PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.20.259507v1?rss=1

Authors: Roongthumskul, Y., Faber, J., Bozovic, D.

Abstract:

The high sensitivity and effective frequency discrimination of sound detection performed by the auditory system rely on the dynamics of a system of hair cells. In the inner ear, these acoustic receptors are primarily attached to an overlying structure which provides mechanical coupling between the hair bundles. While the dynamics of individual hair bundles have been extensively investigated, the influence of mechanical coupling on the motility of the system of bundles remains underdetermined. We developed a technique of mechanically coupling two active hair bundles, enabling us to probe the dynamics of the coupled system experimentally. We demonstrated that the coupling could enhance the coherence of hair bundles' spontaneous oscillation as well as their phase-locked response to sinusoidal stimuli, at the calcium concentration in the surrounding fluid near the physiological level. The empirical data were consistent with numerical results from a model of two coupled nonisochronous oscillators, each displaying a supercritical Hopf bifurcation. The model revealed that weak coupling can poise the system of unstable oscillators closer to the bifurcation by a shift in the critical point. In addition, the dynamics of strongly coupled oscillators far from criticality suggested that individual hair bundles may be regarded as nonisochronous oscillators. An optimal degree of nonisochronicity was required for the observed tuning behavior in the coherence of autonomous motion of the coupled system.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.21.260158v1?rss=1

Authors: G. Rao, A., Wiebeler, C., Sen, S., Cerutti, D. S., Schapiro, I.

Abstract:

Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that bind a linear tetrapyrrole as a chromophore. They show photochromicity by having two stable states that can be interconverted by the photoisomerization of the chromophore. Hence, these photochemical properties make them an attractive target for biotechnological applications. However, their application is impeded by structural heterogeneity that reduces the yield of the photoconversion. The heterogeneity can originate either from the chromophore structure or the protein environment. Here, we study the origin of the heterogeneity in AnPixJg2, a representative member of the red/green cyanobacteriochrome family, that has a red absorbing parental state and a green absorbing photoproduct state. Using molecular dynamics simulations and umbrella sampling we have identified the protonation state of a conserved histidine residue as a trigger for structural heterogeneity. When the histidine is in a neutral form, the chromophore structure is homogenous, while in a positively charged form, the chromophore is heterogeneous with two different conformations. We have identified a correlation between the protonation of the histidine and the structural heterogeneity of the chromophore by detailed characterization of the interactions in the protein binding site. Our findings reconcile seemingly contradicting spectroscopic studies that attribute the heterogeneity to different sources. Furthermore, we predict that circular dichroism can be used as a diagnostic tool to distinguish different substates.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.20.259770v1?rss=1

Authors: Lapointe, C. P., Grosely, R., Johnson, A. G., Wang, J., Fernandez, I. S., Puglisi, J. D.

Abstract:

SARS-CoV-2 recently emerged as a human pathogen and is the causative agent of the COVID-19 pandemic. A molecular framework of how the virus manipulates host cellular machinery to facilitate infection remains unclear. Here, we focus on SARS-CoV-2 NSP1, which is proposed to be a virulence factor that inhibits protein synthesis by directly binding the human ribosome. Using extract-based and reconstitution experiments, we demonstrate that NSP1 inhibits translation initiation on model human and SARS-CoV-2 mRNAs. NSP1 also specifically binds to the small (40S) ribosomal subunit, which is required for translation inhibition. Using single-molecule fluorescence assays to monitor NSP1-40S subunit binding in real time, we demonstrate that eukaryotic translation initiation factors (eIFs) modulate the interaction: NSP1 rapidly and stably associates with most ribosomal pre-initiation complexes in the absence of mRNA, with particular enhancement and inhibition by eIF1 and eIF3j, respectively. Using model mRNAs and an inter-ribosomal-subunit FRET signal, we elucidate that NSP1 competes with RNA segments downstream of the start codon to bind the 40S subunit and that the protein is unable to associate rapidly with 80S ribosomes assembled on an mRNA. Collectively, our findings support a model where NSP1 associates with the open head conformation of the 40S subunit to inhibit an early step of translation, by preventing accommodation of mRNA within the entry channel.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.20.228056v1?rss=1

Authors: Govind Kumar, V., Agrawal, S., Suresh Kumar, T. K., Moradi, M.

Abstract:

Human fibroblast growth factor (FGF) 1 or hFGF1 is a member of the FGF family that isare involved in various vital processes such as cell proliferation, cell differentiation, angiogenesis and wound healing. hFGF1, which is associated with low stability in vivo, is known to be stabilized by binding heparin sulfate, a glycosaminoglycan that aids the protein in the activation of its cell surface receptor. The poor thermal and proteolytic stability of hFGF1 and the stabilizing role of heparin have long been observed experimentally; however, the mechanistic details of these phenomena either phenomenon are still not well understood. Here, we have used a combination of microsecond-level equilibrium molecular dynamics (MD) simulations, and state-of-the-art enhanced sampling MD simulations to quantitatively characterize the structural dynamics of monomeric hFGF1 in the presence and absence of heparin hexasaccharide. We have observed a local conformational changeconformational change in the heparin-binding pocketregion of hFGF1 that only occurs only in the absence of heparin. Several intramolecular hydrogen bonds were also identified within the heparin-binding pocket region, that form only when hFGF1 interacts with heparin. The loss of both intermolecular and intramolecular electrostatic interactions in the absence of heparin plausibly leads to the observed conformational change. This conformational transition results in increased flexibility of the heparin-binding pocket region and provides an explanation for the susceptibility of apo hFGF1 to proteolytic degradation and thermal instability . The hFGF1-heparin interactions) has also been quantified using absolute binding free energy calculations. Binding affinity (Kd) estimates determined computationally using our novel MD approach are in a good quantitative agreement with experimental Kd values from isothermal titration calorimetry experiments. The successful application of a combination of rigorous physics-based simulation techniques microsecond-level MD and accurate free energy calculations and its ability to accurately explain the biomolecular phenomena such as the heparin-mediated stabilization of hFGF1 at a quantitative level, provides open new opportunitiesrepresents a promising approach for studying complex towards understanding biological processesbiomolecular interactions between proteins and their binding partners at a detailed molecular level. using rigorous physics-based simulation techniques.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.19.257774v1?rss=1

Authors: Nguyen, H. C., Melo, A. A., Kruk, J., Frost, A., Gabruk, M.

Abstract:

Chlorophyll (Chl) biosynthesis, crucial to life on Earth, is tightly regulated because its precursors are phototoxic. In flowering plants, the enzyme Light-dependent Protochlorophyllide OxidoReductase (LPOR) captures photons to catalyze the penultimate reaction: the reduction of a double-bond within protochlorophyllide (Pchlide) to generate chlorophyllide (Chlide). In darkness, LPOR oligomerizes to facilitate photon energy transfer and catalysis. However, the complete 3D structure of LPOR, the higher-order architecture of LPOR oligomers, and the implications of these self-assembled states for catalysis, including how LPOR positions Pchlide and the cofactor NADPH, remain unknown. Here we report the atomic structure of LPOR assemblies by electron cryo-microscopy (cryoEM). LPOR polymerizes with its substrates into helical filaments around constricted lipid bilayer tubes. Portions of LPOR and Pchlide insert into the outer membrane leaflet, targeting the product, Chlide, to the membrane for the final reaction site of chlorophyll biosynthesis. In addition to its crucial photocatalytic role, we show that in darkness LPOR filaments directly shape membranes into high-curvature tubules with the spectral properties of the prolammelar body, whose light-triggered disassembly provides lipids for thylakoid assembly. Our structure of the catalytic site, moreover, challenges previously proposed reaction mechanisms. Together, our results reveal a new and unexpected synergy between photosynthetic membrane biogenesis and chlorophyll synthesis in plants orchestrated by LPOR.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.19.257477v1?rss=1

Authors: Elangovan, R., Soman, V., Kumari, S., Nath, S.

Abstract:

Many species of bacteria use flagella to navigate in its environment. The flagellum is a 7-10 m long helical filament with a rotary motor at its base embedded in the cell membrane and almost a dozen stator complexes. Proton motive force across the cell membrane powers the flagellar motors of E.coli and Salmonella. The motor stochastically switches between clockwise and counter-clockwise direction. A chemotaxis system causes the motor to change its direction, but the process is more complex as the switch is sensitive to load and proton motive force as well. NaCl is significant with regard to the flagellar motor as it affects the stator dynamics, proton motive force, and osmotaxis at higher concentration. Chemotaxis helps the bacteria for its growth and survival. E.coli's natural habitat has high osmolarity and the organism uses use various mechanisms for osmoregulation. However, the role of flagellar motor to adapt to the changes in osmolarity, or osmotaxis, is not well studied. In this work, we dissipated the membrane potential of bacteria in pH 7 using step-wise increase in concentration of NaCl in motility buffer and studied the output of E.coli's flagellar motor using tethered bead assay and swimming Salmonella enteritidis cells. We observed decrease in motor speed and switching rates with stepwise increase in NaCl concentration in the motility buffer. The mean speed of the motors decreased with NaCl concentration. The population of swimming cells tumbled more with increase in concentration of NaCl. At the single motor level, the motors biased to CCW rotation with decrease in membrane potential. In this study, we present our observations of the flagellar motor in high NaCl concentration, and explore how NaCl can be used to study various aspects of the bacterial flagellar motor.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.20.230268v1?rss=1

Authors: Brown, C. J., Verma, C. S., Lane, D. P., Lama, D.

Abstract:

Intrinsically disordered regions (IDRs) in proteins can regulate their activity by facilitating protein-protein interactions (PPIs) as exemplified in the recruitment of the eukaryotic translation initiation factor 4E (eIF4E) protein by the protein eIF4G. Deregulation of this PPI module is central to a broad spectrum of cancer related malignancies and its targeted inhibition through bioactive peptides is a promising strategy for therapeutic intervention. We have employed a structure-guided approach to rationally develop peptide derivatives from the intrinsically disordered eIF4G scaffold by incorporating non-natural amino acids that facilitates disorder-to-order transition. The conformational heterogeneity of these peptides and the degree of structural reorganization required to adopt the optimum mode of interaction with eIF4E underscores their differential binding affinities. The presence of a pre-structured local helical element in the ensemble of structures was instrumental in the efficient docking of the peptides on to the protein surface. These insights were exploited to further design features into the peptide to propagate bound-state conformations in solution which resulted in the generation of a potent eIF4E binder. The study illustrates the molecular basis of eIF4E recognition by a disordered epitope from eIF4G and its modulation to generate peptides that can potentially attenuate translation initiation in oncology.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.19.256552v1?rss=1

Authors: Morrell, M. C., Sederberg, A., Nemenman, I.

Abstract:

Understanding the activity of large populations of neurons is difficult due to the combinatorial complexity of possible cell-cell interactions. To reduce the complexity, coarse-graining had been previously applied to experimental neural recordings, which showed over two decades of scaling in free energy, activity variance, eigenvalue spectra, and correlation time, hinting that the mouse hippocampus operates in a critical regime. We model the experiment by simulating conditionally independent binary neurons coupled to a small number of long-timescale stochastic fields and then replicating the coarse-graining procedure and analysis. This reproduces the experimentally-observed scalings, suggesting that they may arise from coupling the neural population activity to latent dynamic stimuli. Further, parameter sweeps for our model suggest that emergence of scaling requires most of the cells in a population to couple to the latent stimuli, predicting that even the celebrated place cells must also respond to non-place stimuli.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.18.255109v1?rss=1

Authors: Fujimura, S., Mio, K., Kuramochi, M., Sekiguchi, H., Keigo, I., Mio, M., Hengphasatporn, K., Shigeta, Y., Kubo, T., Sasaki, Y. C.

Abstract:

Transient receptor potential vanilloid type 1 (TRPV1) channels are activated by heat, vanilloids, and extracellular protons. Cryo-EM has revealed various conformations of TRPV1, and these structures suggest an intramolecular twisting motion in response to ligand binding. However, limited experimental data support this observation. Here we analyzed the intramolecular motion of TRPV1 using diffracted X-ray tracking (DXT). DXT analyzes trajectories of Laue spots generated from attached gold nanocrystals, and provides picometer spatial and microsecond time scale information about intramolecular motion. We observed that both an agonist and a competitive antagonist evoked rotating bias in TRPV1, though these biases were in opposing directions. Furthermore, the rotational bias generated by capsaicin was reversed between the wild type and the capsaicin-insensitive Y511A mutant. Our findings bolster the understanding of the mechanisms used activation and modulation of TRP channels, and this knowledge can be exploited for pharmacological usage such as inhibitor design.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.19.256925v1?rss=1

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

Abstract:

The membrane sculpting ability of BAR domains has been attributed to the intrinsic curvature of their banana-shaped dimeric structure. However, there is often a mismatch between this intrinsic curvature and the diameter of the membrane tubules generated. For example, I-BAR domains are almost flat but generate much higher membrane curvature. Furthermore, F-BAR and I-BAR domains are quite similar, but the former generates positive curvature and the latter negative curvature. Here, we use implicit-solvent computer modeling to show that the membrane bending of the IRSP53 I-BAR domain is dictated by its oligomeric structure, whose curvature is completely unrelated to the intrinsic curvature of the dimer. We find that I-BAR dimers undergo lateral and end-to-end interactions to form higher oligomers. The lateral interactions, which can occur with varying register, are stronger and give a curved shape that has the membrane binding interface on its convex surface. Two other I-BARs (MIM and I-BARa) gave similar results, whereas a flat F-BAR sheet curved to make its membrane binding interface concave, consistent with positive membrane curvature generation. Individual dimers orient parallel to the tube axis when the tube radius is small, whereas perpendicular orientation is preferred for larger diameter tubes. This orientational preference exists even in the higher oligomeric form. Helical spirals on tube interiors are stable at a density comparable to experimental measurements. The sorting ratio computed from our membrane binding energies is also consistent with experimental measurements.

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