PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.12.246322v1?rss=1

Authors: Mehta, N., Shaik, S., Prasad, A., Chaichi, A., Sahu, S. P., Hasan, S. M. A., Donnarumma, F., Murray, K. K., Devireddy, R., Gartia, M. R.

Abstract:

Stem cell-based therapies carry significant promise for treating human diseases. However, clinical translation of stem cell transplants for effective therapy requires precise non-destructive evaluation of the purity of stem cells with high sensitivity (< 0.001% of the number of cells). Here, we report a novel methodology using hyperspectral imaging (HSI) combined with spectral angle mapping (SAM)-based machine learning analysis to distinguish differentiating human adipose derived stem cells (hASCs) from control stem cells. The spectral signature of adipogenesis generated by the HSI method enabled identification of differentiated cells at single cell resolution. The label-free HSI method was compared with the standard methods such as Oil Red O staining, fluorescence microscopy, and qPCR that are routinely used to evaluate adipogenic differentiation of hASCs. Further, we performed Raman microscopy and multiphoton-based metabolic imaging to provide complimentary information for the functional imaging of the hASCs. Finally, the HSI method was validated using matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) imaging of the stem cells. The study presented here demonstrates that multimodal imaging methods enable label-free identification of stem cell differentiation with high spatial and chemical resolution. This could provide a powerful tool to assess the safety and efficacy of stem cell-based regenerative therapies.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.11.244939v1?rss=1

Authors: Raskar, T., Niebling, S., Devos, J. M., Yorke, B. A., Härtlein, M., Huse, N., Forsyth, T. V., Seydel, T., Pearson, A. R.

Abstract:

Incoherent neutron spectroscopy, in combination with dynamic light scattering was used to investigate the effect of ligand binding on the center-of-mass self-diffusion and internal diffusive dynamics of E.coli aspartate -decarboxylase (ADC). The X-ray crystal structure of the D-serine inhibitor complex with ADC was also determined, and molecular dynamics simulations used to further probe the structural rearrangements that occur as a result of ligand binding. These experiments reveal the existence of higher order oligomers of the ADC tetramer on ns-ms time-scales, and also show that ligand binding both affects the ADC internal diffusive dynamics and appears to further increase the size of the higher order oligomers.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.11.246595v1?rss=1

Authors: Forouhesh Tehrani, K., Koukourakis, N., Czarske, J., Mortensen, L.

Abstract:

Wavefront-shaping (WS) enables imaging through scattering tissues like bone, which is important for neuroscience and bone-regeneration research. WS corrects for the optical aberrations at a given depth and field-of-view (FOV) within the sample; the extent of the validity of which is limited to a region known as the isoplanatic patch (IP). Knowing this parameter helps to estimate the number of corrections needed for WS imaging over a given FOV. In this paper, we first present direct transmissive measurement of murine skull IP using digital optical phase conjugation (DOPC) based focusing. Second, we extend our previously reported Phase Accumulation Ray Tracing (PART) method to provide in-situ in-silico estimation of IP, called correlative PART (cPART). Our results show an IP range of 1-3 m for mice within an age range of 8-14 days old and 1.00+/-0.25 m in a 12-week old adult skull. Consistency between the two measurement approaches indicates that cPART can be used to approximate the IP before a WS experiment, which can be used to calculate the number of corrections required within a given field of view.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.11.243733v1?rss=1

Authors: Grobas, I., Polin, M., Asally, M.

Abstract:

Swarming and biofilm formation are two modes of bacterial collective behavior that enable cells to increase their tolerance to anti-microbial stressors. Swarming is a rapid type of surface colonization, and therefore its ability to withstand high antibiotic concentrations could lead to the subsequent establishment of highly resilient biofilms in regions that could not otherwise have been colonized. However, whether swarms can transit into biofilm at all, and how, remains unclear. Using Bacillus subtilis, we reveal that a biophysical mechanism, reminiscent of motility-induced phase separation (MIPS), underpins a swarming-to-biofilm transition through a localized dynamic phase transition. Guided by the MIPS paradigm, we demonstrate that the transition is triggered by environmental stressors such as an antibiotic gradient or even a simple physical barrier. Based on the biophysical insight, we propose a promising strategy of antibiotic treatment to effectively inhibit the transition from swarms to biofilms, by targeting the localized phase transition. The biophysical origin of such a transition suggests that biophysics-based approaches could emerge as a potential tool to control and understand collective stress response in bacterial communities.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.11.245696v1?rss=1

Authors: Zhang, K., Li, S., Pintilie, G., Chmielewski, D., Schmid, M. F., Simmons, G., Jin, J., Chiu, W.

Abstract:

Human coronavirus NL63 (HCoV-NL63) is an enveloped pathogen of the family Coronaviridae that spreads worldwide and causes up to 10% of all annual respiratory diseases. HCoV-NL63 is typically associated with mild upper respiratory symptoms in children, elderly and immunocompromised individuals. It has also been shown to cause severe lower respiratory illness. NL63 shares ACE2 as a receptor for viral entry with SARS-CoV and SARS-CoV-2. Here we present the in situ structure of HCoV-NL63 spike (S) trimer at 3.4-[A] resolution by single-particle cryo-EM imaging of vitrified virions without chemical fixative. It is structurally homologous to that obtained previously from the biochemically purified ectodomain of HCoV-NL63 S trimer, which displays a 3-fold symmetric trimer in a single conformation. In addition to previously proposed and observed glycosylation sites, our map shows density at other amino acid positions as well as differences in glycan structures. The domain arrangement within a protomer is strikingly different from that of the SARS-CoV-2 S and may explain their different requirements for activating binding to the receptor. This structure provides the basis for future studies of spike proteins with receptors, antibodies, or drugs, in the native state of the coronavirus particles.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.10.244558v1?rss=1

Authors: LI, Z., Buck, M.

Abstract:

Despite large differences in behaviors and living conditions, vertebrate organisms share the great majority of proteins often with subtle differences in amino acid sequence. By comparing a set of substantially homologous proteins between model vertebrate organisms at a sub-proteome level, we discover a pattern of amino acid conservation and a shift in amino acid use, noticeably with an apparent distinction between homeotherms (warm-blooded species) and poikilotherms (cold-blooded species). Importantly, we establish a connection between the thermoadaptation of protein sequences manifest in the evolved proteins and two of their physical features: a change in their proteins dynamics and in their solvation. For poikilotherms such as frog and fish, the lower body temperature is expected to increase the association of proteins due to a decrease in protein dynamics and correspondingly lower entropy penalty on binding. In order to prevent overly-sticky protein association at low temperatures, we find that poikilotherms enhance the solvation of their proteins by favoring polar amino acids on their protein surface. This study unveils a general mechanism behind amino acid choices that constitute part of the thermoadaptation of vertebrate organisms at the molecular level.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.10.242719v1?rss=1

Authors: Kubo, S., Kato, S., Nakamura, K., Kodera, N., Takada, S.

Abstract:

High-speed atomic force microscopy (HS-AFM) is a scanning probe microscopy that can capture structural dynamics of biomolecules in real time at single molecule level near physiological condition. Albeit much improvement of the instruments, while scanning one frame of HS-AFM movies, biomolecules often change their conformations largely. Thus, the obtained frame images can be hampered by the time-difference, the asynchronicity, in the data acquisition. Here, to resolve this data asynchronicity in the HS-AFM movie, we developed Kalman filter and smoother methods, some of the sequential Bayesian filtering approaches. The Kalman filter/smoother methods use alternative steps of a short time-propagation by a linear dynamical system and a correction by the likelihood of AFM data acquired pixel by pixel. We first tested the method using a toy model of a diffusing cone, showing that the Kalman smoother method outperforms to reproduce the ground-truth movie, compared to that mimics the raw AFM movie, and the Kalman filter result. We then applied the Kalman smoother to a synthetic movie for conformational change dynamics of a motor protein, i.e., dynein, confirming the superiority of the Kalman smoother. Finally, we applied the Kalman smoother to two real HS-AFM movies, FlhAc and centralspindlin, reducing distortion and noise in the AFM movies. The method is general and can be applied to any HS-AFM movies.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.10.244731v1?rss=1

Authors: Bhattacharjee, T., Amchin, D. B., Ott, J. A., Kratz, F., Datta, S. S.

Abstract:

Chemotactic migration of bacteria--their ability to direct multicellular motion along chemical gradients--is central to processes in agriculture, the environment, and medicine. However, studies are typically performed in bulk liquid, despite the fact that most bacteria inhabit heterogeneous porous media such as soils, sediments, and biological gels. Here, we directly visualize the migration of E. coli populations in 3D porous media. We find that pore-scale confinement is a strong regulator of chemotactic migration. Strikingly, cells use a different primary mechanism to direct their motion in confinement than in bulk liquid. Further, confinement markedly alters the dynamics and morphology of the migrating population--features that can be described by a continuum model, but only when standard motility parameters are substantially altered from their bulk liquid values. Our work thus provides a framework to predict and control the migration of bacteria, and active matter in general, in heterogeneous environments.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.10.244525v1?rss=1

Authors: Malla, T. N., Pandey, S., Poudyal, I., Feliz, D., Noda, M., Phillips, G., Stojkovic, E., Schmidt, M.

Abstract:

The SARS coronavirus 2 main protease 3CLpro tailor cuts various essential virus proteins out of long poly-protein translated from the virus RNA. If the 3CLpro is inhibited, the functional virus proteins cannot form and the virus cannot replicate and assemble. Any compound that inhibits the 3CLpro is therefore a potential drug to end the pandemic. Here we show that the diffraction power of 3CLpro crystals is effectively destroyed by Ebselen. It appears that Ebselen may be a widely available, relatively cost effective way to eliminate the SARS coronavirus 2.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.10.242008v1?rss=1

Authors: Protopopova, A. D., Pumroy, R. A., de la Roche, J., Haug, F. M., Sousa, B. B., Gallo, P. N., Bernardes, G. J. L., Leffler, A., Moiseenkova-Bell, V.

Abstract:

Transient receptor potential vanilloid 2 (TRPV2) plays a critical role in a variety of physiological and pathophysiological processes, putting TRPV2 on the list of important drug targets. Yet, specific TRPV2 agonists and antagonists are currently unavailable. Their development requires a precise knowledge of how the currently known non-specific small molecules interact with TRPV2 at the molecular level. Here we present TRPV2 structures in ligand-bound states resolved by cryo-electron microscopy in the presence of 2-aminoethoxydiphenyl borate (2-ABP), 2-APB with doxorubicin (DOXO), and ruthenium red (RR). We identified a novel 2-APB drug binding site between the S5 helix and S4-S5 linker on two adjacent TRPV2 monomers and determined the mechanism of TRPV2 pore block by RR. We also showed that a large organic molecule like DOXO can enter the TRPV2 pore in the presence of 2-APB. Additionally, we discovered a structural lipid bound in a unique position in the vanilloid pocket, which is absent in the 2-APB-bound state of the channel, allowing us to propose a model for TRPV2 channel gating. Together, this work provides a further understanding of TRPV2 function and a structural framework for the development of TRPV2-specific modulators.

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