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Audio versions of bioRxiv paper abstracts

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Audio versions of bioRxiv paper abstracts

    Asymmetry in Histone Rotation in Forced Unwrapping and Force Quench Rewrapping in a Nucleosome

    Asymmetry in Histone Rotation in Forced Unwrapping and Force Quench Rewrapping in a Nucleosome

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.10.21.348664v1?rss=1

    Authors: Reddy, G., Thirumalai, D.

    Abstract:
    Nucleosomes, the building blocks of chromosomes, are also transcription regulators. Single molecule pulling experiments have shown that nucleosomes unwrap in two major stages, releasing nearly equal length of DNA in each stage. The first stage, attributed to the rupture of the outer turn is reversible, occurs at low forces ({approx} (3 - 5) pNs) whereas in the second stage the inner turn ruptures irreversibly at high forces (between {approx} (9 - 15) or higher) pNs. We show that Brownian dynamics simulations using the Self-Organized Polymer model of the nucleosome capture the experimental findings, thus permitting us to discern the molecular details of the structural changes not only in DNA but also in the Histone Protein Core (HPC). Upon unwrapping of the outer turn, which is independent of the pulling direction, there is a transition from 1.6 turns to 1.0 turn DNA wound around the HPC. In contrast, the rupture of the inner turn, leading to less than 0.5 turn DNA around the HPC, depends on the pulling direction, and is controlled by energetic and kinetic barriers. The latter arises because the mechanical force has to produce sufficient torque to rotate (in an almost directed manner) the HPC by 180{degrees}. In contrast, during the rewrapping process, HPC rotation is stochastic, with the quenched force fQ playing no role. Interestingly, if fQ = 0 the HPC rotation is not required for rewrapping because the DNA ends are unconstrained. The assembly of the outer wrap upon force quench, as assessed by the decrease in the end-to-end distance (Ree) of the DNA, nearly coincides with the increase in Ree as force is increased, confirming the reversible nature of the 1.6 turns to 1.0 turn transition. The asymmetry in HPC rotation during unwrapping and rewrapping accounts for the observed hysteresis in the stretch-release cycles in single molecule pulling experiments. Experiments that could validate the prediction that HPC rotation, which gives rise to the kinetic barrier in the unwrapping process, are proposed.

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    Positive allosteric modulators of lecithin:cholesterol acyltransferase adjust the orientation of the membrane-binding domain and alter its spatial free energy profile

    Positive allosteric modulators of lecithin:cholesterol acyltransferase adjust the orientation of the membrane-binding domain and alter its spatial free energy profile

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.10.20.344978v1?rss=1

    Authors: Niemela, A., Koivuniemi, A. S.

    Abstract:
    Lecithin:cholesterol acyltransferase protein (LCAT) promotes the esterification reaction between cholesterol and phospholipid derived acyl chains. Positive allosteric modulators have been developed to treat LCAT deficiencies and, plausibly, also cardiovascular diseases in the future. The mechanism of action of these compounds is poorly understood. Here computational docking and atomistic molecular dynamics simulations were utilized to study the interactions between LCAT and the activating compounds. Results indicate that all drugs bind to the allosteric binding pocket in the membrane-binding domain in a similar fashion. The presence of the compounds in the allosteric site results in a distinct spatial orientation and sampling of the membrane-binding domain (MBD). The MBD's different spatial arrangement plausibly affects the lid's movement from closed to open state and vice versa, as suggested by steered molecular dynamics simulations.

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    The collapse of the spindle following ablation in S. pombe is mediated by microtubules and the motor protein dynein

    The collapse of the spindle following ablation in S. pombe is mediated by microtubules and the motor protein dynein

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.10.20.347922v1?rss=1

    Authors: Zareiesfandabadi, P., Elting, M. W.

    Abstract:
    A microtubule-based machine called the mitotic spindle segregates chromosomes when eukaryotic cells divide. In the fission yeast S. pombe, which undergoes closed mitosis, the spindle forms a single bundle of microtubules inside the nucleus. During elongation, the spindle extends via antiparallel microtubule sliding by molecular motors. These extensile forces from the spindle are thought to resist compressive forces from the nucleus. We probe the mechanism and maintenance of this force balance via laser ablation of spindles at various stages of mitosis. We find that spindle pole bodies collapse toward each other following ablation, but spindle geometry is often rescued, allowing spindles to resume elongation and segregate chromosomes. While this basic behavior has been previously observed, many questions remain about this phenomenon's dynamics, mechanics, and molecular requirements. In this work, we find that previously hypothesized viscoelastic relaxation of the nucleus cannot fully explain spindle shortening in response to laser ablation. Instead, spindle collapse requires microtubule dynamics and is powered at least partly by the minus-end directed motor protein dynein. These results suggest a role for dynein in redundantly supporting force balance and bipolarity in the S. pombe spindle.

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    High throughput measurements of BMPBMP receptors interactions using bio-layer interferometry

    High throughput measurements of BMPBMP receptors interactions using bio-layer interferometry

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.10.20.348060v1?rss=1

    Authors: KHODR, V., MACHILLOT, P., MIGLIORINI, E., REISER, J.-b., PICART, C.

    Abstract:
    Bone morphogenetic proteins (BMP) are an important family of growth factors playing a role in a large number of physiological and pathological processes, including bone homeostasis, tissue regeneration and cancers. In vivo, BMPs bind successively to both BMP receptors (BMPR) of type I and type II, and a promiscuity has been reported. In this study, we used bio-layer interferometry to perform parallel real-time biosensing and to deduce the kinetic parameters (ka, kd) and the equilibrium constant (KD) for a large range of BMPs/BMPR combinations in similar experimental conditions. We selected four members of the BMP family (BMP-2, 4, 7, 9) known for their physiological relevance and studied their interactions with five type-I BMP receptors (ALK1, 2, 3, 5, 6) and three type-II BMP receptors (BMPR-II, ACTR-IIA, ACTR-IIB). We reveal that BMP-2 and BMP-4 behave differently, especially regarding their kinetic interactions and affinities with the type-II BMPR. We found that BMP-7 has a higher affinity for ACTR-IIA and a tenfold lower affinity with the type-I receptors. While BMP-9 has a high and similar affinity for all type-II receptors, it can interact with ALK5 and ALK2, in addition to ALK1. Interestingly, we also found that all BMPs can interact with ALK5. The interaction between BMPs and both type-I and type II receptors immobilized on the same surface did not reveal further cooperativity. Our work provides a synthetic view of the interactions of these BMPs with their receptors and paves the way for future studies on their cell-type and receptor specific signaling pathways.

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    Targeted modulation of protein liquid-liquid phase separation by evolution of amino-acid sequence

    Targeted modulation of protein liquid-liquid phase separation by evolution of amino-acid sequence

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.10.20.347542v1?rss=1

    Authors: Lichtinger, S. M., Garaizar, A., Collepardo-Guevara, R., Reinhardt, A.

    Abstract:
    Rationally and efficiently modifying the amino-acid sequence of proteins to control their ability to undergo liquid-liquid phase separation (LLPS) on demand is not only highly desirable, but can also help to elucidate which protein features are important for LLPS. Here, we propose an innovative computational method that couples a genetic algorithm to a sequence-dependent coarse-grained protein model to evolve the amino-acid sequences of phase-separating intrinsically disordered protein regions (IDRs), and purposely enhance or inhibit their capacity to phase-separate. We apply it to the phase-separating IDRs of three naturally occurring proteins, namely FUS, hnRNPA1 and LAF1, as prototypes of regions that exist in cells and undergo homotypic LLPS driven by different types of intermolecular interaction. We find that the evolution of amino-acid sequences towards enhanced LLPS is driven in these three cases, among other factors, by an increase in the average size of the amino acids. However, the direction of change in the molecular driving forces that enhance LLPS (such as hydrophobicity, aromaticity and charge) depends on the initial amino-acid sequence: the critical temperature can be enhanced by increasing the frequency of hydrophobic and aromatic residues, by changing the charge patterning, or by a combination of both. Finally, we show that the evolution of amino-acid sequences to modulate LLPS is strongly coupled to the composition of the medium (e.g. the presence or absence of RNA), which may have significant implications for our understanding of phase separation within the many-component mixtures of biological systems.

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    The Mechanical Roles of Chaperons

    The Mechanical Roles of Chaperons

    Link to bioRxiv paper:
    http://biorxiv.org/cgi/content/short/2020.10.20.346973v1?rss=1

    Authors: Haldar, S., chaudhuri, D., banerjee, s., Chakraborty, S.

    Abstract:
    Protein folding under force is an integral source of generating mechanical power to carry out diverse cellular functions. Though chaperones interact with proteins throughout the different stages of folding pathways, how they behave and interact with client proteins under force was not known. Here we introduce the mechanical role of chaperone and explained it with seven independent chaperones using single molecule based real-time microfluidics-magnetic-tweezers. We showed and quantified how chaperones increase or decrease mechanical work output by shifting the folding energy landscape of the client proteins towards the folded or unfolded state. Notably, we found chaperones could behave differently under force. For instance: trigger factor, ribosomal-tunnel associated chaperone, working as a holdase in absence of force, but assist folding under force. This phenomenon generates extra mechanical energy to pull the polyprotein from the stalled ribosome. This is also relevant for SecYEG tunnel associated oxidoreductase DsbA, which act similarly like TF and increases the mechanical energy up to ~59 zJ, to facilitate membrane translocation in an energy efficient manner. However cytoplasmic oxidoreductases such as PDI and Thioredoxin, unlike DsbA, do not have the mechanical folding ability. Interestingly, we observed a highly potential foldase- DnaKJE chaperone complex, only restores the folding ability of the client protein and fails to act like TF or DsbA under force. However, the individual components of this complex, DnaK or DnaJ, act as a mechanical holdase and inhibits folding; similar to that of SecB. Together our study provides an emerging insight of mechanical chaperone behavior, where tunnel associated chaperones generate extra mechanical work whereas the cytoplasmic chaperones are unable to generate that, which might have evolved to minimize the energy consumption in biological processes.

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