PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.02.324087v1?rss=1

Authors: Ferrell, J. B., Remington, J. M., Van Oort, C. M., Sharafi, M., Aboushousha, R., Janssen-Heininger, Y., Schneebeli, S. T., Wargo, M. J., Wshah, S., Li, J.

Abstract:

Antimicrobial peptides (AMPs) are peptides with promising applications for healthcare, veterinary, and agriculture industries. Despite prior success in AMP design using physics- or knowledge-based approaches, there is still a critical need to create new methodologies to design peptides with a low false positive rate and high AMP activity and selectivity. Toward this goal, we invented a cost-effective approach which utilizes a generative model to produce AMP-like sequences and molecular simulations to select peptides based on their structures and interactions. For a proof of concept, we curated a dataset that comprises 500,000 non-AMP peptide sequences and 8,000 labeled AMP sequences to train the generative model, which generated novel and diverse AMP candidates to potentially target a wide variety of microbes. Following a screening process to select peptides that are cationic and likely helical, we assessed 12 candidates by simulating their membrane-binding tendency to a lipid bilayer model. With the umbrella sampling technique, we determined the free energy change during transfer from the solution to the membrane environments for each peptide. Accordingly, we selected the six peptides with the best membrane-binding tendency, synthesized them, and characterized through spectroscopies and biological assays. Three novel peptides were validated with activity to inhibit bacterial growth. In aggregate, the combination of AMP generator and molecular simulations afford an enhanced accuracy in AMP design. Towards future precision AMP design, our methodology and results demonstrate the viability to design novel AMP-like peptides to target selected pathogens and mechanisms.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.02.323782v1?rss=1

Authors: Snoberger, A., Barua, B., Atherton, J. L., Shuman, H., Forgacs, E., Goldman, Y. E., Winkelmann, D. A., Ostap, E. M.

Abstract:

Hypertrophic cardiomyopathies (HCMs) are the leading cause of acute cardiac failure in young individuals. Over 300 mutations throughout {beta}-cardiac myosin, including in the motor domain, are associated with HCM. A {beta}-cardiac myosin motor mutation (R712L) leads to a severe form of HCM. Actin-gliding motility of R712L-myosin is inhibited, despite near normal ATPase kinetics. By optical trapping, the working stroke of R712L-myosin was decreased 4-fold, but actin-attachment durations were normal. A prevalent hypothesis that HCM mutants are hypercontractile is thus not universal. R712 is adjacent to the binding site of the heart failure drug omecamtiv mecarbil (OM). OM suppresses the working stroke of normal {beta}-cardiac myosin, but remarkably, OM rescues the R712L-myosin working stroke. Using a flow chamber to interrogate a single molecule during buffer exchange, we found OM rescue to be reversible. Thus, the R712L mutation uncouples lever arm rotation from ATPase activity and this inhibition is rescued by OM.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.02.323915v1?rss=1

Authors: Yu, A., Pak, A. J., He, P., Monje-Galvan, V., Casalino, L., Gaieb, Z., Dommer, A. C., Amaro, R. E., Voth, G. A.

Abstract:

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Computer simulations of complete viral particles can provide theoretical insights into large-scale viral processes including assembly, budding, egress, entry, and fusion. Detailed atomistic simulations, however, are constrained to shorter timescales and require billion-atom simulations for these processes. Here, we report the current status and on-going development of a largely bottom-up coarse-grained (CG) model of the SARS-CoV-2 virion. Structural data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. We describe how CG molecular interactions can be derived from all-atom simulations, how viral behavior difficult to capture in atomistic simulations can be incorporated into the CG models, and how the CG models can be iteratively improved as new data becomes publicly available. Our initial CG model and the detailed methods presented are intended to serve as a resource for researchers working on COVID-19 who are interested in performing multiscale simulations of the SARS-CoV-2 virion.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.29.318543v1?rss=1

Authors: Croll, T. I., Read, R. J.

Abstract:

When building atomic models into weak and/or low-resolution density, a common strategy is to restrain its conformation to that of a higher-resolution model of the same or similar sequence. When doing so, it is important to avoid over-restraining to the reference model in the face of disagreement with the experimental data. The most common strategy for this is the use of "top-out" potentials. These act like simple harmonic restraints within a defined range, but gradually weaken when the deviation between the model and reference grows larger than a defined transition point. In each current implementation, the rate at which the potential flattens beyond the transition region follows a fixed form - although the form chosen varies between implementations. A restraint potential with a tuneable rate of flattening would provide greater flexibility to encode the confidence in any given restraint. Here we describe two new such potentials: a Cartesian distance restraint derived from a recent generalisation of common loss functions, and a periodic torsion restraint based on a renormalisation of the von Mises distribution. Further, we describe their implementation as user-adjustable/switchable restraints in ISOLDE, and demonstrate their use in some real-world examples.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.29.318840v1?rss=1

Authors: Wilhelm, M. J., Sharifian Gh., M., Chang, C.-M., Wu, T., Li, Y., Ma, J., Dai, H.-L.

Abstract:

Bacterial surface charge is a critical characteristic of the cell's interfacial physiology that influences how the cell interacts with the local environment. A direct, sensitive, and accurate experimental technique capable of quantifying bacterial surface charge is needed to better understand molecular adaptations in interfacial physiology in response to environmental changes. We introduce here the method of second harmonic light scattering (SHS) which is capable of detecting the number of molecular ions adsorbed as counter charges on the exterior bacterial surface, thereby providing a measure of the surface charge. In this first demonstration, we detect the small molecular cation, malachite green, electrostatically adsorbed on the surface of representative strains of Gram-positive and Gram-negative bacteria. Surprisingly, the SHS deduced molecular transport rates through the different cellular ultra-structures are revealed to be nearly identical. However, the adsorption saturation densities on the exterior surfaces of the two bacteria were shown to be characteristically distinct. The negative charge density of the lipopolysaccharide coated outer surface of Gram-negative E. coli (8.7{+/-}1.7 nm-2) was deduced to be seven times larger than that of the protein surface layer of Gram-positive L. rhamnosus (1.2{+/-}0.2 nm-2). The feasibility of SHS deduced bacterial surface charge density for Gram-type differentiation is presented.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.30.321232v1?rss=1

Authors: Rieu, M., Valle-Orero, J., Ducos, B., Allemand, J.-F., Croquette, V.

Abstract:

Fluorescence-free micro-manipulation of nucleic acids (NA) allows the functional characterization of DNA/RNA processing proteins, without the interference of labels, but currently fails to detect and quantify their binding. To overcome this limitation, we developed a new method based on single-molecule force spectroscopy, called kinetic locking, that allows a direct in vitro visualization of protein binding while avoiding any kind of chemical disturbance of the protein's natural function. We validate kinetic locking by measuring accurately the hybridization energy of ultrashort nucleotides (5,6,7 bases) and use it to measure the dynamical interactions of E. coli RecQ helicase with its DNA substrate.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.10.01.321992v1?rss=1

Authors: Okan, O. B., Turgut, D., Atilgan, C., Atilgan, A. R., Ozisik, R.

Abstract:

A direct way to spot structural features that are universally shared among proteins is to find proper analogues from simpler condensed matter systems. In most cases, sphere-packing arguments provide a straightforward route for structural comparison, as they successfully characterize a wide array of materials such as close packed crystals, dense liquids, and structural glasses. In the current study, the feasibility of creating ensembles of artificial structures that can automatically reproduce a large number of geometrical and topological descriptors of globular proteins is investigated. Towards this aim, a simple cubic (SC) arrangement is shown to provide the best background lattice after a careful analysis of the residue packing trends from 210 proteins. It is shown that a minimalistic set of ground rules imposed on this lattice is sufficient to generate structures that can mimic real proteins. In the proposed method, 210 such structures are generated by randomly removing residues (beads) from clusters that have a SC lattice arrangement until a predetermined residue concentration is achieved. All generated structures are checked for residue connectivity such that a path exists between any two residues. Two additional sets are prepared from the initial structures via random relaxation and a reverse Monte Carlo simulated annealing (RMC-SA) algorithm , which targets the average radial distribution function (RDF) of 210 globular proteins. The initial and relaxed structures are compared to real proteins via RDF, bond orientational order parameters, and several descriptors of network topology. Based on these features, results indicate that the structures generated with 40% occupancy via the proposed method closely resemble real residue networks. The broad correspondence established this way indicates a non-superficial link between the residue networks and the defect laden cubic crystalline order. The presented approach of identifying a minimalistic set of operations performed on a target lattice such that each resulting cluster possess structural characteristics largely indistinguishable from that of a coarse-grained globular protein opens up new venues in structural characterization, native state recognition, and rational design of proteins.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.30.320457v1?rss=1

Authors: Buch, M. H. C., Heymann, J. B., Newcomb, W. W., Winkler, D. C., Steven, A. C.

Abstract:

Herpes simplex virus type 1 (HSV-1) packages its genome via the portal protein, pUL6, a dodecameric ring at one of the capsids twelve vertices. While the portal has been visualized in mature capsids, we aimed to describe it in procapsids to elucidate its role in assembly and maturation. Using cryo-electron tomography, we compared procapsids and empty mature capsids (A-capsids) by subtomogram averaging. The portal is located on the interior surface with its narrower end facing outwards in contact with the capsid shell. The portal is embedded in the underlying scaffold, consistent with assembly initiating on a portal-scaffold complex. Maturation involves angularization of the capsid shell, with an accompanying outward movement of the vertices. In A-capsids, the portal translocates further than the surrounding capsomers, enhancing and presumably strengthening its contacts with the capsid shell. We also found a density overlying and offset from the portal vertex corresponding to the expected location of the terminase, the DNA packaging motor.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.30.319814v1?rss=1

Authors: Ham, L., Jackson, M., Stumpf, M. P. H.

Abstract:

Single-cell expression profiling is destructive, giving rise to only static snapshots of cellular states. This loss of temporal information presents significant challenges in inferring dynamics from population data. Here we provide a formal analysis of the extent to which dynamic variability from within individual systems ("intrinsic noise") is distinguishable from variability across the population ("extrinsic noise"). Our results mathematically formalise observations that it is impossible to identify these sources of variability from the transcript abundance distribution alone. Notably, we find that systems subject to population variation invariably inflate the apparent degree of burstiness of the underlying process. Such identifiability problems can be remedied by the dual-reporter method, which separates the total gene expression noise into intrinsic and extrinsic contributions. This noise decomposition, however, requires strictly independent and identical gene reporters integrated into the same cell, which can be difficult to implement experimentally in many systems. Here we demonstrate mathematically that, in some cases, the same noise decomposition can be achieved at the transcriptional level with non-identical and not-necessarily independent reporters. We use our result to show that generic reporters lying in the same biochemical pathways (e.g. mRNA and protein) can replace dual reporters, enabling the noise decomposition to be obtained from only a single gene. Stochastic simulations are used to support our theory, and show that our "pathway-reporter" method compares favourably to the dual-reporter method.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.29.315671v1?rss=1

Authors: Marin, Z., Graff, M., Barentine, A. E. S., Soeller, C., Chung, K. K. H., Fuentes, L. A., Baddeley, D.

Abstract:

Localization-based super-resolution microscopy techniques such as PALM, STORM, and PAINT are an increasingly critical tool for biological discovery. These methods generate lists of single fluorophore positions that capture nanoscale structural details of subcellular organisation, but to develop biological insight, we must post-process and visualize this data in a meaningful way. A large number of algorithms have been developed for localization post-processing, transforming point data into representations which approximate traditional microscopy images, and performing specific quantitative analysis directly on points. Implementations of these algorithms typically stand in isolation, necessitating complex workflows involving multiple different software packages. Here we present PYMEVisualize, an open-source tool for the interactive exploration and analysis of 3D, multicolor, single-molecule localization data. PYMEVisualize brings together a broad range of the most commonly used post-processing, density mapping, and direct quantification tools in an easy-to-use and extensible package. This software is one component of the PYthon Microscopy Environment (python-microscopy.org), an integrated application suite for light microscopy acquisition, data storage, visualization, and analysis built on top of the scientific Python environment

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