Article
Chemistry, Organic
Chia-Hao Chang, Sandra Gomez, Danielle M. Fontaine, Panagiotis Fikas, Bruce R. Branchini, James C. Anderson
Summary: A new synthetic luciferin, designed with rotationally restricted structure, demonstrated enhanced performance for bioluminescence reaction. This luciferin possessed two intramolecular H-bonds to limit degrees of freedom, an amine group to promote indirect light conversion, and an alkenyl group to increase π-conjugation. Spectroscopic and computational studies showed that the synthetic luciferin exhibited longer absorption and fluorescence emission wavelength compared to LH2 and iLH(2). Docking studies suggested that the emission wavelength of the luciferin might be influenced by the twisted structure caused by Asp531 within the enzyme. Further investigation with mutant luciferase FlucRed revealed a major emission peak at 606 nm, a distinct shoulder above 700 nm, and 21% of the spectrum located in the near-infrared range.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Article
Chemistry, Organic
Kesar Jagdev, Damiano Tanini, Jack W. Lownes, Carlotta Figliola, Louise Male, Antonella Capperucci, Richard S. Grainger
Summary: GPx mimics based on 4,5-disubstituted fluorene diselenides show catalytic activities consistent with conformational restriction about the dichalcogen bond, regulating cellular peroxide levels.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Praveen Praveen, Chao Wang, Thomas N. G. Handley, Hongkang Wu, Chrishan S. S. Samuel, Ross A. D. Bathgate, Mohammed Akhter Hossain
Summary: Human relaxin-2 (H2 relaxin) has therapeutic importance due to its anti-fibrotic, vasodilatory, and cardioprotective effects. Relaxin family peptide receptor 1 (RXFP1), the receptor for relaxin, is a potential target for treating fibrosis and related disorders. A single-chain agonist, B7-33 peptide, has been developed based on the B-chain of H2 relaxin but has a short circulation time in vitro.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Inorganic & Nuclear
Andrea Cornia, Adele Mucci, Matteo Briganti, Nathalie Bridonneau, Andrea Nava, Alessio Nicolini
Summary: The study investigates the diamagnetic analogue of tetrametallic, propeller-like single-molecule magnets [Ga-4(L4-Py)(2)(dpm)(6)] in EtOH. Through H-1 NMR spectroscopy and density functional theory calculations, it was found that the two enantiomers interconvert slowly. The solid-state structure suggests the existence of a lower symmetry stereoisomer, which needs to be clearly identified through NMR spectra.
EUROPEAN JOURNAL OF INORGANIC CHEMISTRY
(2022)
Review
Chemistry, Multidisciplinary
David Casanova
Summary: The RASCI methodology is suitable for characterizing medium to large molecular diradicals and polyradicals, as well as studying photophysical processes involving open-shell species and multiexcitonic states. However, limitations arise from the truncation of the excitation operator, leading to inaccuracies and errors that require improvements to be addressed.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Nanoscience & Nanotechnology
Zhipeng Shao, Situo Cheng, Yaxiong Zhang, Hongzhou Guo, Xiaosha Cui, Zhenheng Sun, Yupeng Liu, Yin Wu, Peng Cui, Jiecai Fu, Qing Su, Erqing Xie
Summary: A novel all-in-one structure paper-like zinc ion battery with ultrathin thickness, superior specific capacity, and outstanding cycling stability was designed and assembled in this study. The battery demonstrated excellent flexibility and remarkable temperature resistance in wearable electronic applications, indicating its potential for flexible wearable electronics and implantable biomedical devices.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Chemistry, Multidisciplinary
Qingshan Wu, Hao Yan, Lie Chen, Shuanhu Qi, Tianyi Zhao, Lei Jiang, Mingjie Liu
Summary: Hydrodynamic forces can be used to remove contaminants from underwater surfaces, but their practical applications are limited due to the no-slip condition in the viscous sublayer. Inspired by corals, an active self-cleaning surface with flexible filament-like sweepers is developed. These sweepers can penetrate the viscous sublayer and remove contaminants with high adhesion strength using energy from outer turbulent flows. Under oscillating flow, the single sweeper achieves a removal rate of up to 99.5% through dynamic buckling movements, and the coordinated movements of the sweepers array can completely clean the coverage area within 10 s as symplectic waves. This active self-cleaning surface breaks the concept of conventional self-cleaning by relying on fluid-structure coupling between sweepers and flows.
ADVANCED MATERIALS
(2023)
Article
Mathematics, Interdisciplinary Applications
Ali Raza, Umair Khan, Aurang Zaib, Emad E. Mahmoud, Wajaree Weera, Ibrahim S. Yahia, Ahmed M. Galal
Summary: This article investigates the flow of natural convection viscous unstable fluid on an oscillating infinite inclined plate, considering Newtonian heating effect, boundary wall slip effect, and constant mass diffusion conditions. A semi-analytical solution of transformed governed partial differential equations is obtained using a recent and efficient fractional definition known as Prabhakar, including Fourier and Fick's laws in the thermal profile and concentration field solution.
FRACTAL AND FRACTIONAL
(2022)
Article
Mechanics
Ying Zhang, Dongyan Shi, Dongze He
Summary: This paper uses the Spectro-geometric method to study the vibration behaviors of a submarine-like structure. It establishes a mathematical model and verifies its feasibility through convergence analysis and comparative studies. The effects of parameters on the structural vibration are also investigated.
COMPOSITE STRUCTURES
(2022)
Article
Chemistry, Multidisciplinary
Ruofei Zhang, Lei Chen, Qian Liang, Juqun Xi, Hanqing Zhao, Yiliang Jin, Xingfa Gao, Xiyun Yan, Lizeng Gao, Kelong Fan
Summary: Nanozymes with catalase-like activity, especially ferrihydrite, show potential in relieving tumor hypoxia for adjuvant radiotherapy. The surface iron-associated hydroxyl groups of ferrihydrite dominantly affect its catalytic activity. Moreover, ferrihydrite constantly catalyzes the decomposition of H2O2 to release O-2 in a specific pH range, enhancing the therapeutic effect of radiotherapy in the physiological environment.
Article
Engineering, Aerospace
Govind Mahato, Badam Singh Kushvah, Ashok Kumar Pal, Ravi Kumar Verma
Summary: This paper analyzes the dynamical behavior of the restricted three-body problem with an elongated smaller primary with a disc-like structure. It discusses the zero-velocity curve, equilibrium points, and their stability, emphasizing the impact of the disc-like structure and elongated primary body on the equilibrium points. The proposed problem is considered a credible model for describing motion within a disc-like structure.
ADVANCES IN SPACE RESEARCH
(2022)
Article
Chemistry, Physical
Yunming Zhai, Hongbao Li, Quanwei Ma, Rui Wang, Longhai Zhang, Chaofeng Zhang
Summary: In this study, an organic cathode material HAPN with high redox activity and ideal structural stability was designed and synthesized. HAPN exhibited high Li-storage capacity, remarkable cycling stability, and superior rate capability as a cathode for lithium-ion batteries (LIBs).
Article
Chemistry, Physical
Zhaoxu Jing, Jiacheng Zhang, Jianlong Wang, Mingkang Zhu, Xinxian Wang, Tinghai Cheng, Jianyang Zhu, Zhong Lin Wang
Summary: This study reports a three-dimensional fully-enclosed triboelectric nanogenerator with bionic fish-like structure for harvesting hydrokinetic energy in low flow velocity and shallow water areas. The bionic structure enables zero head power generation, and the effects of external excitations and bionic structures on the electrical performance are studied. Experimental results demonstrate high peak power density and excellent water durability for long-term service in river currents.
Review
Neurosciences
Monica Sathyanesan, Samuel S. Newton
Summary: Antidepressants regulate neurotrophic factors and these factors themselves can produce antidepressant-like effects independently. In addition to brain derived neurotrophic factor (BDNF), there are other structurally diverse trophic factors that have similar behavioral effects. Furthermore, erythropoietin, traditionally used as a hormone for treating anemia, has been found to function as a neurotrophic factor in the central nervous system.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2022)
Article
Engineering, Environmental
Hongyan Nie, Panyu Yan, Xiaomei Wang, Xu Zhang
Summary: A bulk carbon adsorbent with a bionic structure was successfully synthesized. The carbon microcapsules with the internal structure of beef omasum were integrated by interconnected macropores to form the bulk carbon adsorbent ICM-BO. ICM-BO exhibited excellent adsorption capacity and reusability due to the hierarchical nanoscale needle-like structure, interconnected macropores, and monolith nature.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Gogulan Karunanithy, D. Flemming Hansen
Summary: The article introduces a deep neural network architecture called FID-Net, inspired by WaveNet, for analyzing time domain NMR data and demonstrates its effectiveness in reconstructing NUS biomolecular NMR spectra.
JOURNAL OF BIOMOLECULAR NMR
(2021)
Article
Chemistry, Multidisciplinary
Samuel Naudi-Fabra, Maud Tengo, Malene Ringkjobing Jensen, Martin Blackledge, Sigrid Milles
Summary: Studying the conformational landscape of intrinsically disordered and partially folded proteins is challenging and requires an integrated approach using multiple techniques to accurately describe the conformational ensembles of these proteins. This integrated approach has been successfully tested and validated, providing new insights into the conformational landscape of viral proteins and demonstrating its potential for integrative dynamic structural biology.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Gogulan Karunanithy, Harold W. Mackenzie, D. Flemming Hansen
Summary: The study introduces a method of virtual decoupling using deep neural networks, which enhances the resolution of nuclear magnetic resonance experiments and reduces the phase cycles required for experiments. This approach successfully decouples various protein NMR spectra, offering a flexible and effective solution where traditional methods may fail.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Laura Marino Perez, Francesco S. Ielasi, Luiza M. Bessa, Damien Maurin, Jaka Kragelj, Martin Blackledge, Nicola Salvi, Guillaume Bouvignies, Andres Palencia, Malene Ringkjobing Jensen
Summary: This study uncovers the structural rearrangements that occur during ring flipping of a buried tyrosine residue. The results provide insights into protein breathing motions associated with ring flipping and have implications for protein design and structure prediction.
Correction
Biochemistry & Molecular Biology
Tim A. Mollner, Patrick G. Isenegger, Brian Josephson, Charles Buchanan, Lukas Lercher, Daniel Oehlrich, D. Flemming Hansen, Shabaz Mohammed, Andrew J. Baldwin, Veronique Gouverneur, Benjamin G. Davis
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tim A. Mollner, Patrick G. Isenegger, Brian Josephson, Charles Buchanan, Lukas Lercher, Daniel Oehlrich, D. Flemming Hansen, Shabaz Mohammed, Andrew J. Baldwin, Veronique Gouverneur, Benjamin G. Davis
Summary: Post-translational formation of boronoalanine in proteins through C beta-B gamma bond allows for mild, direct, and site-selective access, enabling tunable interactions and de novo function.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Luiza Mamigonian Bessa, Serafima Guseva, Aldo R. Camacho-Zarco, Nicola Salvi, Damien Maurin, Laura Marino Perez, Maiia Botova, Anas Malki, Max Nanao, Malene Ringkjobing Jensen, Rob W. H. Ruigrok, Martin Blackledge
Summary: The genome replication and transcription processes of SARS-CoV-2 are important targets for inhibiting the virus. The interaction between the nucleoprotein (N) and the amino-terminal ubiquitin-like domain of nsp3 (Ubl1), which is a cofactor of the replication-transcription complex, has been described at the atomic level. This interaction involves two linear motifs in the linker domain of N, which fold N around Ubl1 to regulate binding to RNA. The identification of these motifs provides future targets for developing innovative strategies against COVID-19.
Review
Chemistry, Multidisciplinary
Aldo R. Camacho-Zarco, Vincent Schnapka, Serafima Guseva, Anton Abyzov, Wiktor Adamski, Sigrid Milles, Malene Ringkjobing Jensen, Lukas Zidek, Nicola Salvi, Martin Blackledge
Summary: This review introduces the applications of nuclear magnetic resonance (NMR) in understanding the structure, dynamic behavior, and interaction trajectories of intrinsically disordered proteins. NMR provides ensemble averaged structural and dynamic parameters for each assigned resonance, revealing the importance of these parameters in the kinetics and thermodynamics of cellular and extracellular reactions. Furthermore, NMR can uncover the mechanistic basis of functional disordered molecular assemblies that are crucial for human health.
Article
Biochemistry & Molecular Biology
Gogulan Karunanithy, Tairan Yuwen, Lewis E. Kay, D. Flemming Hansen
Summary: This article introduces a DNN for the analysis of CEST data, which can accurately predict the chemical shifts of nuclei in exchanging species involving two or three sites, along with the associated uncertainty. The developed DNN method allows for autonomous analysis of complex NMR data.
JOURNAL OF BIOMOLECULAR NMR
(2022)
Article
Biochemistry & Molecular Biology
Nicolas Bolik-Coulon, D. Flemming Hansen, Lewis E. Kay
Summary: For the past decade, chemical exchange saturation transfer (CEST) experiments have been successfully used to study exchange processes in biomolecules involving sparsely populated, transiently formed conformers. This study shows that the commonly used lengthy sampling schemes may not be optimal and proposes a reduced frequency sampling approach that does not require a priori knowledge of exchange parameters.
JOURNAL OF BIOMOLECULAR NMR
(2022)
Article
Chemistry, Multidisciplinary
Guillaume Hoffmann, Madalen Le Gorrec, Emeline Mestdach, Stephen Cusack, Loic Salmon, Malene Ringkjobing Jensen, Andres Palencia
Summary: This study reveals a novel enzyme-independent prodrug activation mechanism by boron-based compounds targeting leucyl-tRNA synthetase. These benzoxaboroles act as prodrugs that activate their bioconversion by forming a specific and reversible inhibition adduct with ATP, AMP, or the terminal adenosine of the tRNALeu. This adenosine-dependent activation mechanism explains the good druglike properties and broad efficacy of benzoxaboroles against different human pathogens.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Vaibhav Kumar Shukla, Lucas Siemons, D. Flemming Hansen
Summary: Enzymes sample various conformations, and the dynamic sampling of conformations determines both enzymatic activity and inhibitor potency. Precise structures alone often cannot explain the effect of mutations on enzymatic activity and drug potency.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Vaibhav Kumar Shukla, Gabriella T. Heller, D. Flemming Hansen
Summary: Biomolecular nuclear magnetic resonance (NMR) spectroscopy and artificial intelligence (AI) have a strong synergy. AI can improve the acquisition and analysis of NMR spectra, enhancing accuracy and reliability. Deep learning also enables the development of new types of NMR experiments, expanding the scope and potential of biomolecular NMR spectroscopy. The combination of AI and NMR has the potential to revolutionize structural biology and drug discovery.
Article
Chemistry, Multidisciplinary
Vaibhav Kumar Shukla, Lucas Siemons, Francesco L. Gervasio, D. Flemming Hansen
Summary: This study demonstrates a strong correlation between the conformation of aromatic side chains near the active site and the opening and closing of functional loops of HDAC8. Mutations I19S-HDAC8 and S39E-HDAC8 were found to affect product release and substrate binding, providing insights into the mechanism of substantial downregulation caused by allosteric mutations.
Review
Chemistry, Multidisciplinary
Aldo R. Camacho-Zarco, Vincent Schnapka, Serafima Guseva, Anton Abyzov, Wiktor Adamski, Sigrid Milles, Malene Ringkjobing Jensen, Lukas Zidek, Nicola Salvi, Martin Blackledge
Summary: Intrinsically disordered proteins play essential roles in cellular and extracellular biochemistry. Nuclear magnetic resonance is a powerful tool for studying their structural and dynamic behavior, providing insights into reaction kinetics and thermodynamics essential for function. Recent applications of NMR have helped uncover the mechanistic basis of functional disordered molecular assemblies important for human health.