Top 10 Biorxiv Papers Today in Biophysics


2.052 Mikeys
#1. Aggregation dynamics of charged peptides in water: effect of salt concentration
Susmita Ghosh
Extensive molecular dynamics simulations have been employed to probe the effects of salts on the kinetics and dynamics of early-stage aggregated structures of steric zipper peptides in water. The simulations reveal that the chemical identity and valency of cation in the salt play a crucial roles in aggregate morphology of the peptides. Sodium ions induce the most aggregated structures but this is not replicated by potassium ions which are also monovalent. Divalent Magnesium ions induce aggregation, but to a lesser extent than that of sodium and their interactions with the charged peptides are also significantly different. The aggregate morphology in the presence of monovalent sodium ions is a compact structure with interpenetrating peptides, which differs from the more loosely connected peptides in the presence of either potassium or magnesium ions. The different ways in which the cations effectively renormalize the charges of peptides is suggested to be the cause of the differential effects of different salts studied here. These...
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biorxivpreprint: Aggregation dynamics of charged peptides in water: effect of salt concentration https://t.co/FOPm0QuTPo #bioRxiv
biorxiv_biophys: Aggregation dynamics of charged peptides in water: effect of salt concentration https://t.co/kTpG3eJvok #biorxiv_biophys
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Authors: 1
Total Words: 0
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2.015 Mikeys
#2. New High Throughput Approaches to Detect Partial-body and Neutron Exposures on an Individual Basis
Igor Shuryak, Helen C Turner, Jay R Perrier, Lydia Cunha, Monica Pujol Canadell, Mohammad H Durrani, Andrew Harken, Antonella Bertucci, Maria Taveras, Guy Garty, David J Brenner
Biodosimetry-based discrimination between homogeneous total-body photon exposure and complex irradiation scenarios (partial-body shielding and/or neutron + photon mixtures) can improve treatment decisions after mass-casualty radiation-related incidents. Our study objective was to use high-throughput biomarkers to: a) detect partial-body and/or neutron exposure on an individual basis, and b) estimate separately the photon and neutron doses in a mixed exposure. We developed a novel approach, where metrics related to the shapes of micronuclei distributions per binucleated cell in ex-vivo irradiated human lymphocytes (variance/mean, kurtosis, skewness, etc.) served as predictors in machine learning or parametric analyses of the following scenarios: (A) Homogeneous gamma-irradiation, mimicking total-body exposures, vs. mixtures of irradiated blood with unirradiated blood, mimicking partial-body exposures. (B) X rays vs. various neutron + photon mixtures. Classification of samples as homogeneously vs. heterogeneously irradiated...
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biorxivpreprint: New High Throughput Approaches to Detect Partial-body and Neutron Exposures on an Individual Basis https://t.co/jOSy6pi2v0 #bioRxiv
biorxiv_biophys: New High Throughput Approaches to Detect Partial-body and Neutron Exposures on an Individual Basis https://t.co/qHY2O7H8K9 #biorxiv_biophys
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Authors: 11
Total Words: 0
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2.014 Mikeys
#3. Structural characterization of tau in fuzzy tau:tubulin complexes
Ho Yee Joyce Fung, Kushol Gupta, Elizabeth Rhoades
Tau is a neuronal microtubule (MT) associated protein of significant interest due to its association with several neurodegenerative disorders. Tau's intrinsic disorder and the dynamic nature of its interactions with tubulin and MTs make its structural characterization challenging. Here we use an environmentally sensitive fluorophore as a site-specific probe of tau bound to soluble tubulin. Comparison of our results with recently published tau:MT cryo-EM model reveals structural similarities between tubulin- and MT-bound tau. Analysis of residues across the repeat regions reveal a hierarchy in tubulin binding interactions, which may be relevant to tau's ability to differentiate between tubulin and MTs. As binding to soluble tubulin is a critical first step in MT polymerization, our characterization of the structural features of tau in dynamic, fuzzy tau:tubulin assemblies advances our understanding of how tau functions in the cell and how function may be disrupted in disease.
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biorxivpreprint: Structural characterization of tau in fuzzy tau:tubulin complexes https://t.co/UCWTl9IHnC #bioRxiv
biorxiv_biophys: Structural characterization of tau in fuzzy tau:tubulin complexes https://t.co/X3NJASGyKK #biorxiv_biophys
cryoEM_Papers: Structural characterization of tau in fuzzy tau:tubulin complexes https://t.co/Tid0PuRuMU
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Authors: 3
Total Words: 0
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2.01 Mikeys
#4. Two-color nanoscopy of organelles for extended times with HIDE probes
Ling Chu, Jonathan Tyson, Juliana E. Shaw, Felix Rivera-Molina, Anthony J. Koleske, Alanna Schepartz, Derek Toomre
Performing multi-color nanoscopy for extended times is challenging due to the rapid photobleaching rate of most fluorophores. Here we describe a new fluorophore (Yale-595) and a bio-orthogonal labeling strategy that enables both super-resolution (STED) and 3D confocal imaging of two organelles simultaneously for extended times using high-density environmentally sensitive (HIDE) probes. Because HIDE probes are small, cell-permeant molecules, they can visualize organelle pairs (ER + mitochondria, ER + plasma membrane) in hard-to-transfect cell lines at super-resolution for up to 7 minutes. The extended time domain possible using these new tools reveal novel dynamic nanoscale targeting between organelles.
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biorxivpreprint: Two-color nanoscopy of organelles for extended times with HIDE probes https://t.co/O3DdZDbMWl #bioRxiv
biorxiv_biophys: Two-color nanoscopy of organelles for extended times with HIDE probes https://t.co/OLl6L0Pgkn #biorxiv_biophys
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Authors: 7
Total Words: 6049
Unqiue Words: 1597

1.998 Mikeys
#5. Plasticity of cell migration resulting from mechanochemical coupling
Yuansheng Cao, Elisabeth Ghabache, Wouter-Jan Rappel
Eukaryotic cells can migrate using different modes, ranging from amoeboid-like, during which actin filled protrusions come and go, to keratocyte-like, characterized by a stable morphology and persistent motion. How cells can switch between these modes is not well understood but waves of signaling events are thought to play an important role in these transitions. Here we present a simple two-component biochemical reaction-diffusion model based on relaxation oscillators and couple this to a model for the mechanics of cell deformations. Different migration modes, including amoeboid-like and keratocyte-like, naturally emerge through phase transitions determined by interactions between biochemical traveling waves, cell mechanics and morphology. The model predictions are explicitly verified by systematically reducing the protrusive force of the actin network in experiments using Dictyostelium discoideum cells. Our results indicate the importance of coupling signaling events to cell mechanics and morphology and may be applicable in a...
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LilJeanGrey: RT @biorxivpreprint: Plasticity of cell migration resulting from mechanochemical coupling https://t.co/RRbgmmjuFe #bioRxiv
HasreetGill: RT @biorxivpreprint: Plasticity of cell migration resulting from mechanochemical coupling https://t.co/RRbgmmjuFe #bioRxiv
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Authors: 3
Total Words: 10999
Unqiue Words: 2951

1.998 Mikeys
#6. Directional stepping model for yeast dynein: Longitudinal- and side- step distributions
Rony Granek, Itay Fayer
We deduce the directional step distribution of yeast dynein motor protein on the microtubule surface by combing intrinsic features of the dynein and microtubule. These include the probability distribution of the separation vector between the two microtubule binding domains (MTBDs), the angular probability distribution of a single MTBD translation, the existence of a microtubule seam defect, microtubule binding sites, and theoretical extension that accounts for a load force on the motor. Our predictions are in excellent accord with the measured longitudinal step size distributions at various load forces. Moreover, we predict the side-step distribution and its dependence on longitudinal load forces, which shows a few surprising features. First, the distribution is broad. Second, in the absence of load, we find a small right-hand bias. Third, the side-step bias is susceptible to the longitudinal load force; it vanishes at a load equal to the motor stalling force and changes to a left-hand bias above that value. Fourth, our results...
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biorxivpreprint: Directional stepping model for yeast dynein: Longitudinal- and side- step distributions https://t.co/nS7L6wgsHB #bioRxiv
biorxiv_biophys: Directional stepping model for yeast dynein: Longitudinal- and side- step distributions https://t.co/6fhIcqR8PQ #biorxiv_biophys
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Authors: 2
Total Words: 6378
Unqiue Words: 1711

1.998 Mikeys
#7. Detecting and controlling dye effects in single-virus fusion experiments
Robert J. Rawle, Ana M. Villamil Giraldo, Steven G. Boxer, Peter M. Kasson
Fluorescent dye-dequenching assays provide a powerful and versatile means to monitor membrane fusion events. They have been used in bulk assays, for measuring single events in live cells, and for detailed analysis of fusion kinetics for liposomal, viral, and cellular fusion processes; however, the dyes used also have the potential to perturb membrane fusion. Here, using single-virus measurements of influenza membrane fusion, we show that fluorescent membrane probes can alter both the efficiency and the kinetics of lipid mixing in a dye- and illumination-dependent manner. R18, a dye that is commonly used to monitor lipid mixing between membranes, is particularly prone to these effects, while Texas Red is somewhat less sensitive. R18 further undergoes photoconjugation to viral proteins in an illumination-dependent manner that correlates with its inactivation of viral fusion. These results demonstrate how fluorescent probes can perturb measurements of biological activity and provide both data and a method for determining minimally...
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floresromeroh: RT @biorxiv_biophys: Detecting and controlling dye effects in single-virus fusion experiments https://t.co/Ixom0EsuJw #biorxiv_biophys
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Authors: 4
Total Words: 6068
Unqiue Words: 1946

1.997 Mikeys
#8. Mitochondrial dynamics quantitatively revealed by STED nanoscopy with an enhanced squaraine variant probe
Xusan Yang, Zhigang Yang, Ying He, Chunyan Shan, Wei Yan, Zhaoyang Wu, Peiyuan Chai, Junlin Teng, Junle Qu, Peng Xi
Mitochondria play a critical role in generating energy to support the entire lifecycle of biological cells, yet it is still unclear how their morphological structures evolve to regulate their functionality. Conventional fluorescence microscopy can only provide ~300 nm resolution, which is insufficient to visualize mitochondrial cristae. Here, we developed an enhanced squaraine variant dye (MitoESq-635) to study the dynamic structures of mitochondrial cristae in live cells at superresolution. The low saturation intensity and high photostability make it ideal for long-term, high-resolution STED nanoscopy. We demonstrate the time-lapsed imaging of the mitochondrial inner membrane over 50 minutes in living HeLa cells at 35.2 nm resolution for the first time. The forms of the cristae during mitochondrial fusion and fission can be clearly resolved. Our study demonstrates the emerging capability of optical STED nanoscopy to investigate intracellular physiological processes at nanoscale resolution for long periods of time with minimal...
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biorxivpreprint: Mitochondrial dynamics quantitatively revealed by STED nanoscopy with an enhanced squaraine variant probe https://t.co/onrmQzKUAq #bioRxiv
biorxiv_biophys: Mitochondrial dynamics quantitatively revealed by STED nanoscopy with an enhanced squaraine variant probe https://t.co/0ce5Wuue1K #biorxiv_biophys
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Authors: 10
Total Words: 5849
Unqiue Words: 1900

1.997 Mikeys
#9. Quantitative studies of an RNA duplex electrostatics by ion counting
Magdalena Gebala, Dan Herschlag
Ribonucleic acids are one of the most charged polyelectrolytes in nature, and understanding of their electrostatics is fundamental to their structure and biological functions. An effective way to characterize the electrostatic field generated by nucleic acids is to quantify interactions between nucleic acids and ions that surround the molecules. These ions form a loosely associated cloud referred as an ion atmosphere. While theoretical and computational studies can describe the ion atmosphere around RNAs, benchmarks are needed to guide the development of these approaches and experiments to-date that read out RNA-ion interaction are limited. Here we present ion counting studies to quantify the number of ions surrounding well-defined model systems of 24-bp RNA and DNA duplexes. We observe that the RNA duplex attracts more cations and expels fewer anions compared to the DNA duplex and the RNA duplex interacts significantly more strongly with the divalent cation Mg2+. These experimental results strongly suggest that the RNA duplex...
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biorxivpreprint: Quantitative studies of an RNA duplex electrostatics by ion counting https://t.co/tDRoBQYnsc #bioRxiv
biorxiv_biophys: Quantitative studies of an RNA duplex electrostatics by ion counting https://t.co/dh1QryM5YM #biorxiv_biophys
sbotlite: RT @biorxivpreprint: Quantitative studies of an RNA duplex electrostatics by ion counting https://t.co/tDRoBQYnsc #bioRxiv
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Authors: 2
Total Words: 7205
Unqiue Words: 2192

1.997 Mikeys
#10. Cataract-associated deamidations on the surface of γS-crystallin increase protein unfolding and flexibility at distant regions
Heather M Forsythe, Calvin J Vetter, Kayla J Jara, Patrick N Reardon, Larry L David, Elisar J Barbar, Kirsten Lampi
Deamidation is a major age-related modification in the human lens that is highly prevalent in crystallins isolated from cataractous lenses. However, the mechanism by which deamidation causes proteins to become insoluble is not known, because of only subtle structural changes observed in vitro. We have identified Asn14 and Asn76 of γS-crystallin as highly deamidated in insoluble proteins. These sites are on the surface of the N-terminal domain and were mimicked by replacing the Asn with Asp residues. We used heteronuclear NMR spectroscopy to measure their amide hydrogen exchange and 15N relaxation dynamics to identify regions with significantly increased dynamics compared to wildtype-γS. Changes in dynamics were localized to the C-terminal domain, particularly to helix and surface loops distant from the mutation sites. Thus, a potential mechanism for γS deamidation-induced insolubilization in cataractous lenses is altered dynamics due to local regions of unfolding and increased flexibility rather than global structural changes.
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biorxivpreprint: Cataract-associated deamidations on the surface of γS-crystallin increase protein unfolding and flexibility at distant regions https://t.co/0z9BzlnN9F #bioRxiv
biorxiv_biophys: Cataract-associated deamidations on the surface of γS-crystallin increase protein unfolding and flexibility at distant regions https://t.co/phbNaCt8yC #biorxiv_biophys
kirstenlampi: Thank you @mason91 ! Thanks for teaching me how! Here is the link https://t.co/IMCc0FlM50 https://t.co/My26qlamFb
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Sample Sizes : [3, 3, 3]
Authors: 7
Total Words: 7802
Unqiue Words: 2469

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