Article
Biochemical Research Methods
Hai Xu, Lingyi Wu, Daodong Pan, Xiaoqun Zeng, Zhendong Cai, Yuxing Guo, Weijun Wang, Zhen Wu
Summary: The study revealed that the hydrophobicity and auto-aggregation of L. reuteri SH23 were significantly reduced under simulated gastrointestinal conditions, affecting gene expression related to cell envelope, metabolic processes, stress response, regulatory systems, and transporters. Additionally, proteomics analysis showed upregulation of proteins related to ABC transporters and LPxTG anchor domain proteins on the cell surface after exposure to gastrointestinal fluid. Recombinant Mub protein was also found to enhance the survival ability of L. reuteri SH23 in the GIT. Overall, mucus-binding proteins played a crucial role in the adhesion and tolerance of L. reuteri in the gastrointestinal tract.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Wael S. Hassanein, Huemeyra Ispirli, Enes Dertli, Mustafa Tahsin Yilmaz
Summary: Recent reports have shown that modifying potato starch with enzyme treatment increases the amount of a-1,6 linkages, resulting in starch with slow digestible properties. However, the formation of new linkages decreases the thermal resistance of the starch granules. In this study, a novel enzyme GtfB-E81 was used to produce a short length of a-1,6 linkages in potato starch without significantly altering its thermal stability. These findings have important implications for the food industry as they offer potential for regulating the slowly digestible characteristics of potato starch.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Gaurika Garg, Christian Dienemann, Lucas Farnung, Juliane Schwarz, Andreas Linden, Henning Urlaub, Patrick Cramer
Summary: We provide mechanistic insights into the three major steps of human co-transcriptional pre-mRNA capping based on six different cryo-EM structures. The human mRNA capping enzyme, RNGTT, first docks to the Pol II stalk to position its triphosphatase domain near the RNA exit site. The capping enzyme then moves onto the Pol II surface, and its guanylyltransferase receives the pre-mRNA 5'-diphosphate end.
Article
Multidisciplinary Sciences
Adriana Ene, Natalie Stegman, Alan Wolfe, Catherine Putonti
Summary: This study conducted a genomic investigation of Lactobacillus gasseri and Lactobacillus paragasseri. The results showed that the two species cannot be distinguished from short-read sequencing of the 16S rRNA, but average nucleotide identity (ANI) can accurately identify them. The study also found recent divergence and/or frequent gene exchange between the two species, and their genomes frequently harbored intact prophage sequences. Biosynthetic gene clusters for bacteriocins were identified in both species.
Article
Chemistry, Physical
Qingyue Cui, Shengzhong Frank Liu, Kui Zhao
Summary: In the past three years, metal-free perovskites have gained significant interest as promising candidates for next-generation wearable electronics. However, the relationship between the structural details and properties of these perovskites is not well understood. This review summarizes recent insights into their structural and functional aspects, explaining the role of molecular structure in the packing structure and resulting properties. It also discusses important factors and challenges in designing molecular structures for future applications, aiming to enrich the library of potential structures and applications for metal-free perovskites.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Prema L. Mallipeddi, Yongyou Zhang, Hongyun Li, Sanford D. Markowitz, Bruce Posner
Summary: SW033291 is a compound discovered in a high throughput chemical screen as an inhibitor of 15-prostaglandin dehydrogenase (15-PGDH), showing potential in promoting tissue regeneration in in vivo mouse models. Docking and molecular dynamics simulations reveal key binding interactions of SW033291 with specific residues in 15-PGDH, leading to enantioselectivity for the R-enantiomer. Comparisons with other 15-PGDH inhibitors shed light on the unique binding mode of (R)-S(O)-SW033291.
Article
Multidisciplinary Sciences
Florian Altegoer, Tessa E. F. Quax, Paul Weiland, Phillip Nussbaum, Pietro Giammarinaro, Megha Patro, Zhengqun Li, Dieter Oesterhelt, Martin Grininger, Sonja-Verena Albers, Gert Bange
Summary: Signal transduction via phosphorylated CheY is conserved in bacteria and archaea. In this study, the authors employ structural biochemistry combined with cell biology to delineate the mechanism of CheY recognition by the adaptor protein CheF.
NATURE COMMUNICATIONS
(2022)
Review
Pharmacology & Pharmacy
David Machalz, Szymon Pach, Marcel Bermudez, Matthias Bureik, Gerhard Wolber
Summary: This review summarizes recent structural insights into understudied cytochrome P450 enzymes, highlighting the impact of molecular modeling for mechanistically explaining pathophysiological effects and establishing understudied CYPs as promising drug targets.
DRUG DISCOVERY TODAY
(2021)
Article
Biochemistry & Molecular Biology
J. Andrew N. Alexander, Kaspar P. Locher
Summary: Glycosyltransferases of the C superfamily (GT-Cs) are a type of enzyme found in all domains of life, which catalyze the synthesis of oligosaccharides or the transfer of glycans from donor substrates to acceptor proteins. They play essential roles in glycosylation in higher-order eukaryotes. Recent studies have shown that GT-Cs have diverse folds and can be classified into two subclasses, GT-CA and GT-CB. Further research is needed to understand the molecular mechanisms of glycan recognition and catalysis in these subclasses.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Review
Cell Biology
Yang Li, Xue Yang, Yuequan Shen
Summary: Orai channels, belonging to the CRAC channel family, play a crucial role in Ca2+ influx triggered by ER Ca2+ depletion. While structural and functional studies have advanced our understanding of Orai channel activation, the gating mechanism for Ca2+ permeation remains less well understood. This review summarizes existing structural studies, detailing features, comparing closed and open states, and proposing a push-pull model for Ca2+ permeation.
Article
Biology
Paul Lambey, Omolade Otun, Xiaojing Cong, Francois Hoh, Luc Brunel, Pascal Verdie, Claire M. Grison, Fanny Peysson, Sylvain Jeannot, Thierry Durroux, Cherine Bechara, Sebastien Granier, Cedric Leyrat
Summary: The study characterized the interaction of LukE with chemokine receptors ACKR1, CCR2, and CCR5, revealing the location of receptor sulfotyrosine binding sites in the toxins. This work provides new insights into chemokine receptor recognition by leukotoxins and suggests that the conserved sulfotyrosine binding pocket could be a target for future drug development.
Article
Chemistry, Physical
Fatemeh Yazdani, Behzad Shareghi, Sadegh Farhadian, Lida Momeni
Summary: This study investigated the effects of naringenin on the structure of human serum albumin (HSA) using spectroscopic and computational methods. The results showed that naringenin can bind to HSA, increasing its stability and reducing its flexibility.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Rasoul Eslami-Farsani, Sadegh Farhadian, Behzad Shareghi, Lida Momeni
Summary: Valuable and useful information on the biotechnological and medical applications of nanoparticles can be obtained through their interactions with proteins and the resulting structural changes. In this study, the effects of nickel oxide (NiO) nanoparticles on the structure and stability of myoglobin were examined. The results showed that NiO nanoparticles quenched the emission signals of myoglobin and influenced its secondary structure and thermal stability.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Joanna Zamel, Jiaxing Chen, Sofia Zaer, Paul David Harris, Paz Drori, Mario Lebendiker, Nir Kalisman, Nikolay V. Dokholyan, Eitan Lerner
Summary: Parkinson disease is associated with the aggregation of α-synuclein protein. In vitro experiments show that α-synuclein exists primarily as a monomer-dimer equilibrium in nanomolar to micromolar concentrations. By using cross-linking mass spectrometry and molecular dynamics simulations, a compact and stable dimer with partially exposed β-sheet structures is identified. This dimer, characterized by the proximity of tyrosine 39 hydroxyls, may play a role in the formation of α-synuclein amyloid fibrils and have etiological relevance to Parkinson disease.
Article
Biology
Amandeep S. Arora, Hsiang-Ling Huang, Ramanpreet Singh, Yoshie Narui, Andrejus Suchenko, Tomoyuki Hatano, Sarah M. Heissler, Mohan K. Balasubramanian, Krishna Chinthalapudi, Pekka Lappalainen
Summary: The structures of actin isoforms have been determined at high resolution, revealing their specific conformations and isoform-specific interfaces. These findings provide important insights into the function of actin isoforms and contribute to our overall understanding of cytoskeletal physiology.
Article
Pharmacology & Pharmacy
Emelie Ohnstedt, Hava Lofton Tomenius, Peter Frank, Stefan Roos, Evelina Vagesjo, Mia Phillipson
Summary: Non-healing wounds are a growing medical problem that causes significant suffering. In this study, the topical administration of the drug candidate ILP100 proved to be safe and accelerated wound healing in minipigs, using different evaluation methods.
Article
Cell Biology
Conor J. McGrath, Edgaras Laveckis, Andrew Bell, Emmanuelle Crost, Nathalie Juge, Stephanie Schuller
Summary: The gut microbiota plays a crucial role in protecting against enteric infection, but the underlying mechanisms are largely unknown. Researchers developed a new experimental model and optimized the culture medium to study bacterial growth in mucus-producing intestinal cells. They found that L. reuteri and R. gnavus have different effects on EPEC infection and can reduce the secretion of inflammatory factors.
DISEASE MODELS & MECHANISMS
(2022)
Article
Biochemistry & Molecular Biology
Ravindra Pal Singh, Raja Bhaiyya, Raksha Thakur, Jayashree Niharika, Chandrajeet Singh, Dimitrios Latousakis, Gerhard Saalbach, Sergey A. Nepogodiev, Praveen Singh, Sukesh Chander Sharma, Shantanu Sengupta, Nathalie Juge, Robert A. Field
Summary: This study characterized the ability of Limosilactobacillus reuteri and Blautia producta strains to utilize xylan derivatives. The findings revealed the enzymatic properties and mechanisms of these strains in xylooligosaccharide (XOS) utilization and proposed an XOS metabolism pathway model for L. reuteri and B. producta. Additionally, the study highlighted the extended xylanolytic potential of the gut microbiota.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Isabella M. Acquistapace, Emma J. Thompson, Imke Kuhn, Mike R. Bedford, Charles A. Brearley, Andrew M. Hemmings
Summary: The role of the proton donor residue in determining the stereospecificity of the AppA phytase enzyme was investigated. Mutations in the proton donor residue strongly influenced the enzyme's activity and preference for different substrates. High-resolution crystal structures provided evidence for the importance of the proton donor residue in regulating specificity pockets A and B.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Nathalie Juge
Summary: The mucus layer in the gastrointestinal tract is crucial for maintaining gut homeostasis, and the mucosa-associated microbiota (MAM) has a significant impact on immune and metabolic health. Changes in GI microbial communities are associated with human diseases, and MAM signatures show potential for distinguishing between diseased and healthy conditions. However, accessing microbial communities in the human gut remains challenging. This review provides up-to-date information on accessing MAM, the composition of MAM, and the relationship between MAM changes and human health and disease.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Article
Multidisciplinary Sciences
Gregory D. Rix, Colleen Sprigg, Hayley Whitfield, Andrew M. Hemmings, Jonathan D. Todd, Charles A. Brearley
Summary: Phylogenetic analysis, homology modelling, and biochemical methods were used to study a phytase from a Gram-negative soil bacterium. The enzyme showed stability in solution, broad pH activity profile, and specific substrate binding pockets. The transcription of the phytase gene was affected by environmental conditions.
Article
Microbiology
Yanhong Pang, Ludwig Ermann Lundberg, Manuel Mata Forsberg, David Ahl, Helena Bysell, Anton Pallin, Eva Sverremark-Ekstroem, Roger Karlsson, Hans Jonsson, Stefan Roos
Summary: Bacterial extracellular membrane vesicles (MV) are important mediators of microbe-host signals in host-pathogen interactions and interactions between mutualistic bacteria and their hosts. The study focused on MV derived from probiotics and found that they carry numerous bacterial cell surface proteins, some of which are involved in host-bacteria interactions. They can be internalized by epithelial cells, decrease leakage caused by enterotoxigenic Escherichia coli, regulate inflammatory responses in immune cells, and antagonize pain receptor channels. The findings have implications for the development of innovative and more efficient probiotic products.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Hayley L. Whitfield, Sining He, Yinghong Gu, Colleen Sprigg, Hui -Fen Kuo, Tzyy-Jen Chiou, Andrew M. Riley, Barry V. L. Potter, Andrew M. Hemmings, Charles A. Brearley
Summary: This study describes the differences in substrate specificity between two isoforms of ITPK enzymes (ITPK1 and ITPK4) in Arabidopsis, and provides a molecular explanation for the diverse phosphotransferase activity of ITPK4 by analyzing its ATP-coordinated structure. Furthermore, the study reveals a previously unreported N-terminal haloacid dehalogenase-like fold in ITPK4 and its homologues in other plants.
BIOCHEMICAL JOURNAL
(2023)
Article
Microbiology
Irene Vitale, Mattia Spano, Valentina Puca, Simone Carradori, Stefania Cesa, Beatrice Marinacci, Francesca Sisto, Stefan Roos, Gianfranco Grompone, Rossella Grande
Summary: This study evaluated the antibiofilm activity of cell-free supernatant (CFS) and its sub-fractions (SurE 10 K and SurE) produced by Limosilactobacillus reuteri DSM 17938 against biofilm-producing bacterial species. The results showed that CFS exhibited promising antibiofilm activity against biofilms formed by clinically relevant microorganisms. NMR metabolomic analysis identified and quantified several compounds, mainly organic acids and amino acids, with lactate being the most abundant metabolite in all samples. The storage stability of these postbiotics was evaluated using the CIEL*a*b parameters.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Medicine, General & Internal
Emelie Ohnstedt, Evelina Vagesjo, Andreas Fasth, Hava Lofton Tomenius, Pia Dahg, Sofia Jonsson, Nisha Tyagi, Mikael Astrom, Zhanar Myktybekova, Lovisa Ringstad, Margareth Jorvid, Peter Frank, Per Heden, Stefan Roos, Mia Phillipson
Summary: This study aimed to evaluate the safety and tolerability of ILP100-Topical drug in humans and investigate its clinical and biological effects on wound healing. The results showed that ILP100-Topical was safe and well-tolerated in all individuals and doses, and it accelerated wound healing and increased the density of CXCL12+ cells in the wounds.
Article
Biotechnology & Applied Microbiology
Peishun Li, Stefan Roos, Hao Luo, Boyang Ji, Jens Nielsen
Summary: Many studies have shown the link between gut microbiota and human health and disease. Manipulation of gut microbiota, such as supplementation of probiotics, has been suggested as a feasible method, but with limited therapeutic efficacy. In order to develop effective microbiota-targeted diagnostic and therapeutic strategies, metabolic engineering has been applied to construct genetically modified probiotics and synthetic microbial consortia.
METABOLIC ENGINEERING
(2023)
Review
Microbiology
Emmanuelle H. Crost, Erika Coletto, Andrew Bell, Nathalie Juge
Summary: Ruminococcus gnavus, a prevalent member of the gut microbiota, has been identified as a key biomarker of health and diseases due to its immune and metabolic properties. Its study has expanded from specific enzymes or bacteriocins to its association with various intestinal and extraintestinal diseases. The review discusses its biological characterization, occurrence in the gut microbiota, colonization factors, and its role in host health and disease.
FEMS MICROBIOLOGY REVIEWS
(2023)
Article
Biotechnology & Applied Microbiology
Malin Sendelius, Jakob Axelsson, Peidi Liu, Stefan Roos
Summary: This study conducted a systematic safety assessment of Limosilactobacillus reuteri ATCC PTA 4659 through genome analysis, phenotypic characterization, and a human clinical safety study. The results showed that the strain is susceptible to antibiotics and does not possess virulence or antibiotic resistance genes. It was also found to have a high adhesion to mucus and tolerance to gastric pH and bile, indicating its potential as a probiotic strain. The human clinical safety study demonstrated that the strain is safe for human consumption.
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Raquel Faba-Rodriguez, Yinghong Gu, Melissa Salmon, Giuseppe Dionisio, Henrik Brinch-Pedersen, Charles A. Brearley, Andrew M. Hemmings
Summary: This study presents the X-ray crystal structure of the b2 isoform of wheat PAPhy induced during germination, revealing a model for phytate recognition and its impact on the activity of cereal PAPhys, laying the groundwork for rational engineering of phytase activity in plants.
PLANT COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Daniel Demus, Paulina A. Urbanowicz, Richard A. Gardner, Haiyang Wu, Agata Juszczak, Tamara Stambuk, Edita Pape Medvidovic, Katharine R. Owen, Olga Gornik, Nathalie Juge, Daniel I. R. Spencer
Summary: This study developed a high-throughput exoglycosidase plate-based assay to measure alpha 1-3,4 fucosylation levels in blood plasma samples of individuals with HNF1A-MODY, showing good differentiating power in identifying cases with damaging HNF1A variants. The assay has the potential to support future development of a simple diagnostic test for this glycan biomarker in a clinical setting.