Article
Chemistry, Multidisciplinary
Lirong Zheng, Zhuo Liu, Qiang Zhang, Song Li, Juan Huang, Lei Zhang, Bing Zan, Madhusudan Tyagi, He Cheng, Taisen Zuo, Victoria Garcia Sakai, Takeshi Yamada, Chenxing Yang, Pan Tan, Fan Jiang, Hao Chen, Wei Zhuang, Liang Hong
Summary: This study reveals that the onset temperature of surface water is universal, despite the diverse activation temperatures of function-related anharmonic dynamics in different materials. This universal onset results from the switching of hydrogen bonds between neighboring water molecules with a common energy barrier of approximately 35 kJ mol(-1).
Article
Multidisciplinary Sciences
Andrew Z. Lin, Kiersten M. Ruff, Furqan Dar, Ameya Jalihal, Matthew R. King, Jared M. Lalmansingh, Ammon E. Posey, Nadia A. Erkamp, Ian Seim, Amy S. Gladfelter, Rohit V. Pappu
Summary: The authors report that protein-RNA condensates with shared proteins and distinct RNAs can form and persist in vitro and in cells as distinct entities if the nonshared RNA molecules are dynamically arrested, but the shared protein components are dynamically exchangeable.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Romeo C. A. Dubini, Huihun Jung, Chloe H. Skidmore, Melik C. Demirel, Petra Rovo
Summary: A major challenge in developing biomimetic, high-performance, and sustainable products lies in accurately replicating the remarkable properties of biological materials, such as high strength, self-repair, and responsiveness to stimuli. State-of-the-art nuclear magnetic resonance (NMR) spectroscopy has been used to link the atomistic properties of an artificial bioinspired protein to its macroscopic properties, providing insights into the key factors behind its outstanding physical attributes. This in-depth characterization serves as a solid foundation for the development of advanced materials with enhanced properties.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biophysics
Kevin Pounot, Geoffrey W. Grime, Alessandro Longo, Michaela Zamponi, Daria Noferini, Viviana Cristiglio, Tilo Seydel, Elspeth F. Garman, Martin Weik, Vito Fodera, Giorgio Schiro
Summary: This study reveals the crucial role of zinc in insulin dynamics and aggregation kinetics at low pH, where zinc binding stabilizes the native form of insulin by facilitating hydration of this hydrophobic protein. Introducing new binding sites for zinc can improve insulin stability and tune its aggregation propensity.
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Analytical
Nicholas T. Klokkou, David J. Rowe, Bethany M. Bowden, Neil P. Sessions, Jonathan J. West, James S. Wilkinson, Vasilis Apostolopoulos
Summary: A terahertz-compatible PTFE microfluidic flow-cell was fabricated for spectroscopic analysis of BSA, utilizing oxygen plasma treatments and milling to manipulate wettability for liquid confinement. PTFE's inert and bio-compatible properties make it ideal for sub-millimeter wavelength spectroscopy.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Chemistry, Physical
Mohammed Ahmed, Satoshi Nihonyanagi, Tahei Tahara
Summary: In this study, the vibrational relaxation dynamics of free OD molecules at the air/D2O interface were investigated using ultrafast spectroscopy. The results showed that the vibrational relaxation time of free OD molecules did not exhibit any isotopic dilution effect, similar to the behavior of free OH molecules. The relaxation of excited free OD molecules was found to predominantly occur through reorientation, rather than intramolecular energy transfer. The significantly longer relaxation time of free OD compared to free OH suggests the presence of a nuclear quantum effect on the diffusive reorientation of OD molecules. This study provides important insights into the vibrational relaxation behavior of water molecules at interfaces.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Astronomy & Astrophysics
Stephen L. Adler
Summary: In this study, we combine the concepts of a Weyl scaling invariant dark energy action and the gravastar theory. By utilizing the Tolman-Oppenheimer-Volkoff equation, we investigate the structure and dynamics of gravastars. Our Mathematica notebooks demonstrate that the structural changes of gravastars are determined by the action and equation of state, and the radii at which these changes occur are not predetermined. Additionally, we calculate the effects of a very small black hole wind using a relativistic extension of standard pressure-driven isothermal stellar wind theory.
Article
Chemistry, Multidisciplinary
Veronika Slachtova, Simona Bellova, Agustina La-Venia, Juraj Galeta, Martin Dracinsky, Karel Chalupsky, Alexandra Dvorakova, Helena Mertlikova-Kaiserova, Peter Rukovansky, Rastislav Dzijak, Milan Vrabel
Summary: The development of reagents selective in complex biological media is a significant challenge. We demonstrate that N1-alkylation of 1,2,4-triazines produces more reactive triazinium salts when reacting with strained alkynes compared to the parent 1,2,4-triazines. These salts facilitate efficient modification of peptides and proteins through a powerful bioorthogonal ligation. The positively charged N1-alkyl triazinium salts possess favorable cell permeability and outperform analogous 1,2,4,5-tetrazines for intracellular fluorescent labeling applications. These new ionic heterodienes exhibit high reactivity, stability, synthetic accessibility, and improved water solubility, making them valuable additions to the repertoire of modern bioorthogonal reagents.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Thermodynamics
Daniel I. Pineda, Fabio A. Bendana, R. Mitchell Spearrin
Summary: This study experimentally examined the competitive oxidation of methane with C-2 hydrocarbons of different functional groups and its impact on ignition. By using isotopically-labeled fuel mixtures and laser absorption spectroscopy, the researchers generated a novel dataset of multi-isotopologue species time-histories and modified reaction models to incorporate C-13 reactions and species, revealing insights on the influence of each C-2 fuel on methane ignition.
COMBUSTION AND FLAME
(2021)
Article
Chemistry, Physical
V. K. Sharma, H. Srinivasan, R. Mukhopadhyay, V. Garcia Sakai, S. Mitra
Summary: The study focuses on the structure and dynamics of an ionic liquid surfactant system, revealing that the alkyl chains are more ordered, hydration dynamics are slower, and lateral motion is faster in comparison to conventional surfactant micelles.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Biochemistry & Molecular Biology
Luman Haris, Ralf Biehl, Martin Dulle, Aurel Radulescu, Olaf Holderer, Ingo Hoffmann, Andreas M. Stadler
Summary: This study investigates the effects of guanidinium chloride (GndCl) on the structure and dynamics of myelin basic protein (MBP) using small-angle scattering and neutron spin-echo spectroscopy (NSE). The results show that GndCl can perturb the structure of MBP, leading to both compact and expanded conformations, as well as increased internal motions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Tetyana Kyrey, Judith Witte, Jana Lutzki, Michaela Zamponi, Stefan Wellert, Olaf Holderer
Summary: Polymer-solvent interactions play a crucial role in the stimuli-responsive behavior of polymer networks, affecting the swelling/deswelling behavior and dynamics of the polymer chains. Scattering experiments provide insight into the polymer-water interaction, with residual water amount determined by Karl Fischer titration. The relaxation time of water molecules is significantly longer than that of free water, due to strong interactions with the polymer network.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Biology
Ryo Tamura, Fangchao Jiang, Jin Xie, Daichi Kamiyama
Summary: The article describes a method to expand the number of orthogonal split FP systems with spectrally distinct colors, utilizing rational design and cycles of directed evolution to broaden the spectral color palette of FP1-10/11. They demonstrate a multiplexing approach using the new orthogonal split FP systems, allowing simultaneous imaging of four distinct proteins in single cells.
COMMUNICATIONS BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Jessica Spackova, Ieva Goldberga, Rishit Yadav, Guillaume Cazals, Aurelien Lebrun, Pascal Verdie, Thomas-Xavier Metro, Danielle Laurencin
Summary: O-17 NMR spectroscopy is a powerful technique for studying biomolecules. This study presents cost-effective strategies for enriching amino acids and peptides with O-17 using mechanochemistry. The enriched samples showed high levels of enrichment with no loss of purity, making them suitable for future NMR studies.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Astronomy & Astrophysics
N. Andersson, P. Pnigouras
Summary: The proposed model for the effective tidal deformability of a neutron star incorporates frequency dependence associated with the star's oscillation mode, enhancing accuracy during the late stages of binary inspiral. Compared to alternative descriptions, this model proves to accurately represent the dynamical tide up to close to merger. Its simplicity makes it an attractive option for gravitational-wave data analysis implementations, allowing for cost-effective creation of numerous templates spanning the relevant parameter space.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2021)
Article
Biophysics
Kevin Pounot, Geoffrey W. Grime, Alessandro Longo, Michaela Zamponi, Daria Noferini, Viviana Cristiglio, Tilo Seydel, Elspeth F. Garman, Martin Weik, Vito Fodera, Giorgio Schiro
Summary: This study reveals the crucial role of zinc in insulin dynamics and aggregation kinetics at low pH, where zinc binding stabilizes the native form of insulin by facilitating hydration of this hydrophobic protein. Introducing new binding sites for zinc can improve insulin stability and tune its aggregation propensity.
BIOPHYSICAL JOURNAL
(2021)
Article
Physics, Multidisciplinary
Giorgio Schiro, Yann Fichou, Alex P. S. Brogan, Richard Sessions, Wiebke Lohstroh, Michaela Zamponi, Gerald J. Schneider, Francois-Xavier Gallat, Alessandro Paciaroni, Douglas J. Tobias, Adam Perriman, Martin Weik
Summary: The study revealed that solvent-free protein-polymer hybrids can replace hydration water, preserving protein structure and function, with dynamics similar to water's.
PHYSICAL REVIEW LETTERS
(2021)
Review
Biochemistry & Molecular Biology
Harshwardhan Poddar, Derren J. Heyes, Giorgio Schiro, Martin Weik, David Leys, Nigel S. Scrutton
Summary: Dynamic changes in protein structures are crucial for protein function and can be investigated with unprecedented temporal and spatial resolution using X-ray free electron lasers. Light-activated proteins are attractive targets for time-resolved structural studies, as they allow for visualization of early chemical changes and global structural changes.
Article
Biochemistry & Molecular Biology
Camilla B. Andersen, Yuichi Yoshimura, Janni Nielsen, Daniel E. Otzen, Frans A. A. Mulder
Summary: The study demonstrates that (-)-epigallocatechin gallate (EGCG) can reduce the toxicity of α-synuclein (α SN) oligomers by binding to both monomeric and oligomeric forms of α SN. EGCG binds to different regions of α SN with highest affinity for the monomeric form. Furthermore, kinetic data suggest a coupling between EGCG dimerization and α SN association.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
D. Sorigue, K. Hadjidemetriou, S. Blangy, G. Gotthard, A. Bonvalet, N. Coquelle, P. Samire, A. Aleksandrov, L. Antonucci, A. Benachir, S. Boutet, M. Byrdin, M. Cammarata, S. Carbajo, S. Cuine, R. B. Doak, L. Foucar, A. Gorel, M. Grunbein, E. Hartmann, R. Hienerwadel, M. Hilpert, M. Kloos, T. J. Lane, B. Legeret, P. Legrand, Y. Li-Beisson, S. L. Y. Moulin, D. Nurizzo, G. Peltier, G. Schiro, R. L. Shoeman, M. Sliwa, X. Solinas, B. Zhuang, T. R. M. Barends, J-P Colletier, M. Joffre, A. Royant, C. Berthomieu, M. Weik, T. Domratcheva, K. Brettel, M. H. Vos, I Schlichting, P. Arnoux, P. Mueller, F. Beisson
Summary: The study found that Fatty Acid Photodecarboxylase (FAP) exhibits efficient decarboxylation activity, primarily achieved through the reduction of the flavin chromophore and direct removal of carbon dioxide by the substrate carboxyl group. Essential residues R451 and C432 are crucial for substrate stabilization and charge transfer.
Article
Multidisciplinary Sciences
Tiemen Cocquyt, Zhou Zhou, Jeroen Plomp, Lambert van Eijck
Summary: Neutron tomography has allowed us to peer inside Antoni van Leeuwenhoek's single-lens microscopes for the first time, revealing the types of lenses he used. Analysis shows that his microscopes incorporated some innovations indicating awareness of contemporary developments. Van Leeuwenhoek's use of a lens-making procedure popularized by Robert Hooke in 1678 suggests he was not an isolated scholar, but rather influenced by the trends of his time.
Article
Biochemistry & Molecular Biology
Jakob Toudahl Nielsen, Frans A. A. Mulder
Summary: CheSPI is a simple and efficient method that can accurately predict local structure and disorder, even in very small amounts of residual structure. It provides predictions for up to eight structural classes for structured regions and proteins, and generates intuitive numeric and graphical output.
JOURNAL OF BIOMOLECULAR NMR
(2021)
Article
Chemistry, Physical
Bernhard M. H. Weninger, Michel A. Thijs, Jeroen A. C. Nijman, Lambert van Eijck, Fokko M. Mulder
Summary: Iron is a promising material for future energy applications due to its abundance, but its properties in alkaline environments have not been fully understood. Neutron scattering techniques provide unique insights into the behavior of iron electrodes while charging or discharging. This study found that iron electrodes accumulate substantial amounts of iron hydroxide, leading to passivation and the formation of undetectable iron phases inside the electrode.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Editorial Material
Multidisciplinary Sciences
Frans A. A. Mulder
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Physical
Falk Hoffmann, Frans A. A. Mulder, Lars Schaefer
Summary: Solution-state NMR relaxation experiments and molecular dynamics simulations have shown that while most entropy is contained within short-time dynamics, the slow dynamics of side chains on longer timescales significantly affects side-chain conformational entropy and must be considered for accurate extraction of thermodynamic properties.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Allan R. E. Hansen, Kasper Enemark-Rasmussen, Frans A. A. Mulder, Pernille R. Jensen, Sebastian Meier
Summary: Electrochemical reduction allows for the capture and utilization of CO2 by converting it into small chemicals and fuels. However, there is a lack of well-established analytical standard operating procedures for accurately quantifying short-chain acids, aldehydes, and alcohols. The smallest organic compounds produced through electrochemical reduction of CO2 require slow NMR quantifications, which can be improved by using paramagnetic contrast agents or cooling water/DMSO for T-1-optimized measurements. H-1 NMR experiments commonly used in the study of biological mixtures are not suitable for quantitative analysis of T-1-optimized samples.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Humanities, Multidisciplinary
Janneke van der Stok-Nienhuis, Tonny Beentjes, Dominique Ngan-Tillard, Lambert van Eijck, Ineke Joosten, Maarten R. van Bommel
Summary: The structure, manufacturing process and function of five rare filigree spheres from a seventeenth century shipwreck were examined using non-invasive imaging techniques. The study provides decision-making support and insights into their understanding.
Article
Chemistry, Physical
Ahmed A. A. Ali, Falk Hoffmann, Lars Schaefer, Frans A. A. Mulder
Summary: Nuclear magnetic resonance (NMR) spin relaxation and molecular dynamics (MD) simulations are important methods for studying the internal dynamics of proteins. This study establishes a computational framework to extract cross correlation relaxation parameters of methyl groups in proteins from MD simulations and successfully obtains results consistent with experimental data.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemical Research Methods
Kyprianos Hadjidemetriou, Nicolas Coquelle, Thomas R. M. Barends, Elke De Zitter, Ilme Schlichting, Jacques-Philippe Colletier, Martin Weik
Summary: By combining various techniques, researchers have elucidated the catalytic mechanism of fatty-acid photodecarboxylase, which converts free fatty acids into hydrocarbon compounds. The study faced challenges and further experiments are needed to identify the photoproducts and their movements during the catalytic cycle.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Martin Weik, Tatiana Domratcheva
Summary: This review highlights recent advances in studying structural changes of light-sensitive proteins using time-resolved crystallography at X-ray free electron lasers and quantum chemical calculations.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
