-
Simulations predict preferred Mg2+ coordination in a nonenzymatic primer-extension reaction center Biophys. J. (IF 3.4) Pub Date : 2024-05-03 Shriyaa Mittal, Collin Nisler, Jack W. Szostak
The mechanism by which genetic information was copied prior to the evolution of ribozymes is of great interest because of its importance to the origin of life. The most effective known process for the nonenzymatic copying of an RNA template is primer extension by a two-step pathway in which 2-aminoimidazole-activated nucleotides first react with each other to form an imidazolium-bridged intermediate
-
A role for conformational changes in enzyme catalysis Biophys. J. (IF 3.4) Pub Date : 2024-05-03 Olivier Rivoire
The role played by conformational changes in enzyme catalysis is controversial. In addition to examining specific enzymes, studying formal models can help identify the conditions under which conformational changes promote catalysis. Here, we present a model demonstrating how conformational changes can break a generic trade-off due to the conflicting requirements of successive steps in catalytic cycles
-
OrganL: Dynamic triangulation of biomembranes using curved elements Biophys. J. (IF 3.4) Pub Date : 2024-05-03 Christoph Allolio, Balázs Fábián, Mark Dostalík
We describe a method for simulating biomembranes of arbitrary shape. In contrast to other dynamically triangulated surface (DTS) algorithms, our method provides a rich, -tangent-continuous, yet local description of the surface. We use curved Nagata triangles, which we generalize to cubic order to achieve the requisite flexibility. The resulting interpolation can be constructed locally without iterations
-
Protein condensates in the secretory pathway: Deciphering biophysical interactions and functional significance Biophys. J. (IF 3.4) Pub Date : 2024-05-02 Felix Campelo, Javier Vera Lillo, Julia von Blume
The emergence of phase separation phenomena among macromolecules has identified biomolecular condensates as fundamental cellular organizers. These condensates concentrate specific components and accelerate biochemical reactions without relying on membrane boundaries. Although extensive studies have revealed a large variety of nuclear and cytosolic membraneless organelles, we are witnessing a surge
-
Cryo-EM images of phase-separated lipid bilayer vesicles analyzed with a machine-learning approach Biophys. J. (IF 3.4) Pub Date : 2024-04-30 Karan D. Sharma, Milka Doktorova, M. Neal Waxham, Frederick A. Heberle
Lateral lipid heterogeneity (i.e., raft formation) in biomembranes plays a functional role in living cells. Three-component mixtures of low- and high-melting lipids plus cholesterol offer a simplified experimental model for raft domains in which a liquid-disordered (Ld) phase coexists with a liquid-ordered (Lo) phase. Using such models, we recently showed that cryogenic electron microscopy (cryo-EM)
-
A bupropion modulatory site in the Gloeobacter violaceus ligand-gated ion channel Biophys. J. (IF 3.4) Pub Date : 2024-04-27 Hoa Quynh Do, Elham Pirayesh, Garren Ferreira, Akash Pandhare, Zackary Ryan Gallardo, Michaela Jansen
Bupropion is an atypical antidepressant and smoking cessation drug that causes adverse effects such as insomnia, irritability, and anxiety. Bupropion inhibits dopamine and norepinephrine reuptake transporters and eukaryotic cation-conducting pentameric ligand-gated ion channels, such as nicotinic acetylcholine and serotonin type 3A receptors, at clinically relevant concentrations. Here, we demonstrate
-
Mapping the contribution of the C-linker domain to gating polarity in CNBD channels Biophys. J. (IF 3.4) Pub Date : 2024-04-27 Jenna L. Lin, Yongchang Chang, Debanjan Tewari, John Cowgill, Baron Chanda
Ion channels of the cyclic-nucleotide-binding domain (CNBD) family play a crucial role in the regulation of key biological processes, such as photoreception and pacemaking activity in the heart. These channels exhibit high sequence and structural similarity but differ greatly in their functional responses to membrane potential. The CNBD family includes hyperpolarization-activated ion channels and
-
Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics Biophys. J. (IF 3.4) Pub Date : 2024-04-27 Milka Doktorova, George Khelashvili, Rana Ashkar, Michael F. Brown
-
Exploring the pH dependence of an improved PETase Biophys. J. (IF 3.4) Pub Date : 2024-04-25 Cyril Charlier, Sabine Gavalda, Jelena Grga, Laura Perrot, Valeria Gabrielli, Frank Löhr, Julia Schörghuber, Roman Lichtenecker, Grégory Arnal, Alain Marty, Vincent Tournier, Guy Lippens
Enzymatic recycling of plastic and especially of polyethylene terephthalate (PET) has shown great potential to reduce its negative impact on our society. PET hydrolases (PETases) have been optimized using rational design and machine learning, but the mechanistic details of the PET depolymerization process remain unclear. Belonging to the carboxylic-ester hydrolase family with a canonical Ser-His-Asp
-
Directional change during active diffusion of viral ribonucleoprotein particles through cytoplasm Biophys. J. (IF 3.4) Pub Date : 2024-04-25 Kathleen C. Smith, Ryan Oglietti, Steven J. Moran, Jed C. Macosko, Douglas S. Lyles, George Holzwarth
A mesh of cytoskeletal fibers, consisting of microtubules, intermediate filaments, and fibrous actin, prevents the Brownian diffusion of particles with a diameter larger than 0.10 μm, such as vesicular stomatitis virus ribonucleoprotein (RNP) particles, in mammalian cells. Nevertheless, RNP particles do move in random directions but at a lower rate than Brownian diffusion, which is thermally driven
-
New insights into the substrate recognition and transport mechanism of the human sodium-taurocholate cotransporter Biophys. J. (IF 3.4) Pub Date : 2024-04-25 Jana Shen
-
The biophysical function of pulmonary surfactant Biophys. J. (IF 3.4) Pub Date : 2024-04-25 Stephen B. Hall, Yi Y. Zuo
The type II pneumocytes of the lungs secrete a mixture of lipids and proteins that together acts as a surfactant. The material forms a thin film on the surface of the liquid layer that lines the alveolar air sacks. When compressed by the decreasing alveolar surface area during exhalation, the films reduce surface tension to exceptionally low levels. Pulmonary surfactant is essential for preserving
-
Sensing a moving target: A new model reveals how cells sense dynamic signals Biophys. J. (IF 3.4) Pub Date : 2024-04-24 Andrew Mugler
-
Epigenetic marks uniquely tune the material properties of HP1α condensates Biophys. J. (IF 3.4) Pub Date : 2024-04-24 Priyasha Deshpande, Emily Prentice, Alfredo Vidal Ceballos, Patrizia Casaccia, Shana Elbaum-Garfinkle
Biomolecular condensates have emerged as a powerful new paradigm in cell biology with broad implications to human health and disease, particularly in the nucleus where phase separation is thought to underly elements of chromatin organization and regulation. Specifically, it has been recently reported that phase separation of heterochromatin protein 1alpha (HP1α) with DNA contributes to the formation
-
Conformational photo-trapping in NaV1.5: Inferring local motions at the “inactivation gate” Biophys. J. (IF 3.4) Pub Date : 2024-04-24 Samuel J. Goodchild, Christopher A. Ahern
Rapid and effectual inactivation in voltage-gated sodium channels is required for canonical action-potential firing. This “fast” inactivation arises from swift and reversible protein conformational changes that utilize transmembrane segments and the cytoplasmic linker between channel domains III and IV. Until recently, fast inactivation had been accepted to rely on a “ball-and-chain” mechanism whereby
-
Kinetic cooperativity resolves bidirectional clogging within the nuclear pore complex Biophys. J. (IF 3.4) Pub Date : 2024-04-18 Tiantian Zheng, Anton Zilman
As the main gatekeeper of the nucleocytoplasmic transport in eukaryotic cells, the nuclear pore complex (NPC) faces the daunting task of facilitating the bidirectional transport of a high volume of macromolecular cargoes while ensuring the selectivity, speed, and efficiency of this process. The competition between opposing nuclear import and export fluxes passing through the same channel is expected
-
Transmembrane determinants of voltage-gating differences between BK (Slo1) and Slo3 channels Biophys. J. (IF 3.4) Pub Date : 2024-04-18 Qin Li, Guanxing Chen, Jiusheng Yan
Voltage-gated potassium channels are critical in modulating cellular excitability, with Slo (slowpoke) channels forming a unique family characterized by their large conductance and dual regulation by electrical signals and intracellular messengers. Despite their structural and evolutionary similarities, Slo1 and Slo3 channels exhibit significant differences in their voltage-gating properties. This
-
The volume of healthy red blood cells is optimal for advective oxygen transport in arterioles Biophys. J. (IF 3.4) Pub Date : 2024-04-18 Lucas Amoudruz, Athena Economides, Petros Koumoutsakos
Red blood cells (RBCs) are vital for transporting oxygen from the lungs to the body’s tissues through the intricate circulatory system. They achieve this by binding and releasing oxygen molecules to the abundant hemoglobin within their cytosol. The volume of RBCs affects the amount of oxygen they can carry, yet whether this volume is optimal for transporting oxygen through the circulatory system remains
-
-
A structure-based computational model of IP3R1 incorporating Ca and IP3 regulation Biophys. J. (IF 3.4) Pub Date : 2024-04-16 D’Artagnan Greene, Yohannes Shiferaw
The inositol 1,4,5-triphosphate receptor (IPR) mediates Ca release in many cell types and is pivotal to a wide range of cellular processes. High-resolution cryoelectron microscopy studies have provided new structural details of IPR type 1 (IPR1), showing that channel function is determined by the movement of various domains within and between each of its four subunits. Channel properties are regulated
-
Characteristic fingerprint spectrum of α-synuclein mutants on terahertz time-domain spectroscopy Biophys. J. (IF 3.4) Pub Date : 2024-04-16 Xiaofang Zhao, Chenlong Yang, Xin Chen, Yu Sun, Weihai Liu, Qinggang Ge, Jun Yang
-Synuclein, a presynaptic neuronal protein encoded by the gene, is involved in the pathogenesis of Parkinson’s disease. Point mutations and multiplications of -synuclein (A30P and A53T) are correlated with early-onset Parkinson’s disease characterized by rapid progression and poor prognosis. Currently, the clinical identification of variants, especially disease-related A30P and A53T mutants, remains
-
DNA and mRNA as molecular speed bumps in Escherichia coli’s cytoplasm Biophys. J. (IF 3.4) Pub Date : 2024-04-15 Arnold J. Boersma
-
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
-
Map conformational landscapes of intrinsically disordered proteins with polymer physics quantities Biophys. J. (IF 3.4) Pub Date : 2024-04-12 Hossain Shadman, Jesse D. Ziebarth, Caleb E. Gallops, Ray Luo, Zhengxin Li, Hai-Feng Chen, Yongmei Wang
Disordered proteins are conformationally flexible proteins that are biologically important and have been implicated in devastating diseases such as Alzheimer’s disease and cancer. Unlike stably folded structured proteins, disordered proteins sample a range of different conformations that needs to be accounted for. Here, we treat disordered proteins as polymer chains, and compute a dimensionless quantity
-
Nuclear curvature determines Yes-associated protein 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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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,
-
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
-
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
-
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
-
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
-
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
-
Trade-offs in concentration sensing in dynamic environments Biophys. J. (IF 3.4) Pub Date : 2024-03-25 Aparajita Kashyap, Wei Wang, 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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
A hydrophobic nexus at the heart of hERG K channel gating Biophys. J. (IF 3.4) Pub Date : 2024-03-12 Matthew C. Trudeau
-
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
-
WITHDRAWN: 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
This article has been withdrawn: please see Elsevier Policy on Article Withdrawal ().