Article
Physics, Multidisciplinary
Ingo Hoffmann
Summary: This paper discusses the importance of background correction in neutron spin echo measurements, reviews different methods to subtract the buffer, and studies the impact of small errors in background subtraction on results.
In the large dynamic range of modern neutron spin-echo spectrometers, multiple effects become visible in a single measurement, particularly for vesicles where membrane undulations and translational diffusion affect the intermediate scattering function. The study investigates how considering these factors differently can affect the results obtained from data analysis.
FRONTIERS IN PHYSICS
(2021)
Article
Physics, Multidisciplinary
Shang Gao, Michael A. McGuire, Yaohua Liu, Douglas L. Abernathy, Clarina dela Cruz, Matthias Frontzek, Matthew B. Stone, Andrew D. Christianson
Summary: Using neutron scattering, a spiral spin liquid has been realized in the van der Waals honeycomb magnet FeCl3. A continuous ring of scattering is directly observed, indicating the emergence of an approximate U(1) symmetry in momentum space.
PHYSICAL REVIEW LETTERS
(2022)
Review
Chemistry, Multidisciplinary
Jacob J. Kinnun, Haden L. Scott, Rana Ashkar, John Katsaras
Summary: The relationship between cell membrane structure and function is a fundamental principle in biology; neutron scattering techniques can be used to study hydrogen-rich materials such as biomembranes; modeling small-angle neutron scattering data and molecular dynamics simulations can reveal the structure, dynamics, and molecular interactions of biological membranes.
FRONTIERS IN CHEMISTRY
(2021)
Article
Materials Science, Multidisciplinary
M. Bernal-Choban, H. L. Smith, C. N. Saunders, D. S. Kim, L. Mauger, D. L. Abernathy, B. Fultz
Summary: The phonon densities of states (DOSs) of body-centered cubic chromium were studied above the Néel temperature using time-of-flight inelastic neutron scattering. Experimental results showed a significant softening of the phonon DOSs with increasing temperature. The high-transverse phonon branch softened by about 17%, while the low-transverse branch softened by approximately half of that. The calculated vibrational entropies from phonons and electrons agreed well with the entropy obtained by calorimetry, suggesting that there were no explicit temperature-dependent magnetic contributions above 330 K.
Article
Polymer Science
Karin J. Bichler, Bruno Jakobi, Alice Klapproth, Taiki Tominaga, Richard A. Mole, Gerald J. Schneider
Summary: The segmental dynamics of PNB-g-PPO bottlebrush polymer is slower than that of linear PPO due to the stiff backbone. The relaxation time of PNB-g-PPO follows a power law dependence on momentum transfer, indicating more heterogeneous relaxation behavior compared to linear PPO. The time dependent mean square displacement and non-Gaussian parameter also support the slower and more restricted dynamics of PNB-g-PPO compared to linear PPO.
MACROMOLECULAR RAPID COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
D. Subires, A. Korshunov, A. H. Said, L. Sanchez, Brenden R. Ortiz, Stephen D. Wilson, A. Bosak, S. Blanco-Canosa
Summary: The origin and mechanism of the charge density wave in the kagome metal compound AV(3)Sb(5) is still under intense debate. By combining diffuse and inelastic x-ray scattering techniques, this study shows that the charge density wave transition in (Cs,Rb)V3Sb5 is of the order-disorder type. The experimental data indicate that the CDW consists of alternating Star of David and trihexagonal distortions.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Jin Chen, Qingqing Mei, Yinlin Chen, Christopher Marsh, Bing An, Xue Han, Ian P. Silverwood, Ming Li, Yongqiang Cheng, Meng He, Xi Chen, Weiyao Li, Meredydd Kippax-Jones, Danielle Crawshaw, Mark D. Frogley, Sarah J. Day, Victoria Garcia -Sakai, Pascal Manuel, Anibal J. Ramirez-Cuesta, Sihai Yang, Martin Schroeder
Summary: Studying a porous material with rapid proton conduction, researchers have discovered a low activation energy record that allows stable performance over a wide temperature range. By investigating the molecular mechanism of proton diffusion within the material, they have revealed the pathways of proton transport.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Valentina Guccini, Shun Yu, Zhoujun Meng, Eero Kontturi, Franz Demmel, German Salazar-Alvarez
Summary: Cellulose nanofibrils (CNFs) are materials with tunable surface functionality, good mechanical properties, and bio-/environmental friendliness. This study investigates the water movement in hydrated films made of carboxylated CNFs and finds that the surface charge and network structure contribute to moisture uptake.
Article
Materials Science, Multidisciplinary
Sheik Md Kazi Nazrul Islam, Prince Mayank, Yulou Ouyang, Jie Chen, Arun K. Sagotra, Meng Li, Michael B. Cortie, Richard Mole, Claudio Cazorla, Dehong Yu, Xiaolin Wang, Robert A. Robinson, David Laurence Cortie
Summary: The study accurately re-determined the diffusion rates of Cu2Se, revealing a diffusion coefficient of 3.1+/-1.3 x 10(-5) cm(2).s(-1). In the superionic state, there was no major loss of phonon mode intensity, and thermal conductivity was primarily affected by subtle mode broadening associated with anharmonic phonon interactions.
Article
Engineering, Chemical
Velencia J. Witherspoon, Kanae Ito, Chad R. Snyder, Madhusudan Tyagi, Tyler B. Martin, Peter A. Beaucage, Ryan C. Nieuwendaal, Richard S. Vallery, David W. Gidley, Jeffrey D. Wilbur, Dean Welsh, Christopher M. Stafford, Christopher L. Soles
Summary: In order to improve the PA separation layer in reverse osmosis (RO) membranes, the crosslink density of a PA network based on m-phenylene diamine is systematically reduced by substituting part of the crosslinking agent with a difunctional isophthaloyl analog. The resulting changes in the network's properties are evaluated in terms of water flux and salt rejection. The study reveals insights into water diffusion within the PA network and provides design cues for high-performance RO membrane engineering.
JOURNAL OF MEMBRANE SCIENCE
(2023)
Article
Materials Science, Multidisciplinary
Sushanta Dattagupta
Summary: The dissipation in the quantum solid of graphene is studied through the methods of nonequilibrium statistical mechanics of an open quantum system. The response is nonlinear at optical frequencies and for sizable amplitude of the electric field, and a rotating wave approximation simplifies the treatment. The resonant frequency quantifies the tunneling between the valence and the conduction bands across the Dirac point.
Article
Physics, Multidisciplinary
Yao Wang, Yuan Chen, Thomas P. Devereaux, Brian Moritz, Matteo Mitrano
Summary: The manipulation of spins with ultrafast lasers presents a promising approach to control the properties of quantum materials. The study demonstrates that ultrafast pump-induced spin excitations in Mott insulators can lead to a prompt softening of spin excitation energy, with implications for superconducting pairing correlations.
COMMUNICATIONS PHYSICS
(2021)
Article
Chemistry, Physical
Giovanni Romanelli, Carla Andreani, Laura Fazi, Arthur Ishteev, Kamilla Konstantinova, Enrico Preziosi, Roberto Senesi, Aldo Di Carlo
Summary: This study presents an experimental investigation of methylammonium lead tribromide single crystals in different phases using inelastic and deep inelastic neutron scattering experiments. The research found that the changes in average hydrogen nuclear kinetic energy between phases are mainly influenced by zero-point vibrational energies rather than temperature effects. Furthermore, vibrational densities of states in the orthorhombic phase of MAPbBr3 were found to be consistent with previous results on powder samples, with only slight differences in vibrational modes compared to MAPbI3. The study concludes that zero-point energies and average nuclear kinetic energies in two-hybrid organic/inorganic perovskites are expected to be approximately the same within a harmonic framework.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Pablo I. Sepulveda-Medina, Madhusudan Tyagi, Chao Wang, Bryan D. Vogt
Summary: The dynamics of water in amphiphilic hydrogels are influenced by secondary confinement, with changes in composition affecting the spacing between cross-links and altering the temperature dependent dynamics of water. Despite lower water crystallinity, the self-diffusion coefficient of these hydrogels decreases significantly below 260 K, suggesting a chemistry dependent dynamics of water in confined environments.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Yu. S. Ponosov, D. Y. Novoselov
Summary: The study demonstrates that the shapes and energy positions of electronic continua are influenced by temperature and excitations symmetry. Experimental spectra were modeled using ab initio DFT electronic structure calculations, showing promising results.
JOURNAL OF ALLOYS AND COMPOUNDS
(2021)
Article
Chemistry, Physical
Davide Bochicchio, Laura Cantu, Maria Vittoria Cadario, Leonardo Palchetti, Francesca Natali, Luca Monticelli, Giulia Rossi, Elena Del Favero
Summary: Synthetic plastic oligomers can interact with living organisms in various ways, and their effects on cell structure and dynamics are still not well understood. Research has shown that doping doses of polystyrene oligomers can alter the thermal properties of lipid membranes and modify their mechanical properties. This calls for a systematic and interdisciplinary assessment of the interaction mechanisms between synthetic polymers and cell membranes.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Andreas Santamaria, Krishna C. Batchu, Olga Matsarskaia, Sylvain F. Prevost, Daniela Russo, Francesca Natali, Tilo Seydel, Ingo Hoffmann, Valerie Laux, Michael Haertlein, Tamim A. Darwish, Robert A. Russell, Giacomo Corucci, Giovanna Fragneto, Armando Maestro, Nathan R. Zaccai
Summary: This study investigates the role of SARS-CoV-2 Spike fusion peptides in cellular infection using neutron scattering and spectroscopy techniques. The findings reveal that calcium drives the fusion peptides to cross the host plasma membrane, while removal of calcium leads to peptide reorientation and significant changes in lipid properties. Combining with other regions in the fusion domain, the molecular events of cell entry by SARS-CoV-2 are proposed.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Tatsuhito Matsuo, Alessio De Francesco, Judith Peters
Summary: This study investigates the dynamics of two polymorphic fibrils of hen egg white lysozyme, a model for human lysozyme, formed at pH 2.7 and pH 6.0 using neutron scattering techniques. The results show that the pH 6.0 polymorph exhibits higher molecular flexibility and faster diffusive motions compared to the pH 2.7 polymorph.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Multidisciplinary Sciences
Sigurbjorn Markusson, Erik Hallin, Helene J. Bustad, Arne Raasakka, Ju Xu, Gopinath Muruganandam, Remy Loris, Aurora Martinez, Clive R. Bramham, Petri Kursula
Summary: Activity-regulated cytoskeleton-associated protein (Arc) plays a vital role in synaptic plasticity and memory formation. This study used high-affinity anti-Arc nanobodies to investigate the structure and function of Arc. The results suggest that the N-terminal domain of Arc is involved in membrane binding, while the C-terminal domain binds to postsynaptic protein ligands. Furthermore, the NTD and CTD are important for Arc oligomerisation and assembly of capsids.
Article
Genetics & Heredity
Mirella Vinci, Petri Kursula, Donatella Greco, Maurizio Elia, Luigi Vetri, Carmelo Schepis, Valeria Chiavetta, Serena Donadio, Michele Roccella, Marco Carotenuto, Valentino Romano, Francesco Cali
Summary: This study reports a case of CFC-like phenotype in a patient with compound heterozygote missense mutations in the AHNAK2 gene. The mutations were found to be unrelated to known genes associated with CFC syndrome, and their impact on protein function was predicted to be not severe. The mutations were located in flexible regions possibly involved in molecular interactions.
MOLECULAR GENETICS & GENOMIC MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Sigurbjorn Markusson, Jens G. Hjorleifsson, Petri Kursula, Bjarni Asgeirsson
Summary: This study reveals the presence of two chloride binding sites in the structure of marine bacterial alkaline phosphatase (VAP), one in the active site and another at a peripheral site. Binding of chloride ions to the peripheral site decreases structural dynamics, leading to thermal stabilization of the VAP active conformation. The binding of chloride ion in the active site does not displace the bound inorganic phosphate product, but it may promote product release by facilitating rotational stabilization of the substrate-binding Arg129.
Article
Chemistry, Multidisciplinary
Daniele Di Bari, Stepan Timr, Marianne Guiral, Marie-There Giudici-Orticoni, Tilo Seydel, Christian Beck, Caterina Petrillo, Philippe Derreumaux, Simone Melchionna, Fabio Sterpone, Judith Peters, Alessandro Paciaroni
Summary: Temperature variations have a significant impact on bacterial metabolism and death, but a comprehensive understanding of these processes at the molecular level is still lacking. By studying the proteome dynamics of E. coli, it has been found that only a small fraction of the proteome unfolds during cell death. The unfolding of this fraction of proteins, which form an entangling network in the cytoplasm, dominated by hydrophobic interactions, is responsible for the dramatic slowdown in proteome dynamics observed below the cell's death temperature. Understanding the progression of proteome unfolding and its diffusive dynamics is crucial for accurately predicting the growth rate of E. coli.
ACS CENTRAL SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Loreto Misuraca, Josephine LoRicco, Philippe Oger, Judith Peters, Bruno Deme
Summary: Protomembranes at the origin of life may have been composed of readily available short-chain lipids. A new membrane architecture was proposed to validate this assumption due to the less stability and higher permeability of membranes formed by such lipids. In this study, we investigated the incorporation of alkanes into membranes formed by the short-chain phospholipid 1,2-didecanoyl-sn-glycero-3-phophocholine, and found strong indications for the incorporation of two of the three alkanes in the membrane mid-plane.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2023)
Article
Multidisciplinary Sciences
Aleksi Sutinen, Dirk Paffenholz, Giang Thi Tuyet Nguyen, Salla Ruskamo, Andrew E. Torda, Petri Kursula
Summary: Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral polyneuropathy in humans, and its subtypes are linked to mutations in dozens of different genes, including the gene coding for ganglioside-induced differentiation-associated protein 1 (GDAP1). The etiology of GDAP1-linked CMT is poorly understood at the protein level, despite implications for mitochondrial fission and fusion, cytoskeletal interactions, and response to reactive oxygen species. Structural and biophysical analyses on several CMT-linked GDAP1 protein variants have been carried out, and new crystal structures of these variants have been described.
Article
Biochemistry & Molecular Biology
Loreto Misuraca, Roland Winter, Bruno Deme, Philippe M. Oger, Judith Peters
Summary: Lipid membranes play a vital role in living systems and the origin of life. This study investigated the mesophase structure and fluidity of protomembranes formed by ancient lipids. The results showed that these prebiotic model membranes exhibited stable vesicular structures and fluid-like lipid dynamic properties at low temperatures, but formed micellar structures at high temperatures.
Article
Biochemistry & Molecular Biology
Dorothee Houry, Arne Raasakka, Eugenio Ferrario, Marc Niere, Ersilia Bifulco, Petri Kursula, Mathias Ziegler
Summary: In this study, the mechanism of increased substrate affinity of phosphorylated NAMPT is revealed, which includes the coordination of Mg2+ by phospho-His247 to stabilize PRPP in a position favorable for catalysis. Additionally, a stretch of 10 amino acids found only in NAMPTs from deuterostomes is shown to enhance conformational plasticity and stabilize the chemically unstable phosphorylation of His247. Overall, this study provides a structural basis for the important function of NAMPT in recycling Nicotinamide into NAD biosynthesis with high affinity.
JOURNAL OF STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Oda C. Krokengen, Arne Raasakka, Petri Kursula
Summary: Numerous human proteins, known as intrinsically disordered proteins (IDPs), lack high-resolution structural information due to their physicochemical properties. However, IDPs can adopt local ordered structures upon interaction with other proteins or lipid membranes. Using AlphaFold2 predictions and experimental data, we have found that the predicted models of two myelin-specific IDPs closely match their membrane-binding sites. These artificial intelligence-based models provide insight into the ligand-bound state of IDPs and are crucial for understanding the role of IDPs in diseases.
BIOCHEMISTRY AND BIOPHYSICS REPORTS
(2023)
Article
Chemistry, Physical
Josephine G. LoRicco, Ingo Hoffmann, Antonino Calio, Judith Peters
Summary: In this study, the effect of apolar lipid squalane on the dynamics of an archaeal-like membrane under pressure was explored using neutron spin echo spectroscopy. It was found that increasing pressure resulted in a stiffer membrane, and the presence of squalane further increased its rigidity, suggesting its role as a membrane regulator.
Article
Chemistry, Physical
Johal Ruiz, Josephine G. LoRicco, Laurent Soulere, Marta Salvador Castell, Axelle Grelard, Brice Kauffmann, Erick J. Dufourc, Bruno Deme, Florence Popowycz, Judith Peters
Summary: Archaeal membrane lipids have unique structures that enable them to withstand extreme temperature and pressure conditions. A study on the synthesis of an archaeal lipid called 1,2-di-O-phytanyl-sn-glycero-3-phosphoinositol (DoPhPI) derived from myo-inositol reveals its resistance mechanisms. The experiments show that DoPhPI and DoPhPC can form small vesicles in aqueous dispersions, and these dispersions undergo phase transitions from lamellar to cubic and hexagonal phases with increasing temperature. The phytanyl chains in the lipid also contribute to the bilayer's dynamic properties over a wide temperature range. These findings suggest that the unique properties of archaeal lipids provide plasticity and aid in resisting extreme conditions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Loreto Misuraca, Tatsuhito Matsuo, Aline Cisse, Josephine LoRicco, Antonio Calio, Jean-Marc Zanotti, Bruno Deme, Philippe Oger, Judith Peters
Summary: Modern phospholipid membranes are only functional under precise external conditions, and similar principles likely applied to proto-membranes at the origin of life.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
