Top 10 Biorxiv Papers Today in Biophysics


2.099 Mikeys
#1. Single particle diffusion characterization by deep learning
Naor Granik, Lucien E Weiss, Maayan Levine, Michael Chein, Eran Perlson, Yael Roichman, Yoav Shechtman
Diffusion plays a crucial role in many biological processes including signaling, cellular organization, transport mechanisms, and more. Direct observation of molecular movement by single-particle tracking experiments has contributed to a growing body of evidence that many cellular systems do not exhibit classical Brownian motion, but rather anomalous diffusion. Despite this evidence, characterization of the physical process underlying anomalous diffusion remains a challenging problem for several reasons. First, different physical processes can exist simultaneously in a system. Second, commonly used tools to distinguish between these processes are based on asymptotic behavior, which is inaccessible experimentally in most cases. Finally, an accurate analysis of the diffusion model requires the calculation of many observables, since different transport modes can result in the same diffusion power-law α, that is obtained from the commonly used mean-squared-displacement (MSD) in its various forms. The outstanding challenge in the field...
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gp_pulipaka: Single Particle Diffusion Characterization by #DeepLearning. #BigData #Analytics #DataScience #AI #MachineLearning #IoT #IIoT #PyTorch #Python #RStats #TensorFlow #Java #JavaScript #ReactJS #GoLang #CloudComputing #Serverless #DataScientist #Linux https://t.co/aQctrRKMmd https://t.co/gNa5MVZqOG
razoralign: Single particle diffusion characterization by deep learning https://t.co/7lLEOrXESp https://t.co/3RAcOD4XVg
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Authors: 7
Total Words: 0
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2.037 Mikeys
#2. Bidirectional FtsZ filament treadmilling promotes membrane constriction via torsional stress
Diego Alejandro Ramirez-Diaz, Adrian Merino-Salomon, Michael Heymann, Petra Schwille
FtsZ is a key component in bacterial cell division, being the primary protein of the presumably contractile Z ring. Reconstituted in vitro, it shows two distinctive features that could so far however not be mechanistically linked: self-organization into directionally treadmilling vortices on solid supported membranes, and shape deformation of flexible liposomes. In cells, circumferential treadmilling of FtsZ was shown to recruit septum-building enzymes, but an active force production remains elusive. To determine direct contributions of FtsZ to membrane constriction, we designed a novel in vitro assay based on soft lipid tubes pulled from FtsZ decorated giant lipid vesicles (GUVs) by optical tweezers. FtsZ actively transformed these tubes into spring-like structures, where GTPase activity promoted spring compression. Operating the optical tweezers in lateral vibration mode and assigning spring constants to FtsZ coated tubes, we found that that FtsZ indeed exerts pN forces upon GTP hydrolysis, through torsional stress induced by...
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biorxivpreprint: Bidirectional FtsZ filament treadmilling promotes membrane constriction via torsional stress https://t.co/PizfMYEObH #bioRxiv
biorxiv_biophys: Bidirectional FtsZ filament treadmilling promotes membrane constriction via torsional stress https://t.co/i91F66WqQg #biorxiv_biophys
PracheeAC: RT @biorxivpreprint: Bidirectional FtsZ filament treadmilling promotes membrane constriction via torsional stress https://t.co/PizfMYEObH…
seamus_holden: RT @biorxivpreprint: Bidirectional FtsZ filament treadmilling promotes membrane constriction via torsional stress https://t.co/PizfMYEObH…
biochemistries: RT @biorxivpreprint: Bidirectional FtsZ filament treadmilling promotes membrane constriction via torsional stress https://t.co/PizfMYEObH…
BramkampLab: RT @biorxivpreprint: Bidirectional FtsZ filament treadmilling promotes membrane constriction via torsional stress https://t.co/PizfMYEObH…
Figlegend: RT @biorxivpreprint: Bidirectional FtsZ filament treadmilling promotes membrane constriction via torsional stress https://t.co/PizfMYEObH…
Kar__El: RT @biorxivpreprint: Bidirectional FtsZ filament treadmilling promotes membrane constriction via torsional stress https://t.co/PizfMYEObH…
HenrikStrahl: RT @biorxivpreprint: Bidirectional FtsZ filament treadmilling promotes membrane constriction via torsional stress https://t.co/PizfMYEObH…
schraderlab: RT @biorxivpreprint: Bidirectional FtsZ filament treadmilling promotes membrane constriction via torsional stress https://t.co/PizfMYEObH…
Eswara_Lab: RT @biorxivpreprint: Bidirectional FtsZ filament treadmilling promotes membrane constriction via torsional stress https://t.co/PizfMYEObH…
BillSoderstrom: RT @biorxivpreprint: Bidirectional FtsZ filament treadmilling promotes membrane constriction via torsional stress https://t.co/PizfMYEObH…
NguyenThLam: RT @biorxivpreprint: Bidirectional FtsZ filament treadmilling promotes membrane constriction via torsional stress https://t.co/PizfMYEObH…
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Authors: 4
Total Words: 3291
Unqiue Words: 1315

2.027 Mikeys
#3. Polyphosphate initiates tau aggregation through intra- and intermolecular scaffolding
Sanjula P. Wickramasinghe, Justine Lempart, Hope E Merens, Jacob Murphy, Ursula Jakob, Elizabeth Rhoades
The aggregation and deposition of tau is a hallmark of a class of neurodegenerative diseases called tauopathies. Despite intensive study, cellular and molecular factors that trigger tau aggregation are not well understood. Here we provide evidence for two mechanisms relevant to the initiation of tau aggregation in the presence of cytoplasmic polyphosphates (polyP): changes in the conformational ensemble of monomer tau and noncovalent cross-linking of multiple tau monomers. We identified conformational changes throughout full-length tau, most notably diminishment of long-range interactions between the termini coupled with compaction of the microtubule binding and proline rich regions. We found that while the proline rich and microtubule binding regions both contain polyP binding sites, the proline rich region is a requisite for compaction of the microtubule binding region upon binding. Additionally, both the magnitude of the conformational change and the aggregation of tau are dependent on the chain length of the polyP polymer....
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biorxivpreprint: Polyphosphate initiates tau aggregation through intra- and intermolecular scaffolding https://t.co/Q4abNqXcyg #bioRxiv
biorxiv_biophys: Polyphosphate initiates tau aggregation through intra- and intermolecular scaffolding https://t.co/e47GA7Jpim #biorxiv_biophys
kwitschas: RT @biorxiv_biophys: Polyphosphate initiates tau aggregation through intra- and intermolecular scaffolding https://t.co/e47GA7Jpim #biorxi…
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Sample Sizes : [3]
Authors: 6
Total Words: 9775
Unqiue Words: 3047

2.02 Mikeys
#4. Lipid Interactions of a Ciliary Membrane TRP Channel: Simulation and Structural Studies of Polycystin-2 (PC2)
Qinrui Wang, George Hedger, Prafulla Aryal, Mariana Grieben, Chady Nasrallah, Agnese Baronina, Ashley Pike, Jiye Shi, Elisabeth P Carpenter, Mark Sansom
Polycystin-2 (PC2) is a member of the TRPP subfamily of TRP channels and is present in ciliary membranes of the kidney. PC2 can be either homo-tetrameric, or heterotetrameric with PC1. PC2 shares a common transmembrane fold with other TRP channels, in addition to having a novel extracellular domain. Several TRP channels have been suggested to be regulated by lipids, including phosphatidylinositol phosphates (PIPs). We have combined molecular dynamics simulations with cryoelectron microscopy to explore possible lipid interactions sites on PC2. We propose that PC2 has a PIP-binding site close to the equivalent vanilloid/lipid-binding site in the TRPV1 channel. A 3.0 Å cryoelectron microscopy map reveals a binding site for cholesterol on PC2. Cholesterol interactions with the channel at this site are further characterized by MD simulations. These results help to position PC2 within an emerging model of the complex roles of lipids in the regulation and organization of ciliary membranes.
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cryoEM_Papers: Lipid Interactions of a Ciliary Membrane TRP Channel: Simulation and Structural Studies of Polycystin-2 (PC2) https://t.co/8xtLMpszZK
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2.0 Mikeys
#5. Class A GPCRs use the membrane potential to increase their sensitivity and selectivity
Daria Shalaeva, Dmitry Cherepanov, Michael Galperin, Gert Vriend, Armen Mulkidjanian
The human genome contains about 700 genes of G protein-coupled receptors (GPCRs) of class A; these seven-helical membrane proteins are the targets of almost half of all known drugs. In the middle of the helix bundle, crystal structures revealed a highly conserved sodium-binding site, which is connected with the extracellular side by a water-filled tunnel. Sodium ions are observed in GPCRs crystallized in their inactive conformations, but not in GPCRs that were trapped in agonist-bound active conformations. The escape route of the sodium ion upon the inactive-to-active transition and its very direction, either into the cytoplasm or back outside the cell, hitherto remained obscure. We modeled sodium-binding GPCRs as electrogenic carriers of sodium ions. In this model the sodium gradient over the cell membrane would increase the sensitivity of GPCRs if their activation is thermodynamically coupled to the translocation of the sodium ion into the cytoplasm, while decreasing it if the sodium ion retreats into the extracellular space...
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biorxivpreprint: Class A GPCRs use the membrane potential to increase their sensitivity and selectivity https://t.co/0aehc1cDBo #bioRxiv
biorxiv_biophys: Class A GPCRs use the membrane potential to increase their sensitivity and selectivity https://t.co/FbG3dlF8aJ #biorxiv_biophys
JamesEKrause: Impressive structural modeling paper on some recent advances in Class A "GPCRs, the class that represents the targets of some 50% of current #drugs. GPCRs are amazing molecular machines. This field is not for the timid. https://t.co/9Ruld8dpjY
AutonomicAus: Class A GPCRs use the membrane potential to increase their sensitivity and selectivity https://t.co/M4bY69u0Ot #GPCRs #GPCR #membranepotential #Gprotein #receptors #receptor #membraneproteins #membraneprotein #bioinformatics #computationalbiology #lifesciences #biochemistry
ramonguixxa: Class A GPCRs use the membrane potential to increase their sensitivity and selectivity https://t.co/sT7SYOTjwS
DNAed_tech: RT @AutonomicAus: Class A GPCRs use the membrane potential to increase their sensitivity and selectivity https://t.co/M4bY69u0Ot #GPCRs #…
zenbrainest: RT @biorxivpreprint: Class A GPCRs use the membrane potential to increase their sensitivity and selectivity https://t.co/0aehc1cDBo #bioRx…
kwitschas: RT @biorxiv_biophys: Class A GPCRs use the membrane potential to increase their sensitivity and selectivity https://t.co/FbG3dlF8aJ #biorx…
everburningfire: RT @AutonomicAus: Class A GPCRs use the membrane potential to increase their sensitivity and selectivity https://t.co/M4bY69u0Ot #GPCRs #…
kennethkim_: RT @AutonomicAus: Class A GPCRs use the membrane potential to increase their sensitivity and selectivity https://t.co/M4bY69u0Ot #GPCRs #…
jzahratk: RT @biorxivpreprint: Class A GPCRs use the membrane potential to increase their sensitivity and selectivity https://t.co/0aehc1cDBo #bioRx…
poppingjun: RT @biorxivpreprint: Class A GPCRs use the membrane potential to increase their sensitivity and selectivity https://t.co/0aehc1cDBo #bioRx…
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Sample Sizes : [105, 107, 10]
Authors: 5
Total Words: 16733
Unqiue Words: 5084

1.996 Mikeys
#6. Membrane association of VAMP2 SNARE motif in cells and its regulation by different lipid phases of synaptic vesicle membrane
Chuchu Wang, Jia Tu, Shengnan Zhang, Bin Cai, Zhenying Liu, Shouqiao Hou, Zhijun Liu, Jiajie Diao, Zheng-Jiang Zhu, Cong Liu, Dan Li
Vesicle associated membrane protein 2 (VAMP2) contains a conserved SNARE motif that forms helix bundles with the homologous motifs of syntaxin-1 and SNAP25 to assemble into a SNARE complex for the exocytosis of synaptic vesicles (SV). Prior to SNARE assembly, the structure of VAMP2 is unclear. Here, using in-cell NMR spectroscopy, we described the dynamic membrane association of VAMP2 SNARE motif in mammalian cells at atomic resolution, and further tracked the intracellular structural changes of VAMP2 upon the lipid environmental changes. The underlying mechanistic basis was then investigated by solution NMR combined with mass-spectrometry-based lipidomic profiling. We analyzed the lipid compositions of lipid-raft and non-raft phases of SV membrane and revealed that VAMP2 configures distinctive conformations in different phases of SV membrane. The phase of cholesterol-rich lipid rafts could largely weaken the association of SNARE motif with SV membrane and thus, facilitate vesicle docking; While in the non-raft phase, the SNARE...
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Authors: 11
Total Words: 5813
Unqiue Words: 1707

1.996 Mikeys
#7. Modeling the ballistic-to-diffusive transition in nematode motility reveals variation in exploratory behavior across species
Stephen J Helms, W. Mathijs Rozemuller, Antonio Carlos Costa, Leon Avery, Greg J. Stephens, Thomas S. Shimizu
A quantitative understanding of organism-level behavior requires predictive models that can capture the richness of behavioral phenotypes, yet are simple enough to connect with underlying mechanistic processes. Here we investigate the motile behavior of nematodes at the level of their translational motion on surfaces driven by undulatory propulsion. We broadly sample the nematode behavioral repertoire by measuring motile trajectories of the canonical lab strain C. elegans N2 as well as wild strains and distant species. We focus on trajectory dynamics over timescales spanning the transition from ballistic (straight) to diffusive (random) movement and find that salient features of the motility statistics are captured by a random walk model with independent dynamics in the speed, bearing and reversal events. We show that the model parameters vary among species in a correlated, low-dimensional manner suggestive of a common mode of behavioral control and a trade-off between exploration and exploitation. The distribution of phenotypes...
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Authors: 6
Total Words: 16274
Unqiue Words: 4096

1.991 Mikeys
#8. Beyond early development: observing zebrafish over 6 weeks with hybrid optical and optoacoustic imaging
Paul Vetschera, Benno Koberstein-Schwarz, Tobias Schmitt-Manderbach, Christian Dietrich, Wibke Hellmich, Andrei Chekkoury, Panagiotis Symvoulidis, Josefine Reber, Gil Westmeyer, Hernan Lopez-Schier, Murad Omar, Vasilis Ntziachristos
Zebrafish animal models have traditionally been used in developmental biology studies but have recently become promising models of cancer, tissue regeneration and metabolic disorders, as well as efficient platforms for functional genomics and phenotype-based drug discovery. Most studies of zebrafish have examined only the embryonic or larval stages of development, yet many questions in developmental biology and biomedicine require analysis of adults, when zebrafish are large and opaque. Conventional microscopy methods are highly sensitive to light scattering and therefore cannot be applied to zebrafish older than a few weeks. We describe a novel multi-modality system that can observe zebrafish from the larval stage to adulthood. Using a hybrid platform for concurrent selective plane illumination microscopy (SPIM) and optoacoustic mesoscopy we show continuous imaging of fish growth over 47 days of development at a similar object size-to-resolution ratio. Using multiple wavelength illumination over the visible and short-wavelength...
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Authors: 12
Total Words: 7122
Unqiue Words: 2181

1.988 Mikeys
#9. Membrane bending energy and tension govern mitochondrial division
Dora Mahecic, Lina Carlini, Tatjana Kleele, Adai Colom, Antoine Goujon, Stefan Matile, Aurelien Roux, Suliana Manley
Many molecular factors required for mitochondrial division have been identified; however, how they combine to physically trigger division remains unknown. Here, we report that constriction by the division machinery does not ensure mitochondria will divide. Instead, potential division sites accumulate molecular components and can constrict before either dividing, or relaxing back to an unconstricted state. Using time-lapse structured illumination microscopy (SIM), we find that constriction sites with higher local curvatures - reflecting an increased membrane bending energy - are more likely to divide. Furthermore, analyses of mitochondrial motion and shape changes demonstrate that dividing mitochondria are typically under an externally induced membrane tension. This is corroborated by measurements using a newly synthesized fluorescent mitochondrial membrane tension sensor, which reveal that depolymerizing the microtubule network diminishes mitochondrial membrane tension. We find that under reduced tension, the number of...
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Sample Sizes : [112, 57, 61, 30, 13, 10, 69, 43, 69, 43, 70, 43, 69, 70, 101, 88, 10, 57, 33, 16, 16, 33, 33, 22]
Authors: 8
Total Words: 9683
Unqiue Words: 2891

1.91 Mikeys
#10. HDX-MS reveals structural determinants for RORγ hyperactivation by synthetic agonists
Timothy S. Strutzenberg, Ruben Garcia-Ordonez, Scott Novick, HaJeung Park, Mi Ra Chang, Christelle Doebellin, Yuanjun He, Remi Patouret, Theodore Kamenecka, Patrick R Griffin
Members of the nuclear receptor (NR) superfamily regulate both physiological and pathophysiological processes ranging from development and metabolism to inflammation and cancer. As ligand gated transcription factors, synthetic small molecules targeting NRs are often deployed as therapeutics to correct aberrant NR signaling or as chemical probes to explore the role of the receptor in physiology. However, nearly half of NRs do not have specific cognate ligands or its unclear if they possess ligand dependent activities and these receptors are called orphans. Here we demonstrate that ligand dependent action of the orphan nuclear receptor RORG can be defined by selectively disrupting putative endogenous but not synthetic ligand binding. Furthermore, the characterization of a library of RORG modulators reveals that structural dynamics of the receptor assessed by HDX-MS correlate with activity in biochemical and cell-based assays. These findings are corroborated with X-ray co-crystallography and site-directed mutagenesis to collectively...
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