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  • Increased Dissociation of Adamantanamines in Influenza A M2 S31N with Partial Block by Rimantadine
    Biophys. J. (IF 3.854) Pub Date : 2020-09-24
    Kelly L. McGuire; Jonathon T. Hill; David D. Busath

    The ubiquitous mutation from serine (WT) to asparagine at residue 31 (S31N) in the influenza A M2 channel renders it insensitive to amantadine (AMT) and rimantadine (RMT) block, but it is unknown whether the inhibition results from weak binding or incomplete block. Two-electrode voltage clamp (TEVC) of transfected Xenopus oocytes revealed that the M2 S31N channel is essentially fully blocked by AMT

    更新日期:2020-09-25
  • Coupled membrane lipid miscibility and phosphotyrosine-driven protein condensation phase transitions
    Biophys. J. (IF 3.854) Pub Date : 2020-09-24
    Jean K. Chung; William Y.C. Huang; Catherine B. Carbone; Laura M. Nocka; Atul N. Parikh; Ronald D. Vale; Jay T. Groves

    Lipid miscibility phase separation has long been considered to be a central element of cell membrane organization. More recently, protein condensation phase transitions, into three-dimensional droplets or in two-dimensional lattices on membrane surfaces, have emerged as another important organizational principle within cells. Here, we reconstitute the LAT:Grb2:SOS protein condensation on the surface

    更新日期:2020-09-25
  • Effects of ligand binding on the energy landscape of acyl-CoA-binding protein
    Biophys. J. (IF 3.854) Pub Date : 2020-09-24
    Punam Sonar; Luca Bellucci; Alessandro Mossa; Pétur O. Heidarsson; Birthe B. Kragelund; Ciro Cecconi

    Binding of ligands is often crucial for function yet the effects of ligand binding on the mechanical stability and energy landscape of proteins are incompletely understood. Here we use a combination of single-molecule optical tweezers and MD simulations to investigate the effect of ligand binding on the energy landscape of acyl-coenzyme A (CoA) binding protein (ACBP). ACBP is a topologically simple

    更新日期:2020-09-24
  • Dynamics-driven allostery underlies Ca2+-mediated release of SERCA inhibition by phospholamban
    Biophys. J. (IF 3.854) Pub Date : 2020-09-24
    Olga N. Raguimova; Rodrigo Aguayo-Ortiz; Seth L. Robia; L. Michel Espinoza-Fonseca

    Sarcoplasmic reticulum (SR) Ca2+-ATPase (SERCA) and phospholamban (PLB) are essential for intracellular Ca2+ transport in myocytes. Ca2+-dependent control of SERCA–PLB provides a control function that regulates cytosolic and SR Ca2+ levels. While experimental and computational studies alone have led to a greater insight into SERCA–PLB regulation, the mechanisms for Ca2+ binding reverses inhibition

    更新日期:2020-09-24
  • Diffusion of Duffy antigen, glycophorin A, Band 3, and GLUT1 in erythrocytes: Insights into membrane complexes
    Biophys. J. (IF 3.854) Pub Date : 2020-09-23
    Gayani C. Kodippili; Katie Giger; Karson S. Putt; Philip S. Low

    Single particle tracking offers a method to interrogate the organization of transmembrane proteins by measuring their mobilities within a cell’s plasma membrane. Using this technique, the diffusion characteristics of the Duffy antigen (DARC), glycophorin A, Band 3, and GLUT1 were compared under analogous conditions on intact human erythrocyte membranes. Microscopic diffusion coefficients revealed that

    更新日期:2020-09-23
  • ECM stiffness controls the activation and contractility of corneal keratocytes in response to TGF-β1
    Biophys. J. (IF 3.854) Pub Date : 2020-09-23
    Daniel P. Maruri; Miguel Miron-Mendoza; Pouriska B. Kivanany; Joshua M. Hack; David W. Schmidtke; W. Matthew Petroll; Victor D. Varner

    Following surgery or traumatic injury, corneal wound healing can cause a scarring response that stiffens the tissue and impairs ocular function. This fibrosis is caused, in part, by the activation of corneal keratocytes from a native mechanically quiescent state to an activated myofibroblastic state. This transformation is tied to signaling downstream of transforming growth factor beta 1 (TGF-β 1)

    更新日期:2020-09-23
  • Deuterium-Enhanced Raman Spectroscopy for Histidine pKa Determination in a pH-Responsive Hydrogel
    Biophys. J. (IF 3.854) Pub Date : 2020-09-23
    Gabriel A. Braun; Brett H. Pogostin; Milda Pucetaite; Casey H. Londergan; Karin S. Åkerfeldt

    We report here a method for the determination of the pKa of histidine in complex or heterogeneous systems amenable to neither solid-state nor solution NMR spectroscopy. Careful synthesis of an Fmoc- and trityl- protected, C2-deuterated histidine produces a vibrational-probe-equipped amino acid that can readily be incorporated into any peptide accessible by standard solid-phase methods. The frequency

    更新日期:2020-09-23
  • Modelling fibrillogenesis of collagen-mimetic molecules
    Biophys. J. (IF 3.854) Pub Date : 2020-09-23
    Anne E. Hafner; Noemi G. Gyori; Ciaran A. Bench; Luke K. Davis; Andela Šarić

    One of the most robust examples of self-assembly in living organisms is the formation of collagen architectures. Collagen type I molecules are a crucial component of the extracellular-matrix where they self-assemble into fibrils of well defined axial striped patterns. This striped fibrilar pattern is preserved across the animal kingdom and is important for the determination of cell phenotype, cell

    更新日期:2020-09-23
  • Data-driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization
    Biophys. J. (IF 3.854) Pub Date : 2020-09-22
    Yifeng Qi; Alejandro Reyes; Sarah E. Johnstone; Martin J. Aryee; Bradley E. Bernstein; Bin Zhang

    Chromosomes are positioned non-randomly inside the nucleus to coordinate with their transcriptional activity. The molecular mechanisms that dictate the global genome organization and the nuclear localization of individual chromosomes are not fully understood. We introduce a polymer model to study the organization of the diploid human genome: it is data-driven as all parameters can be derived from Hi-C

    更新日期:2020-09-22
  • Desmosomal hyper-adhesion is accompanied with enhanced binding strength of desmoglein 3 molecules
    Biophys. J. (IF 3.854) Pub Date : 2020-09-21
    M. Fuchs; A. Sigmund; J. Waschke; F. Vielmuth

    Intercellular adhesion of keratinocytes depends critically on desmosomes which, during maturation, acquire a hyper-adhesive and thus Ca2+-independent state. Here, we investigated the roles of desmoglein (Dsg) 3 and plakophilins (Pkps) in hyper-adhesion. Atomic force microscopy (AFM) single molecule force mappings revealed increased Dsg3 molecules but not Dsg1 molecules binding strength in murine keratinocytes

    更新日期:2020-09-21
  • Infrared Nanospectroscopy of Air-Sensitive Biological Substrates Protected by Thin Hydrogel Films
    Biophys. J. (IF 3.854) Pub Date : 2020-09-16
    Alexander P. Fellows; Mike T.L. Casford; Paul B. Davies

    The air sensitivity of many substrates, and specifically bio-surfaces, presents an experimental challenge for their analysis by vibrational spectroscopy and, in particular, IR microscopy on a nanometre scale. The recent development of AFM-IR which combines Atomic Force Microscopy with IR spectroscopy to circumvent the Abbe diffraction limit allows nanoscale chemical characterisation of surfaces. Additionally

    更新日期:2020-09-16
  • Liquid phase separation controlled by pH
    Biophys. J. (IF 3.854) Pub Date : 2020-09-16
    Omar Adame-Arana; Christoph A. Weber; Vasily Zaburdaev; Jacques Prost; Frank Jülicher

    We present a minimal model to study the effects of pH on liquid phase separation of macromolecules. Our model describes a mixture composed of water and macromolecules that exist in three different charge states and have a tendency to phase-separate. This phase separation is affected by pH via a set of chemical reactions describing protonation and deprotonation of macromolecules, as well as self-ionisation

    更新日期:2020-09-16
  • A computational analysis of the factors governing the dynamics of α7 nAChR and its homologues
    Biophys. J. (IF 3.854) Pub Date : 2020-09-16
    A. Gulsevin; J. Meiler; N.A. Horenstein

    The α7 nicotinic acetylcholine receptor (nAChR) is a homopentameric ion channel from the Cys-loop receptor superfamily targeted for psychiatric indications and inflammatory pain. Molecular dynamics (MD) studies of the receptor have focused on residue mobility and global conformational changes to address receptor function. However, a comparative analysis of α7 with its homologues that cannot trigger

    更新日期:2020-09-16
  • Mechanisms of Light-Induced Deformations in Photoreceptors
    Biophys. J. (IF 3.854) Pub Date : 2020-09-16
    K.C. Boyle; Z.C. Chen; T. Ling; V.P. Pandiyan; J. Kuchenbecker; R. Sabesan; D. Palanker

    Biological cells deform on a nanometer scale when their transmembrane voltage changes, an effect which has been visualized during the action potential using quantitative phase imaging. Similar changes in the optical path length have been observed in photoreceptor outer segments after a flash stimulus via phase-resolved optical coherence tomography (pOCT). These optoretinograms reveal a fast, ms-scale

    更新日期:2020-09-16
  • Imaging ATP Consumption in Resting Skeletal Muscle: One Molecule at a Time.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-15
    Shane R Nelson,Amy Li,Samantha Beck-Previs,Guy G Kennedy,David M Warshaw

    Striated muscle contraction is the result of sarcomeres, the basic contractile unit, shortening because of hydrolysis of adenosine triphosphate (ATP) by myosin molecular motors. In noncontracting, “relaxed” muscle, myosin still hydrolyzes ATP slowly, contributing to the muscle’s overall resting metabolic rate. Furthermore, when relaxed, myosin partition into two kinetically distinct subpopulations:

    更新日期:2020-09-15
  • Evaluation of Cell's Passability in the ECM Network.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-12
    Yongrou Zhang,Zetao Huang,Shoubin Dong,Zejia Liu,Yiping Liu,Liqun Tang,Taobo Cheng,Xuefeng Zhou

    The microstructure of the extracellular matrix (ECM) plays a key role in affecting cell migration, especially nonproteolytic migration. It is difficult, however, to measure some properties of the ECM, such as stiffness and the passability for cell migration. On the basis of a network model of collagen fiber in the ECM, which has been well applied to simulate mechanical behaviors such as the stress-strain

    更新日期:2020-09-15
  • Nonaxisymmetric Shapes of Biological Membranes from Locally Induced Curvature.
    Biophys. J. (IF 3.854) Pub Date : 2020-07-31
    Yannick A D Omar,Amaresh Sahu,Roger A Sauer,Kranthi K Mandadapu

    In various biological processes such as endocytosis and caveolae formation, the cell membrane is locally deformed into curved morphologies. Previous models to study membrane morphologies resulting from locally induced curvature often only consider the possibility of axisymmetric shapes—an indeed unphysical constraint. Past studies predict that the cell membrane buds at low resting tensions and stalls

    更新日期:2020-09-15
  • Endocytosis Is a Key Mode of Interaction between Extracellular β-Amyloid and the Cell Membrane.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-15
    Jing-Ming Shi,Li Zhu,Xi Lan,Duan-Wei Zhao,Yong-Jun He,Zheng-Qi Sun,Di Wu,Hai-Yun Li

    Interactions between amyloid-β peptide (Aβ) and the cell membrane include interaction with membrane lipids and binding to membrane receptors, both of which are considered to be the toxicity mechanisms of Aβ. However, it is unclear whether both mechanisms lead to cytotoxicity. Thus, we aimed to analyze these two mechanisms of Aβ42 interaction with cell membranes under different Aβ aggregation states

    更新日期:2020-09-15
  • Binding Dynamics of α-Actinin-4 in Dependence of Actin Cortex Tension.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-07
    Kamran Hosseini,Leon Sbosny,Ina Poser,Elisabeth Fischer-Friedrich

    Mechanosensation of cells is an important prerequisite for cellular function, e.g., in the context of cell migration, tissue organization, and morphogenesis. An important mechanochemical transducer is the actin cytoskeleton. In fact, previous studies have shown that actin cross-linkers such as α-actinin-4 exhibit mechanosensitive properties in their binding dynamics to actin polymers. However, to date

    更新日期:2020-09-15
  • Allosteric Priming of E. coli CheY by the Flagellar Motor Protein FliM.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-15
    Paige Wheatley,Sayan Gupta,Alessandro Pandini,Yan Chen,Christopher J Petzold,Corie Y Ralston,David F Blair,Shahid Khan

    Phosphorylation of Escherichia coli CheY protein transduces chemoreceptor stimulation to a highly cooperative flagellar motor response. CheY binds to the N-terminal peptide of the FliM motor protein (FliMN). Constitutively active D13K-Y106W CheY has been an important tool for motor physiology. The crystal structures of CheY and CheY ⋅ FliMN with and without D13K-Y106W have shown FliMN-bound CheY contains

    更新日期:2020-09-15
  • Effect of Protein Structure on Evolution of Cotranslational Folding.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-12
    Victor Zhao,William M Jacobs,Eugene I Shakhnovich

    Cotranslational folding depends on the folding speed and stability of the nascent protein. It remains difficult, however, to predict which proteins cotranslationally fold. Here, we simulate evolution of model proteins to investigate how native structure influences evolution of cotranslational folding. We developed a model that connects protein folding during and after translation to cellular fitness

    更新日期:2020-09-15
  • Allosteric Mechanisms of Nonadditive Substituent Contributions to Protein-Ligand Binding.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-15
    Stephen Boulton,Katherine Van,Bryan VanSchouwen,Jerry Augustine,Madoka Akimoto,Giuseppe Melacini

    Quantifying chemical substituent contributions to ligand-binding free energies is challenging due to nonadditive effects. Protein allostery is a frequent cause of nonadditivity, but the underlying allosteric mechanisms often remain elusive. Here, we propose a general NMR-based approach to elucidate such mechanisms and we apply it to the HCN4 ion channel, whose cAMP-binding domain is an archetypal conformational

    更新日期:2020-09-15
  • Reduction in Dynamics of Base pair Opening upon Ligand Binding by the Cocaine-Binding Aptamer.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-15
    Zachary R Churcher,Devid Garaev,Howard N Hunter,Philip E Johnson

    We have used magnetization transfer NMR experiments to measure the exchange rate constant (kex) of the imino protons in the unbound, cocaine-bound, and quinine-bound forms of the cocaine-binding DNA aptamer. Both long-stem 1 (MN4) and short-stem 1 (MN19) variants were analyzed, corresponding to structures with a prefolded secondary structure and ligand-induced-folding versions of this aptamer, respectively

    更新日期:2020-09-15
  • Amoeboid Swimming Is Propelled by Molecular Paddling in Lymphocytes.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-12
    Laurene Aoun,Alexander Farutin,Nicolas Garcia-Seyda,Paulin Nègre,Mohd Suhail Rizvi,Sham Tlili,Solene Song,Xuan Luo,Martine Biarnes-Pelicot,Rémi Galland,Jean-Baptiste Sibarita,Alphée Michelot,Claire Hivroz,Salima Rafai,Marie-Pierre Valignat,Chaouqi Misbah,Olivier Theodoly

    Mammalian cells developed two main migration modes. The slow mesenchymatous mode, like crawling of fibroblasts, relies on maturation of adhesion complexes and actin fiber traction, whereas the fast amoeboid mode, observed exclusively for leukocytes and cancer cells, is characterized by weak adhesion, highly dynamic cell shapes, and ubiquitous motility on two-dimensional and in three-dimensional solid

    更新日期:2020-09-15
  • Ca2+ Release via IP3 Receptors Shapes the Cardiac Ca2+ Transient for Hypertrophic Signaling.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-13
    Hilary Hunt,Agnė Tilūnaitė,Greg Bass,Christian Soeller,H Llewelyn Roderick,Vijay Rajagopal,Edmund J Crampin

    Calcium (Ca2+) plays a central role in mediating both contractile function and hypertrophic signaling in ventricular cardiomyocytes. L-type Ca2+ channels trigger release of Ca2+ from ryanodine receptors for cellular contraction, whereas signaling downstream of G-protein-coupled receptors stimulates Ca2+ release via inositol 1,4,5-trisphosphate receptors (IP3Rs), engaging hypertrophic signaling pathways

    更新日期:2020-09-15
  • Quantifying Temperature Compensation of Bicoid Gradients with a Fast T-Tunable Microfluidic Device.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-12
    Hongcun Zhu,Yeping Cui,Chunxiong Luo,Feng Liu

    As a reaction-diffusion system strongly affected by temperature, early fly embryos surprisingly show highly reproducible and accurate developmental patterns during embryogenesis under temperature perturbations. To reveal the underlying temperature compensation mechanism, it is important to overcome the challenge in quantitative imaging on fly embryos under temperature perturbations. Inspired by microfluidics

    更新日期:2020-09-15
  • Regulation of Gene Activation by Competitive Cross Talking Pathways.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-19
    Feng Jiao,Chunjuan Zhu

    The phenomenon of a gene expression burst has been attributed to random transitions between the active and inactive states of a gene. However, the mechanisms underlying regulation of the activation process in response to environmental changes remain unclear. Here, we model gene activation as a consequence of the competitive cross talk between a weak basal pathway and an inducible signaling pathway

    更新日期:2020-09-15
  • Requirements for DNA-Bridging Proteins to Act as Topological Barriers of the Bacterial Genome.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-12
    Marc Joyeux,Ivan Junier

    Bacterial genomes have been shown to be partitioned into several-kilobase-long chromosomal domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbors. Both in vivo and in vitro experiments have been performed to question the nature of the topological barriers at play, leading to several predictions on possible molecular

    更新日期:2020-09-15
  • Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-12
    Celine Tse,Lauren Wickstrom,Mamuka Kvaratskhelia,Emilio Gallicchio,Ronald Levy,Nanjie Deng

    We report the free-energy landscape and thermodynamics of the protein-protein association responsible for the drug-induced multimerization of HIV-1 integrase (IN). Allosteric HIV-1 integrase inhibitors promote aberrant IN multimerization by bridging IN-IN intermolecular interactions. However, the thermodynamic driving forces and kinetics of the multimerization remain largely unknown. Here, we explore

    更新日期:2020-09-15
  • Efficient Approximations for Stationary Single-Channel Ca2+ Nanodomains across Length Scales.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-14
    Yinbo Chen,Cyrill B Muratov,Victor Matveev

    We consider the stationary solution for the Ca2+ concentration near a point Ca2+ source describing a single-channel Ca2+ nanodomain in the presence of a single mobile Ca2+ buffer with 1:1 Ca2+ binding. We present computationally efficient approximants that estimate stationary single-channel Ca2+ nanodomains with great accuracy in broad regions of parameter space. The presented approximants have a functional

    更新日期:2020-09-15
  • Membrane Association and Functional Mechanism of Synaptotagmin-1 in Triggering Vesicle Fusion.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-14
    Ramesh Prasad,Huan-Xiang Zhou

    Upon Ca2+ influx, synaptic vesicles fuse with the presynaptic plasma membrane (PM) to release neurotransmitters. Membrane fusion is triggered by synaptotagmin-1, a transmembrane protein in the vesicle membrane (VM), but the mechanism is under debate. Synaptotagmin-1 contains a single transmembrane helix (TM) and two tandem C2 domains (C2A and C2B). This study aimed to use molecular dynamics simulations

    更新日期:2020-09-15
  • The location and rate of the phosphate release step in the muscle crossbridge cycle
    Biophys. J. (IF 3.854) Pub Date : 2020-09-15
    Gerald Offer; K.W. Ranatunga

    It is controversial whether the phosphate (Pi) release step in the crossbridge cycle occurs before or after the first tension-generating step and whether it is fast or slow. We have therefore modified our previous model of the frog crossbridge cycle by including a Pi release step either before (model A) or after (model B) the first tension-generating step and refined by downhill simplex runs the two

    更新日期:2020-09-15
  • Chromosome Structural Mechanics Dictates the Local Spreading of Epigenetic Marks
    Biophys. J. (IF 3.854) Pub Date : 2020-09-12
    Sarah H. Sandholtz; Deepti Kannan; Bruno G. Beltran; Andrew J. Spakowitz

    We present a theoretical model that demonstrates the integral role chromosome organization and structural mechanics play in the spreading of histone modifications involved in epigenetic regulation. Our model shows that heterogeneous nucleosome positioning, and the resulting position-dependent mechanical properties, must be included in order to reproduce several qualitative features of experimental

    更新日期:2020-09-12
  • Insights into the microscopic structure of RNF4-SIM-SUMO complexes from MD simulations
    Biophys. J. (IF 3.854) Pub Date : 2020-09-11
    A. Kötter; H.D. Mootz; A. Heuer

    Posttranslational modification with one of the isoforms of the small ubiquitin-like modifier (SUMO) affects thousands of proteins in the human proteome. The binding of SUMO to SUMO interacting motifs (SIMs) can translate the SUMOylation event into functional consequences. The E3 ubiquitin ligase RNF4 contains multiple SIMs and connects SUMOylation to the ubiquitin pathway. SIM2 and SIM3 of RNF4 were

    更新日期:2020-09-11
  • ATP-driven Non-equilibrium Activation of Kinase Clients by the Molecular Chaperone Hsp90
    Biophys. J. (IF 3.854) Pub Date : 2020-09-11
    Huafeng Xu

    The molecular chaperone 90-kDa heat-shock protein (Hsp90) assists the late-stage folding and activation of diverse types of protein substrates (called clients), including many kinases. Previous studies have established that the Hsp90 homodimer undergoes an ATP-driven cycle through open and closed conformations. Here I propose a model of client activation by Hsp90, which predicts that this cycle enables

    更新日期:2020-09-11
  • Stability of the pH-Dependent Parallel-Stranded d(CGA) Motif.
    Biophys. J. (IF 3.854) Pub Date : 2020-09-11
    Emily M Luteran,Jason D Kahn,Paul J Paukstelis

    Non-canonical DNA structures that retain programmability and structural predictability are increasingly being used in DNA nanotechnology applications, where they offer versatility beyond traditional Watson-Crick interactions. The d(CGA) triplet repeat motif is structurally dynamic and can transition between parallel-stranded homo-base paired duplex and anti-parallel unimolecular hairpin in a pH-dependent

    更新日期:2020-09-11
  • Design of Isoform-Selective Enzyme Inhibitors by Exploring Pocket Size According to the Lock-and-Key Principle
    Biophys. J. (IF 3.854) Pub Date : 2020-09-09
    Virginija Dudutienė; Asta Zubrienė; Visvaldas Kairys; Alexey Smirnov; Joana Smirnovienė; Janis Leitans; Andris Kazaks; Kaspars Tars; Lena Manakova; Saulius Gražulis; Daumantas Matulis

    In the design of high-affinity and enzyme isoform-selective inhibitors, we applied an approach of augmenting the substituents attached to the benzenesulfonamide scaffold in three ways, namely, substitutions at the 3,5- or 2,4,6-positions, or expansion of the condensed ring system. The increased size of the substituents determined the spatial limitations of the active sites of the twelve catalytically

    更新日期:2020-09-10
  • Queuing Models of Gene Expression: Analytical Distributions and Beyond.
    Biophys. J. (IF 3.854) Pub Date : 2020-09-09
    Changhong Shi,Yiguo Jiang,Tianshou Zhou

    Activation of a gene is a multistep biochemical process, involving recruitments of transcription factors and histone kinases as well as modification of histones. Many of these intermediate reaction steps would have been unspecified by experiments. Therefore, classical two-state models of gene expression established based on the memoryless (or Markovian) assumption would not well describe the reality

    更新日期:2020-09-10
  • Membrane tension can enhance adaptation to maintain polarity of migrating cells
    Biophys. J. (IF 3.854) Pub Date : 2020-09-07
    Cole Zmurchok; Jared Collette; Vijay Rajagopal; William R. Holmes

    Migratory cells are known to adapt to environments that contain wide-ranging levels of chemoattractant. While biochemical models of adaptation have been previously proposed, here we discuss a different mechanism based on mechanosensing, where the interaction between biochemical signaling and cell tension facilitates adaptation. We describe and analyze a model of mechanochemical-based adaptation coupling

    更新日期:2020-09-08
  • Editors' Note.
    Biophys. J. (IF 3.854) Pub Date : 2020-09-08
    Meyer B Jackson,Jane Dyson

    更新日期:2020-09-08
  • Disulfide Reduction Allosterically Destabilizes the β-Ladder Subdomain Assembly within the NS1 Dimer of ZIKV.
    Biophys. J. (IF 3.854) Pub Date : 2020-09-06
    Priti Roy,Subhajit Roy,Neelanjana Sengupta

    The Zika virus (ZIKV) was responsible for a recent debilitating epidemic that till date has no cure. A potential way to reduce ZIKV virulence is to limit the action of the non-structural proteins involved in its viral replication. One such protein, NS1, encoded as a monomer by the viral genome, plays a major role via symmetric oligomerization. We examine the homodimeric structure of the dominant β-ladder

    更新日期:2020-09-07
  • Native Cell Environment Constrains Loop Structure in the Escherichia coli Cobalamin Transporter BtuB.
    Biophys. J. (IF 3.854) Pub Date : 2020-09-06
    David A Nyenhuis,Thushani D Nilaweera,David S Cafiso

    The extracellular loops of bacterial outer membrane transporters are thought to sample a range of conformations in the apo state but to undergo a gating motion and assume a more defined conformation upon the binding of substrate. Here, we use pulse EPR to examine the conformations of the extracellular loops of BtuB, the Escherichia coli TonB-dependent vitamin B12 transporter, in whole cells. Unlike

    更新日期:2020-09-07
  • Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA.
    Biophys. J. (IF 3.854) Pub Date : 2020-09-02
    Dhiman Ray,Ioan Andricioaei

    Genetic information is encoded in the DNA double helix which, in its physiological milieu, is characterized by the iconical Watson-Crick nucleobase pairing. Recent NMR relaxation experiments revealed the transient presence of an alternative, Hoogsteen base pairing pattern in naked DNA duplexes and estimated its relative stability and lifetime. In contrast with DNA, such structures were not observed

    更新日期:2020-09-02
  • Four-State Model for Simulating Kinetic and Steady-State Voltage-Dependent Gating of Gap Junctions.
    Biophys. J. (IF 3.854) Pub Date : 2020-09-02
    Mindaugas Snipas,Tadas Kraujalis,Kestutis Maciunas,Lina Kraujaliene,Lukas Gudaitis,Vytas K Verselis

    Gap junction (GJ) channels, formed of connexin (Cx) proteins, provide a direct pathway for metabolic and electrical cell-to-cell communication. These specialized channels are not just passive conduits for the passage of ions and metabolites, but have been shown to gate robustly in response to transjunctional voltage, Vj, the voltage difference between two coupled cells. Voltage gating of GJs could

    更新日期:2020-09-02
  • Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability.
    Biophys. J. (IF 3.854) Pub Date : 2020-09-02
    Chenhan Zhao,Dong Zhang,Yangwei Jiang,Shi-Jie Chen

    The ability to accurately predict RNA hairpin structure and stability for different loop sequences and salt conditions is important for understanding, modeling, and designing larger RNA folds. However, traditional RNA secondary structure models cannot treat loop-sequence and ionic effects on RNA hairpin folding. Here, we describe a general, 3D conformation-based computational method for modeling salt

    更新日期:2020-09-02
  • Orthosteric and Allosteric Activation of Human 5-HT3A Receptors.
    Biophys. J. (IF 3.854) Pub Date : 2020-09-02
    Noelia Rodriguez Araujo,Camila Fabiani,Albano Mazzarini Dimarco,Cecilia Bouzat,Jeremías Corradi

    The serotonin type 3 receptor (5-HT3) is a ligand-gated ion channel that converts the binding of the neurotransmitter serotonin (5-HT) into a transient cation current which mediates fast excitatory responses in peripheral and central nervous systems. Information regarding the activation and modulation of the human 5-HT3 type A receptor has been based only on macroscopic current measurements due to

    更新日期:2020-09-02
  • Piezo1 Forms Specific, Functionally Important Interactions with Phosphoinositides and Cholesterol.
    Biophys. J. (IF 3.854) Pub Date : 2020-09-02
    Amanda Buyan,Charles D Cox,Jonathan Barnoud,Jinyuan Li,Hannah S M Chan,Boris Martinac,Siewert J Marrink,Ben Corry

    Touch, hearing, and blood pressure regulation require mechanically-gated ion channels that convert mechanical stimuli into electrical currents. One such channel is Piezo1, which plays a key role in the transduction of mechanical stimuli in humans, and is implicated in diseases, such as xerocytosis and lymphatic dysplasia. There is building evidence that suggests Piezo1 can be regulated by the membrane

    更新日期:2020-09-02
  • The Multiscale Future of RNA Modeling.
    Biophys. J. (IF 3.854) Pub Date : 2020-09-02
    Petr Šulc

    更新日期:2020-09-02
  • 更新日期:2020-09-02
  • Regulating Lipid Composition Rationalizes Acyl Tail Saturation Homeostasis in Ectotherms.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-06
    Martin Girard,Tristan Bereau

    Cell membranes mainly consist of lipid bilayers with an actively regulated composition. The underlying processes are still poorly understood, in particular, how the hundreds of components are controlled. Cholesterol has been found to correlate with phospholipid saturation for reasons that remain unclear. To better understand the link between cell membrane regulation and chemical composition, we establish

    更新日期:2020-09-01
  • Quantifying Fibrinogen-Dependent Aggregation of Red Blood Cells in Type 2 Diabetes Mellitus.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-07
    Yixiang Deng,Dimitrios P Papageorgiou,Xuejin Li,Nikolaos Perakakis,Christos S Mantzoros,Ming Dao,George Em Karniadakis

    Fibrinogen is regarded as the main glycoprotein in the aggregation of red blood cells (RBCs), a normally occurring phenomenon that has a major impact on blood rheology and hemodynamics, especially under pathological conditions, including type 2 diabetes mellitus (T2DM). In this study, we investigate the fibrinogen-dependent aggregation dynamics of T2DM RBCs through patient-specific predictive computational

    更新日期:2020-09-01
  • Sphingomyelin Acyl Chains Influence the Formation of Sphingomyelin- and Cholesterol-Enriched Domains.
    Biophys. J. (IF 3.854) Pub Date : 2020-07-24
    Oskar Engberg,Kai-Lan Lin,Victor Hautala,J Peter Slotte,Thomas K M Nyholm

    The segregation of lipids into lateral membrane domains has been extensively studied. It is well established that the structural differences between phospholipids play an important role in lateral membrane organization. When a high enough cholesterol concentration is present in the bilayer, liquid-ordered (Lo) domains, which are enriched in cholesterol and saturated phospholipids such as sphingomyelin

    更新日期:2020-09-01
  • Rapid Formation of Peptide/Lipid Coaggregates by the Amyloidogenic Seminal Peptide PAP248-286.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-06
    Eleanor W Vane,Shushan He,Lutz Maibaum,Abhinav Nath

    Protein/lipid coassembly is an understudied phenomenon that is important to the function of antimicrobial peptides as well as the pathological effects of amyloid. Here, we study the coassembly process of PAP248-286, a seminal peptide that displays both amyloid-forming and antimicrobial activity. PAP248-286 is a peptide fragment of prostatic acid phosphatase and has been reported to form amyloid fibrils

    更新日期:2020-09-01
  • Mechanical Unfolding of Proteins-A Comparative Nonequilibrium Molecular Dynamics Study.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-06
    Vasyl V Mykuliak,Mateusz Sikora,Jonathan J Booth,Marek Cieplak,Dmitrii V Shalashilin,Vesa P Hytönen

    Mechanical signals regulate functions of mechanosensitive proteins by inducing structural changes that are determinant for force-dependent interactions. Talin is a focal adhesion protein that is known to extend under mechanical load, and it has been shown to unfold via intermediate states. Here, we compared different nonequilibrium molecular dynamics (MD) simulations to study unfolding of the talin

    更新日期:2020-09-01
  • Interplay of Disorder and Sequence Specificity in the Formation of Stable Dynein-Dynactin Complexes.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-05
    Nikolaus M Loening,Sanjana Saravanan,Nathan E Jespersen,Kayla Jara,Elisar Barbar

    Cytoplasmic dynein is a eukaryotic motor protein complex that, along with its regulatory protein dynactin, is essential to the transport of organelles within cells. The interaction of dynein with dynactin is regulated by binding between the intermediate chain (IC) subunit of dynein and the p150Glued subunit of dynactin. Even though in the rat versions of these proteins this interaction primarily involves

    更新日期:2020-09-01
  • Mechanically Regulated Outside-In Activation of an I-Domain-Containing Integrin.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-05
    Debin Mao,Shouqin Lü,Xiao Zhang,Mian Long

    Integrins are heterodimeric transmembrane proteins that mediate cellular adhesion and bidirectional mechanotransductions through their conformational allostery. The allosteric pathway of an I-domain-containing integrin remains unclear because of its complexity and lack of effective experiments. For a typical I-domain-containing integrin αXβ2, molecular dynamics simulations were employed here to investigate

    更新日期:2020-09-01
  • Conformational Stability and Dynamics in Crystals Recapitulate Protein Behavior in Solution.
    Biophys. J. (IF 3.854) Pub Date : 2020-07-24
    Benedetta Maria Sala,Tanguy Le Marchand,Guido Pintacuda,Carlo Camilloni,Antonino Natalello,Stefano Ricagno

    A growing body of evidences has established that in many cases proteins may preserve most of their function and flexibility in a crystalline environment, and several techniques are today capable to characterize molecular properties of proteins in tightly packed lattices. Intriguingly, in the case of amyloidogenic precursors, the presence of transiently populated states (hidden to conventional crystallographic

    更新日期:2020-09-01
  • Non-Langmuir Kinetics of DNA Surface Hybridization.
    Biophys. J. (IF 3.854) Pub Date : 2020-07-29
    Luka Vanjur,Thomas Carzaniga,Luca Casiraghi,Marcella Chiari,Giuliano Zanchetta,Marco Buscaglia

    Hybridization of complementary single strands of DNA represents a very effective natural molecular recognition process widely exploited for diagnostic, biotechnology, and nanotechnology applications. A common approach relies on the immobilization on a surface of single-stranded DNA probes that bind complementary targets in solution. However, despite the deep knowledge on DNA interactions in bulk solution

    更新日期:2020-09-01
  • A Stochastic Model of Gene Expression with Polymerase Recruitment and Pause Release.
    Biophys. J. (IF 3.854) Pub Date : 2020-08-03
    Zhixing Cao,Tatiana Filatova,Diego A Oyarzún,Ramon Grima

    Transcriptional bursting is a major source of noise in gene expression. The telegraph model of gene expression, whereby transcription switches between on and off states, is the dominant model for bursting. Recently, it was shown that the telegraph model cannot explain a number of experimental observations from perturbation data. Here, we study an alternative model that is consistent with the data and

    更新日期:2020-09-01
  • Modeling the Control of Meiotic Cell Divisions: Entry, Progression, and Exit.
    Biophys. J. (IF 3.854) Pub Date : 2020-07-29
    Prakrati Dangarh,Nishtha Pandey,Palakkad Krishnanunni Vinod

    Upon nitrogen starvation, Schizosaccharomyces pombe exit the mitotic cell cycle and become irreversibly committed to the completion of meiosis program. Meiotic cell divisions are coordinated with sporulation events to produce haploid spores. In the last few decades, experiments on fission yeast have revealed different molecular players involved in two meiotic cell divisions, meiosis I (MI) and meiosis

    更新日期:2020-09-01
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