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Optimizing properties of translocation-enhancing transmembrane proteins Biophys. J. (IF 3.4) Pub Date : 2024-04-13 Ladislav Bartoš, Martina Drabinová, Robert Vácha
Cell membranes act as semi-permeable barriers, often restricting the entry of large or hydrophilic molecules. Nonetheless, certain amphiphilic molecules, such as antimicrobial and cell-penetrating peptides, can cross these barriers. In this study, we demonstrate that specific properties of transmembrane proteins/peptides can enhance membrane permeation of amphiphilic peptides. Using coarse-grained
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Nuclear curvature determines Yes-associated protein nuclear localization and differentiation of mesenchymal stem cells Biophys. J. (IF 3.4) Pub Date : 2024-04-10 Ajinkya Ghagre, Alice Delarue, Luv Kishore Srivastava, Newsha Koushki, Allen Ehrlicher
Controlling mesenchymal stem cell (MSC) differentiation remains a critical challenge in MSCs’ therapeutic application. Numerous biophysical and mechanical stimuli influence stem cell fate; however, their relative efficacy and specificity in mechanically directed differentiation remain unclear. Yes-associated protein (YAP) is one key mechanosensitive protein that controls MSC differentiation. Previous
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A molecular switch in RCK2 triggers sodium-dependent activation of KNa1.1 (KCNT1) potassium channels Biophys. J. (IF 3.4) Pub Date : 2024-04-10 Bethan A. Cole, Antreas C. Kalli, Nadia Pilati, Stephen P. Muench, Jonathan D. Lippiat
The Na-activated K channel K1.1, encoded by the gene, is an important regulator of neuronal excitability. How intracellular Na ions bind and increase channel activity is not well understood. Analysis of K1.1 channel structures indicate that there is a large twisting of the βN-αQ loop in the intracellular RCK2 domain between the inactive and Na-activated conformations, with a lysine (K885, human subunit
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Enhancing micropipette aspiration with artificial-intelligence analysis Biophys. J. (IF 3.4) Pub Date : 2024-04-10 Aldo Abarca-Ortega, Blanca González-Bermúdez, Gustavo R. Plaza
The micropipette-aspiration technique is commonly used in the field of mechanobiology, offering a variety of measurement types. To extract biophysical parameters from the experiments, numerical analysis is required. Although previous works have developed techniques for the partial automation of these analyses, these approaches are relatively time consuming for the researchers. In this article, we describe
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Solving stochastic gene-expression models using queueing theory: A tutorial review Biophys. J. (IF 3.4) Pub Date : 2024-04-09 Juraj Szavits-Nossan, Ramon Grima
Stochastic models of gene expression are typically formulated using the chemical master equation, which can be solved exactly or approximately using a repertoire of analytical methods. Here, we provide a tutorial review of an alternative approach based on queueing theory that has rarely been used in the literature of gene expression. We discuss the interpretation of six types of infinite-server queues
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How much does TRPV1 deviate from an ideal MWC-type protein? Biophys. J. (IF 3.4) Pub Date : 2024-04-06 Shisheng Li, Jie Zheng
Many ion channels are known to behave as an allosteric protein, coupling environmental stimuli captured by specialized sensing domains to the opening of a central pore. The classic Monod-Wyman-Changeux (MWC) model, originally proposed to describe binding of gas molecules to hemoglobin, has been widely used as a framework for analyzing ion channel gating. Here, we address the issue of how accurately
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AI in cellular engineering and reprogramming Biophys. J. (IF 3.4) Pub Date : 2024-04-04 Sara Capponi, Shangying Wang
During the last decade, artificial intelligence (AI) has increasingly been applied in biophysics and related fields, including cellular engineering and reprogramming, offering novel approaches to understand, manipulate, and control cellular function. The potential of AI lies in its ability to analyze complex datasets and generate predictive models. AI algorithms can process large amounts of data from
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Base pair dynamics, electrostatics, and thermodynamics at the LTR-III quadruplex:duplex junction Biophys. J. (IF 3.4) Pub Date : 2024-04-04 Haley M. Michel, Justin A. Lemkul
G-quadruplexes (GQs) play key regulatory roles within the human genome and have also been identified to play similar roles in other eukaryotes, bacteria, archaea, and viruses. Human immunodeficiency virus 1, the etiological agent of acquired immunodeficiency syndrome, can form two GQs in its long terminal repeat (LTR) promoter region, each of which act to regulate viral gene expression in opposing
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Robust spatiotemporal organization of mitotic events in mechanically perturbed C. elegans embryos Biophys. J. (IF 3.4) Pub Date : 2024-04-04 Vincent Borne, Matthias Weiss
Early embryogenesis of the nematode progresses in an autonomous fashion within a protective chitin eggshell. Cell-division timing and the subsequent mechanically guided positioning of cells is virtually invariant between individuals, especially before gastrulation. Here, we have challenged this stereotypical developmental program in early stages by mechanically perturbing the embryo without breaking
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Energy landscapes of homopolymeric RNAs revealed by deep unsupervised learning Biophys. J. (IF 3.4) Pub Date : 2024-04-03 Vysakh Ramachandran, Davit A. Potoyan
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The rotamer of the second-sphere histidine in AA9 lytic polysaccharide monooxygenase is pH dependent Biophys. J. (IF 3.4) Pub Date : 2024-04-02 Ingvild Isaksen, Suvamay Jana, Christina M. Payne, Bastien Bissaro, Åsmund K. Røhr
Lytic polysaccharide monooxygenases (LPMOs) catalyze a reaction that is crucial for the biological decomposition of various biopolymers and for the industrial conversion of plant biomass. Despite the importance of LPMOs, the exact molecular-level nature of the reaction mechanism is still debated today. Here, we investigated the pH-dependent conformation of a second-sphere histidine (His) that we call
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Contribution of different macromolecules to the diffusion of a 40 nm particle in Escherichia coli Biophys. J. (IF 3.4) Pub Date : 2024-03-29 José Losa, Matthias Heinemann
Due to the high concentration of proteins, nucleic acids, and other macromolecules, the bacterial cytoplasm is typically described as a crowded environment. However, the extent to which each of these macromolecules individually affects the mobility of macromolecular complexes, and how this depends on growth conditions, is presently unclear. In this study, we sought to quantify the crowding experienced
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An atomistic characterization of high-density lipoproteins and the conserved “LN” region of apoA-I Biophys. J. (IF 3.4) Pub Date : 2024-03-29 Chris J. Malajczuk, Ricardo L. Mancera
The physicochemical characteristics of the various subpopulations of high-density lipoproteins (HDLs) and, in particular, their surface properties determine their ability to scavenge lipids and interact with specific receptors and peptides. Five representative spheroidal HDL subpopulation models were mapped from a previously reported equilibrated coarse-grained (CG) description to an atomistic representation
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Dynamic conformational changes of acid-sensing ion channels in different desensitizing conditions Biophys. J. (IF 3.4) Pub Date : 2024-03-28 Caroline Marcher Holm, Asli B. Topaktas, Johs Dannesboe, Stephan A. Pless, Stephanie A. Heusser
Acid-sensing ion channels (ASICs) are proton-gated cation channels that contribute to fast synaptic transmission and have roles in fear conditioning and nociception. Apart from activation at low pH, ASIC1a also undergoes several types of desensitization, including acute desensitization, which terminates activation; steady-state desensitization, which occurs at sub-activating proton concentrations and
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The role of shear rates on amyloid formation from biofilm peptide phenol-soluble modulins Biophys. J. (IF 3.4) Pub Date : 2024-03-28 Runyao Zhu, Trevor Stone Jr., Yichun Wang
Biofilms, microbial communities enclosed in the self-produced extracellular matrix, have a significant impact on human health, environment, and industry. The pathogen is recognized as one of the most frequent causes of biofilm-related infections. Phenol-soluble modulins (PSMs) serve as a crucial component, fortifying biofilm matrix through self-assembly into amyloid fibrils, which enhances colonization
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Kinetic network modeling with molecular simulation inputs: A proton-coupled phosphate symporter Biophys. J. (IF 3.4) Pub Date : 2024-03-28 Yu Liu, Chenghan Li, Meghna Gupta, Robert M. Stroud, Gregory A. Voth
Phosphate, an essential metabolite involved in numerous cellular functions, is taken up by proton-coupled phosphate transporters of plants and fungi within the major facilitator family. Similar phosphate transporters have been identified across a diverse range of biological entities, including various protozoan parasites linked to human diseases, breast cancer cells with increased phosphate requirements
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Particle-based simulations shed light on cytoskeleton-membrane dynamics in phagocytosis Biophys. J. (IF 3.4) Pub Date : 2024-03-28 Emmet A. Francis, Padmini Rangamani
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Juggling potassium: A diverse set of K+ channels tune excitability of brain’s capillary pericytes Biophys. J. (IF 3.4) Pub Date : 2024-03-27 Zhihui Fong, L. Fernando Santana
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Single-cell mechanical assay unveils viscoelastic similarities in normal and neoplastic brain cells Biophys. J. (IF 3.4) Pub Date : 2024-03-27 Killian Onwudiwe, Julian Najera, Luke Holen, Alice A. Burchett, Dorielis Rodriguez, Maksym Zarodniuk, Saeed Siri, Meenal Datta
Understanding cancer cell mechanics allows for the identification of novel disease mechanisms, diagnostic biomarkers, and targeted therapies. In this study, we utilized our previously established fluid shear stress assay to investigate and compare the viscoelastic properties of normal immortalized human astrocytes and invasive human glioblastoma (GBM) cells when subjected to physiological levels of
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Molecular mechanisms of Na+-driven bile acid transport in human NTCP Biophys. J. (IF 3.4) Pub Date : 2024-03-27 Xiaoli Lu, Jing Huang
Human Na taurocholate co-transporting protein (hNTCP) is a key bile salt transporter to maintain enterohepatic circulation and is responsible for the recognition of hepatitis B and D viruses. Despite landmark cryoelectron microscopy studies revealing open-pore and inward-facing states of hNTCP stabilized by antibodies, the transport mechanism remains largely unknown. To address this knowledge gap,
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Quantifying single-cell diacylglycerol signaling kinetics after uncaging Biophys. J. (IF 3.4) Pub Date : 2024-03-27 David T. Gonzales, Milena Schuhmacher, H. Mathilda Lennartz, Juan M. Iglesias-Artola, Sascha M. Kuhn, Pavel Barahtjan, Christoph Zechner, Andre Nadler
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Small-angle x-ray scattering investigation of the integration of free fatty acids in polysorbate 20 micelles Biophys. J. (IF 3.4) Pub Date : 2024-03-27 Jörg Ehrit, Tobias W. Gräwert, Hendrik Göddeke, Petr V. Konarev, Dmitri I. Svergun, Norbert Nagel
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Increased vesicular dynamics and nanoscale clustering of IL-2 after T cell activation Biophys. J. (IF 3.4) Pub Date : 2024-03-26 Badeia Saed, Neal T. Ramseier, Thilini Perera, Jesse Anderson, Jacob Burnett, Hirushi Gunasekara, Alyssa Burgess, Haoran Jing, Ying S. Hu
T cells coordinate intercellular communication through the meticulous regulation of cytokine secretion. Direct visualization of vesicular transport and intracellular distribution of cytokines provides valuable insights into the temporal and spatial mechanisms involved in regulation. Employing Jurkat E6-1 T cells and interleukin-2 (IL-2) as a model system, we investigated vesicular dynamics using single-particle
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Mechanical strengthening of cell-cell adhesion during mouse embryo compaction Biophys. J. (IF 3.4) Pub Date : 2024-03-26 Ludmilla de Plater, Julie Firmin, Jean-Léon Maître
Compaction is the first morphogenetic movement of the eutherian mammals and involves a developmentally regulated adhesion process. Previous studies investigated cellular and mechanical aspects of compaction. During mouse and human compaction, cells spread onto each other as a result of a contractility-mediated increase in surface tension pulling at the edges of their cell-cell contacts. However, how
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Two-component macrophage model for active phagocytosis with pseudopod formation Biophys. J. (IF 3.4) Pub Date : 2024-03-25 Shuo Wang, Shuhao Ma, He Li, Ming Dao, Xuejin Li, George Em Karniadakis
Macrophage phagocytosis is critical for the immune response, homeostasis regulation, and tissue repair. This intricate process involves complex changes in cell morphology, cytoskeletal reorganization, and various receptor-ligand interactions controlled by mechanical constraints. However, there is a lack of comprehensive theoretical and computational models that investigate the mechanical process of
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Trade-offs in concentration sensing in dynamic environments Biophys. J. (IF 3.4) Pub Date : 2024-03-25 Aparajita Kashyap, Wei Wang (汪巍), Brian A. Camley
When cells measure concentrations of chemical signals, they may average multiple measurements over time in order to reduce noise in their measurements. However, when cells are in an environment that changes over time, past measurements may not reflect current conditions—creating a new source of error that trades off against noise in chemical sensing. What statistics in the cell’s environment control
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ATOMDANCE: Kernel-based denoising and choreographic analysis for protein dynamic comparison Biophys. J. (IF 3.4) Pub Date : 2024-03-21 Gregory A. Babbitt, Madhusudan Rajendran, Miranda L. Lynch, Richmond Asare-Bediako, Leora T. Mouli, Cameron J. Ryan, Harsh Srivastava, Patrick Rynkiewicz, Kavya Phadke, Makayla L. Reed, Nadia Moore, Maureen C. Ferran, Ernest P. Fokoue
Comparative methods in molecular evolution and structural biology rely heavily upon the site-wise analysis of DNA sequence and protein structure, both static forms of information. However, it is widely accepted that protein function results from nanoscale nonrandom machine-like motions induced by evolutionarily conserved molecular interactions. Comparisons of molecular dynamics (MD) simulations conducted
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Data-driven classification of individual cells by their non-Markovian motion Biophys. J. (IF 3.4) Pub Date : 2024-03-21 Anton Klimek, Debasmita Mondal, Stephan Block, Prerna Sharma, Roland R. Netz
We present a method to differentiate organisms solely by their motion based on the generalized Langevin equation (GLE) and use it to distinguish two different swimming modes of strongly confined unicellular microalgae . The GLE is a general model for active or passive motion of organisms and particles that can be derived from a time-dependent general many-body Hamiltonian and in particular includes
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Self-organization of PIP3 waves is controlled by the topology and curvature of cell membranes Biophys. J. (IF 3.4) Pub Date : 2024-03-21 Sema Erisis, Marcel Hörning
Phosphatidylinositol (3,4,5)-trisphosphate (PIP3) is a signaling lipid on the plasma membrane that plays a fundamental role in cell signaling with a strong impact on cell physiology and diseases. It is responsible for the protruding edge formation, cell polarization, macropinocytosis, and other membrane remodeling dynamics in cells. It has been shown that the membrane confinement and curvature affects
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Tipping points in epithelial-mesenchymal lineages from single-cell transcriptomics data Biophys. J. (IF 3.4) Pub Date : 2024-03-19 Manuel Barcenas, Federico Bocci, Qing Nie
Understanding cell fate decision-making during complex biological processes is an open challenge that is now aided by high-resolution single-cell sequencing technologies. Specifically, it remains challenging to identify and characterize transition states corresponding to “tipping points” whereby cells commit to new cell states. Here, we present a computational method that takes advantage of single-cell
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Testing the feasibility of targeting a conserved region on the S2 domain of the SARS-CoV-2 spike protein Biophys. J. (IF 3.4) Pub Date : 2024-03-16 Pranav Garg, Shawn C.C. Hsueh, Steven S. Plotkin
The efficacy of vaccines against the SARS-CoV-2 virus significantly declines with the emergence of mutant strains, prompting investigation into the feasibility of targeting highly conserved but often cryptic regions on the S2 domain of spike protein. Using tools from molecular dynamics, we find that exposure of a conserved S2 epitope located in the central helices below the receptor binding domains
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Governing principles of transcriptional logic out of equilibrium Biophys. J. (IF 3.4) Pub Date : 2024-03-14 Smruti Dixit, Teije C. Middelkoop, Sandeep Choubey
To survive, adapt, and develop, cells respond to external and internal stimuli by tightly regulating transcription. Transcriptional regulation involves the combinatorial binding of a repertoire of transcription factors to DNA, which often results in switch-like binary outputs akin to Boolean logic gates. Recent experimental studies have demonstrated that in eukaryotes, transcription factor binding
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Bending of a lipid membrane edge by annexin A5 trimers Biophys. J. (IF 3.4) Pub Date : 2024-03-14 Mayank Prakash Pandey, Paulo Cesar Telles de Souza, Weria Pezeshkian, Himanshu Khandelia
Plasma membrane damage occurs in healthy cells and more frequently in cancer cells where high growth rates and metastasis result in frequent membrane damage. The annexin family of proteins plays a key role in membrane repair. Annexins are recruited at the membrane injury site by Ca and repair the damaged membrane in concert with several other proteins. Annexin A4 (ANXA4) and ANXA5 form trimers at the
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Calculation of protein-ligand binding entropies using a rule-based molecular fingerprint Biophys. J. (IF 3.4) Pub Date : 2024-03-13 Ali Risheh, Alles Rebel, Paul S. Nerenberg, Negin Forouzesh
The use of fast in silico prediction methods for protein-ligand binding free energies holds significant promise for the initial phases of drug development. Numerous traditional physics-based models (e.g., implicit solvent models), however, tend to either neglect or heavily approximate entropic contributions to binding due to their computational complexity. Consequently, such methods often yield imprecise
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A hydrophobic nexus at the heart of hERG K channel gating Biophys. J. (IF 3.4) Pub Date : 2024-03-12 Matthew C. Trudeau
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Lipid droplets as substrates for protein phase separation Biophys. J. (IF 3.4) Pub Date : 2024-03-11 Advika Kamatar, Jack P.K. Bravo, Feng Yuan, Liping Wang, Eileen M. Lafer, David W. Taylor, Jeanne C. Stachowiak, Sapun H. Parekh
Membrane-associated protein phase separation plays critical roles in cell biology, driving essential cellular phenomena from immune signaling to membrane traffic. Importantly, by reducing dimensionality from three to two dimensions, lipid bilayers can nucleate phase separation at far lower concentrations compared with those required for phase separation in solution. How might other intracellular lipid
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Investigating the ERG a-wave and Retinal Diseases with Rod Equivalent Circuit Model Based on the APD Biophys. J. (IF 3.4) Pub Date : 2024-03-11 Qing-an Ding, Chunyan Liu, Fangfang Ning, Xiaoyuan Li, Binghui Hou, Yuhua Gao, Jianyu Li, Chaoran Gu
Most empirically supported mathematical models of rod cells lack theoretical support from actual physical devices. Therefore, this paper proposes an equivalent circuit model for the rod is proposed based on the photoconductive properties of the avalanche photodetector (APD) and combined with the electrical properties of the rod. The model employs the photodetector to simulate the source of the photocurrent
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The open channel state in anion channelrhodopsin GtACR1 is a red-absorbing intermediate Biophys. J. (IF 3.4) Pub Date : 2024-03-11 Istvan Szundi, David S. Kliger
Anion channelrhodopsin ACR1 is a powerful optogenetic tool to inhibit nerve activity. Its kinetic mechanism was interpreted in terms of the bacteriorhodopsin photocycle, and the L intermediate was assigned to the open channel state. Here, we report the results of the comparison between the time dependence of the channel currents and the time evolutions of the K-like and L-like spectral forms. Based
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Taking mechanomicrobiology from local to global Biophys. J. (IF 3.4) Pub Date : 2024-03-10 W.R. Harcombe
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The ATPase asymmetry: Novel computational insight into coupling diverse FO motors with tripartite F1 Biophys. J. (IF 3.4) Pub Date : 2024-03-08 Shintaroh Kubo, Yasushi Okada
ATP synthase, a crucial enzyme for cellular bioenergetics, operates via the coordinated coupling of an F motor, which presents variable symmetry, and a tripartite F motor. Despite extensive research, the understanding of their coupling dynamics, especially with non-10-fold symmetrical F motors, remains incomplete. This study investigates the coupling patterns between eightfold and ninefold F motors
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Coupling of zinc and GTP binding drives G-domain folding in Acinetobacter baumannii ZigA Biophys. J. (IF 3.4) Pub Date : 2024-03-08 Maximillian K. Osterberg, Ally K. Smith, Courtney Campbell, Daniel J. Deredge, Timothy L. Stemmler, David P. Giedroc
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Mitigating transcription noise via protein sharing in syncytial cells Biophys. J. (IF 3.4) Pub Date : 2024-03-08 Alex Mayer, Jiayu Li, Grace McLaughlin, Amy Gladfelter, Marcus Roper
Bursty transcription allows nuclei to concentrate the work of transcribing mRNA into short, intermittent intervals, potentially reducing transcriptional interference. However, bursts of mRNA production can increase noise in protein abundances. Here, we formulate models for gene expression in syncytia, or multinucleate cells, showing that protein abundance noise may be mitigated locally via spatial
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How and when to measure mitochondrial inner membrane potentials Biophys. J. (IF 3.4) Pub Date : 2024-03-07 Alicia J. Kowaltowski, Fernando Abdulkader
The 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
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Interplay between environmental yielding and dynamic forcing modulates bacterial growth Biophys. J. (IF 3.4) Pub Date : 2024-03-07 Anna M. Hancock, Sujit S. Datta
Many 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 dispersed in granular hydrogel matrices with
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Hydration water drives the self-assembly of guanosine monophosphate Biophys. J. (IF 3.4) Pub Date : 2024-03-07 Yu Heng Tao, Simon Schulke, Gerhard Schwaab, Gareth L. Nealon, Simone Pezzotti, Stuart I. Hodgetts, Alan R. Harvey, Martina Havenith, Vincent P. Wallace
Guanosine monophosphate (GMP) is a nucleotide that can self-assemble in aqueous solution under certain conditions. An understanding of the process at the molecular level is an essential step to comprehend the involvement of DNA substructures in transcription and replication, as well as their relationship to genetic diseases such as cancer. We present the temperature-dependent terahertz (1.5–12 THz
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Dynamic temperature control in microfluidics for in vivo imaging of cold-sensing in C. elegans Biophys. J. (IF 3.4) Pub Date : 2024-03-06 Sol Ah Lee, Yongmin Cho, William R. Schafer, Hang Lu
The 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. 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
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Mechanical control of cell proliferation patterns in growing epithelial monolayers Biophys. J. (IF 3.4) Pub Date : 2024-03-06 Logan C. Carpenter, Fernanda Pérez-Verdugo, Shiladitya Banerjee
Cell 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
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Distinct potassium channel types in brain capillary pericytes Biophys. J. (IF 3.4) Pub Date : 2024-03-05 Maria Sancho, Nicholas R. Klug, Osama F. Harraz, David Hill-Eubanks, Mark T. Nelson
Capillaries, 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 -actin-expressing, contractile pericytes. These mural cells have a distinctive morphology and express different markers compared with their smooth muscle cell (SMC)
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Interaction with stomatin directs human proton channels into cholesterol-dependent membrane domains Biophys. J. (IF 3.4) Pub Date : 2024-03-05 Artem G. Ayuyan, Vladimir V. Cherny, Gustavo Chaves, Boris Musset, Fredric S. Cohen, Thomas E. DeCoursey
Many membrane proteins are modulated by cholesterol. Here we report profound effects of cholesterol depletion and restoration on the human voltage-gated proton channel, hH1, in excised patches but negligible effects in the whole-cell configuration. Despite the presence of a putative cholesterol-binding site, a CARC motif in hH1, mutation of this motif did not affect cholesterol effects. The murine
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Negative lipid membranes enhance the adsorption of TAT-decorated elastin-like polypeptide micelles Biophys. J. (IF 3.4) Pub Date : 2024-03-05 Vivien Walter, Tatiana Schmatko, Pierre Muller, André P. Schroder, Sarah R. MacEwan, Ashutosh Chilkoti, Carlos M. Marques
A 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
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Calculation of solvation force in molecular dynamics simulation by deep-learning method Biophys. J. (IF 3.4) Pub Date : 2024-03-04 Jun Liao, Mincong Wu, Junyong Gao, Changjun Chen
Electrostatic calculations are generally used in studying the thermodynamics and kinetics of biomolecules in solvent. Generally, this is performed by solving the Poisson-Boltzmann equation on a large grid system, a process known to be time consuming. 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
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Binding equations for the lipid composition dependence of peripheral membrane-binding proteins Biophys. J. (IF 3.4) Pub Date : 2024-03-02 Daniel Kerr, Tiffany Suwatthee, Sofiya Maltseva, Ka Yee C. Lee
The specific recognition of peripheral membrane-binding proteins for their target membranes is mediated by a complex constellation of various lipid contacts. Despite the inherent complexities of the heterogeneous protein-membrane interface, the binding dependence of such proteins is, surprisingly, often reliably described by simple models such as the Langmuir Adsorption Isotherm or the Hill equation
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TRPV4-dependent Ca2+ influx determines cholesterol dynamics at the plasma membrane Biophys. J. (IF 3.4) Pub Date : 2024-03-02 Yutaro Kuwashima, Masataka Yanagawa, Masashi Maekawa, Mitsuhiro Abe, Yasushi Sako, Makoto Arita
The activities of the transient receptor potential vanilloid 4 (TRPV4), a Ca-permeable nonselective 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
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Dual mechanisms contribute to enhanced voltage dependence of an electric fish potassium channel Biophys. J. (IF 3.4) Pub Date : 2024-03-01 Jelena Todorovic, Immani Swapna, Antonio Suma, Vincenzo Carnevale, Harold Zakon
The voltage dependence of different voltage-gated potassium channels, described by the voltage at which half of the channels are open (V), varies over a range of 80 mV and is influenced by factors such as the number of positive gating charges and the identity of the hydrophobic amino acids in the channel’s voltage sensor (S4). Here we explore by experimental manipulations and molecular dynamics simulation
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Design of artificial molecular motor inheriting directionality and scalability Biophys. J. (IF 3.4) Pub Date : 2024-02-29 Kenta I. Ito, Yusuke Sato, Shoichi Toyabe
Realizing artificial molecular motors with autonomous functionality and high performance is a major challenge in biophysics. Such motors not only provide new perspectives in biotechnology but also offer a novel approach for the bottom-up elucidation of biological molecular motors. Directionality and scalability are critical factors for practical applications. However, the simultaneous realization of
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Morphodynamics of T-lymphocytes: Scanning to spreading Biophys. J. (IF 3.4) Pub Date : 2024-02-29 Kheya Sengupta, Pierre Dillard, Laurent Limozin
Binding of the T cell receptor complex to its ligand, the subsequent molecular rearrangement, and the concomitant cell-scale shape changes represent the very first steps of adaptive immune recognition. The first minutes of the interaction of T cells and antigen presenting cells have been extensively scrutinized; yet, gaps remain in our understanding of how the biophysical properties of the environment
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Real-time single-molecule imaging of CaMKII-calmodulin interactions Biophys. J. (IF 3.4) Pub Date : 2024-02-28 Shahid Khan, Justin E. Molloy, Henry Puhl, Howard Schulman, Steven S. Vogel
The binding of calcium/calmodulin (CAM) to calcium/calmodulin-dependent protein kinase II (CaMKII) initiates an ATP-driven cascade that triggers CaMKII autophosphorylation. The autophosphorylation in turn increases the CaMKII affinity for CAM. Here, we studied the ATP dependence of CAM association with the actin-binding CaMKIIβ isoform using single-molecule total internal reflection fluorescence microscopy
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Using a probabilistic approach to derive a two-phase model of flow-induced cell migration Biophys. J. (IF 3.4) Pub Date : 2024-02-28 Yaron Ben-Ami, Joe M. Pitt-Francis, Philip K. Maini, Helen M. Byrne
Interstitial fluid flow is a feature of many solid tumors. In vitro experiments have shown that such fluid flow can direct tumor cell movement upstream or downstream depending on the balance between the competing mechanisms of tensotaxis (cell migration up stress gradients) and autologous chemotaxis (downstream cell movement in response to flow-induced gradients of self-secreted chemoattractants).
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Identical sequences, different behaviors: Protein diversity captured at the single-molecule level Biophys. J. (IF 3.4) Pub Date : 2024-02-28 Rafael Tapia-Rojo, Alvaro Alonso-Caballero, Carmen L. Badilla, Julio M. Fernandez
The classical “one sequence, one structure, one function” paradigm has shaped much of our intuition of how proteins work inside the cell. Partially due to the insight provided by bulk biochemical assays, individual biomolecules are often assumed to behave as identical entities, and their characterization relies on ensemble averages that flatten any conformational diversity into a unique phenotype.
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Cells on a string: Characterizing cellular structure and dynamics through viscoelastic phenotyping Biophys. J. (IF 3.4) Pub Date : 2024-02-27 Dmitry A. Fedosov, Gerhard Gompper