Article
Biochemistry & Molecular Biology
Michael Loukeris, Zahra Assur Sanghai, Jeremie Vendome, Wayne A. Hendrickson, Brian Kloss, Filippo Mancia
Summary: This study presents an enhancement of traditional genomics-based approaches to improve the success of membrane protein structure determination. By selecting orthologs with closely related sequences to expression-positive targets identified through sequence space screening, the study demonstrates an increased percentage of well-expressed and stable targets in detergent, thus increasing the likelihood of identifying candidates for structural information.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Max G. Schubert, Daniel B. Goodman, Timothy M. Wannier, Divjot Kaur, Fahim Farzadfard, Timothy K. Lu, Seth L. Shipman, George M. Church
Summary: RLR is a high-throughput method for genetic variant screening, utilizing retrons' reverse transcription activity to produce ssDNA for editing, introducing multiple genomic variants with barcoding for targeted deep sequencing, and suitable for natural variation screening.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biotechnology & Applied Microbiology
Manman Sun, Alex Xiong Gao, Xiuxia Liu, Yankun Yang, Rodrigo Ledesma-Amaro, Zhonghu Bai
Summary: The demand for faster and more efficient protein production has increased in the post-genomic era. This review presents a holistic high-throughput process development strategy and discusses the challenges, limitations, and future research directions in recombinant protein production.
MICROBIAL CELL FACTORIES
(2023)
Article
Biochemical Research Methods
Jing Xu, Pawan K. Pandoh, Richard D. Corbett, Duane Smailus, Reanne Bowlby, Denise Brooks, Helen McDonald, Simon Haile, Sundeep Chahal, Steve Bilobram, Karen L. Mungall, Andrew J. Mungall, Robin Coope, Richard A. Moore, Yongjun Zhao, Steven J. M. Jones, Marco A. Marra
Summary: This article presents a high-throughput TNA purification protocol based on SPRI beads, which can be used for both genomic and transcriptomic applications. It also introduces modifications to enhance small RNA recovery, addressing the issue of weak binding of small RNA to SPRI beads. The benchmarking results show that the GRAB-ALL protocol efficiently purifies TNA, including small RNA, in a plate-based format suitable for automated high-throughput sample preparation for next-generation sequencing applications.
Article
Biochemistry & Molecular Biology
Swarnendu Tripathi, Nikita R. Dsouza, Angela J. Mathison, Elise Leverence, Raul Urrutia, Michael T. Zimmermann
Summary: This study reports computational scores for interpreting disease-associated genomic variation in the RAS family of genes. By using a combination of experimental datasets and computational methods, the research found a high correlation between 3D structure-based scores and experimental measures, indicating the impact of biochemical scores on the functional behavior of variants.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biotechnology & Applied Microbiology
Chintan Savla, Andre F. Palmer
Summary: By binding heme to human serum albumin and stabilizing it with polyethylene glycol, the anti-inflammatory effects of heme can be realized. This study provides a method for the synthesis and purification of heme protein carriers.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Chemistry, Multidisciplinary
Marta Napiorkowska, Luzius Pestalozzi, Sven Panke, Martin Held, Steven Schmitt
Summary: A high-throughput platform for optimizing microbial protein production is described, using droplet microfluidics and flow cytometry. The platform successfully cultures several industrially relevant bacterial and yeast strains and isolates strains with superior production titers by detecting peptides or proteins released from the cell via autolysis or secretion.
Review
Engineering, Chemical
Xing Yang, Andrea Merenda, Riyadh AL-Attabi, Ludovic F. Dumee, Xiwang Zhang, San H. Thang, Hung Pham, Lingxue Kong
Summary: Membrane chromatography is considered a potential solution for downstream processing in protein purification. Despite limited commercial adoption in large-scale production, significant progress has been made. However, robust evaluation of its performance is still needed, and the disconnection between academic and commercial efforts should be addressed.
JOURNAL OF MEMBRANE SCIENCE
(2022)
Article
Engineering, Chemical
Jose Rodrigues, Vanessa T. Almeida, Ana L. Rosario, Yong Zi Tan, Brian Kloss, Filippo Mancia, Margarida Archer
Summary: This study presents an efficient high-throughput strategy to screen a large number of targets from Mycobacteria in microplates and select the best conditions for large-scale protein production for functional and structural studies.
Article
Biochemistry & Molecular Biology
Nadide Altincekic, Sophie Marianne Korn, Nusrat Shahin Qureshi, Marie Dujardin, Marti Ninot-Pedrosa, Rupert Abele, Marie Jose Abi Saad, Caterina Alfano, Fabio C. L. Almeida, Islam Alshamleh, Gisele Cardoso de Amorim, Thomas K. Anderson, Cristiane D. Anobom, Chelsea Anorma, Jasleen Kaur Bains, Adriaan Bax, Martin Blackledge, Julius Blechar, Anja Bockmann, Louis Brigandat, Anna Bula, Matthias Buetikofer, Aldo R. Camacho-Zarco, Teresa Carlomagno, Icaro Putinhon Caruso, Betul Ceylan, Apirat Chaikuad, Feixia Chu, Laura Cole, Marquise G. Crosby, Vanessa de Jesus, Karthikeyan Dhamotharan, Isabella C. Felli, Jan Ferner, Yanick Fleischmann, Marie-Laure Fogeron, Nikolaos K. Fourkiotis, Christin Fuks, Boris Fuertig, Angelo Gallo, Santosh L. Gande, Juan Atilio Gerez, Dhiman Ghosh, Francisco Gomes-Neto, Oksana Gorbatyuk, Serafima Guseva, Carolin Hacker, Sabine Haefner, Bing Hao, Bruno Hargittay, K. Henzler-Wildman, Jeffrey C. Hoch, Katharina F. Hohmann, Marie T. Hutchison, Kristaps Jaudzems, Katarina Jovic, Janina Kaderli, Gints Kalnins, Iveta Kanepe, Robert N. Kirchdoerfer, John Kirkpatrick, Stefan Knapp, Robin Krishnathas, Felicitas Kutz, Susanne zur Lage, Roderick Lambertz, Andras Lang, Douglas Laurents, Lauriane Lecoq, Verena Linhard, Frank Loehr, Anas Malki, Luiza Mamigonian Bessa, Rachel W. Martin, Tobias Matzel, Damien Maurin, Seth W. McNutt, Nathane Cunha Mebus-Antunes, Beat H. Meier, Nathalie Meiser, Miguel Mompean, Elisa Monaca, Roland Montserret, Laura Marino Perez, Celine Moser, Claudia Muhle-Goll, Thais Cristtina Neves-Martins, Xiamonin Ni, Brenna Norton-Baker, Roberta Pierattelli, Letizia Pontoriero, Yulia Pustovalova, Oliver Ohlenschlaeger, Julien Orts, Andrea T. Da Poian, Dennis J. Pyper, Christian Richter, Roland Riek, Chad M. Rienstra, Angus Robertson, Anderson S. Pinheiro, Raffaele Sabbatella, Nicola Salvi, Krishna Saxena, Linda Schulte, Marco Schiavina, Harald Schwalbe, Mara Silber, Marcius da Silva Almeida, Marc A. Sprague-Piercy, Georgios A. Spyroulias, Sridhar Sreeramulu, Jan-Niklas Tants, Kaspars Tars, Felix Torres, Sabrina Toews, Miguel A. Trevino, Sven Trucks, Aikaterini C. Tsika, Krisztina Varga, Ying Wang, Marco E. Weber, Julia E. Weigand, Christoph Wiedemann, Julia Wirmer-Bartoschek, Maria Alexandra Wirtz Martin, Johannes Zehnder, Martin Hengesbach, Andreas Schlundt
Summary: The international COVID19-NMR consortium aims to gather scientific expertise worldwide to provide new approaches for understanding the molecular components of SARS-CoV-2. By making viral proteins and RNAs available, the consortium accelerates research on the virus and provides protocols for large-scale production. The NMR investigations and resources disclosed through the consortium offer valuable insights and tools for further studies on SARS-CoV-2.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Infectious Diseases
J. Myles Keck, David A. A. Cretella, Kayla R. R. Stover, Jamie L. L. Wagner, Katie E. E. Barber, Tulip A. A. Jhaveri, Prakhar Vijayvargiya, Zerelda Esquer Garrigos, Mary Joyce B. Wingler
Summary: A study evaluated the effects of a micafungin stewardship initiative on treatment duration and clinical outcomes. The initiative was found to decrease treatment days but did not significantly impact other clinical endpoints.
Article
Pharmacology & Pharmacy
Christin Pohl, Sujata Mahapatra, Alina Kulakova, Werner Streicher, Gunther H. J. Peters, Allan Norgaard, Pernille Harris
Summary: This study applies small angle X-ray scattering (SAXS), which is not typically used in industrial protein screening, in a high throughput screening workflow to address problems of contradicting results and reproducibility among different methods. The results demonstrate that SAXS can provide valuable information on interparticle interactions, even without time-consuming modeling, and can be used as a tool for in-depth knowledge highly useful for protein formulation development.
EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS
(2022)
Article
Biochemical Research Methods
Camila Leal-Lopes, Sara 'Angelo, M. Frank Erasmus, Andre A. R. Teixeira, Graham Temples, Jinxiang Zhou, Andrew R. M. Bradbury, Fortunato Ferrara
Summary: The therapeutic use of monoclonal antibodies (mAbs) is diverse, ranging from cancer treatment to immune-mediated conditions, covering infectious and cardiovascular disorders, among others. This work describes a new high-throughput mAb expression and purification method for rapid validation of potential mAb leads, enabling efficient functional validation.
Article
Chemistry, Applied
Wanbao Ouyang, Xin Liu, Yanling Wang, Zhibing Huang, Xiujiang Li
Summary: Adding genistein significantly reduces citrinin production in Monascus, as confirmed by transcriptome analysis and gene expression studies. Quantitative analysis of relevant genes confirms the impact of genistein on biosynthesis process, laying the groundwork for substantial improvements in the Monascus fermentation industry.
Article
Biotechnology & Applied Microbiology
Mi Zhou, Jiangfei Chen, Kuikui Meng, Yu Zhang, Meng Zhang, Panyu Lu, Yongjun Feng, Mai Huang, Qiaoxiang Dong, Xiaokun Li, Haishan Tian
Summary: This study aimed to explore the neuroprotective effects of recombinant humanized FGF12 (rhFGF12) and demonstrated through experiments that the beneficial effects of rhFGF12 may be achieved by promoting cell proliferation and reducing apoptosis.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Logan Tillery, Kayleigh Barrett, Jenna Goldstein, Jared W. Lassner, Bram Osterhout, Nathan L. Tran, Lily Xu, Ryan M. Young, Justin Craig, Ian Chun, David M. Dranow, Jan Abendroth, Silvia L. Delker, Douglas R. Davies, Stephen J. Mayclin, Brandy Calhoun, Madison J. Bolejack, Bart Staker, Sandhya Subramanian, Isabelle Phan, Donald D. Lorimer, Peter J. Myler, Thomas E. Edwards, Dennis E. Kyle, Christopher A. Rice, James C. Morris, James W. Leahy, Roman Manetsch, Lynn K. Barrett, Craig L. Smith, Wesley C. Van Voorhis
Summary: Naegleria fowleri is a pathogenic amoeba that causes primary amebic meningoencephalitis by traveling to the brain via the olfactory nerves, thriving in warm freshwater environments with low drug sensitivity. Efforts have been made to identify potential drug targets through protein production and crystallography, with promising results of pathogen-specific inhibitors.
Article
Biochemistry & Molecular Biology
Nirupa Nagaratnam, Silvia L. Delker, Rebecca Jernigan, Thomas E. Edwards, Janey Snider, Darren Thifault, Dewight Williams, Brent L. Nannenga, Mary Stofega, Lidia Sambucetti, James J. Hsieh, Andrew J. Flint, Petra Fromme, Jose M. Martin-Garcia
Summary: Taspase1 is an Ntn-hydrolase overexpressed in primary human cancers, with its activity closely related to the proliferation, invasion, and metastasis of cancer cells. This study reveals the structure and function of the active site of Taspase1, providing a potential target for the development of anticancer therapeutics.
Article
Multidisciplinary Sciences
Seyed Mohammad Ghafoori, Alyssa M. Robles, Angelika M. Arada, Paniz Shirmast, David M. Dranow, Stephen J. Mayclin, Donald D. Lorimer, Peter J. Myler, Thomas E. Edwards, Misty L. Kuhn, Jade K. Forwood
Summary: Elizabethkingia anophelis is an emerging multidrug resistant pathogen with antibiotic resistance genes including a chloramphenicol acetyltransferase (CAT). The high-resolution crystal structure of CAT protein from E. anophelis NUHP1 strain shows similarity to Type B (CatB) proteins from other bacteria, suggesting its role in chloramphenicol resistance. This research expands the structural and functional understanding of proteins from Flavobacteriaceae pathogens.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Aurore Demars, Armelle Vitali, Audrey Comein, Elodie Carlier, Abdulkader Azouz, Stanislas Goriely, Justine Smout, Veronique Flamand, Megane Van Gysel, Johan Wouters, Jan Abendroth, Thomas E. Edwards, Arnaud Machelart, Eik Hoffmann, Priscille Brodin, Xavier De Bolle, Eric Muraille
Summary: Brucellosis is a common bacterial zoonosis worldwide. The Acod1 gene plays a key role in controlling pulmonary Brucella infection in mice. The ACOD1 enzyme converts cis-aconitate to itaconate and may be a potential target for pharmacological interventions in treating early stages of pulmonary Brucella infection.
Article
Biochemistry & Molecular Biology
Pooja Kesari, Anuradha Deshmukh, Nikhil Pahelkar, Abhishek B. Suryawanshi, Ishan Rathore, Vandana Mishra, John H. Dupuis, Huogen Xiao, Alla Gustchina, Jan Abendroth, Mehdi Labaied, Rickey Y. Yada, Alexander Wlodawer, Thomas E. Edwards, Donald D. Lorimer, Prasenjit Bhaumik
Summary: Plasmodium falciparum plasmepsin X (PfPMX), an essential protein for the survival of the deadliest malaria parasite, has been identified as a potential drug target. The crystal structure of PfPMX zymogen, which contains a novel fold of its prosegment, has been determined for the first time. The study provides insights into the inactivation, maturation, and inhibition of PfPMX, which could aid in the development of potent inhibitors against similar proteases from apicomplexan parasites.
Article
Biochemical Research Methods
Imani Porter, Trinity Neal, Zion Walker, Dylan Hayes, Kayla Fowler, Nyah Billups, Anais Rhoades, Christian Smith, Kaelyn Smith, Bart L. Staker, David M. Dranow, Stephen J. Mayclin, Sandhya Subramanian, Thomas E. Edwards, Peter J. Myler, Oluwatoyin A. Asojo
Summary: Members of the bacterial genus Brucella, which can be used as biological warfare agents, cause brucellosis, a zoonotic disease affecting livestock and wildlife. The structures of FolM alternative dihydrofolate reductases 1 from Brucella suis and Brucella canis were determined and reported in this study. These enzymes show high sequence similarity to each other but low sequence identity with other structurally known homologues. The structures resemble NADPH-dependent short-chain reductases and share their highest tertiary structural similarity with protozoan pteridine reductases.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Dylan K. Beard, Seonna Bristol, Kayla Cosby, Amber Davis, Courtney Manning, Lionel Perry, Lauren Snapp, Arian Toy, Kayla Wheeler, Jeremy Young, Bart Staker, Tracy L. Arakaki, Jan Abendroth, Sandhya Subrahamanian, Thomas E. Edwards, Peter J. Myler, Oluwatoyin A. Asojo
Summary: Giardiasis is the most prevalent diarrheal disease globally, affecting both humans and animals, particularly in developing countries, travelers, and HIV-infected individuals. Treatment involves antibiotics like tinidazole and metronidazole, with ongoing research focusing on characterizing the proteins of Giardia lamblia to develop new therapeutics. This study presents the atomic resolution structure of a 15.6 kDa protein from Giardia lamblia, providing insights into potential targets for drug development.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Dylan K. Beard, Sandhya Subramanian, Jan Abendroth, David M. Dranow, Thomas E. Edwards, Peter J. Myler, Oluwatoyin A. Asojo
Summary: This study reports the crystal structures of the potential drug target BADH from B. pseudomallei. Structural comparison revealed similarities to BADH from Pseudomonas aeruginosa, which could facilitate drug-repurposing studies for B. pseudomallei.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Jasmine Maddy, Bart L. Staker, Sandhya Subramanian, Jan Abendroth, Thomas E. Edwards, Peter J. Myler, Kevin Hybiske, Oluwatoyin A. Asojo
Summary: Chlamydia trachomatis is a leading cause of bacterial sexually transmitted infections worldwide and a common infection in the United States. The development of new therapeutics is necessary due to drug resistance and the failure of current treatments to clear persistent infections. The Seattle Structural Genomics Center for Infectious Disease has determined the structures of potential drug targets for C. trachomatis, including the inorganic pyrophosphatase. The crystal structure of the inorganic pyrophosphatase reveals shared features that could aid in the repurposing of inhibitors for new therapeutics.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Bin Xie, Allison Maker, Andrew Priest, David M. Dranow, Jenny N. Phan, Thomas E. Edwards, Bart L. Staker, Peter J. Myler, Barry M. Gumbiner, Sanjeevi Sivasankar
Summary: The monoclonal antibody 19A11 can interact with Ecad in two distinct modes, one of which enhances the adhesion of Ecad. Adhesion is strengthened by the formation of a salt bridge.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Medicinal
Mattheo Alcaraz, Francoise Roquet-Baneres, Stephen Adonai Leon-Icaza, Jan Abendroth, Yves-Marie Boudehen, Celine Cougoule, Thomas E. Edwards, Laurent Kremer
Summary: There is a significant medical need for effective treatments against Mycobacterium abscessus pulmonary infections, especially in cystic fibrosis (CF) patients. In this study, the antitubercular drug NITD-916 was found to have low minimum inhibitory concentration (MIC) values against M. abscessus in vitro, and it significantly reduced bacterial burden in human macrophages. Furthermore, NITD-916 treatment decreased the number and size of intracellular mycobacterial cords, indicating its potential in treating this difficult-to-treat mycobacterium. The study also confirmed that NITD-916 directly targets InhA(MAB) without activation requirements.
ACS INFECTIOUS DISEASES
(2022)
Review
Infectious Diseases
Mattheo Alcaraz, Thomas E. Edwards, Laurent Kremer
Summary: The treatment options for Mycobacterium abscessus infections are limited. The authors review the potential drug targets in M. abscessus related to the mycolic acid biosynthetic pathway and discuss the activity of inhibitors targeting MmpL3 and InhA. They highlight the potential of NITD-916 as a direct InhA inhibitor for the treatment of multidrug resistant M. abscessus infections.
EXPERT REVIEW OF ANTI-INFECTIVE THERAPY
(2023)
Article
Biochemical Research Methods
Julia Moorefield, Yagmur Konuk, Jordan O. Norman, Jan Abendroth, Thomas E. Edwards, Donald D. Lorimer, Stephen J. Mayclin, Bart L. Staker, Justin K. Craig, Kayleigh F. Barett, Lynn K. Barrett, Wesley C. Van Voorhis, Peter J. Myler, Krystle J. McLaughlin
Summary: Inorganic pyrophosphatases hydrolyze the byproduct PPi and prevent its accumulation in cells, while providing orthophosphates P-i for biosynthetic pathways. L. pneumophila PPase demonstrates hydrolytic activity with Mg2+ as the preferred metal cofactor for catalysis.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2023)
Article
Chemistry, Medicinal
Sneha Basak, Yong Li, Suyuan Tao, Fereidoon Daryaee, Jonathan Merino, Chendi Gu, Silvia L. Delker, Jenny N. Phan, Thomas E. Edwards, Stephen G. Walker, Peter J. Tonge
Summary: UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a potential drug target in Gram-negative bacteria, and the residence time of inhibitors on this target is found to be correlated with their post-antibiotic effect. The study also demonstrates that an analogue has a longer residence time and post-antibiotic effect, providing a platform for rational modulation of inhibitor residence time and the development of antibacterial agents.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Allison Maker, Madison Bolejack, Leslayann Schecterson, Brad Hammerson, Jan Abendroth, Thomas E. Edwards, Bart Staker, Peter J. Myler, Barry M. Gumbiner
Summary: This study utilizes cryo-electron microscopy (EM) and X-ray crystallography to investigate the regulation of E-cadherin adhesion on cell surface. Novel dimer conformations were observed in solution through cryo-EM, and activating antibodies were used to alter the adhesive dimer state. The structures of activating Fabs bound to E-cadherin reveal new insights into the regulation of cell adhesion.