Hydration Water Drives the Self-assembly of Guanosine Monophosphate
We present the temperature-dependent terahertz (1.5-12 THz, 50-400 cm-1) absorptivity spectra of aqueous Na2GMP solution (GMP) in comparison with the aqueous solutions of other RNA nucleotides. Distinct absorption features were observed in the spectrum of GMP, which we attribute to the intramolecular modes of the self-assemblies (i.e., G-complexes) that, at 1 M, start to form at 313 K and below. Changes in broad band features of the terahertz spectrum were also observed, which we associate with the release of hydration water in the temperature-dependent formation of G-quadruplex (G4). Using a state-of-the-art THz calorimet...
Source: Biophysical Journal - March 8, 2024 Category: Physics Authors: Yu Heng Tao Simon Schulke Gerhard Schwaab Gareth L Nealon Simone Pezzotti Stuart I Hodgetts Alan R Harvey Vincent P Wallace Martina Havenith Source Type: research
Interplay between environmental yielding and dynamic forcing modulates bacterial growth
Biophys J. 2024 Mar 7:S0006-3495(24)00173-5. doi: 10.1016/j.bpj.2024.03.008. Online ahead of print.ABSTRACTMany bacterial habitats-ranging from gels and tissues in the body to cell-secreted exopolysaccharides in biofilms-are rheologically complex, undergo dynamic external forcing, and have unevenly-distributed nutrients. How do these features jointly influence how the resident cells grow and proliferate? Here, we address this question by studying the growth of Escherichia coli dispersed in granular hydrogel matrices with defined and highly-tunable structural and rheological properties, under different amounts of external f...
Source: Biophysical Journal - March 8, 2024 Category: Physics Authors: Anna M Hancock Sujit S Datta Source Type: research
How and When to Measure Mitochondrial Inner Membrane Potentials
Biophys J. 2024 Mar 6:S0006-3495(24)00176-0. doi: 10.1016/j.bpj.2024.03.011. Online ahead of print.ABSTRACTThe scientific literature on mitochondria has increased significantly over the years, due to findings that these organelles have widespread roles in the onset and progression of pathological conditions such as metabolic disorders, neurodegenerative and cardiovascular diseases, inflammation, and cancer. Researchers have extensively explored how mitochondrial properties and functions are modified in different models, often using fluorescent inner mitochondrial membrane potential (ΔΨm) probes to assess functional mitoc...
Source: Biophysical Journal - March 8, 2024 Category: Physics Authors: Alicia J Kowaltowski Fernando Abdulkader Source Type: research
Hydration Water Drives the Self-assembly of Guanosine Monophosphate
We present the temperature-dependent terahertz (1.5-12 THz, 50-400 cm-1) absorptivity spectra of aqueous Na2GMP solution (GMP) in comparison with the aqueous solutions of other RNA nucleotides. Distinct absorption features were observed in the spectrum of GMP, which we attribute to the intramolecular modes of the self-assemblies (i.e., G-complexes) that, at 1 M, start to form at 313 K and below. Changes in broad band features of the terahertz spectrum were also observed, which we associate with the release of hydration water in the temperature-dependent formation of G-quadruplex (G4). Using a state-of-the-art THz calorimet...
Source: Biophysical Journal - March 8, 2024 Category: Physics Authors: Yu Heng Tao Simon Schulke Gerhard Schwaab Gareth L Nealon Simone Pezzotti Stuart I Hodgetts Alan R Harvey Vincent P Wallace Martina Havenith Source Type: research
Interplay between environmental yielding and dynamic forcing modulates bacterial growth
Biophys J. 2024 Mar 7:S0006-3495(24)00173-5. doi: 10.1016/j.bpj.2024.03.008. Online ahead of print.ABSTRACTMany bacterial habitats-ranging from gels and tissues in the body to cell-secreted exopolysaccharides in biofilms-are rheologically complex, undergo dynamic external forcing, and have unevenly-distributed nutrients. How do these features jointly influence how the resident cells grow and proliferate? Here, we address this question by studying the growth of Escherichia coli dispersed in granular hydrogel matrices with defined and highly-tunable structural and rheological properties, under different amounts of external f...
Source: Biophysical Journal - March 8, 2024 Category: Physics Authors: Anna M Hancock Sujit S Datta Source Type: research
Mechanical control of cell proliferation patterns in growing epithelial monolayers
Biophys J. 2024 Mar 6:S0006-3495(24)00167-X. doi: 10.1016/j.bpj.2024.03.002. Online ahead of print.ABSTRACTCell proliferation plays a crucial role in regulating tissue homeostasis and development. However, our understanding of how cell proliferation is controlled in densely packed tissues is limited. Here we develop a computational framework to predict the patterns of cell proliferation in growing epithelial tissues, connecting single-cell behaviors and cell-cell interactions to tissue-level growth. Our model incorporates probabilistic rules governing cell growth, division, and elimination, while also taking into account t...
Source: Biophysical Journal - March 7, 2024 Category: Physics Authors: Logan C Carpenter Fernanda P érez-Verdugo Shiladitya Banerjee Source Type: research
Negative lipid membranes enhance the adsorption of TAT-decorated elastin-like polypeptides micelles
Biophys J. 2024 Mar 5:S0006-3495(24)00166-8. doi: 10.1016/j.bpj.2024.03.001. Online ahead of print.ABSTRACTA cell penetrating peptide (CPP) is a short amino-acid sequence capable of efficiently translocating across the cellular membrane of mammalian cells. However, the potential of CPPs as a delivery vector is hampered by the strong reduction of its translocation efficiency when it bears an attached molecular cargo. To overcome this problem, we used previously developed diblock copolymers of elastin-like polypeptides (ELPBC), which we end-functionalized with TAT, an archetypal CPP built from a positively charged amino acid...
Source: Biophysical Journal - March 7, 2024 Category: Physics Authors: Vivien Walter Tatiana Schmatko Pierre Muller Andr é P Schroder Sarah R MacEwan Ashutosh Chilkoti Carlos M Marques Source Type: research
Dynamic temperature control in microfluidics for in vivo imaging of cold-sensing in C. elegans
Biophys J. 2024 Mar 5:S0006-3495(24)00172-3. doi: 10.1016/j.bpj.2024.03.007. Online ahead of print.ABSTRACTThe ability to perceive temperature is crucial for most animals. It enables them to maintain their body temperature and swiftly react to noxiously cold or hot objects. Caenorhabditis elegans is a powerful genetic model for the study of thermosensation as its simple nervous system is well-characterized and its transparent body is suited for in vivo functional imaging of neurons. The behavior triggered by experience-dependent thermosensation has been well studied in C. elegans under temperature gradient environments. Ho...
Source: Biophysical Journal - March 7, 2024 Category: Physics Authors: Sol Ah Lee Yongmin Cho William R Schafer Hang Lu Source Type: research
Interaction with stomatin directs human proton channels into cholesterol dependent membrane domains
Biophys J. 2024 Mar 4:S0006-3495(24)00168-1. doi: 10.1016/j.bpj.2024.03.003. Online ahead of print.ABSTRACTMany membrane proteins are modulated by cholesterol. Here we report profound effects of cholesterol depletion and restoration on the human voltage gated proton channel, hHV1, in excised patches, but with negligible effects in the whole-cell configuration. Despite the presence of a putative cholesterol binding site, a CARC motif in hHV1, mutation of this motif did not affect cholesterol effects. The murine HV1 lacks a CARC sequence but displays similar cholesterol effects. These results argue against a direct effect of...
Source: Biophysical Journal - March 6, 2024 Category: Physics Authors: Artem G Ayuyan Vladimir V Cherny Gustavo Chaves Boris Musset Fredric S Cohen Thomas E DeCoursey Source Type: research
Calculation of solvation force in molecular dynamics simulation by deep learning method
In this study, we developed a deep neural network to predict the decomposed solvation free energies and forces of all atoms in a molecule. To train the network, the internal coordinates of the molecule were used as the input data, and the solvation free energies along with transformed atomic forces from the Poisson-Boltzmann equation were used as labels. Both the training and prediction tasks were accelerated on GPU. Formal tests demonstrated that our method can provide reasonable predictions for small molecules when the network is well-trained with its simulation data. This method is suitable for processing lots of snapsh...
Source: Biophysical Journal - March 6, 2024 Category: Physics Authors: Jun Liao Mincong Wu Junyong Gao Changjun Chen Source Type: research
Distinct Potassium Channel Types in Brain Capillary Pericytes
Biophys J. 2024 Mar 4:S0006-3495(24)00169-3. doi: 10.1016/j.bpj.2024.03.004. Online ahead of print.ABSTRACTCapillaries, composed of electrically coupled endothelial cells and overlying pericytes, constitute the vast majority of blood vessels in the brain. The most arteriole-proximate three to four branches of the capillary bed are covered by alpha actin-expressing, contractile pericytes. These mural cells have a distinctive morphology and express different markers compared with their smooth muscle cell (SMC) cousins but share similar excitation-coupling contraction machinery. Despite this similarity, pericytes are consider...
Source: Biophysical Journal - March 6, 2024 Category: Physics Authors: Maria Sancho Nicholas R Klug Osama F Harraz David Hill-Eubanks Mark T Nelson Source Type: research
Interaction with stomatin directs human proton channels into cholesterol dependent membrane domains
Biophys J. 2024 Mar 4:S0006-3495(24)00168-1. doi: 10.1016/j.bpj.2024.03.003. Online ahead of print.ABSTRACTMany membrane proteins are modulated by cholesterol. Here we report profound effects of cholesterol depletion and restoration on the human voltage gated proton channel, hHV1, in excised patches, but with negligible effects in the whole-cell configuration. Despite the presence of a putative cholesterol binding site, a CARC motif in hHV1, mutation of this motif did not affect cholesterol effects. The murine HV1 lacks a CARC sequence but displays similar cholesterol effects. These results argue against a direct effect of...
Source: Biophysical Journal - March 6, 2024 Category: Physics Authors: Artem G Ayuyan Vladimir V Cherny Gustavo Chaves Boris Musset Fredric S Cohen Thomas E DeCoursey Source Type: research
Calculation of solvation force in molecular dynamics simulation by deep learning method
In this study, we developed a deep neural network to predict the decomposed solvation free energies and forces of all atoms in a molecule. To train the network, the internal coordinates of the molecule were used as the input data, and the solvation free energies along with transformed atomic forces from the Poisson-Boltzmann equation were used as labels. Both the training and prediction tasks were accelerated on GPU. Formal tests demonstrated that our method can provide reasonable predictions for small molecules when the network is well-trained with its simulation data. This method is suitable for processing lots of snapsh...
Source: Biophysical Journal - March 6, 2024 Category: Physics Authors: Jun Liao Mincong Wu Junyong Gao Changjun Chen Source Type: research
Distinct Potassium Channel Types in Brain Capillary Pericytes
Biophys J. 2024 Mar 4:S0006-3495(24)00169-3. doi: 10.1016/j.bpj.2024.03.004. Online ahead of print.ABSTRACTCapillaries, composed of electrically coupled endothelial cells and overlying pericytes, constitute the vast majority of blood vessels in the brain. The most arteriole-proximate three to four branches of the capillary bed are covered by alpha actin-expressing, contractile pericytes. These mural cells have a distinctive morphology and express different markers compared with their smooth muscle cell (SMC) cousins but share similar excitation-coupling contraction machinery. Despite this similarity, pericytes are consider...
Source: Biophysical Journal - March 6, 2024 Category: Physics Authors: Maria Sancho Nicholas R Klug Osama F Harraz David Hill-Eubanks Mark T Nelson Source Type: research
TRPV4-dependent Ca < sup > 2+ < /sup > influx determines cholesterol dynamics at the plasma membrane
Biophys J. 2024 Mar 2:S0006-3495(24)00164-4. doi: 10.1016/j.bpj.2024.02.030. Online ahead of print.ABSTRACTThe activities of the transient receptor potential vanilloid 4 (TRPV4), a Ca2+-permeable non-selective cation channel, are controlled by its surrounding membrane lipids (e.g., cholesterol, phosphoinositides). The transmembrane region of TRPV4 contains a cholesterol recognition amino acid consensus (CRAC) motif and its inverted (CARC) motif located in the plasmalemmal cytosolic leaflet. TRPV4 localizes in caveolae, a bulb-shaped cholesterol-rich domain at the plasma membrane. Here, we visualized the spatiotemporal inte...
Source: Biophysical Journal - March 4, 2024 Category: Physics Authors: Yutaro Kuwashima Masataka Yanagawa Masashi Maekawa Mitsuhiro Abe Yasushi Sako Makoto Arita Source Type: research
