PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.09.375691v1?rss=1

Authors: Stadlbauer, P., Islam, B., Otyepka, M., Chen, J., monchaud, d., Zhou, J., Mergny, J.-L., Sponer, J.

Abstract:

Guanine quadruplex nucleic acids (G4s) are involved in key biological processes such as replication or transcription. Beyond their biological relevance, G4s find applications as biotechnological tools since they readily bind hemin and enhance its peroxidase activity, creating a G4-DNAzyme. The biocatalytic properties of G4-DNAzymes have been thoroughly studied and used for biosensing purposes. Despite hundreds of applications and massive experimental efforts, the atomistic details of the reaction mechanism remain unclear. To help select between the different hypotheses currently under investigation, we use extended explicit-solvent molecular dynamics simulations to scrutinize the G4/hemin interaction. We found that besides the dominant conformation in which hemin is stacked atop the external G-quartets, hemin can also transiently bind to the loops and be brought to the external G-quartets through diverse delivery mechanisms. Importantly, the simulations do not support several mechanistic possibilities (i.e., the wobbling guanine and the iron-bound water molecule) but rather suggest tentative mechanisms in which the external G-quartet itself is responsible for the unique H2O2-promoted biocatalytic properties of the G4/hemin complexes. Our simulations show that once stacked atop a terminal G-quartet, hemin rotates about its vertical axis while readily sampling shifted geometries where the iron transiently contacts oxygen atoms of the adjacent G-quartet. This dynamics is not apparent from the ensemble-averaged structure. We also visualize transient interactions between the stacked hemin and the G4 loops. Finally, we investigated interactions between hemin and on-pathway folding intermediates of the parallel-stranded G4 fold. The simulations suggest that hemin drives the folding of parallel-stranded G4s from slip-stranded intermediates, acting as a G4 chaperone. Limitations of the MD simulation technique are also briefly discussed.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.09.373902v1?rss=1

Authors: Ladefoged, L. K., Schiott, B., Fedosova, N. U.

Abstract:

Kinetic properties and crystal structures of the Na+,K+-ATPase in complex with cardiotonic steroids (CTS) revealed significant differences between CTS subfamilies (Laursen et al., 2015): beneficial effects of K+ on bufadienolide binding strongly contrasted with K+/cardenolide antagonism. To solve this riddle we applied docking and molecular dynamics simulations of the complexes involving Na+,K+-ATPase, bufadienolides (bufalin, cinobufagin), and ions (K+, Na+, Mg2+). The results revealed that bufadienolide binding is affected by i) electrostatic attraction of the lactone ring by a cation, and ii) the ability of a cation to stabilize and ''shape'' the site constituted by transmembrane helices of the -subunit (M1-6). The latter effect was due to varying coordination patterns involving amino acid residues from helix bundles M1-4 and M5-10. Substituents on the steroid core of a bufadienolide add to and modify the cation effects. The above rationale is fully consistent with the ion effects on the kinetics of Na+,K+-ATPase/bufadienolide interactions.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.09.374173v1?rss=1

Authors: Mompean, M., Trevino, M. A., Laurents, D. V.

Abstract:

Intrinsically disordered proteins (IDPs) play essential roles in regulating physiological processes in eukaryotic cells. Many virus use their own IDPs to hack these processes to disactive host defenses and promote viral growth. Thus, viral IDPs are attractive drug targets. While IDPs are hard to study by X-ray crystallography or cryo-EM, atomic level information on their conformational perferences and dynamics can be obtained using NMR spectroscopy. SARS-CoV-2 Nsp2 interacts with human proteins that regulate translation initiation and endosome vesicle sorting, and the C-terminal region of this protein is predicted to be disordered. Molecules that block these interactions could be valuable leads for drug development. To enable inhibitor screening and to uncover conformational preferences and dynamics, we have expressed and purified the 13C,15N-labeled C-terminal region of Nsp2. The 13C{beta} and backbone 13CO, 1HN, 13C and 15N nuclei were assigned by analysis of a series of 2D 1H-15N HSQC and 13C-15N CON as well as 3D HNCO, HNCA, CBCAcoNH and HncocaNH spectra. Overall, the chemical shift data confirm that this region is chiefly disordered, but contains two five-residue segments that adopt a small population of {beta}-strand structure. Whereas the region is flexible on ms/ms timescales as gauged by T1{rho} measurements, the {1H}-15N NOEs reveal a flexibility on ns/ps timescales that is midway between a fully flexible and a completely rigid chain.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.08.373423v1?rss=1

Authors: Koculi, E., Thirumalai, D.

Abstract:

The E. Coli. ATP-consuming chaperonin machinery, a complex between GroEL and GroES, has evolved to facilitate folding of substrate proteins (SPs) that cannot do so spontaneously. A series of kinetic experiments show that the SPs are encapsulated in the GroEL/ES nano cage for a short duration. If confining the SPs in the predominantly polar cage of GroEL in order to help folding, the assisted folding rate, relative to the bulk value, should always be enhanced. Here, we show that this is not the case for the folding of rhodanese in the presence of the full machinery of GroEL/ES and ATP. The assisted folding rate of rhodanese decreases. Based on our finding and those reported in other studies, we suggest that the ATP-consuming chaperonin machinery has evolved to optimize the product of the folding rate and the yield of the folded SPs on the biological time scale. Neither the rate nor the yield is separately maximized.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.09.373969v1?rss=1

Authors: Pärn, O., Lessin, G., Stips, A.

Abstract:

In this study, the effects of sea ice and wind speed on the timing and composition of phytoplankton spring bloom in the central and southern Baltic Sea are investigated by a hydrodynamic-biogeochemical model and observational data. The modelling experiment compared the results of a reference run in the presence of sea ice with those of a run in the absence of sea ice, which confirmed that ecological conditions differed significantly for both the scenarios. It has been found that diatoms dominate the phytoplankton biomass in the absence of sea ice, whereas dinoflagellates dominate the biomass in the presence of thin sea ice. The study concludes that under moderate ice conditions (representing the last few decades), dinoflagellates dominate the spring bloom phytoplankton biomass in the Baltic Sea, whereas diatoms will be dominant in the future as a result of climate change i.e. in the absence of sea ice.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.09.374496v1?rss=1

Authors: Suarez, E., Wiewiora, R. P., Wehmeyer, C., Noe, F., Chodera, J. D., Zuckerman, D. M.

Abstract:

Markov state models (MSMs) have been widely applied to study the kinetics and pathways of protein conformational dynamics based on statistical analysis of molecular dynamics (MD) simulations. These MSMs coarse-grain both configuration space and time in ways that limit what kinds of observables they can reproduce with high fidelity over different spatial and temporal resolutions. Despite their popularity, there is still limited understanding of which biophysical observables can be computed from these MSMs in a robust and unbiased manner, and which suffer from the space-time coarse-graining intrinsic in the MSM model. Most theoretical arguments and practical validity tests for MSMs rely on long-time equilibrium kinetics, such as the slowest relaxation timescales and experimentally observable time-correlation functions. Here, we perform an extensive assessment of the ability of well-validated protein folding MSMs to accuractely reproduce path-based observable such as mean first-passage times (MFPTs) and transition path mechanisms compared to a direct trajectory analysis. We also assess a recently proposed class of history-augmented MSMs (haMSMs) that exploit additional information not accounted for in standard MSMs. We conclude with some practical guidance on the use of MSMs to study various problems in conformational dynamics of biomolecules. In brief, MSMs can accurately reproduce correlation functions slower than the lag time, but path-based observables can only be reliably reproduced if the lifetimes of states exceed the lag time, which is a much stricter requirement. Even in the presence of short-lived states, we find that haMSMs reproduce path-based observables more reliably.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.09.374991v1?rss=1

Authors: Chen, J., Zaer, S., Drori, P., Zamel, J., Joron, K., Kalisman, N., Lerner, E., Dokholyan, N. V.

Abstract:

The intrinsically disordered protein, -synuclein, implicated in synaptic vesicle homeostasis and neurotransmitter release, is also associated with several neurodegenerative diseases. The different roles of -synuclein are characterized by distinct structural states (membrane-bound, dimer, tetramer, oligomer, and fibril), which are originated from its various monomeric conformations. The pathological states, determined by the ensemble of -synuclein monomer conformations and dynamic pathways of interconversion between dominant states, remain elusive due to their transient nature. Here, we use inter-dye distance distributions from bulk time-resolved Forster resonance energy transfer as restraints in discrete molecular dynamics simulations to map the conformational space of the -synuclein monomer. We further confirm the generated conformational ensemble in orthogonal experiments utilizing far-UV circular dichroism and cross-linking mass spectrometry. Single-molecule protein-induced fluorescence enhancement measurements show that within this conformational ensemble, some of the conformations of -synuclein are surprisingly stable, exhibiting conformational transitions slower than milliseconds. Our comprehensive analysis of the conformational ensemble reveals essential structural properties and potential conformations that promote its various functions in membrane interaction or oligomer and fibril formation.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.09.374934v1?rss=1

Authors: Haas, P. A., Goldstein, R. E.

Abstract:

Turing instabilities of reaction-diffusion systems can only arise if the diffusivities of the chemical species are sufficiently different. This threshold is unphysical in generic systems with N=2 diffusing species, forcing experimental realizations of the instability to rely on fluctuations or additional non-diffusing species. Here we ask whether this diffusive threshold lowers for N>2 to allow "true" Turing instabilities. Inspired by May's analysis of the stability of random ecological communities, we analyze the threshold for reaction-diffusion systems whose linearized dynamics near a homogeneous fixed point are given by a random matrix. In the numerically tractable cases of N[≤]6, we find that the diffusive threshold generically decreases as N increases and that these many-species instabilities generally require all species to be diffusing.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.09.375253v1?rss=1

Authors: Liebi, M., Lutz-Bueno, V., Guizar-Sicairos, M., Schoenbauer, B. M., Eichler, J., Martinelli, E., Loeffler, J. F., Weinberg, A., Lichtenegger, H., Gruenewald, T. A.

Abstract:

The nanostructural adaptation of bone is crucial for its compatibility with orthopedic implants. The bone's nanostructure determines its mechanical properties, however little is known about its temporal and spatial adaptation in degrading implants. This study presents insights into this adaptation by applying electron microscopy, elemental analysis, and small-angle X-ray scattering tensor-tomography (SASTT). We extend the SASTT reconstruction to multiple radii of the reciprocal space vector q, providing a 3D reciprocal-space map per voxel. Each scattering curve is spatially linked to one voxel in the volume, and properties such as the thickness of the mineral particles are quantified. This reconstruction provides information on nanostructural adaptation during healing around a degrading ZX10 magnesium implant over the course of 18 months, using a sham as control. The nanostructural adaptation process is observed to start with an initially fast interfacial organization towards the implant direction, followed by a substantial reorganization of the volume around the implant, and an adaptation in the later degradation stages. The study sheds light on the complex bone-implant interaction in 3D, allowing a more guided approach towards the design of future implant materials, which are expected to be of great interest for further clinical studies on the bone-implant interaction.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.09.374157v1?rss=1

Authors: Navikas, V., Leitao, S. M., Grussmayer, K. S., Descloux, A., Drake, B., Yserentant, K., Werther, P., Herten, D.-P., Wombacher, R., Radenovic, A., Fantner, G. E.

Abstract:

High-resolution live-cell imaging is necessary to study complex biological phenomena. Modern fluorescence microscopy methods are increasingly combined with complementary, label-free techniques to put the fluorescence information into the cellular context. The most common high-resolution imaging approaches used in combination with fluorescence imaging are electron microscopy and atomic-force microscopy (AFM), originally developed for solid-state material characterization. AFM routinely resolves atomic steps, however on soft biological samples, the forces between the tip and the sample deform the fragile membrane, thereby distorting the otherwise high axial resolution of the technique. Here we present scanning ion-conductance microscopy (SICM) as an alternative approach for topographical imaging of soft biological samples, preserving high axial resolution on cells. SICM is complemented with live-cell compatible super-resolution optical fluctuation imaging (SOFI). To demonstrate the capabilities of our method we show correlative 3D cellular maps with SOFI implementation in both 2D and 3D with self-blinking dyes for two-color high-order SOFI imaging. Finally, we employ correlative SICM/SOFI microscopy for visualizing actin dynamics in live COS-7 cells with subdiffractional resolution.

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