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On the emergence of orientational order in folded proteins with implications for allostery bioRxiv. Biophys. Pub Date : 2021-03-02 Debayan Chakraborty; Mauro Lorenzo Mugnai; D. Thirumalai
The beautiful structures of single and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully used to describe periodic crystals. For this reason, protein structures are considered to be aperiodic, and may have evolved this way for functional purposes, especially in instances that require a combination of softness
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Identification of the Rigid Core for Aged Liquid Droplets of the TDP-43 Low Complexity Domain bioRxiv. Biophys. Pub Date : 2021-03-02 Blake D Fonda; Khaled M Jami; Natalie R Boulos; Dylan Thomas Murray
The biomolecular condensation of proteins with low complexity sequences plays a functional role in RNA metabolism and a pathogenic role in neurodegenerative diseases. The formation of dynamic liquid droplets brings biomolecules together to achieve complex cellular functions. The rigidification of liquid droplets into β-strand-rich hydrogel structures composed of protein fibrils is thought to be purely
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The Origin of Conductive-Pulse Sensing Inside a Nanopore and the Role of Electro-Hydrodynamics bioRxiv. Biophys. Pub Date : 2021-03-02 Lauren Lastra; Michelle Nguyen; Nasim Farajpour; Kevin J. Freedman
Despite the highly negatively charged backbone of DNA, electroosmotic flow (EOF) within a nanopore can lead to DNA travelling opposite to electrophoretic force at low ionic strengths. However, EOF-pumping and its role in producing current-enhancing events is ambiguous and debated due to the complicated interactions between nanopore walls, DNA grooves, ion mobility, and counterion clouds. Here, we discuss
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Phosphatidylinositol phosphate binding domains exhibit complex dissociation properties at the inner leaflet of plasma membrane sheets bioRxiv. Biophys. Pub Date : 2021-03-01 Madeline R Sponholtz; Eric N Senning
The pleckstrin homology (PH) domain is a lipid targeting motif that binds with high specificity to phosphatidylinositol phosphate (PIP) lipids. Using TIRF microscopy, we followed the dissociation of GFP-tagged PH domains from the plasma membranes of rapidly unroofed cells and found that AKT-PH and PLCδ1-PH dissociation kinetics can be distinguished by their effective koff values determined from fitting
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Cryo-EM structure of lipid embedded human ABCA7 at 3.6 Å resolution bioRxiv. Biophys. Pub Date : 2021-03-01 Le Thi My Le; James R Thompson; Tomonori Aikawa; Takahisa Kanekiyo; Amer Alam
Dysfunction of the ATP Binding Cassette (ABC) transporter ABCA7 alters cellular lipid homeostasis and is linked to Alzheimer′s Disease (AD) pathogenesis through poorly understood mechanisms. Here we determined the cryo-electron microscopy (cryo-EM) structure of human ABCA7 in a lipid environment at 3.6 Å resolution that reveals an open conformation, despite bound nucleotides, and bilayer lipids traversing
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Differential Dynamic Behavior of Prefusion Spike Proteins of SARS Coronaviruses 1 and 2 bioRxiv. Biophys. Pub Date : 2021-03-01 Vivek Govind Kumar; Dylan S Ogden; Ugochi Isu; Adithya Polasa; James Losey; Mahmoud Moradi
The coronavirus spike protein, which binds to the same human receptor in both SARS-CoV-1 and 2, has been implied to be a potential source of their differential transmissibility. However, the mechanistic details of spike protein binding to its human receptor remain elusive at the molecular level. Here, we have used an extensive set of unbiased and biased microsecond-level all-atom molecular dynamics
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Conformational changes in twitchin kinase in vivo revealed by FRET imaging of freely moving C. elegans bioRxiv. Biophys. Pub Date : 2021-03-01 Daniel Porto; Yohei Matsunaga; Barbara Franke; Rhys Williams; Hiroshi Qadota; Olga Mayans; Guy M Benian; Hang Lu
The force-induced unfolding and refolding of proteins is speculated to be a key mechanism in the sensing and transduction of mechanical signals in the living cell. Yet, little evidence has been gathered for its existence in vivo. To test the occurrence of mechanical kinase activation in living working muscle, we generated transgenic C. elegans expressing twitchin containing FRET moieties flanking the
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Avalanches During Epithelial Tissue Growth; Uniform Growth and a Drosophila Eye Disc Model bioRxiv. Biophys. Pub Date : 2021-03-01 George Courcoubetis; Chi Xu; Sergey V Nuzhdin; Stephan Haas
In the physicists' perspective, epithelial tissues constitute an exotic type of active matter with non-linear properties reminiscent of amorphous materials. In the context of a circular proliferating epithelium, modeled by the quasistatic vertex model, we identify novel discrete tissue scale rearrangements, i.e. flow avalanches, which accomplish more compact tissue via cell slipping. After the onset
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Are adaptive chemotherapy schedules robust? A three-strategy stochastic evolutionary game theory model bioRxiv. Biophys. Pub Date : 2021-03-01 Rajvir Dua; Yongqian Ma; Paul K. Newton
We investigate the robustness of adaptive chemotherapy schedules over repeated cycles and a wide range of tumor sizes. We introduce a non-stationary stochastic three-component fitness-dependent Moran process to quantify the variance of the response to treatment associated with multidrug adaptive schedules that are designed to mitigate chemotherapeutic resistance in an idealized (well-mixed) setting
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Dynamic Consequences of Specificity within the Cytidine Repressor DNA-Binding Domain bioRxiv. Biophys. Pub Date : 2021-03-01 Colleen L Moody; Jenaro Soto; Vira Tretyachenko-Ladokhina; Donald F Senear; Melanie J Cocco
The E. coli cytidine repressor (CytR) is a member of the LacR family of bacterial repressors that regulates nine operons with distinct spacing and orientations of recognition sites. Understanding the structural features of the CytR DNA-binding domain (DBD) when bound to DNA is critical to understanding differential mechanisms of gene regulation. We previously reported the structure of the CytR DBD
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Considerations for MESF-bead based assignment of absolute fluorescence values to nanoparticles and extracellular vesicles by flow cytometry bioRxiv. Biophys. Pub Date : 2021-03-01 Estefanía Lozano-Andrés; Tina Van Den Broeck; Lili Wang; Majid Mehrpouyan; Ye Tian; Xiaomei Yan; Marca H.M. Wauben; Ger J.A. Arkesteijn
Flow cytometry is a promising technique to characterize nanoparticles (NPs) and extracellular vesicles (EVs). However, the majority of reported experiments, use arbitrary units to indicate fluorescence intensity. This hampers comparison of results from different laboratories and different platforms. We investigated the advised use of calibrated molecules of equivalent soluble fluorophores (MESF)-beads
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Identification and characterization of a G-quadruplex structure in the pre-core promoter region of hepatitis B virus bioRxiv. Biophys. Pub Date : 2021-02-27 Vaness Meier-Stephenson; Maulik D. Badmalia; Tyler Mrozowich; Keith CK Lau; Sarah K Schultz; Darren L Gemmill; Carla Osiowy; Guido van Marle; Carla S Coffin; Trushar R. Patel
Worldwide, ~250 million people are chronically infected with the hepatitis B virus (HBV) and are at increased risk of cirrhosis and hepatocellular carcinoma. The HBV persists as covalently closed circular DNA (cccDNA), which acts as the template for all HBV mRNA transcripts. Nucleos(t)ide analogs do not directly target the HBV cccDNA and cannot eradicate the HBV. We have discovered a unique structural
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NMR Hydrogen Exchange and Relaxation Reveal Positions Stabilized by p53 Rescue Mutants N239Y and N235K bioRxiv. Biophys. Pub Date : 2021-02-26 Jenaro Soto; Colleen Moody; Ali Alhoshani; Marilyn Sanchez-Bonilla; Daisy Martinon; Melanie J Cocco
Inactivation of p53 is found in over 50% of all cancers; p53 disfunction is often caused by a single missense mutation localized in the DNA binding domain (DBD). Rescue mutants N235K and N239Y stabilize and restore function to multiple p53 cancer mutants. Here, we use NMR to compare protein dynamics between WT and rescue mutants to understand the mechanism of stabilization. We measured and compared
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Allostery in Proteins as Point-to-Point Telecommunication in a Network: Frequency Decomposed Signal-to-Noise Ratio and Channel Capacity Analysis bioRxiv. Biophys. Pub Date : 2021-02-26 Yasemin Bozkurt Varolgunes; Joseph F. Rudzinski; Alper Demir
Allostery in proteins is a phenomenon in which the binding of a ligand induces alterations in the activity of remote functional sites. This can be conceptually viewed as point-to-point telecommunication in a networked communication medium, where a signal (ligand) arriving at the input (binding site) propagates through the network (interconnected and interacting atoms) to reach the output (remote functional
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Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy bioRxiv. Biophys. Pub Date : 2021-02-26 Hiroki Koide; Noriyuki Kodera; Shveta Bisht; Shoji Takada; Tsuyoshi Terakawa
The condensin protein complex compacts chromatin during mitosis using its DNA-loop extrusion activity. Previous studies proposed scrunching and loop-capture models as molecular mechanisms for the loop extrusion process, both of which assume the binding of double-strand (ds) DNA to the so-called hinge domain formed at the interface of the condensin subunits Smc2 and Smc4. However, how the hinge domain
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Decisive Role of Polymer-BSA Interactions in Biofilm Substrates on ‘Philicity’ and EPS Composition bioRxiv. Biophys. Pub Date : 2021-02-26 Suparna Dutta Sinha; Madhumita Choudhuri; Tania Basu; Debkishore Gupta; Alokmay Datta
Formation of extracellular polymeric substances (EPS) is a crucial step for bacterial biofilm growth. Dependence of EPS composition on the growth substrate and the conditioning of the latter is thus of primary importance. Here, we present results of studies on the growth of biofilms of two different strains each, of the Gram negative bacteria Escherichia coli and Klebsiella pneumoniae, on four polymers
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Negative DNA supercoiling tunes protein-mediated looping bioRxiv. Biophys. Pub Date : 2021-02-26 Yan Yan; Wenxuan Xu; Sandip Kumar; Alexander Zhang; Fenfei Leng; David Dunlap; Laura Finzi
Protein-mediated DNA looping is a fundamental mechanism of gene regulation. Such loops occur stochastically, and a calibrated response to environmental stimuli would seem to require more deterministic behavior, so experiments were preformed to determine whether additional proteins and/or DNA supercoiling might be definitive. In experiments on DNA looping mediated by the Escherichia coli lac repressor
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Activity-induced fluidization of arrested coalescence in fusion of cellular aggregates bioRxiv. Biophys. Pub Date : 2021-02-26 Steven Ongenae; Maxim Cuvelier; Jef Vangheel; Herman Ramon; Bart Smeets
At long time scales, tissue spheroids may flow or appear solid depending on their capacity to reorganize their internal structure. Understanding the relationship between intrinsic mechanical properties at the single cell level, and the tissue spheroids dynamics at the long-time scale is key for artificial tissue constructs, which are assembled from multiple tissue spheroids that over time fuse to form
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Dynamic arrest and aging of biomolecular condensates are regulated by low-complexity domains, RNA and biochemical activity bioRxiv. Biophys. Pub Date : 2021-02-26 Miriam Linsenmeier; Maria Hondele; Fulvio Grigolato; Eleonora Secchi; Karsten Weis; Paolo Arosio
Biomolecular condensates require suitable material properties to properly carry out their function. Yet, modulators that affect the material properties of condensates have remained largely unexplored. Here we apply Differential Dynamic Microscopy (DDM) to probe the material properties of an in vitro model of processing bodies (P-bodies) consisting of condensates formed by the DEAD-box ATPase Dhh1 in
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Bone Mineral Density modelled as a Random Field: a Feasibility Study on Pelvic Bone bioRxiv. Biophys. Pub Date : 2021-02-26 Petr Henys; Miroslav Vorechovsky; Michal Kuchar; Axel Heinemann; Jiri Kopal; Benjamin Ondruschka; Niels Hammer
Population variability and correlations in bone mineral density can be described by a spatial random field, which can be inferred from the routine computed tomography (CT) data. Random fields were simulated by transforming pairwise uncorrelated Gaussian random variables into correlated variables through the spectral decomposition of age-detrended correlation matrix estimated from CT. The validity of
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Addressing the Embeddability Problem in Transition Rate Estimation bioRxiv. Biophys. Pub Date : 2021-02-26 Curtis Goolsby; James Losey; Yuchen Xu; Marie-Christine Düker; Mila Getmansky Sherman; David Matteson; Mahmoud Moradi
Markov State Models (MSM) and related techniques have gained significant traction as a tool for analyzing and guiding molecular dynamics (MD) simulations due to their ability to extract structural, thermodynamic, and kinetic information on proteins using computationally feasible MD simulations. The MSM analysis often relies on spectral decomposition of empirically generated transition matrices. Here
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Fitting quantum machine learning potentials to experimental free energy data: Predicting tautomer ratios in solution bioRxiv. Biophys. Pub Date : 2021-02-26 Marcus Wieder; Josh Fass; John D Chodera
The computation of tautomer rations of druglike molecules is enormously important in computer-aided drug discovery, as over a quarter of all approved drugs can populate multiple tautomeric species in solution. Unfortunately, accurate calculations of aqueous tautomer ratios---the degree to which these species must be penalized in order to correctly account for tautomers in modeling binding for computer-aided
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Modulating the voltage sensor of a cardiac potassium channel shows antiarrhythmic effects bioRxiv. Biophys. Pub Date : 2021-02-25 Yangyang Lin; Sam Z. Grinter; Zhongju Lu; Xianjin Xu; Hong Zhan Wang; Hongwu Liang; Panpan Hou; Junyuan Gao; Chris Clausen; Jingyi Shi; Wenshan Zhao; Zhiwei Ma; Yongfeng Liu; Kelli McFarland White; Lu Zhao; Po-Wei Kang; Guohui Zhang; Ira S. Cohen; Xiaoqin Zou; Jianmin Cui
Cardiac arrhythmias are the most common cause of sudden cardiac death worldwide. Lengthening the ventricular action potential duration (APD) either congenitally or via pathologic or pharmacologic means, predisposes to a life-threatening ventricular arrhythmia, Torsade de Pointes. IKs, a slowly activating K+ current plays a role in action potential repolarization. In this study, we screened a chemical
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Self-contained and modular structured illumination microscope bioRxiv. Biophys. Pub Date : 2021-02-25 Robin Van den Eynde; Wim Vandenberg; Siewert Hugelier; Arno Bouwens; Johan Hofkens; Marcel Müller; Peter Dedecker
We present a modular implementation of structured illumination microscopy (SIM) that is fast, largely self-contained and that can be added onto existing fluorescence microscopes. Our instrument, which we call HIT-SIM, can theoretically deliver well over 50 super-resolved images per second and is readily compatible with existing acquisition software packages. We provide a full technical package consisting
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Intrinsic Gating Behavior of Voltage-Gated Sodium Channels Predetermines Regulation by Auxiliary β-subunits bioRxiv. Biophys. Pub Date : 2021-02-25 Niklas Brake; Adamo S Mancino; Yuaho Yan; Takushi Shimomura; Heika Silveira; Yoshihiro Kubo; Anmar Khadra; Derek Bowie
Voltage-gated sodium (Nav) channels mediate rapid millisecond electrical signaling in excitable cells. Auxiliary subunits, β1-β4, are thought to regulate Nav channel function through covalent and/or polar interactions with the channel's voltage-sensing domains. How these interactions translate into the diverse and variable regulatory effects of β-subunits remains unclear. Here, we find that the intrinsic
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A precise and general FRET-based method for monitoring structural transitions in protein self-organization bioRxiv. Biophys. Pub Date : 2021-02-25 Qi Wan; Sara N Mouton; Liesbeth M Veenhoff; Arnold J Boersma
Proteins assemble into a tremendous variety of dynamic and functional structures. Sensitive measurements directly in cells with a high spatiotemporal resolution are needed to distinguish these different assemblies. Here, we demonstrate precise and continuous monitoring of cytoplasmic protein self-assemblies and their structural transitions. Intermolecular FRET with both the donor and acceptor protein
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An integrated multi-wavelength SCATTIRSTORM microscope combining TIRFM and IRM modalities for imaging cellulases and other processive enzymes bioRxiv. Biophys. Pub Date : 2021-02-25 Daguan Nong; Zachary K Haviland; Kate O Vasquez Kuntz; Ming Tien; Charles T Anderson; William O Hancock
We describe a multimodal SCATTIRSTORM microscope for visualizing processive enzymes moving on immobilized substrates. The instrument combines Interference Reflection Microscopy (IRM) with multi-wavelength Total Internal Reflectance Fluorescence Microscopy (TIRFM). The microscope can localize quantum dots with a precision of 2.8 nm at 100 frames/s, and was used to image the dynamics of the cellulase
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Turing's diffusive threshold in random reaction-diffusion systems bioRxiv. Biophys. Pub Date : 2021-02-25 Pierre A Haas; Raymond E. Goldstein
Turing instabilities of reaction-diffusion systems can only arise if the diffusivities of the chemical species are sufficiently different. This threshold is unphysical in most systems with N=2 diffusing species, forcing experimental realizations of the instability to rely on fluctuations or additional nondiffusing species. Here we ask whether this diffusive threshold lowers for N>2 to allow "true"
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Modeling SARS-CoV-2 nsp1-5'-UTR complex via the extended ensemble simulations bioRxiv. Biophys. Pub Date : 2021-02-25 Shun Sakuraba; Xie Qilin; Kota Kasahara; Junichi Iwakiri; Hidetoshi Kono
Nonstructural protein 1 (nsp1) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a 180-residue protein that blocks the translation of SARS-CoV-2 infected cells. Although it has been known that SARS-CoV-2's own RNA evades an nsp1's host translation shutoff, its molecular mechanism has been poorly understood. We performed an extended ensemble molecular dynamics simulation to investigate
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Identical Sequences, Different Behaviors: Protein Diversity Captured at the Single-Molecule Level bioRxiv. Biophys. Pub Date : 2021-02-25 Rafael Tapia-Rojo; Alvaro Alonso-Caballero; Carmen L Badilla; Julio Fernandez
The classical "one sequence, one structure, one function" paradigm has shaped much of our intuition of how proteins work inside the cell. Partially due to the insight provided by bulk biochemical assays, individual biomolecules are assumed to behave as identical entities, and their characterization relies on ensemble averages that flatten any conformational diversity into a unique phenotype. While
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Short hydrogen bonds enhance non-aromatic protein-related fluorescence bioRxiv. Biophys. Pub Date : 2021-02-25 Amberley D Stephens; Muhammad Nawaz Qaisrani; Michael T Ruggiero; Gonzalo Diaz Miron; Uriel Morzan; Mariano C Gonzalez Lebrero; Saul T E Jones; Emiliano Poli; Andrew D Bond; Philippa J Woodhams; Elyse M Kleist; Luca Grisanti; Ralph Gebauer; J Axel Zeitler; Dan Credgington; Ali Hassanali; Gabriele S Kaminski Schierle
Here we show experimentally and computationally that the single amino acid L-glutamine, by undergoing a chemical transformation leading to the formation of a short hydrogen bond, displays optical properties that are significantly enhanced compared to L-glutamine itself. We highlight the importance of the direct local environment on the extent of the Stokes shift observed in fluorescent non-aromatic
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Activation of Cytochrome C Peroxidase Function Through Coordinated Foldon Loop Dynamics upon Interaction with Anionic Lipids bioRxiv. Biophys. Pub Date : 2021-02-25 Mingyue Li; Wanyang Sun; Vladimir A Tyurin; Maria DeLucia; Jinwoo Ahn; Valerian E Kagan; Patrick C.A. van der Wel
Cardiolipin (CL) is a mitochondrial anionic lipid that plays important roles in the regulation and signaling of mitochondrial apoptosis. CL peroxidation catalyzed by the assembly of CL-cytochrome c (cyt c) complexes at the inner mitochondrial membrane is a critical checkpoint. The structural changes in the protein, associated with peroxidase activation by CL and different anionic lipids, are not known
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Structural analysis of Sulfolobus solfataricus TF55β chaperonin in open and filamentous states bioRxiv. Biophys. Pub Date : 2021-02-25 Yi C. Zeng; Meghna Sobti; Alastair G Stewart
Chaperonins are biomolecular complexes that assist protein folding. Thermophilic Factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus that has α, β and γ subunits. Using cryo-electron microscopy, we have determined the structure of the β-only complex of S. solfataricus TF55 complexes to 3.6-4.2 Å resolution and a filamentous form to 5.2 Å resolution. The structures of the
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Nanomechanics of negatively supercoiled diaminopurine-substituted DNA bioRxiv. Biophys. Pub Date : 2021-02-25 Domenico Salerno; Francesco Mantegazza; Valeria Cassina; Matteo Cristofalo; Qing Shao; Laura Finzi; David Dunlap
Single molecule experiments have demonstrated a progressive transition from a B- to an L-form helix as DNA is gently stretched and progressively unwound. Since the particular sequence of a DNA segment influences both base stacking and hydrogen bonding, the conformational dynamics of B-to-L transitions should be tunable. To test this idea, DNA with diaminopurine replacing adenine was synthesized to
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Free Energy Landscape of RNA Binding Dynamics in Start Codon Recognition by Eukaryotic Ribosomal Pre-Initiation Complex bioRxiv. Biophys. Pub Date : 2021-02-25 Takeru Kameda; Katsura Asano; Yuichi Togashi
Specific interaction between the start codon, 5'-AUG-3', and the anticodon, 5'-CAU-3', ensures accurate initiation of translation. Recent studies show that several near-cognate start codons (e.g. GUG and CUG) can play a role in initiating translation in eukaryotes. However, the mechanism allowing initiation through mismatched base-pairs at the ribosomal decoding site is still unclear at an atomic level
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Reconstitution of ultrawide DNA origami pores in liposomes for transmembrane transport of macromolecules bioRxiv. Biophys. Pub Date : 2021-02-24 Alessio Fragasso; Nicola De Franceschi; Pierre Stoemmer; Eli O. Van der Sluis; Hendrik Dietz; Cees Dekker
Molecular traffic across lipid membranes is a vital process in cell biology that involves specialized biological pores with a great variety of pore diameters, from fractions of a nanometer to >30 nm. Creating artificial membrane pores covering similar size and complexity will aid the understanding of transmembrane molecular transport in cells, while artificial pores are also a necessary ingredient
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Effects of substrate stiffness and actin velocity on fibronectin fibril morphometry and mechanics bioRxiv. Biophys. Pub Date : 2021-02-24 Seth H. Weinberg; Navpreet Saini; Christopher Lemmon
Assembly of the extracellular matrix protein fibronectin (FN) into insoluble, viscoelastic fibrils is a critical step during embryonic development and wound healing; misregulation of FN fibril assembly has been implicated in many diseases, including fibrotic diseases and cancer. We have previously developed a computational model of FN fibril assembly that recapitulates the morphometry and mechanics
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Agonist efficiency from concentration-response curves: structural implications and applications bioRxiv. Biophys. Pub Date : 2021-02-24 Dinesh Indurthi; Anthony Auerbach
Agonists are evaluated by a concentration-response curve (CRC), with a midpoint (EC50) that indicates potency, a high-concentration asymptote that indicates efficacy and a low-concentration asymptote that indicates constitutive activity. A third agonist attribute, efficiency (& [eta]), is the fraction of binding energy that is applied to the conformational change that activates the receptor. We show
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AMPGAN v2: Machine Learning Guided Discovery of Anti-Microbial Peptides bioRxiv. Biophys. Pub Date : 2021-02-24 Colin M. Van Oort; Jonathon B. Ferrell; Jacob M. Remington; Safwan Wshah; Jianing Li
Antibiotic resistance is a critical public health problem. Each year ~2.8 million resistant infections lead to more than 35,000 deaths in the U.S. alone. Antimicrobial peptides (AMPs) show promise in treating resistant infections. However, applications of known AMPs have encountered issues in development, production, and shelf-life. To drive the development of AMP-based treatments it is necessary to
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Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel bioRxiv. Biophys. Pub Date : 2021-02-24 Sergio Perez-Conesa; Eric G. Keeler; Dongyu Zhang; Lucie Delemotte; Ann E McDermott
As the first potassium channel with a X-ray structure determined, and given its homology to eukaryotic channels, the pH-gated prokaryotic channel KcsA has been extensively studied. Nevertheless, questions related in particular to the allosteric coupling between its gates remain open. The many currently available X-ray crystallography structures appear to correspond to various stages of activation and
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Light-powered reactivation of flagella and contraction of microtubules network: towards building an artificial cell bioRxiv. Biophys. Pub Date : 2021-02-24 Raheel Ahmad; Christin Kleineberg; Vahid Nasirimarekani; Yu Jung Su; Samira Goli Pozveh; Albert J Bae; Eberhard Bodenschatz; Kai Sundmacher; Isabella Guido; Tanja Vidakovich-Koch; Azam Gholami
Artificial systems capable of self-sustained movement with self-sufficient energy are of high interest with respect to the development of many challenging applications including medical treatments but also technical applications. The bottom-up assembly of such systems in the context of synthetic biology is still a challenging task. In this work, we demonstrate the biocompatibility and efficiency of
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Cortical Tension Initiates the Positive Feedback Loop Between E-cadherin and F-actin bioRxiv. Biophys. Pub Date : 2021-02-24 Qilin Yu; William R. Holmes; Jean Paul Thiery; Rodney Brian Luwor; Vijay Rajagopal
Adherens junctions (AJs) physically link two cells at their contact interface via extracellular homophilic interactions between cadherin molecules and intracellular connections between cadherins and the actomyosin cortex. Both cadherin and actomyosin cytoskeletal dynamics are reciprocally regulated by mechanical and chemical signals, which subsequently determine the strength of cell-cell adhesions
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Calcium Sensitive Allostery Regulates the PI(4,5)P2 Binding Site of the Dysferlin C2A Domain bioRxiv. Biophys. Pub Date : 2021-02-24 Shauna C Otto; Patrick N Reardon; Tanushri M Kumar; Chapman J Kuykendall; Colin P Johnson
C2 domains are the second-most abundant calcium binding module in the proteome. Activity of the muscular dystrophy associated protein dysferlin is dependent on the C2A domain at the N-terminus of the protein, which couples calcium and PI(4,5)P2 binding through an unknown mechanism. Using solution state nuclear magnetic resonance spectroscopy we confirm the phosphoinositide binding site for the domain
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Protein Friction and Filament Bending Facilitate Contraction of Disordered Actomyosin Networks bioRxiv. Biophys. Pub Date : 2021-02-24 Alexander K. Y. Tam; Alex Mogilner; Dietmar B. Oelz
We use mathematical modelling and computation to investigate how protein friction facilitates contraction of disordered actomyosin networks. We simulate two-dimensional networks using an agent-based model, consisting of a system of force-balance equations for myosin motor proteins and semi-flexible actin filaments. A major advantage of our approach is that it enables direct calculation of the network
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Wrinkle force microscopy: a new machine learning based approach to predict cell mechanics from images bioRxiv. Biophys. Pub Date : 2021-02-23 Honghan Li; Daiki Matsunaga; Tsubasa S Matsui; Hiroki Aosaki; Koki Inoue; Amin Doostmohammadi; Shinji Deguchi
Combining experiments with artificial intelligence algorithms, we propose a new machine learning based approach to extract the cellular force distributions from the microscope images. The full process can be divided into three steps. First, we culture the cells on a special substrate allowing to measure both the cellular traction force on the substrate and the corresponding substrate wrinkles simultaneously
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Quantification and demonstration of the collective constriction-by-ratchet mechanism in the dynamin molecular motor bioRxiv. Biophys. Pub Date : 2021-02-23 Oleg Ganichkin; Renee Vancraenenbroeck; Gabriel Rosenblum; Hagen Hofmann; Alexander S Mikhailov; Oliver Daumke; Jeffrey K Noel
Dynamin oligomerizes into helical filaments on tubular membrane templates and, through constriction, cleaves them in a GTPase-driven way. Structural observations of GTP-dependent cross-bridges between neighboring filament turns have led to the suggestion that dynamin operates as a molecular ratchet motor. However, the proof of such mechanism remains absent. Particularly, it is not known whether a powerful
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Consequences of the constitutive NOX2 activity in living cells: cytosol acidification, apoptosis, and localized lipid peroxidation bioRxiv. Biophys. Pub Date : 2021-02-23 Hana Valenta; Sophie Dupré-Crochet; Tania Bizouarn; Laura Baciou; Oliver Nüsse; Ariane Deniset-Besseau; Marie Erard
The phagocyte NADPH oxidase (NOX2) is a key enzyme of the innate immune system generating superoxide anions (O2·-), precursors of reactive oxygen species. The NOX2 protein complex is composed of six subunits: two membrane proteins (gp91phox and p22phox) forming the catalytic core, three cytosolic proteins (p67phox, p47phox and p40phox) and a small GTPase Rac. The sophisticated activation mechanism
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The periodic axon membrane skeleton leads to high-density sodium nanodomains but does not impact action potentials bioRxiv. Biophys. Pub Date : 2021-02-23 Zhaojie Chai; Anastasios V. Tzingounis; George Lykotrafitis
Recent work has established that axons have a periodic skeleton structure comprising of azimuthal actin rings connected via longitudinal spectrin tetramer filaments. This structure endows the axon with structural integrity and mechanical stability. Additionally, voltage-gated sodium channels follow the periodicity of the active-spectrin arrangement, spaced ~190 nm segments apart. The impact of this
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Visualizing multi-protein patterns at the synapse of neuronal tissue with DNA-assisted single-molecule localization microscopy bioRxiv. Biophys. Pub Date : 2021-02-23 Kaarjel K. Narayanasamy; Aleksandar Stojic; Yunqing Li; Steffen Sass; Marina Hesse; Nina S. Deussner-Helfmann; Marina S. Dietz; Maja Klevanski; Thomas Kuner; Mike Heilemann
The development of super-resolution microscopy (SRM) has widened our understanding of biomolecular structure and function in biological materials. Imaging multiple targets within a single area would elucidate their spatial localization relative to the cell matrix and neighboring biomolecules, revealing multi-protein macromolecular structures and their functional co-dependencies. SRM methods are, however
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Local topology, bifurcations and mutation hot-spots in proteins with SARS-CoV-2 spike protein as an example bioRxiv. Biophys. Pub Date : 2021-02-23 Xubiao Peng; Antti Juhani Niemi
Novel topological methods are introduced to protein research. The aim is to identify hot-spot sites where a bifurcation can change the local topology of the protein backbone. Since the shape of a protein is intimately related to its biological function, a mutation that takes place at such a bifurcation hot-spot has an enhanced capacity to change the protein's biological function. The methodology applies
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Multi-fluorescence high-resolution episcopic microscopy (MF-HREM) for three dimensional imaging of adult murine organs bioRxiv. Biophys. Pub Date : 2021-02-23 Claire Walsh; Natalie Holroyd; Eoin Finnerty; Sean G Ryan; Paul W Sweeney; Rebecca J Shipley; Simon Walker-Samuel
Three-dimensional microscopy of large biological samples (>0.5 cm3) is transforming biological research. Many existing techniques require trade-offs between image resolution, sample size and method complexity. A simple robust instrument with the potential to perform large volume 3D imaging currently exists in the form of the Optical HREM, however the development of the instrument to date is limited
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Pulsatile contractions and pattern formation in excitable active gels bioRxiv. Biophys. Pub Date : 2021-02-23 Michael F Staddon; Edwin Munro; Shiladitya Banerjee
The actin cortex is an active adaptive material, embedded with complex regulatory networks that can sense, generate and transmit mechanical forces. The cortex can exhibit a wide range of dynamic behaviours, from generating pulsatory contractions and traveling waves to forming highly organised structures such as ordered fibers, contractile rings and networks that must adapt to the local cellular environment
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Lipid type doping of the sponge (L3) mesophase bioRxiv. Biophys. Pub Date : 2021-02-23 Christopher Brasnett; Adam Squires; Andrew Smith; Annela Seddon
The polymorphism of lipid aggregates has long attracted detailed study due to the myriad factors that determine the final mesophase observed. This study is driven by the need to understand mesophase behaviour for a number of applications, such as drug delivery and membrane protein crystallography. In the case of the latter, the role of the so-called 'sponge' (L3) mesophase has been often noted, but
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The contribution of electrostatics to hydrogen exchange in the unfolded protein state bioRxiv. Biophys. Pub Date : 2021-02-23 Rupashree Dass; Enrico Corlianò Frans AA Mulder
Although electrostatics have long been recognized to play an important role in hydrogen exchange (HX) with solvent, the quantitative assessment of its magnitude in the unfolded state has hitherto been lacking. This limits the utility of HX as a quantitative method to study protein stability, folding and dynamics. Using the intrinsically disordered human protein α-synuclein as a proxy for the unfolded
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Chaperones Skp and SurA dynamically expand unfolded outer membrane protein X and synergistically disassemble oligomeric aggregates bioRxiv. Biophys. Pub Date : 2021-02-23 Neharika Chamachi; Andreas Hartmann; Mai Quynh Ma; Georg Krainer; Michael Schlierf
Periplasmic chaperones Skp and SurA are essential players in outer membrane protein (OMP) biogenesis. They prevent unfolded OMPs from misfolding during their passage through the periplasmic space and aid in the disassembly of OMP aggregates under cellular stress conditions. However, functionally important links between interaction mechanisms, structural dynamics, and energetics that underpin both Skp
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Machine Learning Differentiates Enzymatic and Non-Enzymatic Metals in Proteins bioRxiv. Biophys. Pub Date : 2021-02-22 Ryan Feehan; Meghan W. Franklin; Joanna Sarah Gershkoff Slusky
Metalloenzymes are 40% of all enzymes and can perform all seven classes of enzyme reactions. Because of the physicochemical similarities between the active sites of metalloenzymes and inactive metal binding sites, it is challenging to differentiate between them. Yet distinguishing these two classes is critical for the identification of both native and designed enzymes. Because of similarities between
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Previously uncharacterized interactions between the folded and intrinsically disordered domains impart asymmetric effects on UBQLN2 phase separation bioRxiv. Biophys. Pub Date : 2021-02-22 Tongyin Zheng; Carlos A Castañeda
Shuttle protein UBQLN2 functions in protein quality control (PQC) by binding to proteasomal receptors and ubiquitinated substrates via its N-terminal ubiquitin-like (UBL) and C-terminal ubiquitin-associated (UBA) domains, respectively. Between these two folded domains are intrinsically disordered STI1-I and STI1-II regions, connected by disordered linkers. The STI1 regions bind other components, such
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Tetrameric UvrD helicase is located at the E. coli replisome due to frequent replication blocks bioRxiv. Biophys. Pub Date : 2021-02-22 Adam JM Wollman; Aisha Syeda; Andrew Leech; Colin Guy; Peter McGlynn; Michelle Hawkins; Mark C Leake
DNA replication in all organisms must overcome nucleoprotein blocks to complete genome duplication. Accessory replicative helicases in Escherichia coli, Rep and UvrD, help replication machinery overcome blocks by removing incoming nucleoprotein complexes or aiding the re-initiation of replication. Mechanistic details of Rep function have emerged from recent live cell studies, however, the activities
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E. coli chemotaxis is information-limited bioRxiv. Biophys. Pub Date : 2021-02-22 Henry H Mattingly; Keita Kamino; Benjamin B Machta; Thierry Emonet
Organisms must acquire and use environmental information to guide their behaviors. However, it is unclear whether and how information quantitatively limits behavioral performance. Here, we relate information to behavioral performance in Escherichia coli chemotaxis. First, we derive a theoretical limit for the maximum achievable gradient-climbing speed given a cell's information acquisition rate. Next
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Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies : Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations bioRxiv. Biophys. Pub Date : 2021-02-22 Gennady Verkhivker; Steve Agajanian; Deniz Yazar Oztas; Grace Gupta
In this study, we used an integrative computational approach focused on comparative perturbation-based modeling to examine molecular mechanisms and determine functional signatures underlying role of functional residues in the SARS-CoV-2 spike protein that are targeted by novel mutational variants and antibody-escaping mutations. Atomistic simulations and functional dynamics analysis are combined with
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