PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.19.254706v1?rss=1

Authors: Eeftens, J. M., Kapoor, M., Brangwynne, C. P.

Abstract:

Structural organization of the genome into transcriptionally active euchromatin and silenced heterochromatin is essential for eukaryotic cell function. Heterochromatin is a more compact form of chromatin, and is associated with characteristic post- translational histone modifications and chromatin binding proteins. Phase-separation has recently been suggested as a mechanism for heterochromatin formation, through condensation of heterochromatin associated proteins. However, it is unclear how phase-separated condensates can contribute to stable and robust repression, particularly for heritable epigenetic changes. The Polycomb complex PRC1 is known to be key for heterochromatin formation, but the multitude of Polycomb proteins has hindered our understanding of their collective contribution to chromatin repression. Here, we take a quantitative live cell imaging approach to show that PRC1 proteins form multicomponent condensates through hetero-oligomerization. They preferentially seed at H3K27me3 marks, and subsequently write H2AK119Ub marks. Using optogenetics to nucleate local Polycomb condensates, we show that Polycomb phase separation can induce chromatin compaction, but phase separation is dispensable for maintenance of the compacted state. Our data are consistent with a model in which the time integral of historical Polycomb phase separation is progressively recorded in repressive histone marks, which subsequently drive chromatin compaction. These findings link the equilibrium thermodynamics of phase separation with the fundamentally non-equilibrium concept of epigenetic memory.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.19.256909v1?rss=1

Authors: Zhang, K., Pintilie, G. D., Li, S., Schmid, M. F., Chiu, W.

Abstract:

Breakthroughs in single-particle cryo-electron microscopy (cryo-EM) technology have made near-atomic resolution structure determination possible. Here, we report a ~1.35-Å structure of apoferritin reconstructed from images recorded on a Gatan K3 or a Thermo Fisher Falcon 4 detector in a commonly available 300-kV Titan Krios microscope (G3i) equipped with or without a Gatan post-column energy filter. Our results demonstrate that the atomic-resolution structure determination can be achieved by single-particle cryo-EM with a fraction of a day of automated data collection. These structures resolve unambiguously each heavy atom (C, N, O, and S) in the amino acid side chains with an indication of hydrogen atoms' presence and position, as well as the unambiguous existence of multiple rotameric configurations for some residues. We also develop a statistical and chemical based protocol to assess the positions of the water molecules directly from the cryo-EM map. In addition, we have introduced a B' factor equivalent to the conventional B factor traditionally used by crystallography to annotate the atomic resolution model for determined structures. Our findings will be of immense interest among protein and medicinal scientists engaging in both basic and translational research.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.19.256982v1?rss=1

Authors: Sato, K., Mano, T., Toda, T., Iwata, A.

Abstract:

Objective: We aim to propose a novel method of evaluating the degree of rhythmic irregularity during repetitive tasks in Parkinsons disease (PD) by using autocorrelation to extract serial perturbation in the periodicity of body part movements as recorded by objective devices. Methods: We used publicly distributed sequential joint movement data recorded during a leg agility task or pronation-supination task. The sequences of body part trajectory were processed to extract their short-time autocorrelation (STACF) matrices; the sequences of single task conducted by participants were then divided into two clusters according to their similarity in terms of their STACF representation. The Unified Parkinsons Disease Rating Scale sub-score rated for each task was compared with cluster membership to obtain the area under the curve (AUC) to evaluate the discrimination performance of the clustering. We compared the AUC with those obtained from the clustering of the raw sequence or short-time Fourier transform (STFT). Results: In classifying the pose estimator-based trajectory data of the knee during the leg agility task, the AUC was the highest when the STACF sequence was used for clustering instead of other types of sequences with up to 0.815, being comparable to the results reported in the original analysis of the data using an approach different from ours. In addition, in classifying another dataset of accelerometer-based trajectory data of the wrist during a pronation-supination task, the AUC was again highest up to 0.785 when clustering was performed using the STACF rather than other types of sequence. Conclusion: Our autocorrelation-based method achieved a fair performance in detecting sequences with irregular rhythm, suggesting that it might be used as another evaluation strategy that is potentially widely applicable to qualify the disordered rhythm of PD regardless of the kinds of task or the modality of devices, although further refinement is needed.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.17.252478v1?rss=1

Authors: Moses, D., Yu, F., Ginell, G., Shamoon, N. M., Koenig, P. S., Holehouse, A. S., Sukenik, S.

Abstract:

Intrinsically disordered proteins and protein-regions (IDRs) make up roughly 30% of the human proteome and play vital roles in a wide variety of biological processes. Given a lack of persistent tertiary structure, all of the residues in an IDR are, to some extent, solvent exposed. This extensive surface area, coupled with the absence of strong intramolecular contacts, makes IDRs inherently sensitive to their chemical environment. Despite this sensitivity, our understanding of how IDR structural ensembles are influenced by changes in their chemical environment is limited. This is particularly relevant given a growing body of evidence showing that IDR function is linked to the underlying structural ensemble. We develop and use a combined experimental, computational, and analytical framework for high-throughput characterization of IDR sensitivity we call solution space scanning. Our framework reveals that IDRs show sequence-dependent sensitivity to solution chemistry, with complex behavior that can be interpreted through relatively simple polymer models. Our results imply that solution-responsive IDRs are ubiquitous and can provide an additional layer of biological regulation.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.18.255299v1?rss=1

Authors: Prakashchand, D. D., Mondal, J.

Abstract:

Apolipoprotein E ( ApoE) is a major determinant protein of lipid-metabolism and actively participates in lipid transport in plasma and central nervous system. As a part of its lipid-transport activity, low-density-lipid receptor (LDLR) needs to recognise apoE as a ligand. But, all prior evidences point to the fact that the recognition of apoE by LDLR only takes place in presence of lipid molecules which are assumed to play an important role in conformationally activating apoE upon binding. However, the molecular mechanism underlying the complexation process of apoE with lipid molecules and associated lipid-induced conformational change of apoE are currently elusive. Here we capture the spontaneous complexation process of monomeric apoE3 and phospholipid molecules by employing molecular dynamics simulation at multiple resolution. In particular, our multi scale simulations demonstrate a large-scale conformational change of the full-length apoE3, triggered by two-stage apoE-lipid complexation process. At first stage, lipid molecules assemble close to C-terminal domain of the protein and induce a rapid separation of C-terminal domain of monomeric apoE3 from rest of its tertiary fold. In the second and final stage, long-time scale simulation captures a slow on-the-fly lipid-induced inter-helix separation process in N-terminal domain of the protein. The resultant equilibrated complex, as obtained in the current work resembles an `open conformation' of lipid-stabilised apoE, previously hypothesised based on small-angle X-ray scattering experiments. Taken together, the simulations provide a molecular view of kinetic interplay of apoE and lipid complexation multi-stage process leading to conformational changes in protein, potentially making it conducive for recognising LDLR.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.18.253963v1?rss=1

Authors: Kudella, P. W., Tkachenko, A. V., Maslov, S., Braun, D.

Abstract:

The emergence of longer information-carrying and functional nucleotide polymers from random short strands was a major stepping stone at the dawn of life. But the formation of those polymers under temperature oscillation required some form of selection. A plausible mechanism is template-based ligation where theoretical work already suggested a reduction in information entropy. Here, we show how nontrivial sequence patterns emerge in a system of random 12mer DNA sequences subject to enzyme-based templated ligation reaction and temperature cycling. The strands acted both as a template and substrates of the reaction and thereby formed longer oligomers. The selection for templating sequences leads to the development of a multiscale ligation landscape. A position-dependent sequence pattern emerged with a segregation into mutually complementary pools of A-rich and T-rich sequences. Even without selection for function, the base pairing of DNA with ligation showed a dynamics resembling Darwinian evolution.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.17.255042v1?rss=1

Authors: Basu, A., Bobrovnikov, D. G., Qureshi, Z., Kayikcioglu, T., Ngo, T. T., Ranjan, A., Eustermann, S., Cieza, B., Hejna, M., Rube, T. H., Hopfner, K.-P., Wolberger, C., Song, J. S., Ha, T.

Abstract:

Mechanical deformations of DNA such as bending are ubiquitous and implicated in diverse cellular functions. However, the lack of high-throughput tools to directly measure the mechanical properties of DNA limits our understanding of whether and how DNA sequences modulate DNA mechanics and associated chromatin transactions genome-wide. We developed an assay called loop-seq to measure the intrinsic cyclizability of DNA, a proxy for DNA bendability, in high throughput. We measured the intrinsic cyclizabilities of 270,806 50 bp DNA fragments that span the entire length of S. cerevisiae chromosome V and other genomic regions, and also include random sequences. We discovered sequence-encoded regions of unusually low bendability upstream of Transcription Start Sites (TSSs). These regions disfavor the sharp DNA bending required for nucleosome formation and are co-centric with known Nucleosome Depleted Regions (NDRs). We show biochemically that low bendability of linker DNA located about 40 bp away from a nucleosome edge inhibits nucleosome sliding into the linker by the chromatin remodeler INO80. The observation explains how INO80 can create promoter-proximal nucleosomal arrays in the absence of any other factors by reading the DNA mechanical landscape. We show that chromosome wide, nucleosomes are characterized by high DNA bendability near dyads and low bendability near the linkers. This contrast increases for nucleosomes deeper into gene bodies, suggesting that DNA mechanics plays a previously unappreciated role in organizing nucleosomes far from the TSS, where nucleosome remodelers predominate. Importantly, random substitution of synonymous codons does not preserve this contrast, suggesting that the evolution of codon choice has been impacted by selective pressure to preserve sequence-encoded mechanical modulations along genes. We also provide evidence that transcription through the TSS-proximal nucleosomes is impacted by local DNA mechanics. Overall, this first genome-scale map of DNA mechanics hints at a mechanical code with broad functional implications.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.17.254508v1?rss=1

Authors: Yang, X., Wang, B., Hoop, C. L., Williams, J. K., Baum, J.

Abstract:

Amyloid fibril formation of -synuclein (S) is associated with multiple neurodegenerative diseases, including Parkinson's Disease (PD). Growing evidence suggests that progression of PD is linked to cell-to-cell propagation of S fibrils, which leads to templated seeding of endogenous intrinsically disordered monomer. A molecular understanding of the seeding mechanism and driving interactions is crucial to inhibit progression of amyloid formation. Here, using relaxation-based solution NMR experiments designed to probe large complexes, we identify weak interactions of intrinsically disordered acetylated-S (Ac-S) monomers with seeding-competent Ac-S fibrils and seeding-incompetent off-pathway oligomers to elucidate amyloid promoting interactions at the atomic level. We identify a binding interface in the first 11 residues of the N-terminus that interacts with both fibrils and off-pathway oligomers, under conditions that favor fibril elongation. This common N-terminal hotspot is supported by suppression of seeded amyloid formation by oligomers, as observed through thioflavin-T fluorescence experiments, suggesting competing monomer interactions. This highlights that an amyloid-incompetent species of S itself can act as an auto-inhibitor against S fibril elongation. The similarity between the fibril and oligomer structures lies in their intrinsically disordered termini. Thus, we propose that the monomer-aggregate interactions occur between the intrinsically disordered monomer N-terminus and the intrinsically disordered regions (IDRs) of the fibril/oligomers. Taken together, we propose a novel Ac-S seeding mechanism that is driven by the recruitment of intrinsically disordered monomers by the fibril IDRs, highlighting the potential of the terminal IDRs of the fibril rather than the structured core, as new therapeutic targets against seeded amyloid formation.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.18.256024v1?rss=1

Authors: Kümmerer, F., Orioli, S., Harding-Larsen, D., Hoffmann, F., Gavrilov, Y., Teilum, K., Lindorff-Larsen, K.

Abstract:

Proteins display a wealth of dynamical motions that can be probed using both experiments and simulations. We present an approach to integrate side chain NMR relaxation measurements with molecular dynamics simulations to study the structure and dynamics of these motions. The approach, which we term ABSURDer (Average Block Selection Using Relaxation Data with Entropy Restraints) can be used to find a set of trajectories that are in agreement with relaxation measurements. We apply the method to deuterium relaxation measurements in T4 lysozyme, and show how it can be used to integrate the accuracy of the NMR measurements with the molecular models of protein dynamics afforded by the simulations. We show how fitting of dynamic quantities leads to improved agreement with static properties, and highlight areas needed for further improvements of the approach.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.18.256065v1?rss=1

Authors: Pedebos, C., Verli, H.

Abstract:

Oligosaccharyltransferases (OSTs) are enzymes that catalyze the transfer of a glycan chain to an acceptor protein. Their structure is composed by a transmembrane domain and a periplasmic / C-terminal domain, which can be divided into structural units. The Archaeoglobus fulgidus OST, AfAglB, has unique structural units with unknown functions. Here, we evaluate the stability role proposed for AfAglB units by employing molecular modelling and molecular dynamics simulations, to examine the effect of single and double deletions in the enzyme structure. Our results show a strong effect on the dynamics of the C-terminal domain for the mutated systems with increased fluctuations near the deleted areas. Conformational profile and stability are deeply affected, mainly in the double unit deletion, modifying the enzyme behavior and binding interfaces. Coordination at the catalytic site was not disrupted, indicating that the mutated enzymes could retain activity at some level. Hotspots of variation were identified and rationalized with previous data. Our data shows that structural units may provide stabilization interactions, contributing for integrity of the wild-type enzyme at high temperatures. By correlating our findings to structural units mutagenesis experimental data available, it was observed that structural units deletion can interfere with OSTs stability and dynamics but it is not directly related to catalysis. Instead, they may influence the OST structural integrity, and, potentially, thermostability. This work offers a basis for future experiments involving OSTs structural and functional characterization, as well as for protein engineering.

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