP recognizes partner proteins with directed evolution and combinatorial biosynthetic methods will enhance future discovery and production of new bioactive compounds.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2022)
Article
Chemistry, Medicinal
Takahiro Maruno, Kentaro Ishii, Tetsuo Torisu, Susumu Uchiyama
Summary: This study presents an effective approach for size distribution analysis and component identification of AAV vector samples using a small amount of material. The proposed band sedimentation analytical ultracentrifugation (BS-AUC) method offers higher resolution and allows for accurate determination of component concentration compared to traditional sedimentation velocity AUC (SV-AUC). This approach overcomes the sample amount limitation of SV-AUC.
JOURNAL OF PHARMACEUTICAL SCIENCES
(2023)
Article
Biophysics
Huaying Zhao, Ai Nguyen, Samuel C. To, Peter Schuck
Summary: Analytical ultracentrifugation (AUC) provides absolute measurements of macromolecular parameters, but many instruments suffer from significant systematic errors. External calibration can greatly improve measurement precision and consistency.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2021)
Article
Biochemical Research Methods
Steven A. Berkowitz, Thomas Laue
Summary: Analytical ultracentrifugation (AUC) is the most widely applicable method for characterizing solution properties, with sedimentation velocity AUC (SV-AUC) being particularly important in assessing protein aggregation during drug development. The latest ultracentrifuge model, Optima, has shown evidence of sample convection due to design issues in the temperature control system, primarily affecting low rotor speeds and dilute solvent components used in AAV analysis. Diagnostic features and strategies for reducing this issue are provided.
ANALYTICAL BIOCHEMISTRY
(2021)
Article
Pharmacology & Pharmacy
Songya Zhang, Lin Zhang, Anja Greule, Julien Tailhades, Edward Marschall, Panward Prasongpholchai, Daniel J. Leng, Jingfan Zhang, Jing Zhu, Joe A. Kaczmarski, Ralf B. Schittenhelm, Oliver Einsle, Colin J. Jackson, Fabrizio Alberti, Andreas Bechthold, Youming Zhang, Manuela Tosin, Tong Si, Max J. Cryle
Summary: WS9326A is a peptide antibiotic synthesized by a non-ribosomal peptide synthetase (NRPS). The cytochrome P450 encoded by sas16 (P450Sas) is critical for the formation of an unusual amino acid residue in WS9326A. In this study, the researchers identified the substrate of P450Sas and elucidated its role in the biosynthetic pathway of WS9326A. The results suggest that P450Sas catalyzes the direct dehydrogenation of a dipeptide intermediate, expanding the range of P450 enzymes that can be used for the production of biologically active peptides.
ACTA PHARMACEUTICA SINICA B
(2023)
Article
Biochemistry & Molecular Biology
Sara Garcia-Linares, Rafael Amigot-Sanchez, Carmen Garcia-Montoya, Diego Heras-Marquez, Carlos Alfonso, Juan Roman Luque-Ortega, Jose G. Gavilanes, Alvaro Martinez-Del-Pozo, Juan Palacios-Ortega
Summary: Sticholysins are pore-forming toxins produced by the sea anemone Stichodactyla helianthus. StnII can enhance the activity of StnI and promote its oligomerization. Analytical ultracentrifugation experiments show that StnI is more prone to oligomerization in water solution, but a small amount of StnII in StnI-StnII mixtures can promote oligomerization.
Article
Biochemical Research Methods
Yangjie Wei, JangEun Lee, Michael Dziegelewski, Michael S. Marlow, David B. Hayes
Summary: SLAMF1, a cell surface glycoprotein, is a potential target for inflammatory diseases. Research shows that the dimerization KD value for human SLAMF1 is 0.48μM and its self-association is driven by specific protein-protein interaction.
ANALYTICAL BIOCHEMISTRY
(2021)
Article
Chemistry, Physical
Helmut Coelfen
Summary: Analytical ultracentrifugation (AUC) is a classical polymer and colloid analysis technique invented by Theodor Svedberg 100 years ago. Modern advancements in hardware, software, and computing have expanded the possibilities of AUC beyond its original capabilities. New possibilities include high-resolution simultaneous characterization of particle size and optical property distributions, investigation of nucleation by reaction, characterization of particle interactions at high concentrations, and characterization of complex fluids or osmotic pressures over large concentration ranges. These topics demonstrate the untapped potential of AUC in colloid and polymer science even after 100 years of successful application.
COLLOID AND POLYMER SCIENCE
(2023)
Article
Biology
Jong Il Ahn, Liang Zhang, Harsha Ravishankar, Lixin Fan, Klara Kirsch, Yan Zeng, Lingjun Meng, Jung-Eun Park, Hye-Yeoung Yun, Rodolfo Ghirlando, Buyong Ma, David Ball, Bonsu Ku, Ruth Nussinov, Jeremy D. Schmit, William F. Heinz, Seung Jun Kim, Tatiana Karpova, Yun-Xing Wang, Kyung S. Lee
Summary: Structural, biophysical, and imaging data demonstrate that self-assembly of the pericentrosomal proteins Cep63 and Cep152 is a stepwise and concentration-dependent process. Defects in this process disrupt proper centriole duplication mediated by Plk4. This study provides insights into the organization and function of pericentriolar materials (PCM) and offers a potential model for studying PCM-related diseases in other species.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Giuditta Guerrini, Dora Mehn, Francesco Fumagalli, Sabrina Gioria, Mattia Pedotti, Luca Simonelli, Filippo Bianchini, Davide F. Robbiani, Luca Varani, Luigi Calzolai
Summary: Analytical ultracentrifugation analysis revealed different conformations of the SARS-CoV-2 trimeric Spike protein in solution, with the relative abundance of open and close conformations being temperature-dependent and affected by storage temperature history. Neutralizing antibodies targeting specific domains have different effects on the protein conformations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
X. Edward Zhou, Chad R. Schultz, Kelly Suino Powell, Amy Henrickson, Jared Lamp, Joseph S. Brunzelle, Borries Demeler, Irving E. Vega, Andre S. Bachmann, Karsten Melcher
Summary: Ornithine decarboxylase (ODC) is an enzyme involved in the synthesis of polyamines, and increased ODC activity is associated with cancer and neural over-proliferation. A partial loss-of-function variant, ODC G84R, has been found to be associated with intellectual disability and seizures. This variant may affect ODC activity through misregulation of proteasomal degradation rather than directly reducing its catalytic activity.
Article
Biochemistry & Molecular Biology
Katharina Schmitz, Jan Cox, Lea Marie Esser, Martin Voss, Katja Sander, Antje Loeffler, Frank Hillebrand, Steffen Erkelenz, Heiner Schaal, Thilo Kaehne, Stefan Klinker, Tao Zhang, Luitgard Nagel-Steger, Dieter Willbold, Sabine Seggewiss, David Schluetermann, Bjoern Stork, Matthias Grimmler, Sebastian Wesselborg, Christoph Peter
Summary: The biogenesis of UsnRNPs relies on the methylation of Sm proteins and the SMN complex. ULK1 functions as a key regulator in UsnRNP biogenesis by phosphorylating pICIn, affecting the precursor Sm ring structure and core assembly efficiency. ULK1 has different functions in autophagy or snRNP biosynthesis depending on its complex formation.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biophysics
Chad A. Brautigam
Summary: SViMULATE is a program that allows for quick, straightforward, and interactive simulation of AUC experiments. It generates simulated AUC data based on user-provided parameters, eliminating the need for upfront calculations and allowing for on-the-fly computation of hydrodynamic parameters.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Svetlana Zamakhaeva, Catherine T. Chaton, Jeffrey S. Rush, Sowmya Ajay Castro, Cameron W. Kenner, Alexander E. Yarawsky, Andrew B. Herr, Nina M. van Sorge, Helge C. Dorfmueller, Gregory Frolenkov, Konstantin Korotkov, Natalia Korotkova
Summary: In ovoid-shaped, Gram-positive bacteria, the major cell separation autolysin AtlA was identified as an SCC-binding protein. GroP-deficient immature SCCs were found to localize at cell poles and equators, potentially leading to AtlA mislocalization, dysregulated cellular autolysis, and morphological abnormalities. This indicates a model where maturation of a cell wall polysaccharide plays a role in recruiting cell division machinery for proper daughter cell separation and FtsZ-ring positioning.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Chemistry, Organic
Yongwei Zhao, Robert J. A. Goode, Ralf B. Schittenhelm, Julien Tailhades, Max J. Cryle
JOURNAL OF ORGANIC CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Milda Kaniusaite, Julien Tailhades, Tiia Kittila, Christopher D. Fage, Robert J. A. Goode, Ralf B. Schittenhelm, Max J. Cryle
Summary: The biosynthesis of glycopeptide antibiotics demonstrates the exceptional ability of nonribosomal peptide synthesis to generate diverse and complex structures. An important study on the NRPS assembly lines involved in synthesizing GPAs revealed that they function as dynamic peptide assembly lines, allowing for flexible control over amino acid modifications and peptide formation, which is beneficial for the redesign of important biosynthetic systems.
Article
Microbiology
Rhys Grinter, Blair Ney, Rajini Brammananth, Christopher K. Barlow, Paul R. F. Cordero, David L. Gillett, Thierry Izore, Max J. Cryle, Liam K. Harold, Gregory M. Cook, George Taiaroa, Deborah A. Williamson, Andrew C. Warden, John G. Oakeshott, Matthew C. Taylor, Paul K. Crellin, Colin J. Jackson, Ralf B. Schittenhelm, Ross L. Coppel, Chris Greening
Review
Biochemistry & Molecular Biology
Yongwei Zhao, Y. T. Candace Ho, Julien Tailhades, Max Cryle
Summary: Researchers are intrigued by the complex biosynthesis of glycopeptide antibiotics, particularly the role of the X-domain in recruiting P450 enzymes. In vitro studies have provided insights into the tolerances and limitations of the GPA cyclisation cascade, paving the way for future reengineering of this important antibiotic class.
Article
Biochemistry & Molecular Biology
Milda Kaniusaite, Tiia Kittila, Robert J. A. Goode, Ralf B. Schittenhelm, Max J. Cryle
ACS CHEMICAL BIOLOGY
(2020)
Letter
Biochemistry & Molecular Biology
Daniel L. Machell, Mathias H. Hansen, Max J. Cryle
Summary: Detection of pyrophosphate is crucial for quantifying enzyme activity, especially adenylation domain activity in non-ribosomal peptide synthesis. After screening, viable replacement enzymes with higher activity have been identified, allowing the continued use of the established online assay for pyrophosphate detection.
Article
Biochemistry & Molecular Biology
Y. T. Candace Ho, Ralf B. Schittenhelm, Dumitrita Iftime, Evi Stegmann, Julien Tailhades, Max J. Cryle
Summary: Glycopeptide antibiotics inhibit bacterial cell-wall biosynthesis by sequestration of precursor lipid II. The oxidative crosslinking of the core peptide during GPA biosynthesis is essential and challenging. Understanding the activity and selectivity of Oxy enzymes is important for future engineering of this compound class.
Article
Chemistry, Multidisciplinary
Rania A. A. Hashad, Edwina Jap, Joanne L. L. Casey, Y. T. Candace Ho, Alexander Wright, Claudia Thalmann, Mark Sleeman, David W. W. Lupton, Christoph E. E. Hagemeyer, Max J. J. Cryle, Remy Robert, Karen Alt
Summary: A highly effective 2-step system using engineered methionine residues was used for site-specific antibody modification and conjugation. This system offers a novel way to fundamentally change the process of antibody bioconjugation. The versatility of this system was demonstrated by incorporating a fluorescent dye and can be applied to a wide variety of conjugation partners.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Songya Zhang, Yunliang Chen, Jing Zhu, Qiujie Lu, Max J. Cryle, Youming Zhang, Fu Yan
Summary: Streptomyces bacteria are widely distributed in terrestrial and marine environments and are a rich source of active natural products due to their metabolic diversity. This review highlights the importance of nonribosomal lipopeptides as important natural products with diverse biological activities that play crucial roles in the lifestyle of Streptomyces. Recent advances in the biosynthesis of lipopeptide antibiotics produced by Streptomyces have greatly contributed to our understanding of their structures, properties, biosynthetic mechanisms, chemical and chemoenzymatic synthesis, and biological functions. The use of genome mining techniques has led to the discovery of many novel lipopeptides, further demonstrating their potential for future development in modern medicine.
NATURAL PRODUCT REPORTS
(2023)
Article
Chemistry, Multidisciplinary
Y. T. Candace Ho, Joe A. Kaczmarski, Julien Tailhades, Thierry Izore, David L. Steer, Ralf B. Schittenhelm, Manuela Tosin, Colin J. Jackson, Max J. Cryle
Summary: Nonribosomal peptide synthetases play a significant role in producing essential peptide natural products, with carrier proteins as their core component. By replacing the CP substrate thioesters with stabilized ester analogues, active condensation domain complexes are formed, while amide stabilization leads to non-functional complexes.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Jennifer A. E. Payne, Ketav Kulkarni, Thierry Izore, Alex J. Fulcher, Anton Y. Peleg, Marie-Isabel Aguilar, Max J. Cryle, Mark P. Del Borgo
Summary: A new antimicrobial material was designed, synthesised and characterised by the self-assembly of two distinct beta-peptide monomers, which showed inhibitory effects on drug-resistant bacteria like MRSA. This study provides insights into the design of peptide-based supramolecular assemblies with antibacterial activity.
NANOSCALE ADVANCES
(2021)
Article
Chemistry, Multidisciplinary
Daniel J. Leng, Anja Greule, Max J. Cryle, Manuela Tosin
Summary: Chemical probes were used to capture biosynthetic intermediates generated in the nonribosomal peptide formation of vancomycin in vivo. The putative intercepted intermediates were characterised via HR-LC-MS2, providing insights into the timing of the first chlorination of the peptide backbone by the halogenase VhaA. This information is significant for enzyme engineering towards the production of novel glycopeptides.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Milda Kaniusaite, Robert J. A. Goode, Julien Tailhades, Ralf B. Schittenhelm, Max J. Cryle
Article
Chemistry, Multidisciplinary
Milda Kaniusaite, Julien Tailhades, Edward A. Marschall, Robert J. A. Goode, Ralf B. Schittenhelm, Max J. Cryle
Article
Chemistry, Multidisciplinary
Melanie Schoppet, Madeleine Peschke, Anja Kirchberg, Vincent Wiebach, Roderich D. Suessmuth, Evi Stegmann, Max J. Cryle
Article
Biochemical Research Methods
Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri
Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa
Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Drew S. Sowersby, L. Kevin Lewis
Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li
Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder
Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong
Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong
Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent
Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang
Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic
Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov
Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti
Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.
ANALYTICAL BIOCHEMISTRY
(2024)