Biophysical Journal

Article	Citations
Unraveling the dance of phosphoproteins at adhesion planes: Modeling YAP phosphorylation by a particle-based stochastic model	73
Empagliflozin and ROS-CaMKII-late sodium current signaling in heart failure with preserved ejection fraction	61
Lipids and microparticles, physical characterization as a lung-contamination model	60
Diversity and molecular mechanisms of channelrhodopsins	60
Measurements of cholesterol chemical potential constrain models of cholesterol-phosphatidylcholine interactions	52
Disease mutations of human α3 Na+/K+-ATPase define extracellular Na+ binding/occlusion kinetics at ion binding site III	50
Critical regulation of the voltage-gated sodium channel, Nav1.4, by PIP2	50
Single molecule evidence for linker histone H1 DNA sliding and nucleosomal bypassing regulated by the C-terminal disordered domain	47
“Helicase” activity promoted through dynamic interactions between a ssDNA translocase and a diffusing SSB protein	47
Dissecting metabotropic glutamate receptor activation by single molecule FRET using minimally invasive labeling strategies	47
Differential nuclear translocation of STAT6 regulates the mechanosensitive immune cell activation	46
Myosin-I facilitates symmetry breaking and promotes the growth of actin ‘comet tails’	43
Investigation of nonselective cation permeation through CNGA1 channels by MD simulations	43
How lipids modulate association of proteins in lipid membranes	42
Modulation of potassium channels preserves temporal fidelity in auditory network models	41
Novel biomolecular fingerprint using graph convolutional networks	40
Examining HIV-1 envelope conformational transitions at high temporal resolution	40
Intrinsic stiffening and dynamic softening by cholesterol	40
Unraveling the molecular basis of protein search on ssDNA track and binding specificity of the ssDNA sequences	38
Inter-domain coordination essential for dengue virus non-structural (5) NS5 interaction with stem loop a (SLA)	38
Origins of protein concentration noise in mitochondria	37
A multi-view reflector microscope visualizes six-dimensional single-molecule translational and rotational dynamics with isotropic nanoscale resolution	37
Definition of a saxitoxin (STX) binding code enables discovery and characterization of the anuran saxiphilin family	37
Long-range regulation of cytochrome c binding to bc1 complex	37
Dynamic association of an assembly platform subcomplex of the bacterial type two secretion system	36

Method for direct measuring antibody affinity in biological sample	36
Treatment of osteoarthritis by salvianolic acid derivatives	36
Myosin binding protein-C: Everything, everywhere, all at once	36
Sarcomere dynamics simulations to uncover mechanisms in hypertrophic cardiomyopathy	35
cryo-EM structure of tarantula myosin filament: Implications for analysis of myopathy mutations	35
Fluctuating diffusivity of intrinsically disordered proteins	35
Expansion microscopy through mechanical force	34
Visualizing both nucleosome disassembly and reassembly during FACT chaperone activity	34
The rigidization of water dynamics around proteins: A molecular dynamics study	33
Bacterial brains: How bacteria use electrochemical potentials to solve complex problems	33
FkpA enhances outer membrane protein folding using an extensive interaction surface	33
NFATC1 modulation of atrial excitability in zebrafish	31
Investigating Dnase1L3's role in inflammation and redesigning the enzyme to be used as a therapeutic	30
Novel approaches to understand function and explore inhibition within protein-membrane interfaces	30
Experimental methods and mathematical modeling quantify and predict DUSP1 RNA expression dynamics in response to dexamethasone	30
Using HDX-MS to probe the dynamics and denatured state of GlpG, a helical membrane protein	29
Regioselective metabolism of cannabinoids by cytochrome P450 2J2	29
Extreme-value analysis of intracellular cargo transport by motor proteins	29
Solution NMR studies reveal novel CLIC4 chaperone activity with respect to profilin-1	29
Sensing membrane voltage by reorientation of dipolar transmembrane peptides	28
BPS2025 - On the cooperativity of fold-switching sequences	28
Transmembrane determinants of voltage-gating differences between BK (Slo1) and Slo3 channels	28
A Bayesian framework for systems model refinement and selection of calcium signaling	28
BPS2025 - Optimization of therapeutic T cells through biophysical modeling	28
BPS2025 - Toxic competitors of phospholamban may contribute to dysregulation of SERCA in heart failure	27
BPS2025 - The effects of pH on condensate and cortex formation	27
BPS2025 - Integrating accelerated molecular simulations and AI to elucidate Cas9 specificity factors	27
BPS2025 - Deciphering the relationship between form and inherent electrochemical function during the phase transition of Aβ peptides	27
BPS2025 - Comparison of multi-axes sample handler devices for multiview imaging of lung organoids	27
BPS2025 - Glycan-mediated regulation of IgG1 Fc-CD16a interactions: Insights from all-atom simulations	26
BPS2025 - Electromagnetic dynamics and characterization of cancer cell-magnetic bead interactions	26
BPS2025 - GIRK2 drug repurposing screen identifies treatment options for patients suffering from extremely rare diseases	26
BPS2025 - Real-time tracking of the structural dynamics of adenylate kinase	25
Drug discovery for heart failure: Targeting the myosin-binding protein C interactions with actin	25
BPS2025 - Mechanisms underlying distinct cardiac arrhythmia phenotypes caused by calmodulin mutation D132E in Calm2 and Calm3 genes	25
High throughput mechanotyping via flow cytometry and DNA sequencing	25
Quantitative views of protein dynamics through the computational microscope	25
Storm imaging provides nanodomain-lengthscale observation of coordination between Arabidopsis root hair membrane proteins	25
Quantum-enabled ghost imaging for non-invasive imaging of plants	24
Quantitative fret studies of EphA2-Lyn interactions	24
Characterizing the APOBEC3B closed to open pathway with weighted ensemble	24
RTK-integrin interactions universally modulate αVβ3 integrin-mediated cell adhesion	24
Optimal efficacy in mosquito-host interaction inhibition by 35-60 kHz animal sounds for malaria control	24
Sequence adaptation in various environments across organisms; similar yet different superoxide dismutase	24
Action at a distance along the microtubule couples kinesin motors	24
Engineering of the high-affinity chemokine CXCL13 to screen CXCR5 antagonists to treat cancer and autoimmune diseases	24
RNA structure controls composition and network dynamics of condensates	23
Investigation of G-protein specificity and biased agonism at the beta-2 adrenergic receptor (β2AR)	23
Analysis and comparison of amorphous & amyloid aggregates of the tumor suppressor p53	23
Single-molecule dynamics of ribonuclease H enzymes in Bacillus subtilis	23

Physical determinants of multiphase organisation in multi-component protein/RNA condensates	23
Probing synaptic distribution and arrangement of native surface AMPAR in mouse brain slices with 3D super-resolution microscopy	22
2-d liquid-liquid phase separation of GM130 Golgin protein bound to supported bilayer	22
Compounds specifically enhance IKs by modulating VSD-pore coupling	22
Cataracts and copper: A spectroscopic perspective of copper-induced aggregation of betaB2-crystallin	22
Solution structure of poly(UG) RNA reveals a new fold that drives gene silencing	22
Amplification-free rapid detection of viral genomes at single molecule level	22
Nascent-chain interaction networks and their effect on the bacterial ribosome	22
Functional impact of the interaction between S1 segment and KCNE subunit in the modulation of KCNQ1 channels	22
Insights on plasma membrane asymmetry from studies of asymmetric model membranes	22
BPS2025 - Functional assessment of recombinant human alpha-cardiac myosin and the effect of atrial arrhythmia mutations	21
BPS2025 - Direct quantification of human αβ-tubulin binding kinetics at microtubule ends reveals nucleotide regulation of end-binding affinity	21
BPS2025 - Molecular pharmacology of human P2X7 receptor ligands visualized by cryo-EM	21
BPS2025 - Mavacamten and omecamtiv mecarbil modulate the structure of the interacting-heads motif by inducing distinct subfragment-2 conformations	21
BPS2025 - Activation of TMEM16E scramblase induces ligand-independent growth factor receptor signaling and macropinocytosis for membrane repair	21
BPS2025 - Systematic embedding of biomechanics within dynamical graph grammars with application to actin networks in dendritic spine heads	21
BPS2025 - Structure and dynamics of the p53-MDMX-CK1α complex	21
BPS2025 - Cardiotoxic effects of synthetic cannabinoid receptor agonists: Inhibition of hERG and Kv7.1/KCNE1 channels with proposed hERG binding site	21
BPS2025 - TMEM175 chronicles: A journey from high throughput screening to lysosome	21
BPS2025 - Integrated data acquisition and real-time parameter-free reconstruction for cryo-ET	21
BPS2025 - Recovering true FRET efficiencies from smFRET investigations requires triplet state mitigation	21
BPS2025 - Monitoring conformational dynamics and interactions of p53-TAD via an MspA nanopore	21
BPS2025 - Generative computational modeling with CellPACK reveals interplay between rules of intracellular organization and geometry in hiPSCs	21
BPS2025 - Protein intrinsically disordered regions have nonrandom, modular architectures that influence conformation and function	21
BPS2025 - Developing a model to study iPSC-CM integration with human heart tissue	20
BPS2025 - Differential modulation of beta-cardiac myosin conformations by cardiomyopathy-associated mutations in the converter domain	20
BPS2025 - Molecular dynamics insights into lipid and nucleotide modulation of P-glycoprotein transport cycle	20
BPS2025 - Calcium-mediated structural dynamics and zinc sequestration in S100A12: Insights from NMR and molecular dynamics studies	20
BPS2025 - Cryoprotectant-free lamella preparation of plant and animal tissue for cryo-electron tomography	20
BPS2025 - Characterization of seven new K+ channel blocker peptides of Centruroides bonito revealed that α-KTx 2.24 has a picomolar affinity for Kv1.2	20
BPS2025 - Anticooperative substrate binding in the yeast BC1 complex	20
BPS2025 - Native structure of mosquito salivary protein complexes unveils molecular mechanisms of malaria transmission	20
BPS2025 - Developing an adaptable toolbox for measuring ion channel stoichiometry using stepwise photobleaching	20
BPS2025 - Phospholipase D-derived phosphatidic acid regulates multivesicular body fusion	20
BPS2025 - Studying the interaction of Kv1.3-specific inhibitors with Kv1.3-Kv1.x heterotetrameric ion channels	20
BPS2025 - Synthetic intrinsically disordered proteins that exhibit phase separation	20
BPS2025 - The inaugural flatiron heterogeneity community challenge	20
BPS2025 - Regulated confinement patterns elicit the organized collective migration of rear cells	20
BPS2025 - Investigating the modulation of Kv1.3 channel inactivation by KCNE4	20
BPS2025 - A tool for determining the release rate and number of mRNA molecules released from lipid nanoparticles in cells based on fluorescence readout and simulation	19
BPS2025 - Minimal protein components for chromatin replication-coupled symmetric histone recycling	19
BPS2025 - Replication organelles of arboviruses through the lens of a cryo-electron microscope	19
BPS2025 - Time-resolved fluorometry reveals novel insights into small molecule drug interactions with the HCN channel voltage sensor	19
BPS2025 - COBY: An advanced tool for accurate creation of coarse-grained simulation systems	19
BPS2025 - Simulation of biopolymerization on surfaces—implications for biogenesis	19
BPS2025 - Molecular mechanisms of keratin-based polymer materials for bioengineering applications	19
BPS2025 - Investigation of microtubule-CRMP2-isoforms interaction using high-speed atomic force microscopy	19
BPS2025 - Entropically generated SNARE linker forces maintain a maximally fusogenic, partially unzippered state and drive fusion	19
BPS2025 - Ultrafast fluorescence lifetimes of NADH via FLIM	19
BPS2025 - Inhibition of amyloid beta fibrillation by a heparin binding protein Midkine—a combined spectroscopy, microscopy, and proteomics study	18
BPS2025 - Cryo-EM structures of mitochondrial RNA editing catalytic complexes from Trypanosoma brucei	18
BPS2025 - Deciphering the role of SNARE transmembrane domain palmitoylation in neurotransmitter release	18
Crystal structure of the RNA cleaving 10-23 DNAzyme captured in a pre-catalytic state	18
Predicting side chain conformations in folded proteins by AlphaFold: Perspective and challenges	18
Polarized interfacial tension induces collective migration of cells, as a cluster, in a 3D tissue	18
BPS2025 - Structural dynamics study on mosaic spike heterotrimer provides insights into polyvalent vaccine immunogen display	18
BPS2025 - High-spatial-resolved heat manipulating membrane heterogeneity alters cellular migration and signaling	18
BPS2025 - Characterizing the potassium binding site in human excitatory amino acid transporter	18
BPS2025 - Complex DNA effects on polyphosphate condensate growth and architecture	18
BPS2025 - DNA nanotechnology for large-scale hybrid nanopore integration	18
Blocking uncertain mispriming errors of PCR	18
BPS2025 - Dynamics of IDPs in biomolecular condensates from massive all-atom explicit-solvent simulations	18
BPS2025 - RSV fusion protein conformation transition pathway from prefusion to postfusion	18
BPS2025 - Effective charge of RNA in a fully packaged viral particle	18
BPS2025 - Single-molecule measurements of p44-enhanced XPD helicase activity	18
BPS2025 - Networked interactions in biomolecular condensates formed by disordered proteins reveal structural and dynamic inhomogeneities	18
Structural studies of human serum albumin using cryo-EM up to 0.38 nm resolution	18
Active learning model for extracting elastic modulus of cell on substrate	18
Electrically controlling and optically observing the membrane potential of supported lipid bilayers	17
The substrate and inhibitor binding mechanism of polyspecific transporter OAT1 revealed by high-resolution cryo-EM	17
Small-angle x-ray scattering investigation of the integration of free fatty acids in polysorbate 20 micelles	17
From loops to stacks: Early steps in the DNA folding pathway by protamine	17
Hypertrophic and dilated cardiomyopathy-associatedTNNT2 pathogenic variants induce nucleus remodeling in hiPSC-CM models	17
Organization and dynamics of cross-linked actin filaments in confined environments	17
De novo design of a DNA-binding protein capable of multi-site recognition	17
Calculation of solvation force in molecular dynamics simulation by deep-learning method	17
Structure, dynamics and nanomechanics of wild-type and alpha-variant SARS-CoV-2 virions	17
Protein conformations in Tau condensates probed by smFRET and FLIM-FRET	17
Dynamics of asymmetric membranes and interleaflet coupling as intermediates in membrane fusion	17
Discovering inhibitors against human norovirus protein target 3CLpro using ligand-protein docking	17

Dissecting ER stress signaling with live-cell single-molecule imaging and optogenetics	17
Thank You to Our Reviewers	17
Mathematical modeling as a tool to characterize the role of phosphoinositide metabolism for regulation of neuronal action potential firing	17
Mechanisms of dysfunction in patient-derived cardiomyocytes with the hypertrophic cardiomyopathy-myosin binding protein-C e258K mutation	17
Reversing aberrant phase transitions of ALS-linked disease protein FUS with RNA	16
Investigating how the anionic lipid, BMP, plays a crucial role in the initation of SARS-CoV-2 fusion	16
ERK activation waves are key drivers in the mechanical cell competition that leads to collective onslaught of bacterially infected cells	16
Membrane fission during bacterial spore development requires cellular inflation driven by DNA translocation	16
Enhancing sarcomere function and length-dependent activation in engineered human myocardium via triiodothyronine and dexamethasone treatment	16
Objective unsupervised learning of behavioral dynamics at the frontier of information bottleneck principles, physics informed priors, and maximum mean discrepancy statistical testing	16
Temperature dependence of α-crystallin membrane binding	16
Machine learning for prediction of protein function and elucidation of enzyme function and control	16
Probing the mechanisms of low-voltage activation in T-type CaV3.1 calcium channels	16
2D-dwell-time analysis with simulations of ion-channel gating using high-performance computing	16
Elucidation of a dynamic interplay between beta-adrenergic receptors, its agonists, and stimulatory G protein	16
Impact of mutations near the SARS-CoV-2 furin-cleavage site on viral infectivity	16
Theoretical model for DNA looping by positively charged condensing agents	16
The N-terminus is not the Ca2+-regulated gate in CALHM1 channels	16
Insights into DNA solvation found in protein-DNA structures	16
The Piezo1 channel interacts with the transmembrane channel Tmc1 to exert mechanoelectrical transducer (MET) functions	16
In situ detection of single microRNA molecules by transient hybridization utilizing FRET-based probes	16
A structural model of TCR-pMHC catch bonding	16
Stress-induced BAG3 cleavage and its effects on sarcomere contractile functions	15
Extent of raft composition in a model plasma membrane	15
Phosphomimetic mutations in the C-terminal basic region of troponin T increases actin filament activity	15
Differential regulation of IKs by targeted recruitment of protein kinase A to distinct sites on the KCNQ1/KCNE1 channel complex	15
Does it stick? Long-term outcomes for biology majors from introductory physics for the life sciences	15
Multi-GPU-powered UNRES package for physics-based coarse-grained simulations of structure, dynamics, and thermodynamics of protein systems at biological size- and timescales	15
Cardiac dysfunction in a mouse model of colon cancer cachexia is due to sarcomeric changes	15
Regulation of membrane homeostasis by TMC1 mechanoelectrical transduction channels is essential for hearing	15
Understanding transport processes with simulation	15
Integrative structural dynamics of calmodulin showcases sequence-to-function	15
Changes in cell volume are drivers of plasticity in disordered proteins	15
Structural basis for the intracellular regulation of ferritin degradation	15
Quantifying thermodynamic parameters of multi-step binding using a novel approach to Bayesian inference	15
Quantifying water rigidization near protein surfaces	15
Extracting conformational heterogeneity from 2D and 3D cryo-EM data	15
Biochemical signaling encoded in emergent properties	15
Distinct spatiotemporal dynamics of calmodulin genes in cardiac myocytes under beta-adrenergic stimulation	15
The effects of biomolecular crowding on the behaviour of polymyxin antibiotics within the E. coli cell envelope	15
Local interactions and transient secondary structures govern backbone dynamics of intrinsically disordered proteins	14
Spatial distribution of adhesion force generation in human cardiomyocytes	14
Simultaneous pulsed interleaved excitation (PIE) and alternating-laser excitation (ALEX): an optimized excitation pattern for single molecule FRET	14
Single-molecule dissection of coupling mechanisms between cofactor binding and folding of a complex protein	14
Student usage and perceptions of ChatGPT: The good, the bad, and the ugly	14
Molecular dynamics modeling of polystyrene functionalized carbon nanotubes	14
Nanoscale organization of ryanodine receptor distribution and phosphorylation pattern determines the dynamics of calcium sparks	14
Active-learning-guided and high-throughput synthesis of membrane proteins	14
Escherichia coli JM109 in LB as a model bacterial system to study magnetic field effect in recombination of non-correlated pair of biologically relevant radicals nitric oxide and superoxide anion in h	14
Phase separation of myosin-15 and centrin-2 contributes to stereocilia tip density formation	14
The cancer mucin barrier plays a multifunctional role in providing sustained physical resistance to natural killer cell attack	14
Spelunking with potassium: Functional analysis of the water tunnel in the potassium pump KdpFABC	14
Comparing photosynthetic metabolite free energy and permeability across bacterial microcompartment shell proteins	14
Fluorescent drug analogs to study drug-target interactions in intact cells	14
Kv3.1 channel expression determines the spike waveform in vocal-motor neurons	14
Measuring the effects of infection on disordered viral proteins	14
Establishing the allosteric mechanism in CRISPR-Cas9	14
Graded cleavage of elastic titin in living mouse hearts reveals the role of titin stiffness for cardiac contractility	14
Alchemical free-energy simulations support the formation of the sarco-endoplasmic reticulum calcium pump (SERCA) inhibitory complex from the phospholamban pentamer	14
Exploring a role for the proximity to the plasma membrane miscibility phase transition in the gating of two temperature sensing channels	14
Druggable and allosteric pocket prints of G-protein coupled receptors	14
Chloride intracellular channels regulate spermatogenesis	13
Disparate effects of CaM N- and C-lobe CPVT-linked mutations on SK channel-CaM assembly	13
Computational analyses of SERCA, phospholamban, and sarcolipin complexes	13
Experimental studies of wild type A2A receptor and cholesterol-binding receptor variants support a model for cholesterol as an allosteric modulator of G protein coupling	13
The multiple dimensions of lncRNAS: how 3D structure determines meg3 function	13
Effect of cyclization on the liquid-liquid phase separation of pentaglycine	13
Towards revealing functionally relevant conformational dynamics of the C-terminal tail of β-arrestin	13
Modulation of membrane fusion using a novel fusogenic system composition	13
Ligand discovery for LAT1 with molecular dynamics simulation and virtual screening	13
Membrane composition affects binding and insertion of the influenza virus fusion peptide	13
Bacterial resting membrane potential: a case study with Bacillus subtilis	13
Exploring kinetically controlled protein solubility under physiologically relevant conditions	13
Decoding gene network models and rates from smFISH data	13
Measurement of the specific and non-specific binding energies of Mg2+ to RNA	13
TMEM16 scramblases thin the membrane to enable lipid scrambling	13
Surface densities prewet a near critical membrane	13
Configuring extracellular matrix architectures with dynamic forces	13
Biophysical insights into OR2T7: Investigation of a potential prognostic marker for glioblastoma	13
Superresolution imaging of native surface AMPA receptors in brain tissue	13
Tuning protein condensate selectivity by changing solution composition	13
Engineering inducible dipoles to develop better fluorescent biosensors	13
Collective functionalities emerging in microbial active matter	13
Analysis of membrane fluidity disturbances by mutant huntingtin in different membranal compartments using phasor analysis of local ICS and spectral phasor analysis	13
Intramembrane serine protease catalysis in different physical environments	13
Precision in iterative modulation enhanced single-molecule localization microscopy	13
Elucidating the role of membrane tension in cellular processes using continuum modeling	13
Optogenetic delivery of single molecules to the plasma membrane	13
Structural studies of connexin 32 gap junction channels by cryo-EM	13
Allosteric mechanisms of transcriptional control in FXR	13
Targeting anti-aggregation and anti-oxidation of amyloid deposits for therapeutic intervention of Alzheimer’s using machine learning-enhanced molecular docking	13
A disordered linker with “something” on its N-terminus drives the allostery in the urokinase-type plasminogen activator (uPA)	13
Cryo-EM structures of nanodisc reconstituted ligand-gated ion channel GLIC in various conformations reveal state-dependent protein-lipid interactions and gating mechanism	13
Structural basis of closed groove scrambling by a TMEM16 protein	13
Tetra-gel expansion microscopy combined with superresolution imaging enables superior accuracy	13