PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.22.262931v1?rss=1

Authors: Wayment-Steele, H. K., Kim, D. S., Choe, C. A., Nicol, J. J., Wellington-Oguri, R., Parra Sparberg, R. A., Huang, P., Eterna Massive Open Laboratory,, Das, R.

Abstract:

RNA hydrolysis presents problems in manufacturing, long-term storage, world-wide delivery, and in vivo stability of messenger RNA (mRNA)-based vaccines and therapeutics. A largely unexplored strategy to reduce mRNA hydrolysis is to redesign RNAs to form double-stranded regions, which are protected from in-line cleavage and enzymatic degradation, while coding for the same proteins. The amount of stabilization that this strategy can deliver and the most effective algorithmic approach to achieve stabilization remain poorly understood. Motivated by the need for stabilized COVID-19 mRNA vaccines, we present simple calculations for estimating RNA stability against hydrolysis, and a model that links the average unpaired probability of an mRNA, or AUP, to its overall rate of hydrolysis. To characterize the stabilization achievable through structure design, we compare optimization of AUP by conventional mRNA design methods to results from the LinearDesign algorithm, a new Monte Carlo tree search algorithm called RiboTree, and crowdsourcing through the OpenVaccine challenge on the Eterna platform. Tests were carried out on mRNAs encoding nanoluciferase, green fluorescent protein, and COVID-19 mRNA vaccine candidates encoding SARS-CoV-2 epitopes, spike receptor binding domain, and full-length spike protein. We find that Eterna and RiboTree significantly lower AUP while maintaining a large diversity of sequence and structure features that correlate with translation, biophysical size, and immunogenicity. Our results suggest that increases in in vitro mRNA half-life by at least two-fold are immediately achievable and that further stability improvements may be enabled with thorough experimental characterization of RNA hydrolysis.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.22.262352v1?rss=1

Authors: Basu, A., Bobrovnikov, D. G., Cieza, B., Qureshi, Z., Ha, T.

Abstract:

Sequence features have long been known to influence the local mechanical properties and shapes of DNA. However, a mechanical code (i.e. a comprehensive mapping between DNA sequence and mechanical properties), if it exists, has been difficult to experimentally determine because direct means of measuring the mechanical properties of DNA are typically limited in throughput. Here we use Loop-seq - a recently developed technique to measure the intrinsic cyclizabilities (a proxy for bendability) of DNA fragments in genomic-scale throughput - to characterize the mechanical code. We tabulate how DNA sequence features (distribution patterns of all possible dinucleotides and dinucleotide pairs) influence intrinsic cyclizability, and build a linear model to predict intrinsic cyclizability from sequence. Using our model, we predict that DNA mechanical landscape shapes nucleosome organization around the promoters of various organisms and at the binding site of the transcription factor CTCF, and that hyperperiodic DNA in C. elegans leads to globally curved DNA segments. By performing loop-seq on random libraries in the presence or absence of CpG methylation, we show that CpG methylation leads to global stiffening of DNA in a wide sequence context, and predict based on our model that CpG methylation widely changes the mechanical landscape around mouse promoters. It suggests how epigenetic modifications of DNA might alter gene expression and mediate cellular adaptation by affecting critical processes around promoters that require mechanical deformations of DNA, such as nucleosome organization and transcription initiation. Finally, we show that the genetic code and the mechanical code are linked: sequence-dependent mechanical properties of coding DNA constrains the amino acid sequence despite the degeneracy in the genetic code. Our measurements explain why the pattern of nucleosome organization along genes influences the distribution of amino acids in the translated polypeptide.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.21.262139v1?rss=1

Authors: Li, R., Chen, H., Choi, J. H.

Abstract:

Architectured materials exhibit negative Poisson's ratios and possess enhanced mechanical properties compared with regular materials. Their auxetic behaviors emerge from periodic cellular structures rather than chemistry. The majority of such metamaterials are constructed by top-down approaches and macroscopic with unit cells of microns or larger. On the other extreme, there are molecular-scale auxetics including naturally-occurring crystals which are not designable. There is a gap from few nanometers to microns, which may be filled by bottom-up biomolecular self-assembly. Here we demonstrate two-dimensional (2D) auxetic nanostructures using DNA origami. Structural deformation experiments are performed by strand displacement and complemented by mechanical deformation studies using coarse-grained molecular dynamics (MD) simulations. We find that the auxetic properties of DNA nanostructures are mostly defined by geometrical designs, yet materials' chemistry also plays a role. From elasticity theory, we introduce a set of design principles for auxetic DNA materials which should be useful for diverse applications.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.24.265553v1?rss=1

Authors: Currell, F., Villagomez Bernabe, B., Chan, S.-w., Roseman, A., Coulter, J.

Abstract:

Here we show an interplay between the structures present in ionization tracks and nucleocapsid RNA structural biology, using fast ion beam inactivation of the severe acute respiratory syndrome coronavirus (SARS-CoV) virion as an example. This interplay is one of the key factors in predicting dose-inactivation curves for high energy ion beam inactivation of virions. We also investigate the adaptation of well-established cross-section data derived from radiation interactions with water to the interactions involving the components of a virion, going beyond the density-scaling approximation developed previously. We conclude that solving one of the grand challenges of structural biology - the determination of RNA tertiary/quaternary structure structure - is intimately linked to predicting ion-beam inactivation of viruses and that the two problems can be mutually informative. Indeed, our simulations show that fast ion beams have a key role to play in elucidating RNA tertiary/quaternary structure.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.24.265165v1?rss=1

Authors: Busath, D. D., McGuire, K. L., Ess, D. H., Smit, P., Harrison, R. G., Hill, J. T.

Abstract:

Copper(II) is known to bind in the influenza virus His37 cluster in the homotetrameric M2 proton channel and block the proton current needed for uncoating. Copper complexes based on iminodiacetate also block the M2 proton channel and show reduced cytotoxicity and zebrafish-embryo toxicity. In voltage-clamp oocyte studies using the ubiquitous amantadine-insensitive M2 S31N variant, the current block showed fast and slow phases in contrast to the single phase found for amantadine block of WT M2. Here we evaluate the mechanism of block by copper adamantyl iminodiacitate (Cu(AMT-IDA)) and copper cyclooctyl iminodiacitate (Cu(CO-IDA)) complexes and address whether the complexes can covalently bind to one or more of the His37 imidazoles. The current traces were fitted to parametrized master equations. The energetics of binding and the rate constants suggest that the first step is copper-complex binding within the channel and the slow step in the current block is the covalent bond formation between copper complex and histidine. Isothermal titration calorimetry (ITC) indicates that a single imidazole binds strongly to the copper complexes. Structural optimization using density functional theory (DFT) reveals that the complexes fit inside the channel and project the Cu(II) towards the His37 cluster allowing one imidazole to form a covalent bond with the Cu(II). Electrophysiology and DFT studies also show that the complexes block the G34E amantadine-resistant mutant in spite of some crowding in the binding site by the glutamates.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.24.264465v1?rss=1

Authors: Caruso, I. P., Sanches, K., Da Poian, A., Pinheiro, A., Almeida, F. C. L.

Abstract:

The N protein of betacoronaviruses is responsible for nucleocapsid assembly and other essential regulatory functions. Its N-terminal domain (NTD) interacts and melts the double-stranded transcriptional regulatory sequences (dsTRS), regulating the discontinuous subgenome transcription process. Here, we used molecular dynamics (MD) simulations to study the binding of SARS-CoV-2 N-NTD to non-specific (NS) and TRS dsRNAs. We probed dsRNAs' Watson and Crick (WC) base-pairing over 25 replicas of 100 ns MD simulations, showing that only one N-NTD of dimeric N is enough to destabilize dsRNAs, initiating melting. N-NTD dsRNA destabilizing activity was more efficient for dsTRS than dsNS. N-NTD dynamics, especially a tweezer-like motion of {beta}2-{beta}3 and 2-{beta}5 loops, played a key role in WC base-pairing destabilization. Based on experimental information available in the literature, we constructed kinetics models for N-NTD-mediated dsRNA melting. Our results support a 1:1 stoichiometry (N-NTD:dsRNA), matching MD simulations and raising different possibilities for N-NTD action: (i) two N-NTDs of dimeric N would act independently, increasing efficiency; (ii) two N-NTDs of dimeric N would bind to two different RNA sites, bridging distant regions of the genome; and (iii) monomeric N would be active, opening up the possibility of a regulatory dissociation event.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.24.264663v1?rss=1

Authors: Bu, B., Tian, Z., Li, D., Zhang, K., Ji, B., Diao, J.

Abstract:

Membrane fusion mediated by Soluble N-ethylmaleimide-sensitive factor activating protein receptor (SNARE) proteins is an important cellular process. For neuronal SNAREs, the single transmembrane domain has been proposed to pass zippering energy to membranes for inducing fast fusion. In contrast, the SNARE protein, syntaxin 17, for membrane fusion involved in autophagosome maturation contains an unusual V-shape double-transmembrane domain that may influence its capability to pass energy. Here, we showed that this double-transmembrane domain significantly reduces fusion with an in vitro reconstitution system. Through theoretic modelling, we found that this V-shape double-transmembrane domain increases lipid-protein mismatch, which reduces the energy transduction for fusion. Moreover, our model also revealed the involvement of 2-3 SNAREs in a general fusion process.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.24.264952v1?rss=1

Authors: Hu, M., Zhang, Q., Lin, H.

Abstract:

Electron cryo-microscopy (cryoEM) three-dimensional (3D) reconstruction is based on estimations of orientations of projection images or 3D volumes. It is common that the macromolecules studied by cryoEM have molecular symmetry. However, for neither spatial rotations nor projection directions, cur- rently there is no statistics and classification method which takes molecular symmetry into consideration. This limits the applications of advanced statistical methods in cryoEM. In this research, based on the concept of non-unique-games (NUG), we propose statistics and classification methods of both spatial rotations and projection directions when molecular symmetry is considered. Such methods are realized in the open-source python package pySymStat.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.24.264150v1?rss=1

Authors: Rosenbauer, J., Berghoff, M., Schug, A.

Abstract:

Despite decades of substantial research, cancer remains a ubiquitous scourge in the industrialized world. Effective treatments require a thorough understanding of macroscopic cancerous tumor growth out of individual cells. Clinical imaging methods, however, only detect late-stage macroscopic tumors, while many quantitative experiments focus on small clusters of cancerous cells in microscopic detail but struggle to grow full tumors in-vitro. Here, we introduce the critical scale-bridging link between both these scopes. We are able to simulate the growth of mm-sized tumors composed of 1.5 million m-resolved individual cells by employing highly parallelized code on a supercomputer. We observe the competition for resources and space, which can lead to hypoxic or necrotic tissue regions. Cellular mutations and tumor stem cells can lead to tissue heterogeneity and change tumor properties. We probe the effects of different chemotherapy and radiotherapy treatments and observe selective pressure. This improved theoretical understanding of cancer growth as emerging behavior from single-cells opens new avenues for various scientific fields, ranging from developing better early-stage cancer detection devices to testing treatment regimes in-silico for personalized medicine.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.22.262667v1?rss=1

Authors: Zacharias, M.

Abstract:

Double-strand (ds)DNA formation and dissociation are of fundamental biological importance. The negatively DNA charge influences the dsDNA stability. However, the base pairing and the stacking between neighboring bases are responsible for the sequence dependent stability of dsDNA. The stability of a dsDNA molecule can be estimated from empirical nearest-neighbor models based on contributions assigned to base pair steps along the DNA and additional parameters due to DNA termini. In efforts to separate contributions it has been concluded that base-stacking dominates dsDNA stability whereas base-pairing contributes negligibly. Using a different model for dsDNA formation we re-analyze dsDNA stability contributions and conclude that base stacking contributes already at the level of separate ssDNAs but that pairing contributions drive the dsDNA formation. The theoretical model also predicts that stability contributions of base pair steps that contain only guanine/cytosine, mixed steps and steps with only adenine/thymine follows the order 6:5:4, respectively, as expected based on the formed hydrogen bonds. The model is fully consistent with available stacking data and nearest-neighbor dsDNA parameters. It allows to assign a narrowly distributed value for the effective free energy contribution per formed hydrogen bond during dsDNA formation of -0.72 kcal/mol based entirely on experimental data.

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