PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.14.338293v1?rss=1

Authors: Stefanski, K. M., Russell, C. M., Westerfield, J. M., Lamichhane, R., Barrera, F. N.

Abstract:

The impact of the EphA2 receptor on cancer malignancy hinges on the two different ways it can be activated. EphA2 induces anti-oncogenic signaling after ligand binding, but ligand-independent activation of EphA2 is pro-oncogenic. It is believed that the transmembrane (TM) domain of EphA2 adopts two alternate conformations in the ligand-dependent and the ligand-independent states. However, it is poorly understood how the difference in TM helical crossing angles found in the two conformations impacts the activity and regulation of EphA2. We devised a method that uses hydrophobic matching to stabilize two conformations of a peptide comprising the EphA2 TM domain and a portion of the intracellular juxtamembrane (JM) segment. The two conformations exhibit different TM crossing angles, resembling the ligand-dependent and ligand-independent states. We developed a single-molecule technique using SMALPs to measure dimerization in membranes. We observed that the signaling lipid PIP2 promotes TM dimerization, but only in the small crossing angle state, which we propose corresponds to the ligand-independent conformation. In this state the two TM are almost parallel, and the positively charged JM segments are expected to be close to each other, causing electrostatic repulsion. The mechanism PIP2 uses to promote dimerization might involve alleviating this repulsion due to its high density of negative charges. Our data reveal a conformational coupling between the TM and JM regions, and suggest that PIP2 might directly exert a regulatory effect on EphA2 activation in cells that is specific to the ligand-independent conformation of the receptor.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.14.337840v1?rss=1

Authors: D'Acunto, M.

Abstract:

Protein-DNA interactions play a fundamental role in all life systems. A critical issue of such interactions is given by the strategy of protein search for specific targets on DNA. The mechanisms by which the protein are able to find relatively small cognate sequences, typically 15-20 base pairs (bps) for repressors, and 4-6 bps for restriction enzymes among the millions of bp of non-specific chromosomal DNA have hardly engaged researcher for decades. Recent experimental studies have generated new insights on the basic processes of protein-DNA interactions evidencing the underlying complex dynamic phenomena involved, which combine three-dimensional and one-dimensional motion along the DNA chain. It has been demonstrated that protein molecules spend most of search time on the DNA chain with an extraordinary ability to find the target very quickly, in some cases, with two orders of magnitude faster than the diffusion limit. This unique property of protein-DNA search mechanism is known as facilitated diffusion. Several theoretical mechanisms have been suggested to describe the origin of facilitated diffusion. However, none of such models currently has the ability to fully describe the protein search strategy. In this paper, we suggest that the ability of proteins to identify consensus sequence on DNA is based on the entanglement of {pi}-{pi} electrons between DNA nucleotides and protein amino acids. The {pi}-{pi} entanglement is based on Quantum Walk (QW), through Coin-position entanglement (CPE). First, the protein identifies a dimer belonging to the consensus sequence, and localize a {pi} on such dimer, hence, the other {pi} electron scans the DNA chain until the sequence is identified. By focusing on the example of recognition of consensus sequences by EcoRV or EcoRI, we will describe the quantum features of QW on protein-DNA complexes during search strategy, such as walker quadratic spreading on a coherent superposition of different vertices and environment-supported long-time survival probability of the walker. We will employ both discrete- or continuous-time versions of QW. Biased and unbiased classical Random Walk (CRW) has been used for a long time to describe Protein-DNA search strategy. QW, the quantum version of CRW, have been widely studied for its applications in quantum information applications. In our biological application, the walker (the protein) resides at a vertex in a graph (the DNA structural topology). Differently to CRW, where the walker moves randomly, the quantum walker can hop along the edges in the graph to reach other vertices entering coherently a superposition across different vertices spreading quadratically faster than CRW analogous evidencing the typical speed up features of the QW. When applied to protein-DNA target search problem, QW gives the possibility to achieve the experimental diffusional motion of proteins over diffusion classical limits experienced along DNA chains exploiting quantum features such as CPE and long-time survival probability supported by environment. In turn, we come to the conclusion that, under quantum picture, the protein search strategy does not distinguish between one-dimensional (1D) and three-dimensional (3D) case.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.13.337410v1?rss=1

Authors: Indurthi, D., Auerbach, A.

Abstract:

Concentration-response curves (CRCs) are characterized by a midpoint (EC50) and a high-concentration asymptote (POmax) that relate to agonist affinity and efficacy. A third agonist attribute, efficiency, is the fraction of binding energy that is applied to the conformational change that activates the receptor. Here we show that agonist efficiency can be calculated from EC50 and POmax, and estimate the efficiencies of 17 agonists of adult muscle nicotinic acetylcholine receptors (AChRs). The distribution of efficiency values was bi-modal with mean{+/-}s.d of 52{+/-}2% (n=11) and 41{+/-}3% (n=6). Efficiency is correlated inversely with the volume of the agonists' head-group. For 22 binding site mutations only aY190A affects significantly ACh efficiency, switching it from the high- to the low-efficiency population. If agonist efficiency is known, EC50 can be estimated from POmax and the receptor's level of constitutive activity can be calculated from a CRC.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.14.338509v1?rss=1

Authors: Mohajerani, F., Sayer, E., Neil, C., Inlow, K., Hagan, M. F.

Abstract:

This article describes a theoretical and computational study of the dynamical assembly of a protein shell around a complex consisting of many cargo molecules and long flexible scaffold molecules. Our study is motivated by bacterial microcompartments, which are proteinaceous organelles that assemble around a condensed droplet of enzymes and reactants. As in many examples of cytoplasmic liquid-liquid phase separation, condensation of the microcompartment interior cargo is driven by long flexible scaffold proteins that have weak multivalent interactions with the cargo. We describe a minimal model for the thermodynamics and dynamics of assembly of a protein shell around cargo and scaffold molecules, with scaffold-mediated cargo coalescence and encapsulation. Our results predict that the shell size, amount of encapsulated cargo, and assembly pathways depend sensitively on properties of the scaffold, including its length and valency of scaffold-cargo interactions. Moreover, the ability of self-assembling protein shells to change their size to accommodate scaffold molecules of different lengths depends crucially on whether the spontaneous curvature radius of the protein shell is smaller or larger than a characteristic elastic length scale of the shell. Beyond natural microcompartments, these results have important implications for synthetic biology efforts to target new molecules for encapsulation by microcompartments or viral shells. More broadly, the results elucidate how cells exploit coupling between self-assembly and liquid-liquid phase separation to organize their interiors.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.14.339671v1?rss=1

Authors: Morrison, A. J., Wonderlick, D. R., Harms, M. J.

Abstract:

Non-additivity between mutations--epistasis--profoundly shapes evolution. It can be difficult to understand its mechanistic origins. Here we show that "ensemble epistasis" is likely a universal feature of macromolecules. Using a simple analytical model, we found that epistasis arises when two conditions are met: 1) a macromolecule populates at least three structures and 2) mutations have differential effects on a least two of the inactive structures. To explore the relative magnitude of ensemble epistasis, we performed a virtual deep-mutational scan of the allosteric Ca2+ signaling protein S100A4. We found that 27% of mutation pairs gave ensemble epistasis with a magnitude on the order of thermal fluctuations, 1 kT. We observed many forms of epistasis: magnitude, sign, and reciprocal sign epistasis. Depending on the effector concentration, the same mutation pair could even exhibit different forms of epistasis. The ubiquity of ensembles in biology and its pervasiveness in our dataset suggests that ensemble epistasis may be a universal mechanism of epistasis.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.14.336032v1?rss=1

Authors: van der Wee, E. B., Fokkema, J., Kennedy, C. L., del Pozo, M., de Winter, M., Speets, P. N. A. S., Gerritsen, H. C., van Blaaderen, A.

Abstract:

A multitude of samples is required to monitor and optimize the quality and reliability of quantitative measurements of (super-resolution) light microscopes. Here, we present a single sample to calibrate microscopes, align their laser beams and measure their point spread function (PSF) in 3D. The sample is composed of a refractive index matched colloidal crystal of silica beads with fluorescent and gold cores. The microscope can be calibrated in three dimensions using the periodicity of the crystal; the alignment of the laser beams can be checked using the reflection of the gold cores; and the PSF can be measured at multiple positions and depths using the fluorescent cores. It is demonstrated how this sample can be used to visualize and improve the quality of confocal and super-resolution images. The sample is adjustable to meet the requirements of different NA objectives and microscopy techniques and additionally can be used to evaluate refractive index mismatches as a function of depth quantitatively.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.12.336818v1?rss=1

Authors: Sharma, A., Preece, B., Swann, H., Fan, X., McKenney, R. J., Ori-McKenney, K. M., Saffarian, S., Vershinin, M.

Abstract:

SARS-CoV-2 is a novel coronavirus which has caused the COVID-19 pandemic. Other known coronaviruses show a strong pattern of seasonality, with the infection cases in humans being more prominent in winter. Although several plausible origins of such seasonal variability have been proposed, its mechanism is unclear. SARS-CoV-2 is transmitted via airborne droplets ejected from the upper respiratory tract of the infected individuals. It has been reported that SARS-CoV-2 can remain infectious for hours on surfaces. As such, the stability of viral particles both in liquid droplets as well as dried on surfaces is essential for infectivity. Here we have used atomic force microscopy to examine the structural stability of individual SARS-CoV-2 virus like particles at different temperatures. We demonstrate that even a mild temperature increase, commensurate with what is common for summer warming, leads to dramatic disruption of viral structural stability, especially when the heat is applied in the dry state. This is consistent with other existing non-mechanistic studies of viral infectivity, provides a single particle perspective on viral seasonality, and strengthens the case for a resurgence of COVID-19 in winter.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.13.337964v1?rss=1

Authors: Wang, Z., Estrada, J. B., Arruda, E. M., Garikipati, K.

Abstract:

We present a novel, fully three-dimensional approach to soft material characterization and constitutive modeling with relevance to soft biological tissue. Our approach leverages recent advances in experimental techniques and data-driven computation. The experimental component of this approach involves in situ mechanical loading in a magnetic field (using MRI), yielding the entire deformation tensor field throughout the specimen regardless of the possible irregularities in its three-dimensional shape. Characterization can therefore be accomplished with data at a reduced number of deformation states. We refer to this experimental technique as MR-u. Its combination with powerful approaches to inverse modelling, specifically methods of model inference, would open the door to insightful mechanical characterization for soft materials. In recent computational advances that answer this need, we have developed new, data-driven inverse techniques to infer the model that best explains the physics governing observed phenomena from a spectrum of admissible ones, while maintaining parsimony of representation. This approach is referred to as Variational System Identification (VSI). In this communication, we apply the MR-u approach to characterize soft biological tissue and polymers, and using VSI, we infer the physically best-suited and parsimonious mathematical models of their mechanical response. We demonstrate the performance of our methods in the face of noisy data with physical constraints that challenge the identification of mathematical models, while attaining high accuracy in the predicted response of the inferred models.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.13.330910v1?rss=1

Authors: Jeffet, J., Michaeli-Hoch, Y., Torchinsky, D., Israel-Elgali, I., Shomron, N., Craggs, T. D., Ebenstein, Y.

Abstract:

Color is a fundamental contrast mechanism in fluorescence microscopy, providing the basis for numerous imaging and spectroscopy techniques. The ever-growing need to acquire high-throughput, dynamic data from multicolor species is driving the development of optical schemes that optimize the achievable spectral, temporal, and spatial resolution needed in order to follow biological, chemical and physical processes. Here we introduce Continuously Controlled Spectral-resolution (CoCoS) microscopy, an imaging scheme that encodes color into spatial read-out in the image plane, with continuous control over the spectral resolution. The concept enables single-frame acquisition of multiple color channels, allowing simultaneous, single-molecule colocalization for barcoding and Forster resonance energy transfer (FRET) experiments. The simple control over the spectral dispersion allows switching between imaging modalities at a click of a button. We demonstrate the utility of CoCoS for multicolor localization microscopy of microRNA barcodes in clinical samples, single-molecule FRET measurements, and single-molecule spectroscopy. CoCoS may be integrated as a simple add-on to existing microscopes and will find use in applications that aim to record dynamic, multicolor localization events such as in multiplex FRET and tracking of multi-component, interacting complexes.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.12.335679v1?rss=1

Authors: Giuliani, N., Rossi, M., Noselli, G., DeSimone, A.

Abstract:

Euglena gracilis is a unicellular organism that swims by beating a single anterior flagellum. We study the nonplanar waveforms spanned by the flagellum during a swimming stroke, and the three-dimensional flows that they generate in the surrounding fluid. Starting from a small set of time-indexed images obtained by optical microscopy on a swimming Euglena cell, we construct a numerical interpolation of the stroke. We define an optimal interpolation (which we call synthetic stroke) by minimizing the discrepancy between experimentally measured velocities (of the swimmer) and those computed by solving numerically the equations of motion of the swimmer driven by the trial interpolated stroke. The good match we obtain between experimentally measured and numerically computed trajectories provides a first validation of our synthetic stroke. We further validate the procedure by studying the flow velocities induced in the surrounding fluid. We compare the experimentally measured flow fields with the corresponding quantities computed by solving numerically the Stokes equations for the fluid flow, in which the forcing is provided by the synthetic stroke, and find good matching. Finally, we use the synthetic stroke to derive a coarse-grained model of the flow field resolved in terms of a few dominant singularities. The far field is well approximated by a time-varying Stresslet, and we show that the average behavior of Euglena during one stroke is that of an off-axis puller. The reconstruction of the flow field closer to the swimmer body requires a more complex system of singularities. A system of two Stokeslets and one Rotlet, that can be loosely associated with the force exerted by the flagellum, the drag of the body, and a torque to guarantee rotational equilibrium, provides a good approximation.

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