PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.27.271080v1?rss=1

Authors: Huang, H., Zheng, C.-J., Wang, L.-F., Che-Nordin, N., Wang, Y.-X.

Abstract:

Objectives: To establish reference values for middle aged subjects and investigate age and gender dependence of liver diffusion MRI parameters. Methods: The IVIM type of liver diffusion scan was based on a single-shot spin-echo type echo-planar sequence using a 1.5-T magnet with 16 b-values. DDVD (diffusion-derived vessel density) was the signal difference between b=0 and b=2 s/mm2 images after removing visible vessels. IVIM analysis was performed with full-fitting and segmented-fitting, and with threshold b-value of 60 or 200 s/mm2, and fitting started from b=2 s/mm2. 32 men (age range: 25-71 years) and 26 men (age: 22-69 years) had DDVD and IVIM analysis respectively, while 36 women (age: 20-71 years) had DDVD and IVIM analysis. Results: DDVD had an age-related reduction noted for women. IVIM results of full fitting had good agreement with segmented fitting with threshold b of 60 s/mm2 results, but less so with results of threshold b of 200 s/mm2. As age increases, female subjects Dslow measure had significant reduction, and PF and Dfast measure had significant increase. Conclusion: DDVD measure suggest that aging may be associated with reduction in liver perfusion. Lower Dslow measurement can lead to artificial higher PF and Dfast measurement, providing the evidence of IVIM modeling of perfusion component is constrained by diffusion component.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.27.270496v1?rss=1

Authors: Plochberger, B., Sych, T., Weber, F., Novacek, J., Axmann, M., Stangl, H., Sezgin, E.

Abstract:

Lipid transfer from lipoprotein particles to cells is essential for lipid homeostasis. High density lipoprotein (HDL) particles are mainly captured by cell-membrane-associated scavenger receptor class B type 1 (SR-B1) from the blood stream while low and very low density lipoprotein (LDL, VLDL) particles are mostly taken up by receptor-mediated endocytosis. However, the role of the target lipid membrane itself in the transfer process has been largely neglected so far. Here, we study how lipoprotein particles (HDL, LDL and VLDL) interact with synthetic lipid bilayers and cell-derived membranes and transfer their cargo subsequently. Employing cryo-electron microscopy, spectral imaging and fluorescence (cross) correlation spectroscopy allowed us to observe integration of all major types of lipoprotein particles into the membrane and delivery of their cargo in a receptor-independent manner. Importantly, biophysical properties of the target cell membranes change upon cargo delivery. The concept of receptor-independent interaction of lipoprotein particles with membranes helps to better understand lipoprotein particle biology and can be exploited for novel treatments of dyslipidemia diseases.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.27.270991v1?rss=1

Authors: Jin, F., Sun, M., Fujii, T., Yamada, Y., Wang, J., Maturana, A., Wada, M., Su, S., Ma, J., Takeda, H., Kusakizako, T., Tomita, A., Nakura, Y. N., Liu, K., Uemura, T., Nomura, Y., Nomura, N., Ito, K., Nureki, O., Namba, K., Iwata, S., Yu, Y., Hattori, M.

Abstract:

MgtE is a Mg2+ channel conserved in organisms ranging from prokaryotes to eukaryotes, including humans, and plays an important role in Mg2+ homeostasis. The previously determined MgtE structures in the Mg2+-bound, closed state and structure-based functional analyses of MgtE revealed that the binding of Mg2+ ions to the MgtE cytoplasmic domain induces channel inactivation to maintain Mg2+ homeostasis. However, due to the lack of a structure of the MgtE channel, including its transmembrane domain in Mg2+-free conditions, the pore-opening mechanism of MgtE has remained unclear. Here, we determined the cryoelectron microscopy (cryo-EM) structure of the MgtE-Fab complex in the absence of Mg2+ ions. The Mg2+-free MgtE transmembrane domain structure and its comparison with the Mg2+-bound, closed-state structure, together with functional analyses, showed the Mg2+-dependent pore opening of MgtE on the cytoplasmic side and revealed the kink motions of the TM2 and TM5 helices at the glycine residues, which are important for channel activity. Overall, our work provides structure-based mechanistic insights into the channel gating of MgtE.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.28.271809v1?rss=1

Authors: Bobone, S., Pannone, L., Biondi, B., Solman, M., Flex, E., Canale, V., Calligari, P., De Faveri, C., Gandini, T., Quercioli, A., Torini, G., Venditti, M., Lauri, A., Fasano, G., Hoeksma, J., Santucci, V., Cattani, G., Bocedi, A., Carpentieri, G., Tirelli, V., Sanchez, M., Peggion, C., Formaggio, F., Den Hertog, J., Martinelli, S., Bocchinfuso, G., Tartaglia, M., Stella, L.

Abstract:

Mutations of PTPN11, the gene coding for the Src homology 2 domain-containing phosphatase 2 (SHP2), cause childhood leukemias and developmental disorders. SHP2 inhibitors targeting the catalytic site or an allosteric pocket lack specificity or are ineffective on pathogenic variants. In addition, several data indicate that increased association with cognate proteins, through its SH2 domains, rather than enhanced catalytic activity, is the main effect of mutations causing hyperactivation of SHP2-mediated signaling. We developed peptide-based molecules with low nM affinity to the N-SH2 domain and high specificity. These molecules bind to pathogenic variants of SHP2 with an affinity up to 20 times higher than to the wild-type protein, in contrast to allosteric inhibitors, and were able to revert the effects of a pathogenic SHP2 mutation in zebrafish embryos. Our results provide a novel route for SHP2-targeted therapies and a tool to investigate the role of protein-protein interactions in the function of SHP2.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.28.272104v1?rss=1

Authors: Manka, S. W., Brew, K.

Abstract:

Local unwinding of the collagen triple helix is a necessary step for initiating the collagen degradation cascade in extracellular matrices. A few matrix metalloproteinases (MMPs) are known to support this key process, but its energetic aspects remain unknown. Here, we captured the thermodynamics of the triple helix unwinding by monitoring interactions between a collagen peptide and MMP-1(E200A) - an active-site mutant of an archetypal vertebrate collagenase - at increasing temperatures, using isothermal titration calorimetry (ITC). Coupled binding and unwinding manifests as a curved relationship between the total enthalpy change and temperature of the reaction, producing increasingly negative heat capacity change ({Delta}{Delta}Cp {approx} -36.3 kcal/molK2). A specially designed solid-phase binding and cleavage assay (SPBCA) reported strain in the catalytically relevant unwound state, suggesting that this state is distinct from the horizon of sampled conformations of the collagenase-susceptible site. MMP-1 appears to blend selected fit with induced fit mechanisms to catalyse collagen unwinding prior to cleavage of individual collagen chains.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.27.270934v1?rss=1

Authors: Stern, C. D., Bayly, C. I., Smith, D. G. A., Fass, J., Wang, L.-P., Mobley, D. L., Chodera, J. D.

Abstract:

Accurate molecular mechanics force fields for small molecules are essential for predicting protein-ligand binding affinities in drug discovery and understanding the biophysics of biomolecular systems. Torsion potentials derived from quantum chemical (QC) calculations are critical for determining the conformational distributions of small molecules, but are computationally expensive and scale poorly with molecular size. To reduce computational cost and avoid the complications of distal through-space intramolecular interactions, molecules are generally fragmented into smaller entities to carry out QC torsion scans. However, torsion potentials, particularly for conjugated bonds, can be strongly affected by through-bond chemistry distal to the torsion itself. Poor fragmentation schemes have the potential to significantly disrupt electronic properties in the region around the torsion by removing important, distal chemistries, leading to poor representation of the parent molecule's chemical environment and the resulting torsion energy profile. Here we show that a rapidly computable quantity, the fractional Wiberg bond order (WBO), is a sensitive reporter on whether the chemical environment around a torsion has been disrupted. We show that the WBO can be used as a surrogate to assess the robustness of fragmentation schemes and identify conjugated bond sets. We use this concept to construct a validation set by exhaustively fragmenting a set of druglike organic molecules and examine their corresponding WBO distributions derived from accessible conformations that can be used to evaluate fragmentation schemes. To illustrate the utility of the WBO in assessing fragmentation schemes that preserve the chemical environment, we propose a new fragmentation scheme that uses rapidly-computable AM1 WBOs, which are available essentially for free as part of standard AM1-BCC partial charge assignment. This approach can simultaneously maximize the chemical equivalency of the fragment and the substructure in the larger molecule while minimizing fragment size to accelerate QC torsion potential computation for small molecules and reducing undesired through-space steric interactions.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.28.271940v1?rss=1

Authors: Weber, D. K., Hernandez, M. S., Reddy, V. U., Wang, S., Larsen, E. K., Tata, G., Gustavsson, M., Cornea, R. L., Thomas, D. D., De Simone, A., Veglia, G.

Abstract:

Phospholamban (PLN) is a mini-membrane protein that directly controls the cardiac Ca2+-transport response to {beta}-adrenergic stimulation, thus modulating cardiac output during the fight-or-flight response. In the sarcoplasmic reticulum membrane, PLN binds to the sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA), keeping this enzyme's function within a narrow physiological window. PLN phosphorylation or increase in Ca2+ concentration reverses the inhibitory effects. Despite a plethora of X-ray studies, the structural mechanism of SERCA regulation by PLN remains unknown. Using solid-state NMR spectroscopy and replica-averaged NMR-restrained structural refinement, we found that the transmembrane region of PLN is in equilibrium between inhibitory and non-inhibitory topologies within SERCA's binding groove. Phosphorylation of PLN at Ser16, or increase in Ca2+ concentration, shifts the equilibrium toward the non-inhibitory topologies, augmenting Ca2+ transport and muscle contractility. This type of allosteric regulation, via topological changes (topological allostery), may constitute a general mechanism for the other regulins that modulate SERCA activity in cardiac and skeletal muscle.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.28.272195v1?rss=1

Authors: de Lannoy, C. V., Filius, M., Kim, S. H., Joo, C., de Ridder, D.

Abstract:

Forster resonance energy transfer (FRET) is a useful phenomenon in biomolecular investigations, as it can be leveraged for nano-scale measurements. The optical signals produced by such experiments can be analyzed by fitting a statistical model. Several software tools exist to fit such models in an unsupervised manner, but their operating system-dependent installation requirements and lack of flexibility impede wide-spread adoption. Here we propose to fit such models more efficiently and intuitively by adopting a semi-supervised approach, in which the user interactively guides the model to fit a given dataset, and introduce FRETboard, a web tool that allows users to provide such guidance. We show that our approach is able to closely reproduce ground truth FRET statistics in a wide range of simulated single-molecule scenarios, and correctly estimate parameters for up to eleven states. On in vitro data we retrieve parameters identical to those obtained by laborious manual classification in a fraction of the required time. Moreover, we designed FRETboard to be easily extendable to other models, allowing it to adapt to future developments in FRET measurement and analysis.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.28.271510v1?rss=1

Authors: Thomson, N. J., Vickery, O. N., Ives, C. M., Zachariae, U.

Abstract:

G-protein-coupled receptors (GPCRs) are membrane proteins that transmit signals across the cell membrane by activating intracellular G-proteins in response to extracellular ligand binding. A large majority of GPCRs are characterised by an evolutionarily conserved activation mechanism, involving the reorientation of helices and the conformation of key residue side chains, rearrangement of an internal hydrogen bonding network, and the expulsion of a sodium ion from a binding site in the transmembrane region. However, how sodium, internal water, and protein residues interplay to determine the overall receptor state remains elusive. Here, we develop and apply "State Specific Information" (SSI), a novel methodology based on information theory, to resolve signal transmission pathways through the proteins. Using all-atom molecular dynamics simulations of pharmaceutically important GPCRs, we find that sodium plays a causal role in the formation and regulation of a communication channel from the ion binding site to the G-protein binding region. Our analysis reveals that the reorientation of specific water molecules is essential to enable coupled conformational state changes of protein residues along this pathway, ultimately modulating the G-protein binding site. Furthermore, we show that protonation of the ion binding site creates a conformational coupling between two previously separate motifs, entirely controlled by the orientation of two water molecules, priming the receptor for activation. Taken together, our results demonstrate that sodium serves as a master switch, acting in conjunction with the network of internal water molecules, to determine the micro- and macrostates of GPCRs during the receptors' transition to activation.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.27.270058v1?rss=1

Authors: Kapoor, S., Kodesia, A., Kalidas, N., Ganguly, A., Thakur, K. G.

Abstract:

Myxococcus xanthus displays two types of motilities i.e. Social (S) and Adventurous (A). The pole-to-pole reversals of these motility regulator proteins is the key to this process. Here, we determined ~1.85 angstrom resolution crystal structure of MglC, which revealed that despite sharing <9% sequence identity, both MglB and MglC adopt Regulatory Light Chain 7 (RLC7) family fold. Interestingly, MglC is structurally unique compared to the other known RLC7 family proteins having ~30{ring}-40{ring} shift in the orientation of functionally important 2 helix. Using isothermal titration calorimetry and gel filtration chromatography, we show that MglC binds MglB in 2:4 stoichiometry with submicromolar range dissociation constant. Using combination of small angle X-ray scattering and molecular docking studies, we show that MglBC complex is formed by MglC homodimer sandwiched between two homodimers of MglB.

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