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bioRxiv2020

Molecular structure of a prevalent amyloid-β fibril polymorph from Alzheimer's disease brain tissue

Amyloid-{beta} (A{beta}) fibrils exhibit self-propagating, molecular-level polymorphisms that may underlie variations in clinical and pathological characteristics of Alzheimers disease. We report the molecular structure of a specific brain-derived polymorph that has been identified as the most prevalent polymorph of 40-residue A{beta} fibrils in cortical tissue of Alzheimers disease patients. This structure, developed from cryo-electron microscopy and supported by solid state NMR data, differs qualitatively from all previously described A{beta} fibril structures, both in its molecular conformation and its organization of cross-{beta} subunits. Knowledge of this brain-derived fibril structure may contribute to the development of structure-specific amyloid imaging agents and aggregation inhibitors with greater diagnostic and therapeutic utility.

biophysics↗

bioRxiv2020

Kinetics of charged polymer collapse: effects of additional salt

Extensive molecular dynamics simulations, using simple charged polymer models, have been employed to probe the kinetics and dynamics of early-stage collapse of charged polymers and the effect of additional monovalent salt on such kinetics. The exponents characterizing the coarsening dynamics during such early-collapse stage via finite size scaling for the case of charged polymers are found to be different from the neutral polymers, suggesting that the collapse kinetics of charged polymers are inherently different from that neutral polymers. The kinetics of coarsening of the clusters along the collapsed trajectory also depends significantly on the counterion valency and for higher valency counterions, multiple regimes are observed and unlike the neutral polymer case, the collapse kinetics are a function of charge density along the charged polymer. Inclusion of additional salt affects the kinetics and conformational landscape along the collapse trajectory. Addition of salt increases the value of critical charge density required to initiate collapse for all the counterion valencies, though the effect is more pronounced for monovalent counterion systems. The addition of salt significantly affects the collapse trajectory in the presence of trivalent counterions via promotion of transient long-distance loop structures inducing a parallel and hierarchical local collapsed conformation leading to faster global collapsed states. This may play a role in understanding the fast folding rates of biopolymers such as proteins and RNA from extended state to a collapsed state in the presence of multivalent counterions before reorganizing into a native fold.

biophysics↗

bioRxiv2020

Characterization of fluorescent proteins with intramolecular photostabilization

Genetically encodable fluorescent proteins have revolutionized biological imaging in vivo and in vitro. Since there are no other natural fluorescent tags with comparable features, the impact of fluorescent proteins for biological research cannot be overemphasized. Despite their importance, their photophysical properties, i.e., brightness, count-rate and photostability, are relatively poor compared to synthetic organic fluorophores or quantum dots. Intramolecular photostabilizers were recently rediscovered as an effective approach to improve photophysical properties. The approach uses direct conjugation of photostablizing compounds such as triplet-state quenchers or redox-active substances to an organic fluorophore, thereby creating high local concentrations of photostabilizer. Here, we introduce an experimental strategy to screen for the effects of covalently-linked photostabilizers on fluorescent proteins. We recombinantly produced a double cysteine mutant (A206C/L221C) of -GFP for attachment of photostabilizer-maleimides on the {beta}-barrel in close proximity to the chromophore. Whereas labelling with photostabilizers such as Trolox, Nitrophenyl, and Cyclooctatetraene, which are often used for organic fluorophores, had no effect on -GFP-photostability, a substantial increase of photostability was found upon conjugation of -GFP to an azobenzene derivative. Although the mechanism of the photostabilizing effects remains to be elucidated, we speculate that the higher triplet-energy of azobenzene might be crucial for triplet-quenching of fluorophores in the near-UV and blue spectral range. Our study paves the way towards the development and design of a second generation of fluorescent proteins with photostabilizers placed directly in the protein barrel by methods such as unnatural amino acid incorporation.

biophysics↗

bioRxiv2020

Structural basis for targeting human cancer antigen STEAP1 with antibodies

Six-transmembrane epithelial antigen of the prostate (STEAP1) is an integral membrane protein that is highly upregulated on the cell surface of several human cancers, making it a promising therapeutic target. It shares sequence homology with three enzymes (STEAP2-4) that catalyze the NADPH-dependent reduction of iron(III). However, STEAP1 lacks an intracellular NADPH-binding domain and does not exhibit cellular ferric-reductase activity. Thus, both the molecular function of STEAP1 and its role in cancer progression remain elusive. Here, we present a ~3.0 [A] cryo-electron microscopy structure of trimeric human STEAP1 bound to three Fab-fragments of the clinically employed antibody mAb120.545. STEAP1 adopts a reductase-like conformation and interacts with the Fabs through its extracellular helices. Enzymatic assays in human cells reveal that STEAP1 promotes iron(III) reduction when fused to the intracellular NADPH-binding domain of its family member STEAP4, implicating STEAP1 as a functional ferric reductase in STEAP hetero-trimers. Our work provides a foundation for deciphering the molecular mechanisms of STEAP1 and will be instrumental in the design of new therapeutic strategies to target STEAP1 in cancer.

biophysics↗

bioRxiv2020

Protein induced membrane phase transition facilitates leishmania infection

Although host membrane is known to play critical roles in the internalization of leishmania parasites inside macrophages (M{phi}), any detailed mechanistic understanding is missing. We show here that KMP-11, a small immunogenic protein of Leishmania Donovani (LD) facilitates the infection process by binding to M{phi} membrane through its N-terminal domain (1-19AA). This binding results in a membrane phase transition that occurs at a threshold protein/lipid ratio, which is linked to the change in membrane tension. KMP-11 induced phase transition is also associated with lipid raft disruption and T-cell deactivation. Finally, using a combination of tryptophan-scanning mutagenesis and synthesized peptides, we develop a mathematical exposition, which demonstrates that hydrophobic moment (H) and the number of residues involved in a mirror sequence (N) at the interacting N-terminal are governing factors for the membrane phase transition, which facilitates infection process.

biophysics↗

bioRxiv2020

Fine-tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides

Determination of RNA structural-dynamic properties is challenging for experimental methods. Thus atomistic molecular dynamics (MD) simulations represent a helpful technique complementary to experiments. However, contemporary MD methods still suffer from limitations of force fields (ffs), including imbalances in the non-bonded ff terms. We have recently demonstrated that some improvement of state-of-the-art AMBER RNA ff can be achieved by adding a new term for H-bonding called gHBfix, which increases tuning flexibility and reduces the risk of side-effects. Still, the first gHBfix version did not fully correct simulations of short RNA tetranucleotides (TNs). TNs are key benchmark systems due to availability of unique NMR data, although giving too much weight on improving TN simulations can easily lead to over-fitting to A-form RNA. Here we combine the gHBfix version with another term called tHBfix, which separately treats H-bond interactions formed by terminal nucleotides. This allows to refine simulations of RNA TNs without affecting simulations of other RNAs. The approach is in line with adopted strategy of current RNA ffs, where the terminal nucleotides possess different parameters for the terminal atoms than the internal nucleotides. The combination of gHBfix with tHBfix significantly improves the behavior of RNA TNs during well-converged enhanced-sampling simulations. TNs mostly populate canonical A-form like states while spurious intercalated structures are largely suppressed. Still, simulations of r(AAAA) and r(UUUU) TNs show some residual discrepancies with the primary NMR data which suggests that future tuning of some other ff terms might be useful.

biophysics↗

bioRxiv2020

Human Mammary Cells in a Mature, Stratified Epithelial Layer Flatten and Stiffen Compared to Confluent and Single Cells

The epithelium forms a protective barrier against external biological, chemical and physical insults. So far, AFM-based, micro-mechanical measurements have only been performed on single cells and confluent cells, but not yet on cells in the physiologically relevant, mature epithelial layer. Using a combination of atomic force, fluorescence and confocal microscopy, we determined the changes in stiffness, morphology and actin distribution of human mammary epithelial cells (HMECs) as they transition from single cells to confluency to a mature epithelial layer. Single cells have a tall, round (planoconvex) morphology, have actin stress fibers at the base, have diffuse cortical actin, and have a stiffness of 1 kPa. Confluent cells become flatter, basal actin stress fibers start to disappear, and actin accumulates laterally where cells abut. Overall stiffness is still 1 kPa with two-fold higher stiffness in the abutting regions. Cells in an epithelial layer are flat on top and seven times stiffer (average, 7 kPa) than single and confluent cells. Epithelial layer cells show strong actin accumulation in the regions where cells adjoin and in the apical regions. Stiffness is significantly enhanced in the regions of adjoining cells, compared to the central regions of cells. Physiologically, this previously unrecognized, drastic stiffness increase may be important to the protective function of the epithelium.

biophysics↗

bioRxiv2020

Quantitating denaturation by formic acid: Imperfect repeats are essential to the stability of the functional amyloid protein FapC

Bacterial functional amyloids are evolutionarily optimized to aggregate to help them fulfil their biological functions, e.g. to provide mechanical stability to biofilm. Amyloid is formed in Pseudomonas sp. by the protein FapC which contains 3 imperfect repeats connected by long linkers. Stepwise removal of these repeats slows down aggregation and increases the propensity of amyloids to fragment during the fibrillation process, but how these mechanistic properties link to fibril stability is unclear. Here we address this question. The extreme robustness of functional amyloid makes them resistant to conventional chemical denaturants, but they dissolve in formic acid (FA) at high concentrations. To quantify this, we first measured the denaturing potency of FA using 3 small acid-resistant proteins (S6, lysozyme and ubiquitin). This revealed a linear relationship between [FA] and the free energy of unfolding with a slope of mFA, as well as a robust correlation between protein residue size and mFA. We then measured the solubilisation of fibrils formed from different FapC variants (with varying number of repeats) as a function of [FA]. The resulting mFA values revealed a decline in the number of residues driving amyloid formation when at least 2 repeats were deleted. The midpoint of denaturation declined monotonically with progressive removal of repeats and correlated with solubility in SDS. Complete removal of all repeats led to fibrils which were solubilized at FA concentrations 2-3 orders of magnitude lower than the repeat-containing variants, showing that at least one imperfect repeat is required for the stability of functional amyloid.

biophysics↗

bioRxiv2020

A Data-driven Surrogate Model for Work Computation of a Periodically Forced Half-Sarcomere

Muscle force generation follows from molecular scale interactions that drive macroscopic behaviors and macroscopic processes that influence those at the molecular scale. A particuarly challenging issue is that models at the molecular level of organization are often quite difficult to apply to larger spatial scales. This is particularly true of moleuclar models driven by Monte-Carlo simulations. This challenge of multiscale dynamics requires methods to extract reduced order behaviors from detailed high-dimensional simulations. In this work we present a novel deterministic simulation method yielding accurate predictions of force-length behaviors of contracting muscle sarcomeres undergoing periodic length changes (work loops). The model maintains interpretability by tracking macroscopic state variables throughout the simulation while using data-driven representations of dynamics. Parameters of the data-driven dynamics are learned from trajectories from Monte-Carlo simulations of a half-sarcomere. Our method significantly reduces computational cost by tracking the state of the sarcomere in a course grained set of variables while maintaining accurate prediction of macroscopic level observables and time series for course grained variables. This allows for rapid sampling of the models output and builds towards the ability to scale to multiple-sarcomere simulations. Author SummaryWe develop a data-driven surrogate model for the dynamics of the half-sarcomere. This model achieves the same behavior with respect to force traces as more sophisticated Monte Carlo models at a substantially lower computational cost. The model is built by finding a course grained description of the full state space of the Monte Carlo simulation and learning dynamical models on the course grained space. Data-driven representations of the dynamics in the course grained space are trained using data from the full model. Data-driven models for forcing are also learned, and the result fed back into the dynamics. In doing so, the model seeks to replicate the effects of filament compliance on macro scale dynamics without explicitly tracking micro scale features. We withhold some input parameter regimes and demonstrate accurate reconstruction of course grained state and force traces using the data-driven model and given only knowledge of the initial condition and input. This work allows for faster computation of the forcing behavior of the half-sarcomere, as well as consistent representations of the course grained state variables. It is therefore promising as a step towards multi-sarcomere or even tissue scale models of skeletal muscle.

biophysics↗

bioRxiv2020

Rapid growth and fusion of protocells in surface-adhered membrane networks

Elevated temperatures might have promoted the nucleation, growth and replication of protocells on the early Earth. Recent reports have shown evidence that moderately high temperatures not only permit protocell assembly at the origin of life, but could have actively supported it. Here we show the fast nucleation and growth of vesicular compartments from autonomously formed lipid networks on solid surfaces, induced by a moderate increase in temperature. Branches of the networks, initially consisting of self-assembled interconnected nanotubes, rapidly swell into microcompartments which can spontaneously encapsulate RNA fragments. The increase in temperature further causes fusion of adjacent network-connected compartments, resulting in the redistribution of the RNA. The experimental observations and the mathematical model indicate that the presence of nanotubular interconnections between protocells facilitates the fusion process.

biophysics↗

bioRxiv2020

In vivo corneal and lenticular microscopy with asymmetric fundus retroillumination

We describe a new technique for non-contact in vivo corneal and lenticular microscopy. It is based on fundus retro-reflection and back-illumination of the crystalline lens and cornea. To enhance phase-gradient contrast, we apply asymmetric illumination by illuminating one side of the fundus. The technique produces micron-scale lateral resolution across a 1-mm diagonal field of view. We show representative images of the epithelium, the subbasal nerve plexus, large stromal nerves, dendritic immune cells, endothelial nuclei, and the anterior crystalline lens, demonstrating the potential of this instrument for clinical applications.

biophysics↗

bioRxiv2020

Amplitude Analysis of Polarization Modulation Data and 3D-Polarization Demodulation (3D-SPoD)

Super-resolution optical fluctuation imaging (SOFI) is a technique that uses the amplitude of fluorescence correlation data for improved resolution of fluorescence images. Here, we explore if also the amplitude of superresolution by polarisation demodulation (SPoD) data can be used to gain additional information about the underlying structures. Highly organized experimental as well a simulated actin filament data demonstrate a principle information gain from this approach. In addition, we explored theoretically the benefits of analyzing the entire 3D-polarization information instead of only 2D-projections thereof. Due to fundamental principles, the probability of finding parallel orientations is approaching zero in 3D-SPoD in contrast to 2D-approaches. Using the modulation-amplitude based analysis we explored systematically simulated 3D-single molecules data (for which the true structures are known) under different conditions that are typically observed in experiments. We found that this approach can significantly improve the distinction, reconstruction and localization. In addition, these approaches are less sensitive to uncertainties in the knowledge about the true experimental point-spread-function (PSF) used for reconstruction compared to approaches using non-modulated data. Finally, they can effectively remove higher levels of non-modulated back-ground intensity.

biophysics↗

bioRxiv2020

Charge density of cation determines inner versus outer shell coordination to phosphate in RNA

Divalent cations are often required to fold RNA, which is a highly charged polyanion. Condensation of ions, such as Mg2+ or Ca2+, in the vicinity of RNA renormalizes the effective charges on the phosphate groups, thus minimizing the intra RNA electrostatic repulsion. The prevailing view is that divalent ions bind diffusively in a non-specific manner. In sharp contrast, we arrive at the exact opposite conclusion using a theory for the interaction of ions with the phosphate groups using RISM theory in conjunction with simulations based on an accurate Three Interaction Site RNA model. The divalent ions bind in a nucleotide-specific manner using either the inner (partially dehydrated) or outer (fully hydrated) shell coordination. The high charge density Mg2+ ion has a preference to bind to the outer shell whereas the opposite is the case for Ca2+. Surprisingly, we find that bridging interactions, involving ions that are coordinated to two or more phosphate groups, play a crucial role in maintaining the integrity of the folded state. Their importance could become increasingly prominent as the size of the RNA increases. Because the modes of interaction of divalent ions with DNA are likely to be similar, we propose that specific inner and outer shell coordination could play a role in DNA condensation, and perhaps genome organization as well.

biophysics↗

bioRxiv2020

Effect of thermal and high-pressure processing on the thermo-rheological and functional properties of common bean (Phaseolus vulgaris L.) flours

The effect of hydrothermal (HT) (boiling for 15 or 120min) and high-hydrostatic pressure (HHP) (150, 300, 450, and 600MPa for 5, 10 or 15min) processing on the rheological, pasting, thermal and functional properties of bean flours was investigated. HT and HHP treatments differently affected these properties. HT120 led to maximum values of elastic and viscous moduli (G', G''), and gel strength of bean flours. HHP enhanced G', G'' and gel strength as the pressure and holding time increased. The viscoelastic properties of HT120 and HHP600/5-treated bean flours correlated with the increased viscosity of these samples. The pasting profiles and thermograms indicated a full, partial, and limited starch gelatinization in HT120, HHP600/5 and HHP [≤] 450MPa samples, respectively. Enthalpy values showed that HT120 caused a higher degree of protein denaturation than HHP, with protein denaturation increasing as pressurization and time increased. This had an impact on protein solubility and emulsifying activity of flours which were significantly diminished by HT15/HT120, but maintained or slightly decreased by HHP. Nevertheless, HHP-treated samples showed enhanced emulsifying stability with increased pressure and holding time. These results demonstrate that HHP has the technological potential to manufacture bean flours with a range of functionalities into diverse food products.

biophysics↗

bioRxiv2020

A device for exploring the full angular excitation space - Can more angular projections improve determination of a molecules 3D-orientation in the presence of noise?

In the past, different methods have been presented to determine the 3D orientation of single molecules in a microscopic set-up by excitation polarization modulation. Using linearly polarized illumination from different directions and thereby measuring different 2D projections enables reconstructing the full 3D orientation. Theoretically, two projections suffice for a full 3D orientation determination if the intensities are properly calibrated. If they are not, a third projection will enable unambiguous orientation measurements. The question arises if three projections already contain the maximum information on the 3D orientation when also considering the limited number of available photons and shot noise in an experiment, or if detecting more projections or even continuously changing the projection direction during a measurement provides more information with an identical number of available photons. To answer this principle question, we constructed a simple device allowing for exploring any projection direction available with a particular microscope objective and tested several different excitation modulation schemes using simulated as well as experimental single molecule data. We found that three different projections in fact already do provide the maximum information also for noisy data. Our results do not indicate a significant improvement in angular precision in comparison to three projections, both when increasing the number of projections and when modulating the projection direction and polarization simultaneously during the measurement. In fluorescence microscopy polarized illumination from different directions enables the determination of the 3D orientation of single molecules by combining the 2D information of different projection directions. Ambiguities that emerge when using only two projections can be eliminated using a third projection. In a systematic study we show that - also considering the limited number of available photons and shot noise in an experiment - three projection directions already contain the maximum information on the 3D orientation. Our results do not indicate a significant improvement in angular precision in comparison to three projections, both when increasing the number of projections and when modulating the projection direction and polarization simultaneously during the measurement.

biophysics↗

bioRxiv2020

Binding dynamics of α-actinin-4 in dependence of actin cortex tension

Mechano-sensation of cells is an important prerequisite for cellular function, e.g. in the context of cell migration, tissue organisation and morphogenesis. An important mechano-chemical-transducer is the actin cytoskeleton. In fact, previous studies have shown that actin cross-linkers, such as -actinin-4, exhibit mechanosensitive properties in its binding dynamics to actin polymers. However, to date, a quantitative analysis of tension-dependent binding dynamics in live cells is lacking. Here, we present a new technique that allows to quantitatively characterize the dependence of cross-linking lifetime of actin cross-linkers on mechanical tension in the actin cortex of live cells. We use an approach that combines parallel plate confinement of round cells, fluorescence recovery after photo-bleaching, and a mathematical mean-field model of cross-linker binding. We apply our approach to the actin cross-linker -actinin-4 and show that the cross-linking time of -actinin-4 homodimers increases approximately twofold within the cellular range of cortical mechanical tension rendering -actinin-4 a catch bond in physiological tension ranges.

biophysics↗

bioRxiv2020

Network Organisation and the Dynamics of Tubules in the Endoplasmic Reticulum

The endoplasmic reticulum (ER) is a eukaryotic subcellular organelle composed of tubules and sheet-like areas of membrane connected at junctions. The tubule network is highly dynamic and undergoes rapid and continual rearrangement. There are currently few tools to evaluate network organisation and dynamics. We quantified ER network organisation in Vero and MRC5 cells, and developed a classification system for ER dynamics in live cells. The persistence length, tubule length, junction coordination number and angles of the network were quantified. Hallmarks of imbalances in ER tension, indications of interactions with microtubules and other subcellular organelles, and active reorganisation and dynamics were observed. Live cell ER tubule dynamics were classified using a Gaussian mixture model, defining tubule motion as active or thermal and conformational phase space analysis allowed this classification to be refined by tubule curvature states. STATEMENT OF SIGNIFICANCEThe endoplasmic reticulum (ER), a subcellular organelle, is an underexplored real-world example of active matter. Many processes essential to cell survival are performed by the ER, the efficacy of which may depend on its organisation and dynamics. Abnormal ER morphology is linked to diseases such as hereditary spastic paraplegias and it is possible that the dynamics are also implicated. Therefore, analysing the ER network in normal cells is important for the understanding of disease-related alterations. In this work, we outline the first thorough quantification methods for determining ER organisation and dynamics, deducing that tubule motion has a binary classification as active or thermal. Active reorganisation and dynamics along with indications of tension imbalances and membrane contact sites were observed.

biophysics↗

bioRxiv2020

Myelin water imaging depends on white matter fiber orientation in the human brain

The multiexponential T2 decay of the magnetic resonance imaging (MRI) signal from cerebral white matter can be separated into short components sensitive to myelin water and long components related to intra- and extracellular water. In this study we investigated to what degree the myelin water fraction (MWF) depends on the angle between white matter fibers and the main magnetic filed. Maps of MWF were acquired using multi echo CPMG and GRASE sequences. The CPMG sequence was acquired with a TR of 1073 ms, 1500 ms and 2000 ms. The fiber orientation was mapped with diffusion tensor imaging. By angle-wise pooling the voxels across the brains white matter, an orientation dependent MWF curve was generated. We found that MWF varied between 25% and 35% across different fiber orientations. The orientation dependency of the MWF is characterized by a dipole-dipole interaction model. Furthermore, the selection of the TR influences the orientation dependent and global white matter MWF. White matter fiber orientation induces a strong systematic bias on the estimation of MWF. This finding has important implications for future research and the interpretation of MWI results in previously published studies.

biophysics↗