SEARCH · Search bioRxiv

Results for “Biophysics”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 757 records · Page 42Linked to original sources

bioRxiv2017

Statistical Mechanics Of Phase Space Partitioning In Large-Scale Spiking Neuron Circuits

Synaptic interactions structure the phase space of the dynamics of neural circuits and constrain neural computation. Understanding how requires methods that handle those discrete interactions, yet few exist. Recently, it was discovered that even random networks exhibit dynamics that partitions the phase space into numerous attractor basins. Here we utilize this phenomenon to develop theory for the geometry of phase space partitioning in spiking neural circuits. We find basin boundaries structuring the phase space are pre-images of spike-time collision events. Formulating a statistical theory of spike-time collision events, we derive expressions for the rate of divergence of neighboring basins and for their size distribution. This theory reveals that the typical basin diameter grows with inhibitory coupling strength and shrinks with the rate of spike events. Our study provides an analytical and generalizable approach for dissecting how connectivity, coupling strength, single neuron dynamics and population activity shape the phase space geometry of spiking circuits.

biophysics↗

bioRxiv2017

Cell-cycle dependent organization and dynamics of RNA Polymerase I in live human cells

RNA Polymerase I (Pol I) is responsible for over 60% of transcriptional output in human cells, yet basic questions concerning the spatial and temporal organization of the polymerase remain unanswered. Here we investigate how mammalian cells rely on Pol I organization throughout the cell cycle to balance different needs, from complete transcription shut down to massive increase in protein synthesis (and thus ribosomal RNA synthesis) before cell division. In contrast to our previous reports on RNA Polymerase II, Pol I clusters are stable with active transcription, and the presence of transient Pol I clusters correlates with inactive ribosomal transcription. Our results suggest that both stable and transient populations Pol I clusters co-exist in individual living cells, and their relative fraction may directly reflect the global gene expression need of the cell.

biophysics↗

bioRxiv2017

Nanoscale Dynamics of Centromere Nucleosomes and the Critical Roles of CENP-A

In the absence of a functioning centromere, chromosome segregation becomes aberrant, leading to an increased rate of aneuploidy. The highly specific recognition of centromeres by kinetochores suggests that specific structural characteristics define this region, however, the structural details and mechanism underlying this recognition remains a matter of intense investigation. To address this, High speed atomic force microscopy was used for direct visualization of the spontaneous dynamics of CENP-A nucleosomes at the sub-second time scale. We report that CENP-A nucleosomes change conformation spontaneously and reversibly, utilizing two major pathways: unwrapping, and looping of the DNA; enabling core transfer between neighboring DNA substrates. Along with these nucleosome dynamics we observed that CENP-A stabilizes the histone core against dissociating to histone subunits, unique from H3 cores which are only capable of such plasticity in the presence of remodeling factors. These findings have implications for the dynamics and integrity of nucleosomes at the centromere.

biophysics↗

bioRxiv2017

Self-Organisation And Positioning Of Bacterial Protein Clusters

Many cellular processes require sub-cellular positioning of proteins. This can be due to passive mechanisms such as recruitment by existing landmarks or curvature sensing. However, in bacteria active self-positioning is likely to play a role in multiple processes, including the positioning of the future division site and cytoplasmic protein clusters. How can such dynamic clusters be formed and positioned? Here, we present a model for the self-organization and positioning of dynamic protein clusters into regularly repeating patterns based on a phase-locked Turing pattern. A single peak in the concentration is always positioned at mid-domain (mid-cell) while two peaks are positioned one at each quarter-position etc. Furthermore, domain growth results in peak-splitting and pattern doubling. We argue that the model may explain the regular positioning of the highly conserved Structural Maintenance of Chromosomes (SMC) complexes on the bacterial nucleoid and provides an attractive mechanism for the self-positioning of dynamic protein clusters in other systems.

biophysics↗

bioRxiv2017

The N-terminal domain of ALS-linked TDP-43 assembles without misfolding

TDP-43 forms inclusions in several neurodegenerative diseases, and both its N- and C-terminal domains are implicated in this process. We show that the folded TDP-43 N-terminal domain oligomerizes under physiological conditions and propose that, in full-length TDP-43, association between folded N-terminal domains enhances the propensity of the intrinsically unfolded C-terminal domains to drive pathological aggregation.

biophysics↗

bioRxiv2017

FCS In Closed Systems And Application For Membrane Nanotubes

In the present study, we developed the fluorescence correlation spectroscopy theory for closed systems with either periodic or reflective boundaries. The illumination could be any arbitrary function. We tested our theory with simulated data of both boundary conditions. We also tested the theory with experimental data of membrane nanotubes, whose circular direction is a closed system. The result shows that the correlation function for nanotubes falls between 1D and 2D diffusion model. The fitting with our model gives an accurate recovery of the diffusion time and nanotube radius. We also give some examples of single molecule experiments for which our theory can be potentially useful.

biophysics↗

bioRxiv2017

Transient Thresholding: A Mechanism Enabling Non-Cooperative Transcriptional Circuitry To Form A Switch

Threshold generation in fate-selection circuits is often achieved through deterministic bistability, which requires cooperativity (i.e., nonlinear activation) and associated hysteresis. However, the Tat positive-feedback loop that controls HIVs fate decision between replication and proviral latency lacks self-cooperativity and deterministic bistability. Absent cooperativity, it is unclear how HIV can temporarily remain in an off state long enough for the kinetically slower epigenetic silencing mechanisms to act-- expression fluctuations should rapidly trigger active positive feedback and replication, precluding establishment of latency. Here, using flow cytometry and single-cell imaging, we find that the Tat circuit exhibits a transient activation threshold. This threshold largely disappears after [~]40 hours--accounting for the lack of deterministic bistability--and promoter activation shortens the lifetime of this transient threshold. Continuous differential equation models do not recapitulate this phenomenon. However, chemical reaction (master equation) models where the transcriptional transactivator and promoter toggle between inactive and active states can recapitulate the phenomenon since they intrinsically create a single-molecule threshold transiently requiring excess molecules in the inactive state to achieve at least one molecule (rather than a continuous fractional value) in the active state. Given the widespread nature of promoter toggling and transcription factor modifications, transient thresholds may be a general feature of inducible promoters.

biophysics↗

bioRxiv2017

Two Loci Single Particle Trajectories Analysis: Constructing A First Passage Time Statistics Of Local Chromatin Exploration

Stochastic single particle trajectories are used to explore the local chromatin organization. We present here a statistical analysis of the first contact time distributions between two tagged loci recorded experimentally. First, we extract the association and dissociation times from data for various genomic distances between loci and we show that the looping time occurs in confined nanometer regions. Second, we characterize the looping time distribution for two loci in the presence of multiple DNA damages. Finally, we construct a polymer model that accounts for the local chromatin organization before and after a double-stranded DNA break (DSB) to estimate the level of chromatin decompaction. This novel passage time statistics method allows extracting transient dynamic at scales from one to few hundreds of nanometers, predicts the local changes in the number of binding molecules following DSB and can be used to better characterize the local dynamic of the chromatin.

biophysics↗

bioRxiv2017

3D Single-Molecule Super-Resolution Microscopy With A Tilted Light Sheet

Tilted light sheet microscopy with 3D point spread functions (TILT3D) combines a novel, tilted light sheet illumination strategy with long axial range point spread functions (PSFs) for low-background, 3D super-localization of single molecules as well as 3D super-resolution imaging in thick cells. Because the axial positions of the single emitters are encoded in the shape of each single-molecule image rather than in the position or thickness of the light sheet, the light sheet need not be extremely thin. TILT3D is built upon a standard inverted microscope and has minimal custom parts. The result is simple and flexible 3D super-resolution imaging with tens of nm localization precision throughout thick mammalian cells. We validated TILT3D for 3D super-resolution imaging in mammalian cells by imaging mitochondria and the full nuclear lamina using the double-helix PSF for single-molecule detection and the recently developed Tetrapod PSFs for fiducial bead tracking and live axial drift correction.

biophysics↗

bioRxiv2017

Epigenetic Transitions And Knotted Solitons In Stretched Chromatin

The spreading and regulation of epigenetic marks on chromosomes is crucial to establish and maintain cellular identity. Nonetheless, the dynamical mechanism leading to the establishment and maintenance of a given, cell-line specific, epigenetic pattern is still poorly understood. In this work we propose, and investigate in silico, a possible experimental strategy to illuminate the interplay between 3D chromatin structure and epigenetic dynamics. We consider a set-up where a reconstituted chromatin fibre is stretched at its two ends (e.g., by laser tweezers), while epigenetic enzymes (writers) and chromatin-binding proteins (readers) are flooded into the system. We show that, by tuning the stretching force and the binding affinity of the readers for chromatin, the fibre undergoes a sharp transition between a stretched, epigenetically disordered, state and a crumpled, epigenetically coherent, one. We further investigate the case in which a knot is tied along the chromatin fibre, and find that the knotted segment enhances local epigenetic order, giving rise to \"epigenetic solitons\" which travel and diffuse along chromatin. Our results point to an intriguing coupling between 3D chromatin topology and epigenetic dynamics, which may be investigated via single molecule experiments.

biophysics↗

bioRxiv2017

Torque and buckling in stretched intertwined double-helix DNAs

We present a statistical-mechanical model for the behavior of intertwined DNAs, with a focus on their torque and extension as a function of their catenation (linking) number and applied force, as studied in magnetic tweezers experiments. Our model produces results in good agreement with available experimental data, and predicts a catenation-dependent effective twist modulus distinct from what is observed for twisted individual double-helix DNAs. We find that buckling occurs near to the point where experiments have observed a kink in the extension versus linking number, and that the subsequent \"supercoiled braid\" state corresponds to a proliferation of multiple small plectoneme structures. We predict a discontinuity in extension at the buckling transition corresponding to nucleation of the first plectoneme domain. We also find that buckling occurs for lower linking number at lower salt; the opposite trend is observed for supercoiled single DNAs.

biophysics↗

bioRxiv2017

Millisecond Dynamics Of BTK Reveal Kinome-Wide Conformational Plasticity Within The Apo Kinase Domain

Bruton tyrosine kinase (BTK) is a key enzyme in B-cell development whose improper regulation causes severe immunodeficiency diseases. Design of selective BTK therapeutics would benefit from improved, in-silico structural modeling of the kinases solution ensemble. However, this remains challenging due to the immense computational cost of sampling events on biological timescales. In this work, we combine multi-millisecond molecular dynamics (MD) simulations with Markov state models (MSMs) to report on the thermodynamics, kinetics, and accessible states of BTKs kinase domain. Our conformational landscape links the active state to several inactive states, connected via a structurally diverse intermediate. Our calculations predict a kinome-wide conformational plasticity, and indicate the presence of several new potentially druggable BTK states. We further find that the population of these states and the kinetics of their inter-conversion are modulated by protonation of an aspartate residue, establishing the power of MD & MSMs in predicting effects of chemical perturbations.

biophysics↗

bioRxiv2017

Facilitated Dissociation Of Transcription Factors From Single DNA Binding Sites

The binding of transcription factors (TFs) to DNA controls most aspects of cellular function, making the understanding of their binding kinetics imperative. The standard description of bimolecular interactions posits TF off-rates are independent of TF concentration in solution. However, recent observations have revealed that proteins in solution can accelerate the dissociation of DNA-bound proteins. To study the molecular basis of facilitated dissociation (FD), we have used single-molecule imaging to measure dissociation kinetics of Fis, a key E. coli TF and major bacterial nucleoid protein, from single dsDNA binding sites. We observe a strong FD effect characterized by an exchange rate {bsim}1 x 104 M-1s-1, establishing that FD of Fis occurs at the single-binding-site level, and we find that the off-rate saturates at large Fis concentrations in solution. While spontaneous (i.e., competitor-free) dissociation shows a strong salt dependence, we find that facilitated dissociation depends only weakly on salt. These results are quantitatively explained by a model in which partially dissociated bound proteins are susceptible to invasion by competitor proteins in solution. We also report FD of NHP6A, a yeast TF whose structure differs significantly from Fis. We further perform molecular dynamics simulations, which indicate that FD can occur for molecules that interact far more weakly than those we have studied. Taken together, our results indicate that FD is a general mechanism assisting in the local removal of TFs from their binding sites and does not necessarily require cooperativity, clustering, or binding site overlap.\n\nSIGNIFICANCE STATEMENTTranscription factors (TFs) control biological processes by binding and unbinding to DNA. Therefore it is crucial to understand the mechanisms that affect TF binding kinetics. Recent studies challenge the standard picture of TF binding kinetics by demonstrating cases of proteins in solution accelerating TF dissociation rates through a facilitated dissociation (FD) process. Our study shows that FD can occur at the level of single binding sites, without the action of large protein clusters or long DNA segments. Our results quantitatively support a model of FD in which competitor proteins invade partially dissociated states of DNA-bound TFs. FD is expected to be a general mechanism for modulating gene expression by altering the occupancy of TFs on the genome.\n\nAuthor ContributionsRamsey I. Kamar\n\ndesigned research, performed research, contributed new reagents/analytic tools, analyzed data, wrote the paper\n\nEdward J. Banigan\n\ndesigned research, performed research, contributed new reagents/analytic tools, analyzed data, wrote the paper\n\nAykut Erbas\n\ndesigned research, performed research, contributed new reagents/analytic tools, analyzed data, wrote the paper\n\nRebecca D. Giuntoli\n\ndesigned research, performed research, contributed new reagents/analytic tools, analyzed data, wrote the paper\n\nMonica Olvera de la Cruz\n\ndesigned research, performed research, wrote the paper\n\nReid C. Johnson\n\ndesigned research, performed research, contributed new reagents/analytic tools, analyzed data, wrote the paper\n\nJohn F. Marko\n\ndesigned research, performed research, contributed new reagents/analytic tools, analyzed data, wrote the paper

biophysics↗

bioRxiv2017

Pushing The Limits Of Detection Of Weak Binding Using Fragment Based Drug Discovery: Identification Of New Cyclophilin Binders

Fragment Based Drug Discovery (FBDD) is an increasingly popular method to identify novel small-molecule drug candidates. One of the limitations of the approach is the difficulty of accurately characterizing weak binding events. This work reports a combination of X-ray diffraction, surface plasmon resonance (SPR) experiments and molecular dynamics (MD) simulations, for the characterisation of binders to different isoforms of the cyclophilin (Cyp) protein family. Although several Cyp inhibitors have been reported in the literature, it has proven challenging to achieve high binding selectivity for different isoforms of this protein family. The present studies have led to the identification of several structurally novel fragments that bind to diverse Cyp isoforms in distinct pockets with low millimolar dissociation constants. A detailed comparison of the merits and drawbacks of the experimental and computational techniques is presented, and emerging strategies for designing ligands with enhanced isoform specificity are described.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC=\"FIGDIR/small/136101_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (18K):\norg.highwire.dtl.DTLVardef@5d2d48org.highwire.dtl.DTLVardef@147f922org.highwire.dtl.DTLVardef@356562org.highwire.dtl.DTLVardef@1933853_HPS_FORMAT_FIGEXP M_FIG C_FIG Research Highlights O_LIFBDD is a popular method but weak binding is difficult to detect\nC_LIO_LIThere is a need for pushing the limits of weak binding detection\nC_LIO_LICombination of X-ray, SPR and MD methodologies increases successful characterization of weak binding events\nC_LIO_LISeveral novel Cyclophilin fragment binders were identified\nC_LI

biophysics↗

bioRxiv2017

A Systematic Analysis Of Atomic Protein-Ligand Interactions In The PDB

As the protein databank (PDB) recently passed the cap of 123,456 structures, it stands more than ever as an important resource not only to analyze structural features of specific biological systems, but also to study the prevalence of structural patterns observed in a large body of unrelated structures, that may reflect rules governing protein folding or molecular recognition. Here, we compiled a list of 11,016 unique structures of small-molecule ligands bound to proteins - 6,444 of which have experimental binding affinity - representing 750,873 protein-ligand atomic interactions, and analyzed the frequency, geometry and impact of each interaction type. We find that hydrophobic interactions are generally enriched in high-efficiency ligands, but polar interactions are over-represented in fragment inhibitors. While most observations extracted from the PDB will be familiar to seasoned medicinal chemists, less expected findings, such as the high number of C-H ...O hydrogen bonds or the relatively frequent amide-{pi} stacking between the backbone amide of proteins and aromatic rings of ligands, uncover underused ligand design strategies.

biophysics↗

bioRxiv2017

Element-Free Multiscale Modeling Of Large Deformation Behavior Of Red Blood Cell Membrane With Malaria Infection

In normal physiological and healthy conditions, red blood cells (RBCs) deform readily as they pass through the microcapillaries and the spleen. In this paper, we examine the effects of Plasmodium falciparum infection and maturation on the large deformation behavior of malaria-infected red blood cells (iRBCs) by means of a three-dimensional (3D) multiscale meshfree method. We numerically simulated the optical tweezers experiment and observed the force-displacement response of the iRBC membrane as malaria infection progresses. Our simulation results agree well with experimental data and confirm that the deformability of malaria-infected cells decreases significantly as malaria infection progresses.

biophysics↗

bioRxiv2017

Boosting The Localization Precision Of dSTORM By Biocompatible Metal-Dielectric Coated Glass Coverslips

Super-resolution techniques such as direct Stochastic Optical Reconstruction Microscopy (dSTORM) have become versatile and well-established tools for biological imaging over the last century. Here, we theoretically and experimentally show that clever combination of different fluorescence modalities allows further improvements. We found that the interaction of fluorophores with plasmonic surfaces boost super-resolution performance in dSTORM approaches as it allows for tailoring the excitation and emission properties. The strength of the approach is that no further specialized microscope setup is required as the described enhancement solely rely on metal-dielectric coated glass coverslips that are straightforward to fabricate. Such biocompatible plasmonic nanolayers enhance the signal-to-noise ratio of dSTORM, and thus sharpens the localization precision by a factor of two.

biophysics↗

bioRxiv2017

Does Temperature Change Worsen Or Mitigate The Effect Of Malaria Infection On Erythrocyte Deformability?

INTRODUCTION INTRODUCTION METHODS RESULTS AND DISCUSSION REFERENCES This paper attempts to investigate whether temperature change worsen or mitigate the effect of Plasmodium falciparum (P. falciparum) infection and maturation on the deformability of malaria-infected red blood cells (iRBCs) or erythrocytes. P. falciparum infection is the most lethal malaria parasitic infection affecting humans [1]. Upon infection, the merozoites enter the bloodstream and develop through the ring (Pf-rRBC), trophozoite (Pf-tRBC) and schizont (Pf-tRBC) stages, which is usually accompanied by significant changes in body temperature. Hence, this study aims to draw a connection between temperature change and erythrocyte deformability upon malaria infection. ...

biophysics↗