Article
Multidisciplinary Sciences
Anubhav Tamrakar, Rahul Singh, Amit Kumar, Ravindra D. Makde, Ashish, Prashant Kodgire
Summary: Our study focused on exploring the structure of the HomA and HomB proteins from H. pylori using computational, biophysical, and SAXS techniques. Analysis revealed that HomA/B consist of 8 discontinuous N and C terminal beta-strands forming a small beta-barrel with a large surface-exposed globular domain. Biophysical experiments indicated that HomA and HomB are likely dimeric and that cysteine residues on surface-exposed loops may be involved in protein-protein interactions. This structural information provides insight into the pathogenesis of H. pylori.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Marie Wensien, Fabian Rabe von Pappenheim, Lisa-Marie Funk, Patrick Kloskowski, Ute Curth, Ulf Diederichsen, Jon Uranga, Jin Ye, Pan Fang, Kuan-Ting Pan, Henning Urlaub, Ricardo A. Mata, Viktor Sautner, Kai Tittmann
Summary: The discovery of a covalent crosslink between a cysteine and a lysine residue with a NOS bridge as an allosteric redox switch in the transaldolase enzyme of Neisseria gonorrhoeae is reported in this study. This redox switch leads to a structural relaxation mechanism that increases enzymatic activity in a significant way. The NOS bridge, found in diverse protein families across different organisms, can serve as a potential target for the development of new drugs and antibodies.
Article
Chemistry, Physical
Eugenia Chukwu Cornelius, Michael Bartl, Louise J. Persson, Ruisheng Xiong, Daniela Cederfelt, Farshid Mashayekhy Rad, Thomas Norberg, Sarah Engel, Erik G. Marklund, Doreen Dobritzsch, Mikael Widersten
Summary: A triple mutant of FSA was engineered to generate new enzyme variants capable of catalyzing aldol reactions between aryl substituted ketones and aldehydes. Saturation mutagenesis was performed on residues L107 and L163, resulting in a library of FSA variants that were screened for catalytic activity. Some aldolase variants were identified that catalyze the synthesis of 2,3-dihydroxy-1,4-diphenylbutanone. The most active variants contained an L163C substitution. Further testing showed that an L107C/L163C variant produced diphenyl substituted butanones with good diastereoselectivities and reasonable to good enantioselectivities.
CATALYSIS SCIENCE & TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Heladia Salgado, Socorro Gama-Castro, Paloma Lara, Citlalli Mejia-Almonte, Gabriel Alarcon-Carranza, Andres G. Lopez-Almazo, Felipe Betancourt-Figueroa, Pablo Pena-Loredo, Shirley Alquicira-Hernandez, Daniela Ledezma-Tejeida, Lizeth Arizmendi-Zagal, Francisco Mendez-Hernandez, Ana K. Diaz-Gomez, Elizabeth Ochoa-Praxedis, Luis J. Muniz-Rascado, Jair S. Garcia-Sotelo, Fanny A. Flores-Gallegos, Laura Gomez, Cesar Bonavides-Martinez, Victor M. del Moral-Chavez, Alfredo J. Hernandez-Alvarez, Alberto Santos-Zavaleta, Salvador Capella-Gutierrez, Josep Lluis Gelpi, Julio Collado-Vides
Summary: RegulonDB is a database that contains comprehensive knowledge on the regulation of transcription initiation of Escherichia coli K-12. The latest version, 12.0, offers improved data storage, retrieval, and accessibility, as well as intuitive graphical tools for data interpretation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Xiaorui Lou, Jianyu Zhang, Shimeng Liu, Runhao Wang, Weiping Li, Ruihua Liu, Qionglin Zhang, Mark Bartlam
Summary: This paper reports the structure and functional characteristics of an L-fuculose 1-phosphate aldolase from Klebsiella pneumoniae. This enzyme has potential applications in pathogenesis and biosynthesis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Tse-Wei Hsu, Jim-Min Fang
Summary: Instead of using labeled lipid II substrate, this study quantitatively measures the released UPP product to probe the formation of peptidoglycan in bacterial transglycosylation. Two assay methods were employed, identifying moenomycin A as a potent transglycosylase inhibitor with a consistent IC50 value.
Article
Biochemistry & Molecular Biology
Simeng Chen, Chenxi Liu, Chenchen Zhou, Zhihui Wei, Yuting Li, Lei Xiong, Liang Yan, Jun Lv, Liang Shen, Lei Xu
Summary: A new photolyase, SePhrB, has been characterized in Synechococcus elongatus, demonstrating its ability to repair 6-4 photoproducts in DNA. SePhrB contains an antenna chromophore called 8-HDF and can be photoreduced without external electron donors. These findings suggest a greater diversity of FeS-BCPs than previously thought and warrant further investigation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Shan-Chi Hsieh, Joseph E. Peters
Summary: The CRISPR-Cas defense systems have been coopted for guide RNA-directed transposition by bacterial transposons. Cyanobacterial genomes contain various Tn7-like elements, including guide RNA-directed transposons and CRISPR-Cas based systems. A type I-D CRISPR-Cas system was discovered, which showed flexibility in guide RNA length requirements and had naturally fused transposase proteins. These findings provide new possibilities for future gene editing work. In addition, the analysis revealed a broader understanding of the evolution of Tn7-like elements, including extensive swapping of targeting systems among cyanobacteria.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Dariusz Czernecki, Frederic Bonhomme, Pierre-Alexandre Kaminski, Marc Delarue
Summary: Cyanophage S-2L incorporates 2-aminoadenine into its DNA, altering its biophysical properties. Through investigation of the genes and synthesis pathways involved, the researchers successfully incorporated 2-aminoadenine into the bacterial genome, opening up possibilities for studying synthetic organisms containing ZTGC-DNA.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Lucas Harrison, Shaohua Zhao, Cong Li, Patrick F. McDermott, Gregory H. Tyson, Errol Strain
Summary: Lociq is a computational method that generates typing schema to aid investigations into the origin, evolution, and epidemiology of multidrug resistant plasmids. It classifies plasmids by variations in the sequence and arrangement of core plasmid genetic elements, providing a way to track and characterize the origin, evolution, and epidemiology of these plasmids.
COMMUNICATIONS BIOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Seon-Hwa Lee, Soo-Jin Yeom, Seong-Eun Kim, Deok-Kun Oh
Summary: Aldol chemicals are synthesized by condensation reactions between ketones and aldehydes using aldolases. Improving the catalytic properties of aldolases through engineering and design, as well as combining them with other catalysts, enables the efficient synthesis of complex organic chemicals. Current challenges and emerging solutions for aldolase-based catalysts are also discussed.
TRENDS IN BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Sitao Zhang, Yongchang Xu, Hongxin Guan, Tao Cui, Yuling Liao, Wenhui Wei, Jun Li, Bachar H. Hassan, Huimin Zhang, Xu Jia, Songying Ouyang, Youjun Feng
Summary: A novel pathway for biotin precursor synthesis involving BioZ has been identified and characterized, offering a different approach from the canonical pathway found in Escherichia coli. Genetic and biochemical characterization has elucidated the role of BioZ in biotin synthesis. Furthermore, crystal structure analysis of Agrobacterium tumefaciens BioZ provides insight into the molecular basis of its activity in biotin biosynthesis.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Qingqing Fang, Yu Feng, Alan McNally, Zhiyong Zong
Summary: Fang et al. identified two previously unidentified phages that can inhibit the growth and decrease the virulence of carbapenem-resistant Klebsiella pneumoniae (CRKP). They also found that CRKP can develop phage resistance but can still be eliminated in a mouse intestinal colonization model, highlighting the potential of phage therapy as a treatment against drug-resistant pathogens.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Nadine Abraham, Kurt L. Schroeter, Yan Zhu, Jonathan Chan, Natasha Evans, Matthew S. Kimber, Jason Carere, Ting Zhou, Stephen Y. K. Seah
Summary: Deoxynivalenol (DON) is a mycotoxin produced by filamentous fungi that causes significant yield losses of cereal crops. One promising method to detoxify DON is enzymatic epimerization to 3-epi-DON, and the enzyme DepB plays a critical role in this process.
SCIENTIFIC REPORTS
(2022)
Article
Agriculture, Dairy & Animal Science
Jonathan J. Lopez-Islas, Estela T. Mendez-Olvera, Daniel Martinez-Gomez, Andres M. Lopez-Perez, Libertad Orozco, Gerardo Suzan, Carlos Eslava
Summary: Emerging diseases pose a constant challenge in public health, and wild carnivores can be carriers of atypical strains of pathogenic microorganisms, highlighting the importance of natural environments in studying emerging diseases.
Article
Multidisciplinary Sciences
Yun Yang, Jiwei Liu, Bradley R. Clarke, Laura Seidel, Jani R. Bolla, Philip N. Ward, Peijun Zhang, Carol V. Robinson, Chris Whitfield, James H. Naismith
Summary: Bacterial extracellular polysaccharides play critical roles in virulence, with the Wzc protein serving as a key regulator through cycling between phosphorylation states to control both synthesis and export of glycan polymers.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Jiandong Huo, Halina Mikolajek, Audrey Le Bas, Jordan J. Clark, Parul Sharma, Anja Kipar, Joshua Dormon, Chelsea Norman, Miriam Weckener, Daniel K. Clare, Peter J. Harrison, Julia A. Tree, Karen R. Buttigieg, Francisco J. Salguero, Robert Watson, Daniel Knott, Oliver Carnell, Didier Ngabo, Michael J. Elmore, Susan Fotheringham, Adam Harding, Philip N. Ward, Maud Dumoux, Tessa Prince, Yper Hall, Julian A. Hiscox, Andrew Owen, William James, Miles W. Carroll, James P. Stewart, James H. Naismith, Raymond J. Owens, Lucile Moynie
Summary: Nanobodies engineered as homotrimers show promising potential in neutralizing SARS-CoV-2 viral strains for COVID-19 treatment, especially when administered through respiratory routes. The study characterizes four nanobodies with high affinity for the receptor binding domain of the spike protein, demonstrating efficacy in inhibiting disease progression in animal models.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Halina Mikolajek, Miriam Weckener, Z. Faidon Brotzakis, Jiandong Huo, Evmorfia Dalietou, Audrey Le Bas, Pietro Sormanni, Peter J. Harrison, Philip N. Ward, Steven Truong, Lucile Moynie, Daniel K. Clare, Maud Dumoux, Joshua Dormon, Chelsea Norman, Naveed Hussain, Vinod Vogirala, Raymond J. Owens, Michele Vendruscolo, James H. Naismith
Summary: This study generated nanobodies with different affinities using the receptor binding domain (RBD) of SARS-CoV-2 spike protein and a naive library. By analyzing the structure-activity relationship, it was found that higher conformational entropy losses were associated with tighter binding. Structural ensembles and conformational fluctuations were investigated to enhance the affinity of nanobodies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Charles J. Buchanan, Ben Gaunt, Peter J. Harrison, Yun Yang, Jiwei Liu, Aziz Khan, Andrew M. Giltrap, Audrey Le Bas, Philip N. Ward, Kapil Gupta, Maud Dumoux, Tiong Kit Tan, Lisa Schimaski, Sergio Daga, Nicola Picchiotti, Margherita Baldassarri, Elisa Benetti, Chiara Fallerini, Francesca Fava, Annarita Giliberti, Panagiotis Koukos, Matthew J. Davy, Abirami Lakshminarayanan, Xiaochao Xue, Georgios Papadakis, Lachlan P. Deimel, Virginia Casablancas-Antras, Timothy D. W. Claridge, Alexandre M. J. J. Bonvin, Quentin J. Sattentau, Simone Furini, Marco Gori, Jiandong Huo, Raymond J. Owens, Christiane Schaffitzel, Imre Berger, Alessandra Renieri, James H. Naismith, Andrew J. Baldwin, Benjamin G. Davis
Summary: This study utilizes universal saturation transfer analysis to reveal the interaction between the novel coronavirus and glycan compounds, and identifies protein mutations related to pathogenicity and zoonosis.
Article
Chemistry, Medicinal
Lucile Moynie, Francoise Hoegy, Stefan Milenkovic, Mathilde Munier, Aurelie Paulen, Veronique Gasser, Aline L. Faucon, Nicolas Zill, James H. Naismith, Matteo Ceccarelli, Isabelle J. Schalk, Gaetan L. A. Mislin
Summary: This study found that TCV can mimic the binding of ENT to the outer membrane transporter PfeA in Pseudomonas aeruginosa and can cross the bacterial outer membrane through this protein. This finding provides a promising vector for using the Trojan horse strategy against P. aeruginosa.
ACS INFECTIOUS DISEASES
(2022)
Article
Biochemistry & Molecular Biology
Talya S. Levitz, Miriam Weckener, Ivan Fong, James H. Naismith, Catherine L. Drennan, Edward J. Brignole, Daniel K. Clare, Michele C. Darrow
Summary: The specimen preparation process is crucial for the success of cryo electron microscopy (cryoEM) structural studies. Traditional manual methods have limitations in speed and efficiency, while new automated technologies offer improved controllability and stability. As early users of the chameleon system, we share our experiences and lessons learned through case studies, providing recommendations for future users and the field of cryoEM specimen preparation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Wenbo Li, Georgina C. Girt, Ashish Radadiya, James J. P. Stewart, Nigel G. J. Richards, James H. Naismith
Summary: The biosynthetic enzyme ForT catalyzes the formation of a C-C bond and distinguishes between different molecules, providing insights for biocatalytic production. This study utilizes biophysical measurements, structural biology, and quantum chemical calculations to understand ForT-catalyzed C-C bond formation and conformational changes. The findings have implications for the production of novel anti-viral compounds.
Article
Multidisciplinary Sciences
Casper Berger, Maud Dumoux, Thomas Glen, Neville B. -y. Yee, John M. Mitchels, Zuzana Patakova, Michele C. Darrow, James H. Naismith, Michael Grange
Summary: Plasma-coupled ion sources are used to thin vitrified human cells, allowing for in situ structural biology studies inside cells and tissues.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Miriam Weckener, Laura S. Woodward, Bradley R. Clarke, Huanting Liu, Philip N. Ward, Audrey Le Bas, David Bhella, Chris Whitfield, James H. Naismith
Summary: The study reveals the regulatory mechanism of polysaccharide polymerization in Enterobacteriaceae bacteria. It demonstrates the formation of a complex between WzyE polymerase and WzzE polysaccharide co-polymerase, which together participate in the polymerization and regulation of polysaccharides. These findings provide important structural insights into the mechanism of polysaccharide chain length regulation in bacteria.
Article
Biology
Maud Dumoux, Thomas Glen, Jake L. R. Smith, Elaine M. L. Ho, Luis M. A. Perdigao, Avery Pennington, Sven Klumpe, Neville B. Y. Yee, David Andrew Farmer, Pui Y. A. Lai, William Bowles, Ron Kelley, Juergen M. Plitzko, Liang Wu, Mark Basham, Daniel K. Clare, C. Alistair Siebert, Michele C. Darrow, James H. Naismith, Michael Grange, Giulia Zanetti
Summary: Cryogenic plasma FIB/SEM overcomes challenges in imaging non-stained biological samples, producing high-quality images with automated workflows. This technique allows for three-dimensional imaging of bacteria, human cells, and tissue with resolutions typically ranging from 20-50 nm.
Article
Chemistry, Multidisciplinary
James M. Parkhurst, Adam D. Crawshaw, C. Alistair Siebert, Maud Dumoux, C. David Owen, Pedro Nunes, David Waterman, Thomas Glen, David I. Stuart, James H. Naismith, Gwyndaf Evans
Summary: Three-dimensional electron diffraction from nanocrystals of biological macromolecules requires the use of very small crystals, typically less than 300 nm-thick. Focused-ion-beam milling has been used to prepare thin samples for this purpose, but little work has been done to quantify the damage caused to delicate biological samples. This study analyzed the effect of plasma FIB milling on lysozyme crystals and compared argon and xenon plasmas with a gallium source. The results showed an upper bound and a lower bound for the depth of the milling damage layer.
Review
Multidisciplinary Sciences
Anagha Madhusudanan, Christopher Iddon, Muge Cevik, James H. Naismith, Shaun Fitzgerald
Summary: The purpose of this review was to identify the effectiveness of environmental control non-pharmaceutical interventions (NPIs) in reducing transmission of SARS-CoV-2. A systematic review was conducted, and a total of 19 references provided evidence for the effectiveness of certain NPIs, such as ventilation and air cleaning devices. However, there was low confidence in the findings due to the low quality and certainty of the evidence.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2023)
Article
Biology
Audrey Le Bas, Halina Mikolajek, Jiandong Huo, Chelsea Norman, Joshua Dormon, James H. Naismith, Raymond J. Owens
Summary: The receptor binding domain (RBD) of the spike protein of SARS-CoV-2 interacts with angiotensin converting enzyme-2 (ACE-2) on epithelial cells, allowing the virus to enter the cell. However, llama-derived nanobodies (VHHs) can block this interaction and neutralize the virus. X-ray crystallography analysis of VHH-RBD complexes helps identify VHH epitopes and predict the effects of variant mutations. A workflow for expressing and purifying the proteins and screening conditions for high-quality crystals has been established.
Article
Multidisciplinary Sciences
Georgina C. Girt, Abirami Lakshminarayanan, Jiandong Huo, Joshua Dormon, Chelsea Norman, Babak Afrough, Adam Harding, William James, Raymond J. Owens, James H. Naismith
Summary: Detection of SARS-CoV-2 Spike protein using engineered nanobodies in a sandwich ELISA has shown promising results, with an optimal combination identified to capture antigens effectively and measure sub-picomolar amounts. This method allows for routine detection of infectious SARS-CoV-2 in samples, with a detection limit of less than seven focus-forming units.
ROYAL SOCIETY OPEN SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Heba Barnawi, Laura Woodward, Natalie Fava, Mikhail Roubakha, Steve D. Shaw, Chelsea Kubinec, James H. Naismith, Carole Creuzenet
Summary: Many bacteria produce polysaccharide capsules for protection and virulence, and understanding their synthesis could lead to new ways to combat bacterial infections. Two pairs of enzymes involved in the biosynthesis of capsular sugar precursors in Campylobacter jejuni were characterized, with specificities observed in heptose substrates. The enzymes demonstrated unique features and mechanisms, with potential for therapeutic applications and glycobiology research.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)