PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.01.322982v1?rss=1

Authors: Yan, S., Fang, Q.

Abstract:

Over the past decade, an increasing body of evidence has suggested that three-dimensional (3-D) Monte Carlo (MC) light transport simulations are affected by the inherent limitations and errors of voxel-based domain boundaries. In this work, we specifically address this challenge using a hybrid MC algorithm, namely split-voxel MC or SVMC, that combines both mesh and voxel domain information to greatly improve MC simulation accuracy while remaining highly flexible and efficient in parallel hardware, such as graphics processing units (GPU). We achieve this by applying a marching-cubes algorithm to a pre-segmented domain to extract and encode sub-voxel information of curved surfaces, which is then used to inform ray-tracing computation within boundary voxels. This preservation of curved boundaries in a voxel data structure demonstrates significantly improved accuracy in several benchmarks, including a human brain atlas. The accuracy of the SVMC algorithm is comparable to that of mesh-based MC (MMC), but runs 2x-6x faster and requires only a lightweight preprocessing step. The proposed algorithm has been implemented in our open-source software and is freely available at http://mcx.space.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.01.322156v1?rss=1

Authors: Davis, L. K., Saric, A., Hoogenboom, B., Zilman, A.

Abstract:

In the nuclear pore complex (NPC), intrinsically disordered proteins (FG Nups) along with their interactions with more globular proteins called nuclear transport receptors (NTRs) are vital to the selectivity of transport into and out of the cell nucleus. While such interactions can be modelled at different levels of coarse graining, in-vitro experimental data have been quantitatively described by minimal models that describe FG Nups as cohesive homogeneous polymers and NTRs as uniformly cohesive spheres, where the heterogeneous effects have been smeared out. By definition, these minimal models do not account for the explicit heterogeneities in FG Nup sequences, essentially a string of cohesive and non-cohesive polymer units, and at the NTR surface. Here, we develop computational and analytical models that do take into account such heterogeneity at a level of minimal complexity, and compare them to experimental data on single-molecule interactions between FG Nups and NTRs. Overall, we find that the heterogeneous nature of FG Nups and NTRs plays a minor role for their equilibrium binding properties, but is of significance when it comes to (un)binding kinetics. Using our models, we predict how binding equilibria and kinetics depend on the distribution of cohesive blocks in the FG Nup sequences and of the binding pockets at the NTR surface, with multivalency playing a key role. Finally, we observe that single-molecule binding kinetics has a rather minor influence on the diffusion of NTRs in polymer melts consisting of FG-Nup-like sequences.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.02.323956v1?rss=1

Authors: Sepehri, A., Nepal, B., Lazaridis, T.

Abstract:

The actinoporins are cytolytic toxins produced by sea anemones. Upon encountering a membrane, preferably containing sphingomyelin, they oligomerize and insert their N-terminal helix into the membrane, forming a pore. Whether sphingomyelin is specifically recognized by the protein or simply induces phase coexistence in the membrane has been debated. Here, we perform multimicrosecond molecular dynamics simulations of an octamer of fragaceatoxin C, a member of the actinoporin family, in lipid bilayers containing either pure 1,2-Dioleoyl-sn-Glycero-3-Phosphocholine (DOPC) or a 1:1 mixture of DOPC and palmitoyl sphingomyelin (PSM). The complex is highly stable in both environments, with only slight fraying of the inserted helices near their N-termini. Analyzing the structural parameters of the mixed membrane in the course of the simulation we see signs of a phase transition for PSM in the inner leaflet of the bilayer. In both leaflets, cross-interactions between lipids of different type decrease over time. Surprisingly, the aromatic loop thought to be responsible for sphingomyelin recognition interacts more with DOPC than PSM by the end of the simulation. These results support the notion that the key membrane property that actinoporins recognize is lipid phase coexistence.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.02.324129v1?rss=1

Authors: Stroberg, W., Schnell, S.

Abstract:

Signal transduction within crowded cellular compartments is essential for the physiological function of cells and organisms. While the accuracy with which receptors can probe the concentration of ligands has been thoroughly investigated in dilute systems, the effect of macromolecular crowding on the inference of concentration remains unknown. In this work we develop a novel algorithm to simulate reversible reactions between reacting Brownian particles. This facilitates the calculation of reaction rates and correlation times for ligand-receptor systems in the presence of macromolecular crowding. Using this method, we show that it is possible for crowding to increase the accuracy of estimated ligand concentration based on receptor occupancy. In particular, we find that crowding can enhance the effective association rates between small ligands and receptors to a large enough degree to overcome the increased chance of rebinding due to caging by crowding molecules. For larger ligands, crowding decreases the accuracy of the receptor's estimate primarily by decreasing the microscopic association and dissociation rates.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.02.323527v1?rss=1

Authors: Lachetta, M., Sandmeyer, H., Sandmeyer, A., Schulte am Esch, J., Huser, T., Müller, M.

Abstract:

Digital micromirror devices (DMDs) are spatial light modulators that employ the electro-mechanical movement of miniaturized mirrors to steer and thus modulate the light reflected of a mirror array. Their wide availability, low cost and high speed make them a popular choice both in consumer electronics such as video projectors, and scientific applications such as microscopy. High-end fluorescence microscopy systems typically employ laser light sources, which by their nature provide coherent excitation light. In super-resolution microscopy applications that use light modulation, most notably structured illumination microscopy (SIM), the coherent nature of the excitation light becomes a requirement to achieve optimal interference pattern contrast. The universal combination of DMDs and coherent light sources, especially when working with multiple different wavelengths, is unfortunately not straight forward. The substructure of the tilted micromirror array gives rise to a blazed grating, which has to be understood and which must be taken into account when designing a DMD-based illumination system. Here, we present a set of simulation frameworks that explore the use of DMDs in conjunction with coherent light sources, motivated by their application in SIM, but which are generalizable to other light patterning applications. This framework provides all the tools to explore and compute DMD-based diffraction effects and to simulate possible system alignment configurations computationally, which simplifies the system design process and provides guidance for setting up DMD-based microscopes.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.03.322354v1?rss=1

Authors: Bashirzadeh, Y., Redford, S. A., Lorpaiboon, C., Groaz, A., Litschel, T., Schwille, P., Hocky, G. M., Dinner, A., Liu, A. P.

Abstract:

Robust spatiotemporal organization of cytoskeletal networks is crucial, enabling cellular processes such as cell migration and division. -Actinin and fascin are two actin crosslinking proteins localized to distinct regions of eukaryotes to form actin bundles with optimized spacing for cell contractile machinery and sensory projections, respectively. In vitro reconstitution assays and coarse-grained simulations have shown that these actin bundling proteins segregate into distinct domains with a bundler size-dependent competition-based mechanism, driven by the minimization of F-actin bending energy. However, it is not known how physical confinement imposed by the cell membrane contributes to sorting of actin bundling proteins and the concomitant reorganization of actin networks in intracellular environment. Here, by encapsulating actin, -actinin, and fascin in giant unilamellar vesicles (GUVs), we show that the size of such a spherical boundary determines equilibrated structure of actin networks among three typical structures: single rings, astral structures, and star-like structures. We show that -actinin bundling activity and its tendency for clustering actin is central to the formation of these structures. By analyzing physical features of crosslinked actin networks, we show that spontaneous sorting and domain formation of -actinin and fascin are intimately linked to the resulting structures. We propose that the observed boundary-imposed effect on sorting and structure formation is a general mechanism by which cells can select between different structural dynamical steady states.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.02.323303v1?rss=1

Authors: Pradhan, T., Annamalai, K., Sarkar, R., Huhn, S., Hegenbart, U., Schoenland, S., Faendrich, M., Reif, B.

Abstract:

Systemic antibody light chains (AL) amyloidosis is characterized by deposition of amyloid fibrils derived from a particular antibody light chain. Cardiac involvement is a major risk factor for mortality. Using MAS solid-state NMR, we study the fibril structure of a recombinant light chain fragment corresponding to the fibril protein from patient FOR005, together with fibrils formed by protein sequence variants that reflect the closest germline (GL) sequence. Both analyzed fibril structures were seeded with ex-vivo amyloid fibrils purified from the explanted heart of this patient. We find that residues 11-42 and 69-102 adopt {beta}-sheet conformation in patient protein fibrils. We identify glycine-49 that is mutated with respect to the germline sequence into arginine-49 as a key residue that forms a salt bridge to aspartate-25 in the patient protein fibril structure. Fibrils from the GL protein and from the patient protein harboring the single point mutation R49G can be both heterologously seeded using patient ex-vivo fibrils. Seeded R49G fibrils show an increased heterogeneity for the C-terminal residues 80-102 which is reflected by the disappearance of all resonances of these residues. By contrast, residues 11-42 and 69-77, which are visible in the MAS solid-state NMR spectra show 13C chemical shifts that are highly similar to patient fibrils. The mutation R49G thus induces a conformational heterogeneity at the C-terminus in the fibril state, while the overall fibril topology is retained.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.01.322800v1?rss=1

Authors: Shams, S., LeVan, P., Chen, J.

Abstract:

The desire to enhance the sensitivity and specificity of resting-state (rs-fMRI) measures has prompted substantial recent research into removing noise components. Chief among contributions to noise in rs-fMRI are physiological processes, and the neuronal implications of respiratory-volume variability (RVT), a main rs-fMRI-relevant physiological process, is incompletely understood. The potential implications of RVT in modulating and being modulated by autonomic nervous regulation, has yet to be fully understood by the rs-fMRI community. In this work, we use high-density electroencephalography (EEG) along with simultaneously acquired RVT recordings to help address this question. We hypothesize that (1) there is a significant relationship between EEG and RVT in multiple EEG bands, and (2) that this relationship varies by brain region. Our results confirm our first hypothesis, although all brain regions are shown to be equally implicated in RVT-related EEG-signal fluctuations. The lag between RVT and EEG is consistent with previously reported values. However, an interesting finding is related to the polarity of the correlation between RVT and EEG. Our results reveal potentially two main regimes of EEG-RVT association, one in which EEG leads RVT with a positive association between the two, and one in which RVT leads EEG but with a positive association between the two. We propose that these two patterns can be interpreted differently in terms of the involvement of higher cognition. These results further suggest that treating RVT simply as noise is likely a questionable practice, and that more work is needed to avoid discarding cognitively relevant information when performing physiological correction rs-fMRI.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.01.322610v1?rss=1

Authors: Fisher, M. E., Bovo, E., Cho, E. E., Pribadi, M. P., Dalton, M. P., Lemieux, M. J., Rathod, N., Aquayo-Ortiz, R., Espinoza-Fonseca, L. M., Robia, S. L., Zima, A. V., Young, H. S.

Abstract:

The cardiac sarcoplasmic reticulum calcium pump, SERCA, sequesters calcium in the sarco-endoplasmic reticulum (SR/ER) and plays a critical role in the contraction-relaxation cycle of the heart. A well-known regulator of SERCA in cardiac muscle is phospholamban (PLN), which interacts with the pump and reduces its apparent calcium affinity. A newly discovered SERCA regulatory subunit in cardiac muscle, dwarf open reading frame (DWORF), has added a new level of SERCA regulation. In this report, we modeled the structure of DWORF and evaluated it using molecular dynamics simulations. DWORF structure was modeled as a discontinuous helix with an unwound region at Pro15. This model orients an N-terminal amphipathic helix along the membrane surface and leaves a relatively short C-terminal transmembrane helix. We determined the functional regulation of SERCA by DWORF using a membrane reconstitution system. Surprisingly, we observed that DWORF directly activated SERCA by increasing its turnover rate. Furthermore, in-cell imaging of calcium dynamics demonstrated that DWORF increased SERCA-dependent ER calcium load, calcium reuptake rate, and spontaneous calcium release. Together, these functional assays suggest opposing effects of DWORF and PLN on SERCA function. The results agree with fluorescence resonance energy transfer experiments, which revealed changes in the affinity of DWORF for SERCA at low versus high cytosolic calcium concentrations. We found that DWORF has a higher affinity for SERCA in the presence of calcium, while PLN had the opposite behavior, a higher affinity for SERCA in low calcium. We propose a new mechanism for DWORF regulation of cardiac calcium handling in which DWORF directly enhances SERCA turnover by stabilizing the conformations of SERCA that predominate during elevated cytosolic calcium.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.02.323352v1?rss=1

Authors: Chen, T.-Y., Kwon, H. C., Yu, Y., Fairclough, R. H.

Abstract:

CLC-0, a prototype Cl - channel in the CLC family, employs two gating mechanisms that control its ion-permeation pore: fast gating and slow gating. The negatively-charged sidechain of a pore glutamate residue, E166, is known to be the fast gate, and the swinging of this sidechain opens or closes the pore of CLC-0 on the millisecond time scale. The other gating mechanism, slow gating, operates with much slower kinetics in the range of seconds to tens or even hundreds of seconds, and it is thought to involve still-unknown conformational rearrangements. Here, we find that low intracellular pH (pH i ) facilitates the closure of the CLC-0s slow gate, thus generating current inhibition. The rate of low pH i -induced current inhibition increases with intracellular H + concentration ([H + ] i )--the time constants of current inhibition by low pH i = 4.5, 5.5 and 6 are roughly 0.1, 1 and 10 sec, respectively, at room temperature. In comparison, the time constant of the slow gate closure at pH i = 7.4 at room temperature is hundreds of seconds. The inhibition by low pH i is significantly less prominent in mutants favoring the slow-gate open state (such as C212S and Y512A), further supporting the fact that intracellular H + enhances the slow-gate closure in CLC-0. A fast inhibition by low pH i causes an apparent inverted voltage-dependent activation in the wild-type CLC-0, a behavior similar to those in some channel mutants such as V490W in which only membrane hyperpolarization can open the channel. Interestingly, when V490W mutation is constructed in the background of C212S or Y512A mutation, the inverted voltage-dependent activation disappears. We propose that the slow kinetics of CLC-0s slow-gate closure may be due to low [H + ] i rather than due to the proposed large conformational change of the channel protein. Our results also suggest that the inverted voltage-dependent opening observed in some mutant channels may result from fast closure of the slow gate by the mutations.

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