Top 10 Biorxiv Papers Today in Biophysics


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#1. CryoEM structure of the Nipah virus nucleocapsid assembly
De-Sheng Ker, Huw T. Jenkins, Sandra J. Greive, Alfred A. Antson
Nipah virus is a highly pathogenic zoonotic RNA virus, causing fatal encephalitis in humans. Like other negative-strand RNA viruses including Ebola and measles, its genome is wrapped by the nucleocapsid (N) protein forming a helical assembly. Here we report the CryoEM structure of the Nipah nucleocapsid protein-RNA assembly, at near atomic resolution. The N protein wraps the RNA genome with a periodicity of six nucleotides per protomer, around the outer edge of the helical assembly, in common with other paramyxoviruses. This structure uncovers details of the nucleocapsid assembly, demonstrating the role of the N-terminal arm of the N protein in the formation of the helical assembly and revealing details of the sequence-independent coordination of RNA binding in the "3-bases-in, 3-bases-out" conformation. CryoEM analysis also reveals formation of clam-shaped assemblies of the N-protein, mediated by intersubunit interactions involving several N protein loop regions.
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biorxivpreprint: CryoEM structure of the Nipah virus nucleocapsid assembly https://t.co/GWtoTJC4QP #bioRxiv
biorxiv_biophys: CryoEM structure of the Nipah virus nucleocapsid assembly https://t.co/kJuzAYnHTJ #biorxiv_biophys
cryoEM_Papers: CryoEM structure of the Nipah virus nucleocapsid assembly https://t.co/ZtFrlziXun
DanielHurdiss: RT @cryoEM_Papers: CryoEM structure of the Nipah virus nucleocapsid assembly https://t.co/ZtFrlziXun
_socalledexpert: RT @cryoEM_Papers: CryoEM structure of the Nipah virus nucleocapsid assembly https://t.co/ZtFrlziXun
roponpallab: RT @biorxiv_biophys: CryoEM structure of the Nipah virus nucleocapsid assembly https://t.co/kJuzAYnHTJ #biorxiv_biophys
dmborek: RT @cryoEM_Papers: CryoEM structure of the Nipah virus nucleocapsid assembly https://t.co/ZtFrlziXun
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Authors: 4
Total Words: 0
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#2. Lipidomics of human adipose tissue reveals diversity between body areas
Naba Al-Sari, Tommi Suvitaival, Ismo Mattila, Ashfaq Ali, Linda Ahonen, Kajetan Trost, Trine Foged Henriksen, Flemming Pociot, Lars Ove Dragsted, Cristina Legido-Quigley
Background and aims: Adipose tissue plays a pivotal role in storing excess fat and its composition reflects the history of person's lifestyle and metabolic health. Broad profiling of lipids with mass spectrometry has potential for uncovering new knowledge on the pathology of obesity, metabolic syndrome, diabetes and other related conditions. Here, we developed a lipidomic method for analyzing human subcutaneous adipose biopsies. We applied the method to four body areas to understand the differences in lipid composition between these areas. Materials and methods: Adipose tissue biopsies from 10 participants were analyzed using ultra-high-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. The method development included the optimization of the lipid extraction, the sample amount and the sample dilution factor to detect lipids in an appropriate concentration range. Lipidomic analyses were performed for adipose tissue collected from the abdomen, breast, thigh and lower back. Differences in lipid...
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biorxivpreprint: Lipidomics of human adipose tissue reveals diversity between body areas https://t.co/B36bx2WW41 #bioRxiv
biorxiv_biophys: Lipidomics of human adipose tissue reveals diversity between body areas https://t.co/bbzeJNYrw0 #biorxiv_biophys
HubBucket: RT @biorxivpreprint: Lipidomics of human adipose tissue reveals diversity between body areas https://t.co/B36bx2WW41 #bioRxiv
Astro_Erik: RT @biorxivpreprint: Lipidomics of human adipose tissue reveals diversity between body areas https://t.co/B36bx2WW41 #bioRxiv
AyalaTovy: RT @biorxivpreprint: Lipidomics of human adipose tissue reveals diversity between body areas https://t.co/B36bx2WW41 #bioRxiv
Jonatha14158813: RT @biorxivpreprint: Lipidomics of human adipose tissue reveals diversity between body areas https://t.co/B36bx2WW41 #bioRxiv
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Sample Sizes : [3, 4, 4, 10]
Authors: 10
Total Words: 6687
Unqiue Words: 2386

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#3. vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy
Alexander Spark, Alexandre Kitching, Daniel Esteban-Ferrer, Anoushka Handa, Alexander R. Carr, Lisa-Maria Needham, Aleks Ponjavic, Mafalda Da Cunha Santos, James McColl, Christophe Leterrier, Simon J. Davis, Ricardo Henriques, Steven F. Lee
Super-Resolution (SR) Microscopy based on 3D Single-Molecule Localization Microscopy (SMLM) is now well established and its wide-spread adoption has led to the development of more than 36 software packages, dedicated to quantitative evaluation of the spatial and temporal detection of fluorophore photoswitching. While the initial emphasis in the 3D SMLM field has clearly been on improving resolution and data quality, there is now a marked absence of 3D visualization approaches that enable the straightforward, high-fidelity exploration of this type of data. Inspired by the horological phosphorescence points that illuminate watch-faces in the dark, we present vLUME (Visualization of the Universe in a Micro Environment, pronounced 'volume') a free-for-academic-use immersive virtual reality-based (VR) visualization software package purposefully designed to render large 3D-SMLM data sets. vLUME enables robust visualization, segmentation and quantification of millions of fluorescence puncta from any 3D SMLM technique. vLUME has an...
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SteveTheChemist: Ever wanted to squish an immune cell, you need vLUME (pronounced 'volume'). VR for SMLM @lumeVR @AnoushkaHanda @SteveTheChemist @LisaMariaN91 @christlet @HenriquesLab pre-print now available, any questions please ask https://t.co/BsLkvCvI7d @biorxiv_biophys https://t.co/VUQoov0Gng
biophotonicat: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy (relevance: 100%) https://t.co/0ukAuxpcmw #biophotonics #biomedicaloptics https://t.co/1FkJxBguwW
HubBucket: RT @biorxivpreprint: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/2Zf1m2RyGE #bioRxiv
Olu_GH: RT @biorxiv_biophys: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/dtNAh5HXI3 #biorxiv_biophys
Craggs_Lab: RT @biorxiv_biophys: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/dtNAh5HXI3 #biorxiv_biophys
Nicolas26538817: RT @biorxiv_biophys: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/dtNAh5HXI3 #biorxiv_biophys
kaaskac: RT @biorxiv_biophys: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/dtNAh5HXI3 #biorxiv_biophys
AnoushkaHanda: RT @biorxiv_biophys: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/dtNAh5HXI3 #biorxiv_biophys
nanxiaolin: RT @biorxiv_biophys: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/dtNAh5HXI3 #biorxiv_biophys
Superresolved: RT @biorxiv_biophys: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/dtNAh5HXI3 #biorxiv_biophys
DanielE42587767: RT @biorxiv_biophys: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/dtNAh5HXI3 #biorxiv_biophys
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Authors: 13
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#4. Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge
Mehtap Işık, Teresa Danielle Bergazin, Thomas Fox, Andrea Rizzi, John D. Chodera, David L. Mobley
The SAMPL Challenges aim to focus the biomolecular and physical modeling community on issues that limit the accuracy of predictive modeling of protein-ligand binding for rational drug design. In the SAMPL5 log D Challenge, designed to benchmark the accuracy of methods for predicting drug-like small molecule transfer free energies from aqueous to nonpolar phases, participants found it difficult to make accurate predictions due to the complexity of protonation state issues. In the SAMPL6 log P Challenge, we asked participants to make blind predictions of the octanol-water partition coefficients of neutral species of 11 compounds and assessed how well these methods performed absent the complication of protonation state effects. This challenge builds on the SAMPL6 pKa Challenge, which asked participants to predict pKa values of a superset of the compounds considered in this log P challenge. Blind prediction sets of 91 prediction methods were collected from 27 research groups, spanning a variety of quantum mechanics (QM) or molecular...
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biorxivpreprint: Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge https://t.co/jzTjR3DZgT #bioRxiv
biorxiv_biophys: Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge https://t.co/ASEBLPqrGg #biorxiv_biophys
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#5. Effect of flagellar beating pattern on sperm rheotaxis and boundary-dependent navigation
Meisam Zaferani, Farhad Javi, Amir Mokhtare, Alireza Abbaspourrad
The study of navigational mechanisms used by mammalian sperm inside a microenvironment yields better understanding of sperm locomotion during the insemination process, which aids in the design of tools for overcoming infertility. Near- and far-field hydrodynamic interactions with nearby boundaries and rheotaxis are known to be some of the steering strategies that keep sperm on the correct path toward the egg. However, it is not known how the beating patterns of sperm may influence these navigational strategies. In this study, we investigate the effect of flagellar beating pattern on navigation of sperm cells both theoretically and experimentally using a two-step approach. We first isolate bovine sperm based on their rheotactic behavior in a zone with quiescent medium using a microfluidic system. This step ensures that the swimmers are able to navigate upstream and have motilities higher than a selected value, even though they feature various flagellar beating patterns. We then explore the flagellar beating pattern of these...
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biorxivpreprint: Effect of flagellar beating pattern on sperm rheotaxis and boundary-dependent navigation https://t.co/Mif23rlRbp #bioRxiv
biorxiv_biophys: Effect of flagellar beating pattern on sperm rheotaxis and boundary-dependent navigation https://t.co/cIgE9YvmO1 #biorxiv_biophys
biophotonicat: Effect of flagellar beating pattern on sperm rheotaxis and boundary-dependent navigation (relevance: 46%) https://t.co/HyX4VqqSqD #biophotonics #biomedicaloptics https://t.co/tdglwojRUp
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#6. Middle-level IM-MS and CIU experiments for improved therapeutic immunoglobulin isotype fingerprinting
Thomas Botzanowski, Oscar HERNANDEZ-ALBA, Martine Malissard, Elsa Wagner-Rousset, Evolene Desligniere, Olivier Colas, Jean-Francois Haeuw, Alain Beck, Sarah CIANFERANI
Currently approved therapeutic monoclonal antibodies (mAbs) are based on immunoglobulin G (IgG) 1, 2 or 4 isotypes, which differ in their specific inter-chains disulfide bridge connectivities. Different analytical techniques have been reported for mAb isotyping, among which native ion mobility mass spectrometry (IM-MS) and collision induced unfolding (CIU) experiments. However, mAb isotyping by these approaches is based on detection of subtle differences and thus remains challenging at the intact-level. We report here on middle-level (after IdeS digestion) IM-MS and CIU approaches to afford better differentiation of mAb isotypes. Our method provides simultaneously CIU patterns of F(ab)2 and Fc domains within a single run. Middle-level CIU patterns of F(ab)2 domains enable more reliable classification of mAb isotypes compared to intact level CIU, while CIU fingerprints of Fc domains are overall less informative for mAb isotyping. F(ab)2 regions can thus be considered as diagnostic domains providing specific CIU signatures for mAb...
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biorxivpreprint: Middle-level IM-MS and CIU experiments for improved therapeutic immunoglobulin isotype fingerprinting https://t.co/AKzCi6lboW #bioRxiv
biorxiv_biophys: Middle-level IM-MS and CIU experiments for improved therapeutic immunoglobulin isotype fingerprinting https://t.co/zlwavbyqZj #biorxiv_biophys
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#7. Creating supported plasma membrane bilayers using acoustic pressure
Erdinc Sezgin, Dario Carugo, Ilya Levental, Eleanor Stride, Christian Eggeling
Model membrane systems are essential tools for biology, enabling study of biological processes in a simplified setting to reveal the underlying physicochemical principles. As cell-derived membrane systems, giant plasma membrane vesicles (GPMVs) constitute an intermediate model between native cellular plasma and artificial membranes. Certain applications, however, require planar membrane surfaces. Here, we report a novel approach for creating supported plasma membrane bilayers (SPMBs) by bursting cell-derived GPMVs using an ultrasonic pressure field generated within an acoustofluidic device. We show that the mobility of outer leaflet molecules is preserved in SPMBs, suggesting that they are accessible on the surface of the bilayers. Such model membrane systems will be useful for many applications requiring detailed characterization of plasma membrane dynamics.
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biorxivpreprint: Creating supported plasma membrane bilayers using acoustic pressure https://t.co/ywBi3yBoLx #bioRxiv
biorxiv_biophys: Creating supported plasma membrane bilayers using acoustic pressure https://t.co/xYMZuupMks #biorxiv_biophys
kwitschas: RT @biorxiv_biophys: Creating supported plasma membrane bilayers using acoustic pressure https://t.co/xYMZuupMks #biorxiv_biophys
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Total Words: 4085
Unqiue Words: 1640

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#8. Membrane-mediated ligand unbinding of the PK-11195 ligand from the translocator protein (TSPO)
Tom Dixon, Arzu Uyar, Shelagh Ferguson-Miller, Alex Dickson
The translocator protein (TSPO), previously known as the peripheral benzodiazepine receptor, is of longstanding medical interest as both a biomarker for neuroinjury and a potential drug target for neuroinflammation and other disorders. Recently it was shown that ligand residence time is a key factor determining steroidogenic efficacy of TSPO-binding compounds. This spurs interest in simulations of (un)binding pathways of TSPO ligands, which could reveal the molecular interactions governing ligand residence time. In this study, we use a weighted ensemble algorithm to determine the unbinding pathway for different poses of PK-11195, a TSPO ligand used in neuroimaging. In contrast with previous studies, our results show that PK-11195 does not dissociate directly into solvent but instead dissociates via the lipid membrane by going between the transmembrane helices. We analyze this path ensemble in detail, constructing descriptors that can facilitate a general understanding of membrane-mediated ligand binding.
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biorxivpreprint: Membrane-mediated ligand unbinding of the PK-11195 ligand from the translocator protein (TSPO) https://t.co/08ZJz30qcJ #bioRxiv
biorxiv_biophys: Membrane-mediated ligand unbinding of the PK-11195 ligand from the translocator protein (TSPO) https://t.co/R4fnafKdFX #biorxiv_biophys
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#9. High-resolution cryo-EM using beam-image shift at 200 keV
Jennifer N Cash, Sarah Kearns, Yilai A Li, Michael A Cianfrocco
Recent advances in single-particle cryo-electron microscopy (cryo-EM) data collection utilizes beam-image shift to improve throughput. Despite implementation on well-aligned 300 keV cryo-EM instruments, it remains unknown how well beam-image shift data collection affects data quality on 200 keV instruments and whether any aberrations can be computationally corrected. To test this, we collected and analyzed a cryo-EM dataset of aldolase at 200 keV using beam-image shift. This analysis shows that beam tilt on the instrument initially limited the resolution of aldolase to 5.6Å. After iterative rounds of aberration correction and particle polishing in RELION, we were able to obtain a 2.8Å structure. This analysis indicates that software correction of microscope misalignment can provide a dramatic improvement in resolution.
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biorxivpreprint: High-resolution cryo-EM using beam-image shift at 200 keV https://t.co/f7tEqwxYav #bioRxiv
biorxiv_biophys: High-resolution cryo-EM using beam-image shift at 200 keV https://t.co/0HQmabT1lO #biorxiv_biophys
biophotonicat: High-resolution cryo-EM using beam-image shift at 200 keV (relevance: 47%) https://t.co/MqfpgkmtKm #biophotonics #biomedicaloptics https://t.co/uW14kFHKr8
cryoEM_Papers: High-resolution cryo-EM using beam-image shift at 200 keV https://t.co/UUvarYuP8N
emeKato: RT @biorxivpreprint: High-resolution cryo-EM using beam-image shift at 200 keV https://t.co/f7tEqwxYav #bioRxiv
SingleParticle: RT @cryoEM_Papers: High-resolution cryo-EM using beam-image shift at 200 keV https://t.co/UUvarYuP8N
AlexanderSobol6: RT @cryoEM_Papers: High-resolution cryo-EM using beam-image shift at 200 keV https://t.co/UUvarYuP8N
t2438: RT @cryoEM_Papers: High-resolution cryo-EM using beam-image shift at 200 keV https://t.co/UUvarYuP8N
a__jomaa: RT @cryoEM_Papers: High-resolution cryo-EM using beam-image shift at 200 keV https://t.co/UUvarYuP8N
pietro1968: RT @cryoEM_Papers: High-resolution cryo-EM using beam-image shift at 200 keV https://t.co/UUvarYuP8N
dmborek: RT @cryoEM_Papers: High-resolution cryo-EM using beam-image shift at 200 keV https://t.co/UUvarYuP8N
MalettaMax: RT @cryoEM_Papers: High-resolution cryo-EM using beam-image shift at 200 keV https://t.co/UUvarYuP8N
AlHSJCKtEfpFXtm: RT @cryoEM_Papers: High-resolution cryo-EM using beam-image shift at 200 keV https://t.co/UUvarYuP8N
MarjetaPodobnik: RT @cryoEM_Papers: High-resolution cryo-EM using beam-image shift at 200 keV https://t.co/UUvarYuP8N
JinfanW: RT @cryoEM_Papers: High-resolution cryo-EM using beam-image shift at 200 keV https://t.co/UUvarYuP8N
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#10. High Force Catch Bond Mechanism of Bacterial Adhesion in the Human Gut
Zhaowei Liu, Haipei Liu, Andrés M. Vera, Rafael C. Bernardi, Philip Tinnefeld, Michael A. Nash
Bacterial colonization of the human intestine requires firm adhesion of bacteria to insoluble targets under hydrodynamic flow. Here we report the molecular mechanism behind an mechanostable protein complex responsible for resisting high shear forces and adhering bacteria to cellulose fibers in the human gut. Using single-molecule force spectroscopy (SMFS), single-molecule FRET (smFRET), and molecular dynamics (MD) simulations, we resolved two binding modes and three unbinding reaction pathways of a mechanically ultrastable R. champanellensis (Rc) Dockerin-Cohesin (Doc-Coh) complex. The complex assembles in two discrete binding modes with significantly different mechanical properties, with one breaking at ~500 pN and the other at ~200 pN at loading rates from 1-100 nN/sec. A neighboring X-module domain allosterically regulates the binding interaction and inhibits one of the low-force pathways at high loading rates, giving rise to a new mechanism of catch bonding that manifests under force ramp protocols. Multi-state Monte Carlo...
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