Article
Biochemistry & Molecular Biology
Anabela Martinez, Jorge Cantero, Antonio J. Melendez-Martinez, Margot Paulino
Summary: This study investigates the interaction of BCO1 and BCO2 with carotenoids through homology modeling and molecular dynamics simulations. The results show that the structures of these two enzymes are conserved, with β-carotene positioned optimally for catalysis. Additionally, BCO1 and BCO2 interact with different numbers and types of amino acid residues.
Article
Multidisciplinary Sciences
Kamil Nosol, Rose Bang-Sorensen, Rossitza N. Irobalieva, Satchal K. Erramilli, Bruno Stieger, Anthony A. Kossiakoff, Kaspar P. Locher
Summary: ABCB4 is expressed in hepatocytes and plays a key role in translocating phosphatidylcholine into bile canaliculi. Cryogenic electron microscopy structures of ABCB4 reveal its specificity for phosphatidylcholine and the essential role of key residues in this process. These findings provide a structural basis for understanding bile generation and its sensitivity to azole drugs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Plant Sciences
Ruphi Naz, Andleeb Khan, Badrah S. Alghamdi, Ghulam Md Ashraf, Maimonah Alghanmi, Altaf Ahmad, Sheikh Shanawaz Bashir, Qazi Mohd Rizwanul Haq
Summary: Ionotropic glutamate receptors (iGluRs) play an important role in neurons, with involvement in memory, neuronal development, and synaptic plasticity. Arabidopsis thaliana has genes comparable to human iGluRs, affecting plant growth and physiological activities. The evolutionary relationship between animal and plant glutamate receptors suggests a correlation, which can be utilized for early detection of neurodegenerative diseases. This review updates knowledge on Arabidopsis glutamate receptors, their evolution, functions, and expression, in comparison with iGluRs. Additionally, the use of FRET nanosensors for understanding neurotransmitter signaling via glutamate receptors in animals and plants is discussed.
Article
Chemistry, Multidisciplinary
Binbin Gu, Jeroen S. Dickschat
Summary: The researchers synthesized two terpenoid substrate analogs and enzymatically converted them with nine diterpene and two sesterterpene synthases. While two of the analogs were converted into diterpenes similar to the native substrate, the other nine cases resulted in disrupted or redirected cyclisation reactions, leading to the formation of products called ruptenes. The ruptenes were identified as deprotonation products of cationic intermediates, providing insights into the complex reaction mechanisms of terpene synthase mediated biosynthesis.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Biochemistry & Molecular Biology
Susanna Tornroth-Horsefield, Clara Chivasso, Helin Strandberg, Claudia D'Agostino, Carla V. T. O'Neale, Kevin L. Schey, Christine Delporte
Summary: This review provides a comprehensive overview of the current knowledge of AQP interactomes and discusses the molecular basis and functional significance of these protein-protein interactions in health and diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Danyil Grybchuk, Michaela Prochazkova, Tibor Fuzik, Aleksandras Konovalovas, Saulius Serva, Vyacheslav Yurchenko, Pavel Plevka
Summary: This study determined the structure and assembly mechanism of the L-BC virus using cryo-electron microscopy. The L-BC capsid has an icosahedral symmetry and the capsid proteins are stabilized by domain swapping. Additionally, some L-BC virus particles were found to be open and lacked one decamer of capsid proteins.
COMMUNICATIONS BIOLOGY
(2022)
Article
Engineering, Geological
Andreas-Nizar Granitzer, Franz Tschuchnigg, Saman Hosseini, Sandro Brasile
Summary: This paper proposes an enhanced embedded finite element model for simulating pile-type structures embedded in a soil continuum. The implicit surface-to-volume coupling scheme improves the well-posedness of the stiffness matrix, making the proposed model computationally efficient.
INTERNATIONAL JOURNAL FOR NUMERICAL AND ANALYTICAL METHODS IN GEOMECHANICS
(2023)
Review
Virology
Arpita Kar, Abhisekh Samanta, Soumyadeep Mukherjee, Subhasis Barik, Avik Biswas
Summary: Hepatitis B virus (HBV) is a major cause of hepatocellular carcinoma (HCC), the most common primary liver malignancy. The study of HBV-host interactions has identified various mechanisms involved in the development and progression of HBV-associated HCC. This review provides a comprehensive summary of the existing knowledge on HBV-host interplay and highlights new therapeutic strategies for HBV-induced HCC.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Review
Genetics & Heredity
Qingan Jia, Binghui Xu, Yaoyao Zhang, Arshad Ali, Xia Liao
Summary: The communication between tumor cells and TME activates signaling pathways that contribute to cancer progression. Targeting multiple components rather than single molecules could be more effective in cancer therapy, with CCN family proteins showing promise. The diverse functions of CCN proteins in different cancers are influenced by the TME and its truncated isoforms, suggesting a potential anti-cancer strategy by targeting CCN proteins to rebalance the TME.
FRONTIERS IN GENETICS
(2021)
Article
Chemistry, Multidisciplinary
Carolyn L. Hartley, Melody L. Kessler, Jillian L. Dempsey
Summary: Surface structure and reactivity are crucial for optimizing the properties of nanocrystals. Semiconductor nanocrystals face a technical disadvantage due to the lack of specific chemical formula, requiring innovative approaches to obtain a molecular-level surface image.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Janusz Wisniewski, Jakub Barciszewski, Jakub Turlik, Karolina Baran, Przemyslaw Duda, Mariusz Jaskolski, Dariusz Rakus
Summary: This study presents the crystal structure of PGAM2 and identifies its nuclear localization sequence. PGAM2 is found to stabilize nucleolar structure, maintain mRNA expression, and assist in the assembly of pre-ribosomal subunits. The insulin/IGF1-PI3K-Akt-mTOR signaling pathway is responsible for the nuclear localization of PGAM2.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Linguo Lu, Shansheng Yu, Hongwei Tian
Summary: Pentlandite ((Fe, Ni)(9)S-8) is a promising transition-metal catalyst for the hydrogen evolution reaction, but the long activation process and facet-dependent hydrogen evolution activity are not fully understood. Density functional theory calculations reveal that small metal cubes play a crucial role in surface stability and the linking sites between them act as the main catalytic active sites for hydrogen evolution.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Article
Chemistry, Physical
Shubham Tiwari, B. Moses Abraham, Jayant K. Singh
Summary: This study investigates the combined effect of surfactants and nanoparticles at the air-water interface, showing that the presence of nanoparticles reduces the efficiency of Triton X-100 and Tween 20 surfactants primarily due to the adsorption of surfactants on the nanoparticles. Density functional theory simulations reveal that the adsorption of non-ionic surfactants on silica nanoparticles decreases as the degree of ionization of the nanoparticles increases, in agreement with experimental observations.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Physics, Multidisciplinary
Long Li, Jinglei Hu, Huaping Wu, Fan Song
Summary: Cell adhesion on a supported lipid bilayer functionalized with ligand proteins is widely used to study trans receptor-ligand interaction, with attractive cis-interaction between ligands on the SLB amplifying both affinity and cooperativity of the binding, suggesting careful consideration of ligand-ligand cis-interaction in experiments.
SCIENCE CHINA-PHYSICS MECHANICS & ASTRONOMY
(2021)
Article
Multidisciplinary Sciences
Izabela Zglobicka, Juergen Gluch, Zhongquan Liao, Stephan Werner, Peter Guttmann, Qiong Li, Piotr Bazarnik, Tomasz Plocinski, Andrzej Witkowski, Krzysztof J. Kurzydlowski
Summary: The diatom shell serves as a complex siliceous structure that demonstrates the process of digging into the third dimension using modern visualization techniques. This paper highlights the importance of a comprehensive multi-length scale approach to bio-structures/materials, utilizing state-of-the-art imaging techniques to gain deeper insights into their morphology. Using visible light, electron, and X-ray microscopy to image diatoms allows for a more comprehensive understanding of their frustules.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Jessica E. Martyn, Giulia Pilla, Sarah Hollingshead, Kristoffer S. Winther, Susan Lea, Gareth McVicker, Christoph M. Tang
Summary: Shigella sonnei is a major cause of bacillary dysentery and becoming more concerning due to multidrug resistance. It spontaneously becomes avirulent during laboratory growth through loss of its virulence plasmid (pINV). This study investigated the mechanisms of avirulence in S. sonnei and found that it mainly results from pINV loss. The limited repertoire and amino acid sequences of plasmid-encoded toxin-antitoxin (TA) systems contribute to plasmid loss in S. sonnei. These findings provide new insights for reducing plasmid loss in S. sonnei and facilitating research and vaccine development.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Multidisciplinary Sciences
Andrea Arsiccio, Clive Metcalfe, Roberto Pisano, Sanj Raut, Carmen Coxon
Summary: Allosteric disulfide bonds have responsive and transient properties that make them suitable for processes requiring rapid and localized responses. This study used molecular dynamics (MD) to analyze the impact of reduction on the structure and function of coagulation factor VIII (FVIII). The results identified a specific disulfide bond that is most likely to undergo reduction and showed that this reduction leads to a more open conformation. These findings have implications for molecular engineering strategies to improve FVIII's activity and stability while reducing immunogenicity.
Article
Multidisciplinary Sciences
Katharina Braunger, Jiyoon Ahn, Matthijs M. Jore, Steven Johnson, Terence T. L. Tang, Dennis V. Pedersen, Gregers R. Andersen, Susan M. Lea
Summary: The authors report the identification and characterisation of a species-specific properdin inhibitor CirpA derived from tick saliva, opening avenues for future therapeutic approaches.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Di Wu, Carol Robinson
Summary: Oligomerization and glycosylation play important roles in the stability and efficacy of therapeutic glycoproteins, but the interplay between these two attributes is often difficult to define. In this study, a native top-down mass spectrometry approach was used to assess the glycosylation status of therapeutic cytokine and hormone assemblies and to relate interfacial glycan occupancy to complex stability. The study found that interfacial O-glycan stabilizes tumor necrosis factor-alpha trimer, while interferon-beta 1a dimerization is independent of glycosylation. Furthermore, a unique distribution of N-glycans on the follicle-stimulating hormone alpha subunit was discovered, and the interfacial N-glycan was found to interact extensively with the beta subunit to regulate dimer assembly.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Medicinal
Lisbeth R. Kjolbye, Lars Sorensen, Jun Yan, Nils A. Berglund, Jesper Ferkinghoff-Borg, Carol V. Robinson, Birgit Schiott
Summary: This study used molecular dynamics simulations and native mass spectrometry to investigate the interaction between PI(4,5)P-2 lipids and GCGR, revealing differential affinities of the lipids to different conformations of GCGR. Furthermore, the study uncovered the role of a conserved binding site in stabilizing the inactive conformation of GCGR in class B GPCRs.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Multidisciplinary Sciences
Longfei Wang, Di Wu, Carol Robinson, Tian-Min Fu
Summary: This study identifies a new protein called mEAK-7 that interacts with V-ATPases and may regulate its function while also being involved in mTOR signaling.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Di Wu, Manman Guo, Carol V. Robinson
Summary: Understanding the impact of genetic variations and post-translational modifications on protein interactions is made possible by using native mass spectrometry (MS). In this study, we characterized the proteoforms of plasma serine protease inhibitors and found that different fucosylation linkages have opposing effects on protein interactions.
Article
Chemistry, Multidisciplinary
Tarick J. El-Baba, Corinne A. Lutomski, Sean A. Burnap, Jani R. Bolla, Lindsay A. Baker, Andrew J. Baldwin, Weston B. Struwe, Carol V. Robinson
Summary: In this study, the impact of glycans on mediating ACE2 dimerization and interactions with Spike was investigated. The researchers found that glycans play a regulatory role in ACE2 dimerization and that positive cooperativity drives ACE2 to complex with multiple Spike trimers. These findings are important for developing strategies to neutralize the virus.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Correction
Biochemistry & Molecular Biology
Rei Matsuoka, Roman Fudim, Sukkyeong Jung, Chenou Zhang, Andre Bazzone, Yurie Chatzikyriakidou, Carol V. Robinson, Norimichi Nomura, So Iwata, Michael Landreh, Laura Orellana, Oliver Beckstein, David Drew
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Review
Pharmacology & Pharmacy
Hsin-Yung Yen, Ali Jazayeri, Carol Robinson
Summary: GPCRs are important drug targets due to their involvement in physiological processes. Mass spectrometry techniques, such as HDX-MS and native-MS, provide opportunities to investigate GPCR pharmacology and discover new drugs. This review highlights the potential of MS techniques for in-depth investigations of GPCR biology.
PHARMACOLOGICAL REVIEWS
(2023)
Article
Multidisciplinary Sciences
Benjamin J. Hardy, Alvaro Martin Hermosilla, Dinesh K. Chinthapalli, Carol V. Robinson, J. L. Ross Anderson, Paul Curnow
Summary: In this study, a minimal diheme membrane cytochrome was computationally designed and produced in live bacteria. The synthetic construct mimics a four-helix bundle found in respiratory complexes and has no sequence homology to natural polypeptides. This artificial membrane metalloprotein has the potential to function as an electron transfer module in both synthetic protocells and living systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Gabriela Dias Noske, Yun Song, Rafaela Sachetto Fernandes, Rod Chalk, Haitem Elmassoudi, Lizbe Koekemoer, C. David J. Owen, Tarick V. El-Baba, Carol Robinson, Glaucius Oliva, Andre Schutzer Godoy
Summary: The main protease of SARS-CoV-2, M-pro, is responsible for cleaving the viral polyprotein and is crucial for enzyme dimerization and activity. N-terminal cleavage is not critical for dimerization, and different types of inhibitors can affect the oligomeric states. This study provides insights into the maturation process of M-pro and how it can be targeted by inhibitors.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Kenneth R. R. Durbin, Matthew T. T. Robey, Lilien N. N. Voong, Ryan T. T. Fellers, Corinne A. A. Lutomski, Tarick J. J. El-Baba, Carol V. V. Robinson, Neil L. L. Kelleher
Summary: Native mass spectrometry has become an important technique for determining the composition of protein complexes. However, there is a lack of software tools for comprehensive analysis of native mass spectrometry data. In this study, we introduce ProSight Native as an informatics platform that can determine the complete composition of protein complexes. We demonstrated its features by successfully determining the composition of a homotetrameric membrane complex and a heterodimer complex with associated ligands.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Hongmiao Hu, Anne-Marie M. van Roon, George E. Ghanim, Bilal Ahsan, Abraham O. Oluwole, Sew-Yeu Peak-Chew, Carol V. Robinson, Thi Hoang Duong Nguyen
Summary: Shelterin and nucleosomes interact at mammalian telomeres, but the mechanism is not yet understood. Cryo-electron microscopy was used to study the structure of a human telomeric nucleosome bound to the shelterin factor TRF1. The study revealed that TRF1 binds to unwrapped nucleosomal DNA ends by engaging both the DNA and the histone octamer, resulting in a shift in the nucleosomal DNA. Phosphorylation of TRF1 and a noncanonical DNA binding surface on TRF1 were found to be crucial for its association with telomeric nucleosomes. These findings provide important insights into shelterin-chromatin interactions and its roles at telomeres.
Article
Multidisciplinary Sciences
Luke Smithers, Oksana Degtjarik, Dietmar Weichert, Chia-Ying Huang, Coilin Boland, Katherine Bowen, Abraham Oluwole, Corinne Lutomski, Carol V. Robinson, Eoin M. Scanlan, Meitian Wang, Vincent Olieric, Moran Shalev-Benami, Martin Caffrey
Summary: This study investigates the structural changes of the enzyme apolipoprotein N-acyltransferase (Lnt) during its reaction. The study confirms the ping-pong mechanism of Lnt and explains the molecular basis for its ability to bind different substrates.
