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Molecular mechanisms of precise timing in cell lysis Biophys. J. (IF 3.2) Pub Date : 2024-07-06 Anupam Mondal, Hamid Teimouri, Anatoly B. Kolomeisky
Many biological systems exhibit precise timing of events, and one of the most known examples is cell lysis, which is a process of breaking bacterial host cells in the virus infection cycle. However, the underlying microscopic picture of precise timing remains not well understood. We present a novel theoretical approach to explain the molecular mechanisms of effectively deterministic dynamics in biological
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Effects of pH on opioid receptor activation and implications for drug design Biophys. J. (IF 3.2) Pub Date : 2024-07-05 Christoph Stein
G-protein-coupled receptors are integral membrane proteins that transduce chemical signals from the extracellular matrix into the cell. Traditional drug design has considered ligand-receptor interactions only under normal conditions. However, studies on opioids indicate that such interactions are very different in diseased tissues. In such microenvironments, protons play an important role in structural
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A colloidal model for the equilibrium assembly and liquid-liquid phase separation of the reflectin A1 protein Biophys. J. (IF 3.2) Pub Date : 2024-07-04 Tse-Chiang Huang, Robert Levenson, Youli Li, Phillip Kohl, Daniel E. Morse, M. Scott Shell, Matthew E. Helgeson
Reflectin is an intrinsically disordered protein known for its ability to modulate the biophotonic camouflage of cephalopods based on its assembly-induced osmotic properties. Its reversible self-assembly into discrete, size-controlled clusters and condensed droplets are known to depend sensitively on the net protein charge, making reflectin stimuli-responsive to pH, phosphorylation, and electric fields
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Optical torque calculations and measurements for DNA torsional studies Biophys. J. (IF 3.2) Pub Date : 2024-07-03 Yifeng Hong, Fan Ye, Jin Qian, Xiang Gao, James T. Inman, Michelle D. Wang
The angular optical trap (AOT) is a powerful instrument for measuring the torsional and rotational properties of a biological molecule. Thus far, AOT studies of DNA torsional mechanics have been carried out using a high numerical aperture oil-immersion objective, which permits strong trapping but inevitably introduces spherical aberrations due to the glass-aqueous interface. However, the impact of
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Phalloidin-PAINT: Enhanced quantitative nanoscale imaging of F-actin Biophys. J. (IF 3.2) Pub Date : 2024-07-03 Hirushi Gunasekara, Thilini Perera, Chih-Jia Chao, Joshua Bruno, Badeia Saed, Jesse Anderson, Zongmin Zhao, Ying S. Hu
We present phalloidin-based points accumulation for imaging in nanoscale topography (phalloidin-PAINT), enabling quantitative superresolution imaging of filamentous actin (F-actin) in the cell body and delicate membrane protrusions. We demonstrate that the intrinsic phalloidin dissociation enables PAINT superresolution microscopy in an imaging buffer containing low concentrations of dye-conjugated
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Proton diffusion on the surface of mixed lipid membranes highlights the role of membrane composition Biophys. J. (IF 3.2) Pub Date : 2024-07-02 Ambili Ramanthrikkovil Variyam, Mateusz Rzycki, Anna Yucknovsky, Alexei A. Stuchebrukhov, Dominik Drabik, Nadav Amdursky
Proton circuits within biological membranes, the foundation of natural bioenergetic systems, are significantly influenced by the lipid compositions of different biological membranes. In this study, we investigate the influence of mixed lipid membrane composition on the proton transfer (PT) properties on the surface of the membrane. We track the excited-state PT (ESPT) process from a tethered probe
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FimH-mannose noncovalent bonds survive minutes to hours under force Biophys. J. (IF 3.2) Pub Date : 2024-07-02 Laura A. Carlucci, Keith C. Johnson, Wendy E. Thomas
The adhesin FimH is expressed by commensal and is implicated in urinary tract infections, where it mediates adhesion to mannosylated glycoproteins on urinary and intestinal epithelial cells in the presence of a high-shear fluid environment. The FimH-mannose bond exhibits catch behavior in which bond lifetime increases with force, because tensile force induces a transition in FimH from a compact native
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Sarcomere, troponin, and myosin X-ray diffraction signals can be resolved in single cardiomyocytes Biophys. J. (IF 3.2) Pub Date : 2024-07-02 Hendrik Bruns, Titus S. Czajka, Michael Sztucki, Sören Brandenburg, Tim Salditt
Cardiac function relies on the autonomous molecular contraction mechanisms in the ventricular wall. Contraction is driven by ordered motor proteins acting in parallel to generate a macroscopic force. The averaged structure can be investigated by diffraction from model tissues such as trabecular and papillary cardiac muscle using collimated synchrotron beams, offering high resolution in reciprocal space
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Insight into molecular basis and dynamics of full-length CRaf kinase in cellular signaling mechanisms Biophys. J. (IF 3.2) Pub Date : 2024-06-29 Van A. Ngo
Raf kinases play key roles in signal transduction in cells for regulating proliferation, differentiation, and survival. Despite decades of research into functions and dynamics of Raf kinases with respect to other cytosolic proteins, understanding Raf kinases is limited by the lack of their full-length structures at the atomic resolution. Here, we present the first model of the full-length CRaf kinase
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Bioelectricity and molecular signaling Biophys. J. (IF 3.2) Pub Date : 2024-06-29 Marcel P. Goldschen-Ohm, Baron Chanda
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Core-shell model of the clusters of CPEB4 isoforms preceding liquid-liquid phase separation Biophys. J. (IF 3.2) Pub Date : 2024-06-28 Maria Oranges, Chandrima Jash, Gonen Golani, Manas Seal, Sidney R. Cohen, Irit Rosenhek-Goldian, Alexey Bogdanov, Samuel Safran, Daniella Goldfarb
Protein solutions can undergo liquid-liquid phase separation (LLPS), where a dispersed phase with a low protein concentration coexists with coacervates with a high protein concentration. We focus on the low complexity N-terminal domain of cytoplasmic polyadenylation element binding-4 protein, CPEB4, and its isoform depleted of the Exon4, CPEB4Δ4. They both exhibit LLPS, but in contrast to most systems
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Conformational rigidity of cytochrome c'-α from a thermophile is associated with slow NO binding Biophys. J. (IF 3.2) Pub Date : 2024-06-26 Sotaro Fujii, Michael T. Wilson, Hannah R. Adams, Halina Mikolajek, Dimitri A. Svistunenko, Peter Smyth, Colin R. Andrew, Yoshihiro Sambongi, Michael A. Hough
Cytochromes ′-α are nitric oxide (NO)-binding heme proteins derived from bacteria that can thrive in a wide range of temperature environments. Studies of mesophilic cytochrome ′-α (AxCP-α) have revealed an unusual NO-binding mechanism involving both heme faces, in which NO first binds to form a distal hexa-coordinate Fe(II)-NO (6cNO) intermediate and then displaces the proximal His to form a proximal
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Conformations of influenza A M2 protein in DOPC/DOPS and E. coli native lipids and proteins Biophys. J. (IF 3.2) Pub Date : 2024-06-25 Griffin Sanders, Peter P. Borbat, Elka R. Georgieva
We compared the conformations of the transmembrane domain (TMD) of influenza A M2 (IM2) protein reconstituted in 1,2-dioleoyl-sn-glycero-3-phosphocholine/1,2-dioleoyl-sn-glycero-3-phospho-L-serine (DOPC/DOPS) bilayers to those in isolated () membranes, having preserved its native proteins and lipids. IM2 is a single-pass transmembrane protein known to assemble into a homo-tetrameric proton channel
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Hi-C-guided many-polymer model to decipher 3D genome organization Biophys. J. (IF 3.2) Pub Date : 2024-06-25 Chen Shi, Lei Liu, Changbong Hyeon
We propose a high-throughput chromosome conformation capture data-based many-polymer model that allows us to generate an ensemble of multi-scale genome structures. We demonstrate the efficacy of our model by validating the generated structures against experimental measurements and employ them to address key questions regarding genome organization. Our model first confirms a significant correlation
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Time-resolved fluorescence of tryptophan characterizes membrane perturbation by cyclic lipopeptides Biophys. J. (IF 3.2) Pub Date : 2024-06-22 Iulia Carabadjac, Jessica Steigenberger, Niels Geudens, Vic De Roo, Penthip Muangkaew, Annemieke Madder, José C. Martins, Heiko Heerklotz
Viscosin is a membrane-permeabilizing, cyclic lipopeptide (CLiP) produced by species. Here, we have studied four synthetic analogs (L1W, V4W, L5W, and L7W), each with one leucine (Leu; L) or valine residue exchanged for tryptophan (Trp; W) by means of time-resolved fluorescence spectroscopy of Trp. To this end, we recorded the average fluorescence lifetime, rotational correlation time and limiting
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Modulating Ca2+ influx into adrenal chromaffin cells with short-duration nanosecond electric pulses Biophys. J. (IF 3.2) Pub Date : 2024-06-21 Sung Hae Yun, Vasilii Mansurov, Lisha Yang, Jihwan Yoon, Normand Leblanc, Gale L. Craviso, Josette Zaklit
Isolated bovine adrenal chromaffin cells exposed to single 2-, 4-, or 5-ns pulses undergo a rapid, transient rise in intracellular Ca mediated by Ca entry via voltage-gated Ca channels (VGCCs), mimicking the activation of these cells in vivo by acetylcholine. However, pulse durations 150 ns or longer elicit larger amplitude and longer-lived Ca responses due to Ca influx via both VGCCs and a yet to
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Coupling the role of lipids to the conformational dynamics of the ABC transporter P-glycoprotein Biophys. J. (IF 3.2) Pub Date : 2024-06-21 Dario De Vecchis, Lars V. Schäfer
The ATP-binding cassette transporter P-glycoprotein (P-gp) is a multidrug efflux pump that is overexpressed in a variety of cancers and associated with the drug-resistance phenomenon. P-gp structures were previously determined in detergent and in nanodiscs, in which different transmembrane helix conformations were found, “straight” and “kinked,” respectively, indicating a possible role of the lipid
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Auxin-mediated stress relaxation in pericycle and endoderm remodeling drives lateral root initiation Biophys. J. (IF 3.2) Pub Date : 2024-06-20 João R.D. Ramos, Blanca Jazmin Reyes-Hernández, Karen Alim, Alexis Maizel
Plant development relies on the precise coordination of cell growth, which is influenced by the mechanical constraints imposed by rigid cell walls. The hormone auxin plays a crucial role in regulating this growth by altering the mechanical properties of cell walls. During the postembryonic formation of lateral roots, pericycle cells deep within the main root are triggered by auxin to resume growth
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After the gold rush: Getting far from the shallow in studying asymmetric membranes Biophys. J. (IF 3.2) Pub Date : 2024-06-19 Georg Pabst, Heiko Heerklotz
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Kismet/CHD7/CHD8 affects gut microbiota, mechanics, and the gut-brain axis in Drosophila melanogaster Biophys. J. (IF 3.2) Pub Date : 2024-06-19 Angelo Niosi, Nguyên Henry Võ, Punithavathi Sundaramurthy, Chloe Welch, Aliyah Penn, Yelena Yuldasheva, Adam Alfareh, Kaitlyn Rausch, Takhmina Amin-Rahbar, Jeffery Cavanaugh, Prince Yadav, Stephanie Peterson, Raina Brown, Alain Hu, Any Ardon-Castro, Darren Nguyen, Robert Crawford, Wendy Lee, Eliza J. Morris, Mikkel Herholdt Jensen, Kimberly Mulligan
The gut microbiome affects brain and neuronal development and may contribute to the pathophysiology of neurodevelopmental disorders. However, it is unclear how risk genes associated with such disorders affect gut physiology in a manner that could impact microbial colonization and how the mechanical properties of the gut tissue might play a role in gut-brain bidirectional communication. To address this
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Hydrodynamic and thermodynamic analysis of PEGylated human serum albumin Biophys. J. (IF 3.2) Pub Date : 2024-06-18 John J. Correia, Walter F. Stafford, Heidi Erlandsen, James L. Cole, Sanduni H. Premathilaka, Dragan Isailovic, John David Dignam
Covalent labeling of therapeutic drugs and proteins with polyethylene glycol (PEGylation) is an important modification for improving stability, solubility, and half-life. PEGylation alters protein solution behavior through its impact on thermodynamic nonideality by increasing the excluded volume, and on hydrodynamic nonideality by increasing the frictional drag. To understand PEGylation’s impact, we
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Cracked actin filaments as mechanosensitive receptors Biophys. J. (IF 3.2) Pub Date : 2024-06-17 Vilmos Zsolnay, Margaret L. Gardel, David R. Kovar, Gregory A. Voth
Actin filament networks are exposed to mechanical stimuli, but the effect of strain on actin filament structure has not been well established in molecular detail. This is a critical gap in understanding because the activity of a variety of actin-binding proteins has recently been determined to be altered by actin filament strain. We therefore used all-atom molecular dynamics simulations to apply tensile
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Molecular mechanism of anion permeation through aquaporin 6 Biophys. J. (IF 3.2) Pub Date : 2024-06-17 Eiji Yamamoto, Keehyoung Joo, Jooyoung Lee, Mark S.P. Sansom, Masato Yasui
Aquaporins (AQPs) are recognized as transmembrane water channels that facilitate selective water permeation through their monomeric pores. Among the AQP family, AQP6 has an intriguing characteristic as an anion channel, which is allosterically controlled by pH conditions and is eliminated by a single amino acid mutation. However, the molecular mechanism of anion permeation through AQP6 remains unclear
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Quantification of membrane fluidity in bacteria using TIR-FCS Biophys. J. (IF 3.2) Pub Date : 2024-06-13 Aurélien Barbotin, Cyrille Billaudeau, Erdinc Sezgin, Rut Carballido-López
Plasma membrane fluidity is an important phenotypic feature that regulates the diffusion, function, and folding of transmembrane and membrane-associated proteins. In bacterial cells, variations in membrane fluidity are known to affect respiration, transport, and antibiotic resistance. Membrane fluidity must therefore be tightly regulated to adapt to environmental variations and stresses such as temperature
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Impact of trypsin on cell cytoplasm during detachment of cells studied by terahertz sensing Biophys. J. (IF 3.2) Pub Date : 2024-06-13 Blandine Lordon, Tiffany Campion, Laure Gibot, Guilhem Gallot
Trypsin is a very common enzyme used in cell culture to harvest cells by cleaving the proteins responsible for cell adhesion. However, trypsin also induces undesirable effects on cells, such as altering membrane proteins and the cytoskeleton, changing the composition of the cytoplasm and the cell volume, and even leading to cell death when used improperly. Using attenuated total reflection in the terahertz
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Integrin mechanosensing relies on a pivot-clip mechanism to reinforce cell adhesion Biophys. J. (IF 3.2) Pub Date : 2024-06-13 Andre R. Montes, Anahi Barroso, Wei Wang, Grace D. O’Connell, Adrian B. Tepole, Mohammad R.K. Mofrad
Cells intricately sense mechanical forces from their surroundings, driving biophysical and biochemical activities. This mechanosensing phenomenon occurs at the cell-matrix interface, where mechanical forces resulting from cellular motion, such as migration or matrix stretching, are exchanged through surface receptors, primarily integrins, and their corresponding matrix ligands. A pivotal player in
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Transient pores in hemifusion diaphragms Biophys. J. (IF 3.2) Pub Date : 2024-06-11 Russell K.W. Spencer, Yuliya G. Smirnova, Alireza Soleimani, Marcus Müller
Exchange of material across two membranes, as in the case of synaptic neurotransmitter release from a vesicle, involves the formation and poration of a hemifusion diaphragm (HD). The nontrivial geometry of the HD leads to environment-dependent control, regarding the stability and dynamics of the pores required for this kind of exocytosis. This work combines particle simulations, field-based calculations
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Biophysics of claudin proteins in tight junction architecture: Three decades of progress Biophys. J. (IF 3.2) Pub Date : 2024-06-10 Patrick Marsch, Nandhini Rajagopal, Shikha Nangia
Tight junctions are cell-cell adhesion complexes that act as gatekeepers of the paracellular space. Formed by several transmembrane proteins, the claudin family performs the primary gate-keeping function. The claudin proteins form charge and size-selective diffusion barriers to maintain homeostasis across endothelial and epithelial tissue. Of the 27 known claudins in mammals, some are known to seal
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Coarse-grained modeling of annexin A2-induced microdomain formation on a vesicle Biophys. J. (IF 3.2) Pub Date : 2024-06-10 S. Lindsay, Y. Li
Annexin A2 (A2)-induced microdomain formation is a key step in biological processes such as Ca-mediated exocytosis in neuroendocrine cells. In this work, a total of 15 coarse-grained molecular dynamics simulations were performed on vesicle models having a diameter of approximately 250 Å for 15 s each using the Martini2 force field. Five simulations were performed in the presence of 10 A2, 5 in the
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Fluidic shear stress alters clathrin dynamics and vesicle formation in endothelial cells Biophys. J. (IF 3.2) Pub Date : 2024-06-08 Tomasz J. Nawara, Jie Yuan, Leslie D. Seeley, Elizabeth Sztul, Alexa L. Mattheyses
Endothelial cells (ECs) experience a variety of highly dynamic mechanical stresses. Among others, cyclic stretch and increased plasma membrane tension inhibit clathrin-mediated endocytosis (CME) in non-ECs. It remains elusive how ECs maintain CME in these biophysically unfavorable conditions. Previously, we have used simultaneous two-wavelength axial ratiometry (STAR) microscopy to show that endocytic
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Identifying the molecular basis of Laminin N-terminal domain Ca2+ binding using a hybrid approach Biophys. J. (IF 3.2) Pub Date : 2024-06-08 Scott Legare, Fabian Heide, Haben Gabir, Faride Rafiei, Markus Meier, Gay Pauline Padilla-Meier, Manuel Koch, Jörg Stetefeld
Ca is a highly abundant ion involved in numerous biological processes, particularly in multicellular eukaryotic organisms where it exerts many of these functions through interactions with Ca binding proteins. The laminin N-terminal (LN) domain is found in members of the laminin and netrin protein families where it plays a critical role in the function of these proteins. The LN domain of laminins and
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AbMelt: Learning antibody thermostability from molecular dynamics Biophys. J. (IF 3.2) Pub Date : 2024-06-07 Zachary A. Rollins, Talal Widatalla, Alan C. Cheng, Essam Metwally
Antibody thermostability is challenging to predict from sequence and/or structure. This difficulty is likely due to the absence of direct entropic information. Herein, we present AbMelt where we model the inherent flexibility of homologous antibody structures using molecular dynamics simulations at three temperatures and learn the relevant descriptors to predict the temperatures of aggregation (T)
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Varying the position of phospholipid acyl chain unsaturation modulates hopanoid and sterol ordering Biophys. J. (IF 3.2) Pub Date : 2024-06-06 Ha-Ngoc-Anh Nguyen, Liam Sharp, Edward Lyman, James P. Saenz
The cell membrane must balance mechanical stability with fluidity to function as both a barrier and an organizational platform. Key to this balance is the ordering of hydrocarbon chains and the packing of lipids. Many eukaryotes synthesize sterols, which are uniquely capable of modulating the lipid order to decouple membrane stability from fluidity. Ancient sterol analogs known as hopanoids are found
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Confinement energy landscape classification reveals membrane receptor nano-organization mechanisms Biophys. J. (IF 3.2) Pub Date : 2024-06-06 Chao Yu, Maximilian Richly, Thi Thuy Hoang, Mohammed El Beheiry, Silvan Türkcan, Jean-Baptiste Masson, Antigoni Alexandrou, Cedric I. Bouzigues
The cell membrane organization has an essential functional role through the control of membrane receptor confinement in micro- or nanodomains. Several mechanisms have been proposed to account for these properties, although some features have remained controversial, notably the nature, size, and stability of cholesterol- and sphingolipid-rich domains or lipid rafts. Here, we probed the effective energy
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On the response of elongating ribosomes to forces opposing translocation Biophys. J. (IF 3.2) Pub Date : 2024-06-06 Peter B. Moore
The elongation phase of protein synthesis is a cyclic, steady-state process. It follows that its directionality is determined by the thermodynamics of the accompanying chemical reactions, which strongly favor elongation. Its irreversibility is guaranteed by its coupling to those reactions, rather being a consequence of any of the conformational changes that occur as it unfolds. It also follows that
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Beyond stiffness: Multiscale viscoelastic features as biomechanical markers for assessing cell types and states Biophys. J. (IF 3.2) Pub Date : 2024-06-04 Zhuo Chang, Li-Ya Li, Zhi-Jun Shi, Wenjia Liu, Guang-Kui Xu
Cell mechanics are pivotal in regulating cellular activities, diseases progression, and cancer development. However, the understanding of how cellular viscoelastic properties vary in physiological and pathological stimuli remains scarce. Here, we develop a hybrid self-similar hierarchical theory-microrheology approach to accurately and efficiently characterize cellular viscoelasticity. Focusing on
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SANS reveals lipid-dependent oligomerization of an intramembrane aspartyl protease from H. volcanii Biophys. J. (IF 3.2) Pub Date : 2024-06-01 Gwendell M. Thomas, Yuqi Wu, Wellington Leite, Sai Venkatesh Pingali, Kevin L. Weiss, Arshay J. Grant, Monneh W. Diggs, Ingeborg Schmidt-Krey, Gvantsa Gutishvili, James C. Gumbart, Volker S. Urban, Raquel L. Lieberman
Reactions that occur within the lipid membrane involve, at minimum, ternary complexes among the enzyme, substrate, and lipid. For many systems, the impact of the lipid in regulating activity or oligomerization state is poorly understood. Here, we used small-angle neutron scattering (SANS) to structurally characterize an intramembrane aspartyl protease (IAP), a class of membrane-bound enzymes that use
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Effect of leaflet asymmetry on the stretching elasticity of lipid bilayers with phosphatidic acid Biophys. J. (IF 3.2) Pub Date : 2024-05-31 Dominik Drabik, Piotr Hinc, Mareike Stephan, Rafaela R.M. Cavalcanti, Aleksander Czogalla, Rumiana Dimova
The asymmetry of membranes has a significant impact on their biophysical characteristics and behavior. This study investigates the composition and mechanical properties of symmetric and asymmetric membranes in giant unilamellar vesicles (GUVs) made of palmitoyloleoyl phosphatidylcholine (POPC) and palmitoyloleoyl phosphatidic acid (POPA). A combination of fluorescence quantification, zeta potential
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Triacylglycerol-droplet-induced bilayer spontaneous curvature in giant unilamellar vesicles Biophys. J. (IF 3.2) Pub Date : 2024-05-31 Chiho Kataoka-Hamai
This study investigated the incorporation of triacylglycerol droplets in the bilayers of giant unilamellar vesicles (GUVs) using four triacylglycerols and four phosphatidylcholines by confocal laser scanning microscopy. The triacylglycerol droplets were incorporated between the monolayer leaflets of the GUVs. Among the spherical droplets protruding on only one side of the bilayers, the droplets bound
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Competing mechanisms in bacterial invasion of human colon mucus probed with agent-based modeling Biophys. J. (IF 3.2) Pub Date : 2024-05-31 Zhongyu Yan, Jingjie Yeo
The gastrointestinal tract is inhabited by a vast community of microorganisms, termed the gut microbiota. Large colonies can pose a health threat, but the gastrointestinal mucus system protects epithelial cells from microbiota invasion. The human colon features a bilayer of mucus lining. Due to imbalances in intestinal homeostasis, bacteria may successfully penetrate the inner mucus layer, which can
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Shape of the membrane neck around a hole during plasma membrane repair Biophys. J. (IF 3.2) Pub Date : 2024-05-31 Martin Berg Klenow, Magnus Staal Vigsø, Weria Pezeshkian, Jesper Nylandsted, Michael Andersen Lomholt, Adam Cohen Simonsen
Plasma membrane damage and rupture occurs frequently in cells, and holes must be sealed rapidly to ensure homeostasis and cell survival. The membrane repair machinery is known to involve recruitment of curvature-inducing annexin proteins, but the connection between membrane remodeling and hole closure is poorly described. The induction of curvature by repair proteins leads to the possible formation
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Preserving condensate structure and composition by lowering sequence complexity Biophys. J. (IF 3.2) Pub Date : 2024-05-31 Amogh Sood, Bin Zhang
Biomolecular condensates play a vital role in organizing cellular chemistry. They selectively partition biomolecules, preventing unwanted cross talk and buffering against chemical noise. Intrinsically disordered proteins (IDPs) serve as primary components of these condensates due to their flexibility and ability to engage in multivalent interactions, leading to spontaneous aggregation. Theoretical
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A multiscale sensorimotor model of experience-dependent behavior in a minimal organism Biophys. J. (IF 3.2) Pub Date : 2024-05-29 María Sol Vidal-Saez, Oscar Vilarroya, Jordi Garcia-Ojalvo
To survive in ever-changing environments, living organisms need to continuously combine the ongoing external inputs they receive, representing present conditions, with their dynamical internal state, which includes influences of past experiences. It is still unclear in general, however 1) how this happens at the molecular and cellular levels and 2) how the corresponding molecular and cellular processes
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Cardiac length-dependent activation driven by force-dependent thick-filament dynamics Biophys. J. (IF 3.2) Pub Date : 2024-05-28 Alexandre Lewalle, Gregory Milburn, Kenneth S. Campbell, Steven A. Niederer
The length-dependent activation (LDA) of maximum force and calcium sensitivity are established features of cardiac muscle contraction but the dominant underlying mechanisms remain to be fully clarified. Alongside the well-documented regulation of contraction via the thin filaments, experiments have identified an additional force-dependent thick-filament activation, whereby myosin heads parked in a
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Photoinhibition of the hERG potassium channel PAS domain by ultraviolet light speeds channel closing Biophys. J. (IF 3.2) Pub Date : 2024-05-24 Sara J. Codding, Matthew C. Trudeau
hERG potassium channels are critical for cardiac excitability. hERG channels have a Per-Arnt-Sim (PAS) domain at their N-terminus, and here, we examined the mechanism for PAS domain regulation of channel opening and closing (gating). We used TAG codon suppression to incorporate the noncanonical amino acid 4-benzoyl-L-phenylalanine (BZF), which is capable of forming covalent cross-links after photoactivation
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Controlling heme redox properties in peptide amphiphile fibers with sequence and heme loading ratio Biophys. J. (IF 3.2) Pub Date : 2024-05-23 Chiranjit Dutta, Virginia Lopez, Conner Preston, Nimesh Rudra, Alex Mauricio Valdivia Chavez, Abigail M. Rogers, Lee A. Solomon
Controlling the reduction midpoint potential of heme B is a key factor in many bioelectrochemical reactions, including long-range electron transport. Currently, there are a number of globular model protein systems to study this biophysical parameter; however, there are none for large polymeric protein model systems (e.g., the OmcS protein from ). Peptide amphiphiles, short peptides with a lipid tail
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Mimicking the retinal neuron functions by a photoresponsive single transistor with a double gate Biophys. J. (IF 3.2) Pub Date : 2024-05-23 Qing-an Ding, Chaoran Gu, Jianyu Li, Xiaoyuan Li, BingHui Hou, Yandong Peng, Bing Chen, Youli Yao
To realize a low-cost neuromorphic visual system, employing an artificial neuron capable of mimicking the retinal neuron functions is essential. A photoresponsive single transistor neuron composed of a vertical silicon nanowire is proposed. Similar to retinal neurons, various photoresponsive characteristics of the single transistor neuron can be modulated by light intensity as well as wavelength and
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Mechanical characterization of regenerating Hydra tissue spheres Biophys. J. (IF 3.2) Pub Date : 2024-05-23 Thomas Perros, Anaïs Biquet-Bisquert, Zacchari Ben Meriem, Morgan Delarue, Pierre Joseph, Philippe Marcq, Olivier Cochet-Escartin
, long known for its remarkable regenerative capabilities, is also a long-standing source of inspiration for models of spontaneous patterning. Recently it became clear that early patterning during regeneration is an integrated mechanochemical process whereby morphogen dynamics is influenced by tissue mechanics. One roadblock to understanding self-organization is our lack of knowledge about the mechanical
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Mechanical control of antigen detection and discrimination by T and B cell receptors Biophys. J. (IF 3.2) Pub Date : 2024-05-23 Jhordan Rogers, Anna T. Bajur, Khalid Salaita, Katelyn M. Spillane
The adaptive immune response is orchestrated by just two cell types, T cells and B cells. Both cells possess the remarkable ability to recognize virtually any antigen through their respective antigen receptors—the T cell receptor (TCR) and B cell receptor (BCR). Despite extensive investigations into the biochemical signaling events triggered by antigen recognition in these cells, our ability to predict
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The molecular basis for hydrodynamic properties of PEGylated human serum albumin Biophys. J. (IF 3.2) Pub Date : 2024-05-22 Patrick J. Fleming, John J. Correia, Karen G. Fleming
Polyethylene glycol (PEG) conjugation provides a protective modification that enhances the pharmacokinetics and solubility of proteins for therapeutic use. A knowledge of the structural ensemble of these PEGylated proteins is necessary to understand the molecular details that contribute to their hydrodynamic and colligative properties. Because of the large size and dynamic flexibility of pharmaceutically
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The role of the STAS domain in SLC26A9 for chloride ion transporter function Biophys. J. (IF 3.2) Pub Date : 2024-05-21 Satoshi Omori, Yuya Hanazono, Hafumi Nishi, Kengo Kinoshita
The anion exchanger solute carrier family 26 (SLC26)A9, consisting of the transmembrane (TM) domain and the cytoplasmic STAS domain, plays an essential role in regulating chloride transport across cell membranes. Recent studies have indicated that C-terminal helices block the entrance of the putative ion transport pathway. However, the precise functions of the STAS domain and C-terminal helix, as well
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The contribution and mechanism of hypoxia/USP19/Beclin-1 feed-forward loop in cervical cancer Biophys. J. (IF 3.2) Pub Date : 2024-05-21 Guocai Xu, Shengjun Chai, Rong Zhang, Meiqi Chen, Xiaoxia Fan, Yao Zhang, Chunmei Cai, Ri-Li Ge
Cervical cancer ranks fourth in female mortality. Since the mechanisms for pathogenesis of cervical cancer are still poorly understood, the effective treatment options are lacking. Beclin-1 exhibits an inhibitory role in cervical cancer via suppressing the proliferation, invasion, and migration of cervical cancer cells. It is reported that USP19 removes the K11-linked ubiquitination of Beclin-1 to
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Structure-independent machine-learning predictions of the CDK12 interactome Biophys. J. (IF 3.2) Pub Date : 2024-05-18 Aleksandra Karolak, Konstancja Urbaniak, Andrii Monastyrskyi, Derek R. Duckett, Sergio Branciamore, Paul A. Stewart
Cyclin-dependent kinase 12 (CDK12) is a critical regulatory protein involved in transcription and DNA repair processes. Dysregulation of CDK12 has been implicated in various diseases, including cancer. Understanding the CDK12 interactome is pivotal for elucidating its functional roles and potential therapeutic targets. Traditional methods for interactome prediction often rely on protein structure information
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Parallel photocycle kinetic model of anion channelrhodopsin GtACR1 function Biophys. J. (IF 3.2) Pub Date : 2024-05-18 Istvan Szundi, David S. Kliger
The light-gated anion channelrhodopsin ACR1 is an important optogenetic tool for neuronal silencing. Its photochemistry, including its photointermediates, is poorly understood. The current mechanistic view presumes BR-like kinetics and assigns the open channel to a blue-absorbing L intermediate. Based on time-resolved absorption and electrophysiological data, we recently proposed a red-absorbing spectral
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Modeling reveals the strength of weak interactions in stacked-ring assembly Biophys. J. (IF 3.2) Pub Date : 2024-05-18 Leonila Lagunes, Koan Briggs, Paige Martin-Holder, Zaikun Xu, Dustin Maurer, Karim Ghabra, Eric J. Deeds
Cells employ many large macromolecular machines for the execution and regulation of processes that are vital for cell and organismal viability. Interestingly, cells cannot synthesize these machines as functioning units. Instead, cells synthesize the molecular parts that must then assemble into the functional complex. Many important machines, including chaperones such as GroEL and proteases such as
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Emerging biophysical principles of macromolecular phase separation Biophys. J. (IF 3.2) Pub Date : 2024-05-17 Galia T. Debelouchina, Keren Lasker, Samrat Mukhopadhyay
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Molecular dynamics simulations of lipid-protein interactions in SLC4 proteins Biophys. J. (IF 3.2) Pub Date : 2024-05-17 Hristina R. Zhekova, Daniel P. Ramirez Echemendía, Besian I. Sejdiu, Alexander Pushkin, D. Peter Tieleman, Ira Kurtz
The SLC4 family of secondary bicarbonate transporters is responsible for the transport of HCO, CO, Cl, Na, K, NH, and H, which are necessary for regulation of pH and ion homeostasis. They are widely expressed in numerous tissues throughout the body and function in different cell types with different membrane properties. Potential lipid roles in SLC4 function have been reported in experimental studies
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Protective effect of trehalose sugar on amyloid-membrane interactions using BLM electrophysiology Biophys. J. (IF 3.2) Pub Date : 2024-05-15 Yue Xu, Carina Teresa Filice, Zoya Leonenko
Alzheimer’s disease (AD) is a neurodegenerative disease characterized by dementia and memory loss in the elderly population. The amyloid-β peptide (Aβ) is one of the main pathogenic factors in AD and is known to cause damage to neuronal cellular membranes. There is no cure currently available for AD, and new approaches, including preventive strategies, are highly desirable. In this work, we explore
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MHC-Fine: Fine-tuned AlphaFold for precise MHC-peptide complex prediction Biophys. J. (IF 3.2) Pub Date : 2024-05-15 Ernest Glukhov, Dmytro Kalitin, Darya Stepanenko, Yimin Zhu, Thu Nguyen, George Jones, Taras Patsahan, Carlos Simmerling, Julie C. Mitchell, Sandor Vajda, Ken A. Dill, Dzmitry Padhorny, Dima Kozakov
The precise prediction of major histocompatibility complex (MHC)-peptide complex structures is pivotal for understanding cellular immune responses and advancing vaccine design. In this study, we enhanced AlphaFold’s capabilities by fine-tuning it with a specialized dataset consisting of exclusively high-resolution class I MHC-peptide crystal structures. This tailored approach aimed to address the generalist
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Peptide diffusion in biomolecular condensates Biophys. J. (IF 3.2) Pub Date : 2024-05-15 Riley J. Workman, Caleb J. Huang, Gillian C. Lynch, B. Montgomery Pettitt
Diffusion determines the turnover of biomolecules in liquid-liquid phase-separated condensates. We considered the mean square displacement and thus the diffusion constant for simple model systems of peptides GGGGG, GGQGG, and GGVGG in aqueous solutions after phase separation by simulating atomic-level models. These solutions readily separate into aqueous and peptide-rich droplet phases. We noted the