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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 613 records · Page 34Linked to original sources

bioRxiv2016

Self assembly of HIV-1 Gag protein on lipid membranes generates PI(4,5)P2/Cholesterolnanoclusters.

The self-assembly of HIV-1 Gag polyprotein at the inner leaflet of the cell host plasma membrane is the key orchestrator of virus assembly. The binding between Gag and the plasma membrane is mediated by specific interaction of the Gag matrix domain and the PI(4,5)P2 lipid (PIP2). It is unknown whether this interaction could lead to local reorganization of the plasma membrane lipids. In this study, using model membranes, we examined the ability of Gag to segregate specific lipids upon self-assembly. We show for the first time that Gag self-assembly is responsible for the formation of PIP2 lipid nanoclusters, enriched in cholesterol but not in sphingomyelin. We also show that Gag mainly partition into liquid-disordered domains of these lipid membranes. Our work strongly suggests that, instead of targeting pre-existing plasma membrane lipid domains, Gag is more prone to generate PIP2/Cholesterol lipid nanodomains at the inner leaflet of the plasma membrane during early events of virus assembly.

biophysics↗

bioRxiv2016

ULTRAFAST LASER-PROBING SPECTROCOPY FOR STUDYING MOLECULAR STRUCTURE OF POLYMERIC PROTEINS

We report the development of a new technique to screen protein crystallinity quantitatively based on laser-probing spectroscopy with sub-picosecond resolution. First, we show theoretically that the temperature dependence of the refractive index of a polymeric protein is correlated to its crystallinity. Then, we performed time-domain thermo-transmission experiments on purified semi-crystalline proteins, both native and recombinant (i.e., silk and squid ring teeth), and also on intact E. coli cells bearing overexpressed recombinant protein. Our results demonstrate, for the first time, quantification of crystallinity in real time for polymeric proteins. Our approach can potentially be used for screening an ultra-large number of polymeric proteins in vivo.

biophysics↗

bioRxiv2016

How to fold intricately: using theory and experiments to unravel the properties of knotted proteins

Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native state. Here, we review such developments by paying particular attention to the complementarity of experimental and computational studies. Key open issues that could be tackled with either or both approaches are finally pointed out.

biophysics↗

bioRxiv2016

Probing the effect of uniaxial compression on cell migration

The chemical, physical and mechanical properties of the extra-cellular environment have a strong effect on cell migration. Aspects such as pore-size or stiffness of the matrix influence the selection of the mechanism used by cells to propel themselves, including pseudopod or blebbing. How a cell perceives its environment, and how such a cue triggers a change in behaviour are largely unknown, but mechanics is likely to be involved. Because mechanical conditions are often controlled by modifying the composition of the environment, separating chemical and physical contributions is difficult and requires multiple controls. Here we propose a simple method to impose a mechanical compression on individual cells without altering the composition of the gel. Live imaging during compression provides accurate information about the cells morphology and migratory phenotype. Using Dictyostelium as a model, we observe that a compression of the order of 500 Pa flattens the cells under gel by up to 50%. This uniaxial compression directly triggers a transition in the mode of migration, from primarily pseudopodial to bleb driven, in less than 30 sec. This novel device is therefore capable of influencing cell migration in real time and offers a convenient approach to systematically study mechanotransduction in confined environments.

biophysics↗

bioRxiv2016

Energy Conservation as a Measure of Simulation Accuracy

Energy conservation is widely used as a measure of accuracy for molecular simulations. When reporting rates of energy drift, researchers usually assume it is linear in the simulation length, temperature, and system size. We study these assumptions and find that all three are incorrect. Energy drift is too complicated to characterize with a single number, and a more sophisticated analysis is needed to identify the effects of systematic versus random drift, and of integration error versus numerical error. We further argue that energy conservation is not a reliable measure of accuracy. Having small overall drift on long time scales is not a sufficient condition, and in some cases not a necessary condition, for a simulation to produce meaningful results.

biophysics↗

bioRxiv2016

Applying Corrections in Single-Molecule FRET

Single-molecule Forster resonance energy transfer (smFRET) experiments can detect the distance between a donor and an acceptor fluorophore on the 3-10nm scale. In ratiometric smFRET experiments, the FRET efficiency is estimated from the ratio of acceptor and total signal (donor + acceptor). An excitation scheme involving two alternating lasers (ALEX) is often employed to discriminate between singly- and doubly-labeled populations thanks to a second ratiometric parameter, the stoichiometry S. Accurate FRET and S estimations requires applying three well-known correction factors: donor emission leakage into the acceptor channel, acceptor direct excitation by the donor excitation laser and the \"gamma factor\" (i.e. correction for the imbalance between donor and acceptor signals due to different fluorophores quantum yields and photon detection effciencies).\n\nExpressions to directly correct both raw FRET and S values have been reported in [1] in the context of freely-diffusing smFRET. Here we extend Lee et al. work providing several expressions for the direct excitation coeffcient and highlighting a clear interpretation in terms of physical parameters and experimental quantities. Moreover, we derive a more complete set of analytic expressions for correcting FRET and S. We aim to provide a clear and concise reference for different definitions of correction coeffcients and correction formulas valid for any smFRET experiment both in immobilized and freely-diffusing form.

biophysics↗

bioRxiv2016

Analyzing Single Molecule Localization MicroscopyData Using Cubic Splines

The resolution of super-resolution microscopy based on single molecule localization is in part determined by the accuracy of the localization algorithm. In most published approaches to date this localization is done by fitting an analytical function that approximates the point spread function (PSF) of the microscope. However, particularly for localization in 3D, analytical functions such as a Gaussian, which are computationally inexpensive, may not accurately capture the PSF shape leading to reduced fitting accuracy. On the other hand, analytical functions that can accurately capture the PSF shape, such as those based on pupil functions, can be computationally expensive. Here we investigate the use of cubic splines as an alternative fitting approach. We demonstrate that cubic splines can capture the shape of any PSF with high accuracy and that they can be used for fitting the PSF with only a 2-3x increase in computation time as compared to Gaussian fitting. We provide an open-source software package that measures the PSF of any microscope and uses the measured PSF to perform 3D single molecule localization microscopy analysis with reasonable accuracy and speed.

biophysics↗

bioRxiv2016

Effects of of dimethyl sulfoxide on surface water near phospholipid bilayers

Despite much effort to probe the properties of dimethyl sulfoxide (DMSO) solution, effects of DMSO on water, especially near plasma membrane surfaces still remain elusive. By performing molecular dynamics (MD) simulations at varying DMSO concentrations (XDMSO), we study how DMSO affects structural and dynamical properties of water in the vicinity of phospholipid bilayers. As proposed by a number of experiments, our simulations confirm that DMSO induces dehydration from bilayer surfaces and disrupts the H-bond structure of water. However, DMSO enhanced water diffusivity at solvent-bilayer interfaces, an intriguing discovery reported by a spin-label measurement, is not confirmed in our simulations. In order to resolve this discrepancy, we examine the location of the spin-label (Tempo), relative to the solvent-bilayer interface. In accord with the evidence in the literature, our simulations, which explicitly model Tempo-PC, find that the Tempo moiety is equilibrated at ~ 8 - 10 [A] below the bilayer surface. Furthermore, the DMSO-enhanced surface water diffusion is confirmed only when water diffusion is analyzed around the Tempo moiety that is immersed below the bilayer surface, which implies that the experimentally detected signal of water using Tempo stems from the interior of bilayers, not from the interface. Our analysis finds that the increase of water diffusion below the bilayer surface is coupled to the increase of area per lipid with an increasing XDMSO ([lsim] 10 mol%). Underscoring the hydrophobic nature of Tempo moiety, our study calls for careful re-evaluation of the use of Tempo in the measurement on lipid bilayer surfaces.

biophysics↗

bioRxiv2016

MSMBuilder: Statistical Models for Biomolecular Dynamics

MSMBuilder is a software package for building statistical models of high-dimensional time-series data. It is designed with a particular focus on the analysis of atomistic simulations of biomolecular dynamics such as protein folding and conformational change. MSMBuilder is named for its ability to construct Markov State Models (MSMs), a class of models that has gained favor among computational biophysicists. In addition to both well-established and newer MSM methods, the package includes complementary algorithms for understanding time-series data such as hidden Markov models (HMMs) and time-structure based independent component analysis (tICA). MSMBuilder boasts an easy to use command-line interface, as well as clear and consistent abstractions through its Python API (application programming interface). MSMBuilder is developed with careful consideration for compatibility with the broader machine-learning community by following the design of scikit-learn. The package is used primarily by practitioners of molecular dynamics but is just as applicable to other computational or experimental time-series measurements. http://msmbuilder.org

biophysics↗

bioRxiv2016

Chromosome interactome inferred from mitosis-G1 transition

The progress in experimental techniques aimed at 3D genome study is yet to bring about revelation of basic principles of genome folding. Chromosome conformation capture Hi-C technologies provide genome wide mapping of genomic loci interactions but spatial organization of chromosomes remains unknown. Here, we develop a polymer modeling approach to generate the ensemble of 3D chromosome conformations for mapping genetic loci contacts and the positions of megabase chromosomal domains in interphase chromosome at different time of mitosis-interphase transition. We demonstrate that (*) whole chromosome contact map (interactome) generated for mouse chromosome 18 structure and (**) contact patterns, observed soon after mitotic decondensation and remaining similar during G1, correlate well with the experimental Hi-C contact data. The results suggest that contact map formation and spatial compartmentalization of an interphase chromosome are driven by interactions between different types of domains during formation of globular chromosome state at the end of mitotis-G1 transition.

biophysics↗

bioRxiv2016

THE CREATION OF A NEGATIVE SLOPE CONDUCTANCE REGION BY THE ACTIVATION OF THE PERSISTENT SODIUM CURRENT PROLONGS NEAR-THRESHOLD SYNAPTIC POTENTIALS

A change of the input resistance (Rin) of the neuron involves a change in the membrane conductances by opening and closing of ion channels. In passive membranes, i.e., membranes with only linear leak conductances, the increase or decrease of these conductances leads to a decrease or increase of the Rin and the membrane time constant ({tau}m). However, the presence of subthreshold voltage dependent currents can produce non-linear effects generating deviations from this relationship, especially the contradictory effect of negative conductances, as produced by the sodium-persistent current (INaP), on the Rin. In this work we aimed to analyze experimentally and theoretically the impact of the negative conductance produced by INaP on Rin. Experiments of whole-cell patch-clamp conducted in CA1 hippocampus pyramidal cells from brain slices showed a paradoxical voltage-dependent decrease of the Rin and the {tau}m in subthreshold membrane potentials close to the firing threshold after the perfusion with TTX, which inhibits INaP. This effect is postulated to be a result of the negative slope conductance in the subthreshold region produced by this conductance. The analysis of the experimental data, together with simulations found that the slope conductance of INaP is negative for subthreshold membrane potentials and its magnitude is voltage dependent in the same range observed for the voltage-dependence of Rin and {tau}m. The injection of an artificial INaP using dynamic-clamp in the presence of TTX restored the Rin and {tau}m to its original values. Additionally the injection of an artificial leak current with a negative conductance in the presence of TTX restored the Rin and {tau}m as the artificial Inap did. On the other hand, the injection of an artificial leak current with a positive conductance in the presence of TTX had no effect on the Rin and {tau}m. We conclude that INaP increases the Rin and {tau}m by the negative slope conductance observed in its non-monotonic I-V relationship. These results demonstrate that the effect of Inap on Rin and {tau}m is stronger in potentials near the firing threshold, which could potentiate the temporal summation of the EPSPs increasing their temporal integration and facilitating action potential firing. Because of its negative slope conductance, INaP is more effective in increasing excitability near threshold than a depolarizing leak current.

biophysics↗

bioRxiv2016

Entropy Transfer between Residue Pairs Shows that Allostery is an Intrinsic Propertyof Proteins: Quantifying Allosteric Communication in Ubiquitin

AbstractIt has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we apply Schreibers transfer entropy formulation to the non-allosteric protein Ubiquitin and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. Calculations show that specific residues act as entropy reservoirs in Ubiquitin and others as entropy sinks. Using the plausible conjecture that extracting entropy from a residue makes it more susceptible for interaction with a partner, we explain the ternary complex formation of Ubiquitin in terms of entropy transfer. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins.\n\nAuthor SummaryAllosteric communication is essential for the function of proteins. Recent work shows that allostery results from dynamic processes in the protein associated with atomic fluctuations leading to entropic interactions that involve ensemble of pathways rather than discrete two state transitions. Based on this new picture of allostery, it was proposed that allostery may indeed be an intrinsic property of all proteins. In order to test this hypothesis, we derive the computational tools for quantifying allosteric communication, and explain allostery in terms of entropy transfer, a new concept based on information theory. We use long molecular dynamics simulations of proteins from which we calculate the transfer of entropy between pairs of residues. Results of simulations show that certain residues act as entropy sources while others as entropy sinks. Evaluation of time delayed correlations shows the presence of causality of interactions that allow us to differentiate between residues that are drivers in allosteric activity and those that are driven. Identification of driver-driven relations is important for drug design. Using the example of Ubiquitin, a protein that is not known to be allosteric, we identify paths of information transfer that control its binding to diverse partners in the Ubiquitin-Proteasome System. We conclude that allosteric communication resulting from entropy transfer between residues is an intrinsic property of all proteins.

biophysics↗

bioRxiv2016

Causality, Transfer Entropy and Allosteric Communication Landscapes inProteins with Harmonic Interactions

A fast and approximate method of generating allosteric communication landscapes is presented by using Schreiber's entropy transfer concept in combination with the Gaussian Network Model of proteins. Predictions of the model and the allosteric communication landscapes generated show that information transfer in proteins does not necessarily take place along a single path, but through an ensemble of pathways. The model emphasizes that knowledge of entropy only is not sufficient for determining allosteric communication and additional information based on time delayed correlations has to be introduced, which leads to the presence of causality in proteins. The model provides a simple tool for mapping entropy sink-source relations into pairs of residues. Residues that should be manipulated to control protein activity may be determined with this approach. This should be of great importance for allosteric drug design and for understanding the effects of mutations on protein function. The model is applied to determine allosteric communication in two proteins, Ubiquitin and Pyruvate Kinase. Predictions are in agreement with detailed molecular dynamics simulations and experimental evidence.\n\nSignificanceProteins perform their function by an exchange of information within themselves and with their environments through correlated fluctuations of their atoms. Fluctuations of one atom may drive the fluctuations of another. Information transmitted in this way leads to allosteric communication which is described as the process in which action at one site of the protein is transmitted to another site at which the protein performs its activity. Disruption of allosteric communication by mutation for example leads to disease. The present paper incorporates information theoretic concepts into the well known Gaussian Network Model of proteins and allows for rapid characterization of allosteric communication landscapes for normal functioning as well as malfunctioning proteins.

biophysics↗

bioRxiv2016

Multispot single-molecule FRET: high-throughput analysis of freely diffusing molecules

We describe an 8-spot confocal setup for high-throughput smFRET assays and illustrate its performance with two characteristic experiments. First, measurements on a series of freely diffusing doubly-labeled dsDNA samples allow us to demonstrate that data acquired in multiple spots in parallel can be properly corrected and result in measured sample characteristics identical to those obtained with a standard single-spot setup. We then take advantage of the higher throughput provided by parallel acquisition to address an outstanding question about the kinetics of the initial steps of bacterial RNA transcription. Our real-time kinetic analysis of promoter escape by bacterial RNA polymerase confirms results obtained by a more indirect route, shedding additional light on the initial steps of transcription.\n\nFinally, we discuss the advantages of our multispot setup, while pointing potential limitations of the current single laser excitation design, as well as analysis challenges and their solutions.

biophysics↗

bioRxiv2016

Folding Principle of Chromosome Emerges from Mapping of Genome Features onto its 3D Structure

How chromosomes fold into 3D structures and how genome functions are affected or even controlled by their spatial organization remain challenging questions. Hi-C experiment has provided important structural insights for chromosome, and Hi-C data are used here to construct the 3D chromatin structure which are characterized by two spatially segregated chromatin compartments A and B. By mapping a plethora of genome features onto the constructed 3D chromatin model, we show vividly the close connection between genome properties and the spatial organization of chromatin. We are able to dissect the whole chromatin into two types of chromatin domains which have clearly different Hi-C contact patterns as well as different sizes of chromatin loops. The two chromatin types can be respectively regarded as the basic units of chromatin compartments A and B, and also spatially segregate from each other as the two chromatin compartments. Therefore, the chromatin loops segregate in the space according to their sizes, suggesting the excluded volume or entropic effect in chromatin compartmentalization as well as chromosome positioning. Taken together, these results provide clues to the folding principles of chromosomes, their spatial organization, and the resulted clustering of many genome features in the 3D space.

biophysics↗

bioRxiv2016

A looping-based model for quenching repression

We model the regulatory role of proteins bound to looped DNA using a simulation in which dsDNA is represented as a self-avoiding chain, and proteins as spherical protrusions. We simu-late long self-avoiding chains using a sequential importance sampling Monte-Carlo algorithm, and compute the probabilities for chain looping with and without a protrusion. We find that a protrusion near one of the chains termini reduces the probability of looping, even for chains much longer than the protrusion-chain-terminus distance. This effect increases with protrusion size, and decreases with protrusion-terminus distance. The reduced probability of looping can be explained via an eclipse-like model, which provides a novel inhibitory mechanism. We test the eclipse model on two possible transcription-factor occupancy states of the eve 3/7 enhancer, and show that it provides a possible explanation for the experimentally-observed eve stripe 3 and 7 expression patterns.\n\nThe authors declare no conflict of interests

biophysics↗

bioRxiv2016

Using the Volta phase plate with defocus for cryo-EM single particle analysis

Previously, we reported an in-focus data acquisition method for cryo-EM single particle analysis with the Volta phase plate (VPP) (Danev and Baumeister, 2016). Here, we extend the technique to include a small amount of defocus which enables contrast transfer function measurement and correction. This hybrid approach simplifies the experiment and increases the data acquisition speed. It also enables 3D reconstructions with resolutions in the 2 [A] range, demonstrating that, in practice, there are no resolution limitations imposed by the VPP.

biophysics↗

bioRxiv2016

Gentle, fast and effective crystal soaking by acoustic dispensing

SynopsisA high-throughput method is described for crystal soaking using acoustic droplet ejection, and its effectiveness demonstrated.\n\nAbstractBright light sources, agile robotics, and fast detectors are continually reducing the time it takes to perform an X-ray diffraction experiment, making high throughput experiments more feasible than ever. But this is also pushing the upstream bottleneck towards sample preparation, even for robust and well characterised crystal systems. Crystal soaking is routinely used to generate protein-ligand complex structures, yet protein crystals are often sensitive to changes in solvent composition, and frequently require gentle or careful stepwise soaking techniques, limiting overall throughput. Here, we describe the use of acoustic droplet ejection for soaking of protein crystals with small molecules, and show that it is both gentle on crystals and allows very high throughput, with 1000 unique soaks easily performed in under 10 minutes. In addition to having very low compound consumption (tens of nanolitres per sample), the positional precision of acoustic droplet ejection enables targeted placement of the compound/solvent away from crystals and towards drop edges, allowing for gradual diffusion of solvent across the drop. This ensures both an improvement in reproducibility of X-ray diffraction and an increased solvent tolerance of the crystals, thus enabling higher effective compound soaking concentrations. We detail the technique here with examples from the protein target JMJD2D, a histone lysine demethylase, having roles in cancer and the focus of active structure based drug design efforts.

biophysics↗