PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.05.369744v1?rss=1

Authors: Torrillo, P. A., Bogetti, A. T., Chong, L.

Abstract:

A promising approach for simulating rare events with rigorous kinetics is the weighted ensemble path sampling strategy. One challenge of this strategy is the division of configurational space into bins for sampling. Here we present the minimal adaptive binning (MAB) scheme for the automated, adaptive placement of bins along a progress coordinate within the framework of the weighted ensemble strategy. In this scheme, a fixed number of bins are evenly spaced between the positions of trailing and leading trajectories along a progress coordinate after each resampling interval. To further enhance the sampling of bottleneck regions, additional bins are dedicated to trajectories residing in the least visited regions of the free energy landscape. On average, bins are more finely spaced along steeper regions of the landscape and further apart along flatter regions of the landscape. We applied the scheme to simulations of the following processes, listed in order of increasing complexity: (i) transitions between states of a double-well toy potential; (ii) association of Na+ and Cl- ions; and (iii) conformational sampling of a tumor suppressor p53 peptide fragment. Results reveal that our binning scheme, despite its simplicity, efficiently estimates rate constants for rare-event processes with large free energy barriers and enhances conformational sampling.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.05.369934v1?rss=1

Authors: Gupta, A., Abdul, W., Mondal, J.

Abstract:

A seemingly random and disorganized bacterial chromosome, in reality, is a well organized nucleus-like structure, called the nucleoid, which is maintained by several nucleoid associated proteins(NAPs). Here we present an application of a previously developed Hi-C based computational method to study the effects of some of these proteins on the E. coli chromosome. Simulations with encoded Hi-C data for mutant, hupAB deficient, E. coli cells, revealed a decondensed, axially expanded chromosome with enhanced short range and diminished long range interactions. Simulations for mutant cells deficient in FIS protein revealed that the effects are similar to that of the hupAB mutant, but the absence of FIS led to a greater disruption in chromosome organization. Absence of another NAP, MatP, known to mediate Ter macrodomain isolation, led to enhanced contacts between Ter and its flanking macrodomains but lacked any change in matS sites' localization. Deficiency of MukBEF, the only SMC complex present in E. coli, led to disorganization of macrodomains. Upon further analysis, it was observed that the above mutations do not significantly impact the local chromosome organization (~ 100 Kb) but only affect the chromosome on a larger scale (>100 Kb). These observations shed more light on the sparsely explored effects of NAPs on the overall chromosome organization and helps us understand the myriad complex interactions NAPs have with the chromosome.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.05.369629v1?rss=1

Authors: Belan, O., Barroso, C., Kaczmarczyk, A., Anand, R., Federico, S., O'Reilly, N., Newton, M. D., Maeots, E., Enchev, R. I., Martinez-Perez, E., Rueda, D. S., Boulton, S. J.

Abstract:

Homologous recombination (HR) is an essential DNA double-strand break (DSBs) repair mechanism frequently inactivated in cancer. During HR, RAD51 forms nucleoprotein filaments on RPA-coated resected DNA and catalyses strand invasion into homologous duplex DNA. How RAD51 displaces RPA and assembles into long HR-proficient filaments remains uncertain. Here, we employ single-molecule imaging to investigate the mechanism of nematode RAD-51 filament growth in the presence of BRC-2 (BRCA2) and RAD-51 paralogs, RFS-1/RIP-1. BRC-2 nucleates RAD-51 on RPA-coated DNA, while RFS-1/RIP-1 acts as a "chaperone" to promote 3' to 5' filament growth via highly dynamic engagement with 5' filament ends. Inhibiting ATPase or mutation in RFS-1 Walker box leads to RFS-1/RIP-1 retention on RAD-51 filaments and hinders growth. rfs-1 Walker box mutants display sensitivity to DNA damage and accumulate RAD-51 complexes non-functional for HR in vivo. Our work reveals the mechanism of RAD-51 nucleation and filament growth in the presence of recombination mediators.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.05.369835v1?rss=1

Authors: Deng, Z., Zhao, Y., Feng, J., Zhang, J., Zhao, H., Rau, M. J., Fitzpatrick, J., Hu, H., Yuan, P.

Abstract:

TMEM206 has been recently identified as an evolutionarily conserved chloride channel that underlies ubiquitously expressed, proton-activated, outwardly rectifying anion currents. Here we report the cryo-electron microscopy structure of pufferfish TMEM206, which forms a trimeric channel, with each subunit comprising two transmembrane segments, the outer and inner helices, and a large extracellular domain. An ample vestibule in the extracellular region is accessible laterally from the three side portals. The central pore contains multiple constrictions preventing ion conduction. A conserved lysine residue near the cytoplasmic end of the inner helix forms the presumed chloride ion selectivity filter. Unprecedentedly, the core structure and assembly closely resemble those of the epithelial sodium channel/degenerin family of sodium channels that are unrelated in amino acid sequence and conduct cations instead of anions. Together with electrophysiology, this work provides insights into ion conduction and gating for a new class of chloride channels that is architecturally distinct from previously characterized chloride channel families.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.05.370189v1?rss=1

Authors: Girard, M., Bereau, T.

Abstract:

The lipid raft hypothesis postulates that cell membranes possess some degree of lateral organization. The last decade has seen a large amount of experimental evidence for rafts. Yet, the underlying mechanism remains elusive. One hypothesis that supports rafts relies on the membrane to lie near a critical point. While supported by experimental evidence, the role of regulation is unclear. Using both a lattice model and molecular dynamics simulations, we show that lipid regulation of a many-component membrane can lead to critical behavior over a large temperature range. Across this range, the membrane displays a critical composition due to finite-size effects. This mechanism provides a rationale as to how cells tune their composition without the need for specific sensing mechanisms. It is robust and reproduces important experimentally verified biological trends: membrane-demixing temperature closely follows cell growth temperature, and the composition evolves along a critical manifold. The simplicity of the mechanism provides a strong argument in favor of the critical membrane hypothesis.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.04.366658v1?rss=1

Authors: Fortune, G. T., Worley, A., Sendova-Franks, A., Franks, N., Leptos, K. C., Goldstein, R. E.

Abstract:

Circular milling, a stunning manifestation of collective motion, is found across the natural world, from fish shoals to army ants. It has been observed recently that the plant-animal worm Symsagittifera roscoffensis exhibits circular milling behaviour, both in shallow pools at the beach and in Petri dishes in the laboratory. Here we investigate this phenomenon, through experiment and theory, from a fluid dynamical viewpoint, focusing on the effect that an established circular mill has on the surrounding fluid. Unlike systems such as confined bacterial suspensions and collections of molecular motors and filaments that exhibit spontaneous circulatory behaviour, and which are modelled as force dipoles, the front-back symmetry of individual worms precludes a stresslet contribution. Instead, singularities such as source dipoles and Stokes quadrupoles are expected to dominate. A series of models is analyzed to understand the contributions of these singularities to the azimuthal flow fields generated by a mill, in light of the particular boundary conditions that hold for flow in a Petri dish. A model that treats a circular mill as a rigid rotating disc that generates a Stokes flow is shown to capture basic experimental results well, and gives insights into the emergence and stability of multiple mill systems.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.04.369017v1?rss=1

Authors: Posey, A. E., Ruff, K. M., Lalmansingh, J. M., Kandola, T. S., Lange, J. J., Halfmann, R., Pappu, R. V.

Abstract:

The combination of phase separation and disorder-to-order transitions can give rise to ordered, semi-crystalline fibrillar assemblies that underlie prion phenomena namely, the non-Mendelian transfer of information across cells. Recently, a method known as Distributed Amphifluoric Foerster Resonance Energy Transfer (DAmFRET) was developed to study the convolution of phase separation and disorder-to-order transitions in live cells. In this assay, a protein of interest is expressed to a broad range of concentrations and the acquisition of local density and order, measured by changes in FRET, is used to map phase transitions for different proteins. The high-throughput nature of this assay affords the promise of uncovering sequence-to-phase behavior relationships in live cells. Here, we report the development of a supervised method to obtain automated and accurate classifications of phase transitions quantified using the DAmFRET assay. Systems that we classify as undergoing two-state discontinuous transitions are consistent with prion-like behaviors, although the converse is not always true. We uncover well-established and surprising new sequence features that contribute to two-state phase behavior of prion-like domains. Additionally, our method enables quantitative, comparative assessments of sequence-specific driving forces for phase transitions in live cells. Finally, we demonstrate that a modest augmentation of DAmFRET measurements, specifically time-dependent protein expression profiles, can allow one to apply classical nucleation theory to extract sequence-specific lower bounds on the probability of nucleating ordered assemblies. Taken together, our approaches lead to a useful analysis pipeline that enables the extraction of mechanistic inferences regarding phase transitions in live cells.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.04.368928v1?rss=1

Authors: Kefer, P., Iqbal, F., Locatelli, M., Lawrimor, J., Zhang, M., Bloom, K., Bonin, K., Vidi, P.-A., Liu, J.

Abstract:

Image-based particle tracking is an essential tool to answer research questions in cell biology and beyond. A major challenge of particle tracking in living systems is that low light exposure is required to avoid phototoxicity and photobleaching. In addition, high-speed imaging used to fully capture particle motion dictates fast image acquisition rates. Short exposure times come at the expense of tracking accuracy. This is generally true for quantitative microscopy approaches and particularly relevant to single molecule tracking where the number of photons emitted from a single chromophore is limited. Image restoration methods based on deep learning dramatically improve the signal-to-noise ratio in low-exposure datasets. However, it is not clear whether images generated by these methods yield accurate quantitative measurements such as diffusion parameters in (single) particle tracking experiments. Here, we evaluate the performance of two popular deep learning denoising software packages for particle tracking, using synthetic datasets and movies of diffusing chromatin as biological examples. With synthetic data, both supervised and unsupervised deep learning restored particle motions with high accuracy in two-dimensional datasets, whereas artifacts were introduced by the denoisers in 3D datasets. Experimentally, we found that, while both supervised and unsupervised approaches improved the number of trackable particles and tracking accuracy, supervised learning generally outperformed the unsupervised approach, as expected. We also highlight that with extremely noisy image sequences, deep learning algorithms produce deceiving artifacts, which underscores the need to carefully evaluate the results. Finally, we address the challenge of selecting hyper-parameters to train convolutional neural networks by implementing a frugal Bayesian optimizer that rapidly explores multidimensional parameter spaces, identifying networks yielding optional particle tracking accuracy. Our study provides quantitative outcome measures of image restoration using deep learning. We anticipate broad application of the approaches presented here to critically evaluate artificial intelligence solutions for quantitative microscopy.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.04.368233v1?rss=1

Authors: Tiwari, V., Borchardt, J. S., Schuh, A., Klug, C. S., Czajkowski, C.

Abstract:

Signaling in the brain depends on rapid opening and closing of pentameric ligand-gated ion channels (pLGICs). These proteins are the targets of various clinical drugs and, defects in their function is linked to a variety of diseases including myasthenia, epilepsy and sleep-disorders. While recent high-resolution structures of prokaryotic and eukaryotic pLGICs have shed light on the molecular architecture of these proteins, describing their conformational dynamics in physiological lipids is essential for understanding their function. Here, we used site-directed spin labeling electron paramagnetic resonance (SDSL EPR) spectroscopy and functional channels reconstituted in liposomes to reveal ligand-induced structural changes in the extracellular domain (ECD) of GLIC. Proton-activation caused an inward motion of labeled sites at the top of {beta}-strands ({beta}1, 2, 5, 6, 8) towards the channel lumen, consistent with an agonist-induced inward tilting motion of the ECD. Similar proton-dependent GLIC ECD motions were detected in the presence of a non-activating (gating deficient) mutation, suggesting that the inward tilting of the ECD does not accompany channel opening but is associated with an agonist-induced closed pre-activated channel state. These findings provide new insights into the protein dynamics underlying pLGIC gating transitions.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.03.366310v1?rss=1

Authors: Shrivastava, S.

Abstract:

Action potentials in neurons are known to annihilate each other upon collision, while there are cases where they might penetrate each other. Compression waves that travel within the plasma membrane of a neuron have previously been proposed as a thermodynamic basis for the propagation of action potentials. In this context, it was recently shown that two dimensional compressive shock waves in the model system of lipid monolayers can nearly annihilate each other upon head on collision when excited close to a phase transition. However, weaker shock waves showed penetration. In general, once the approximation of small perturbation is not valid, compression waves do not interact linearly anymore. While experiments in lipid monolayers demonstrated this principle, a mechanism remained unclear. In this article, we summarise the fundamentals of shock physics as applied to an interface and how it previously explained the observation of threshold and saturation of shockwaves in the lipid monolayer (all or none). While the theory has the same fundamental premise as the soliton model, i.e. the conservation laws and thermodynamics, we elaborate on how the two approaches make different predictions with regards to collisions and the detailed structure of the wave-front. As a case study and a new result, we show that previously unexplained annihilation of shock waves in the lipid monolayer is a direct consequence of the nature of state changes, i.e. jump conditions, within these shockwaves, and elaborate on the consequence of these results for the general understanding of the excitation waves in a thermo-fluids framework.

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