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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 1,171 records · Page 65Linked to original sources

bioRxiv2018

Irreversible temperature gating in trpv1 sheds light on channel activation

Temperature activated TRP channels or thermoTRPs are among the only proteins that can directly convert temperature changes into changes in channel open probability. In spite of a wealth of information, including several experimentally determined structural models of TRP channels, the mechanism of temperature activation remains unknown. We have carefully characterized the repeated activation of TRPV1 by thermal stimuli and discovered a previously unknown inactivation process, which is irreversible. This inactivation is associated with specific conformational changes in the membrane proximal domain. We propose that this form of gating in TRPV1 channels is a consequence of the heat absorption process that leads to channel opening.

biophysics↗

bioRxiv2018

A label-free approach to detect ligand binding to cell surface proteins in real time

Electrophysiological recordings allow for monitoring the operation of proteins with high temporal resolution down to the single molecule level. This technique has been exploited to track either ion flow arising from channel opening or the synchronized movement of charged residues and/or ions within the membrane electric field. Here, we describe a novel type of current by using the serotonin transporter (SERT) as a model. We examined transient currents elicited on rapid application of specific SERT inhibitors. Our analysis shows that these currents originate from ligand binding and not from a conformational change. The Gouy-Chapman model predicts that a ligand-induced elimination/neutralization of surface charge must produce a displacement current and related apparent changes in membrane capacitance. Here we verified these predictions with SERT. Our observations demonstrate that ligand binding to a protein can be monitored in real time and in a label-free manner by recording the membrane capacitance.

biophysics↗

bioRxiv2018

Measurement of the Persistence Length of Cytoskeletal Filaments using Curvature Distributions

Cytoskeletal filaments such as microtubules and actin filaments play important roles in the mechanical integrity of cells and the ability of cells to respond to their environment. Measuring the mechanical properties of cytoskeletal structures is crucial for gaining insight into intracellular mechanical stresses and their role in regulating cellular processes. One of the ways to characterize these mechanical properties is by measuring their persistence length, the average length over which filaments stay straight. There are several approaches in the literature for measuring filament deformations, including Fourier analysis of images obtained using fluorescence microscopy. Here, we show how curvature distributions can be used as an alternative tool to quantify bio-filament deformations, and investigate how the apparent stiffness of filaments depends on the resolution and noise of the imaging system. We present analytical calculations of the scaling curvature distributions as a function of filament discretization, and test our predictions by comparing Monte Carlo simulations to results from existing techniques. We also apply our approach to microtubules and actin filaments obtained from in vitro gliding assay experiments with high densities of non-functional motors, and calculate the persistence length of these filaments. The presented curvature analysis is significantly more accurate compared to existing approaches for small data sets, and can be readily applied to both in vitro or in vivo filament data through the use of an ImageJ plugin we provide.

biophysics↗

bioRxiv2018

In Vivo Measurements of the Frequency-Dependent Impedance of the Spinal Cord

Improved knowledge of the electrode-tissue impedance will be useful in optimizing the clinical protocols and resulting efficacy of the existing and emerging approaches to spinal cord stimulation. Toward that end, the complex impedance (amplitude and phase) of in vivo ovine spinal cord tissue was measured at the electrode-pial subdural surface interface from 5 Hz to 1 MHz, and with the bi-polar electrodes oriented both parallel and perpendicular to the rostral-caudal axis of the spinal cord. At stimulation frequencies above 10 kHz, most of the impedance then becomes resistive in nature and the phase diference between the stimulation signal and the resulting current drops to {approx} 10{ring}, thus maximizing power transfer to the tissues. Also, at these higher frequencies, the current pulse maintains significantly greater fidelity to the shape of the stimulation signal applied across the electrodes. Lastly, there were lower impedances associated with parallel as opposed to perpendicular orientation of the electrodes, thus reflecting the effects of fiber orientation within the spinal cord. Impedance differences of this kind have not been reported with epidural stimulation because of the electrical shunting effects of the intervening layer of relatively high conductivity cerebrospinal fluid. These observations provide a quantitative basis for improved models of spinal cord stimulation and suggest certain advantages for direct intradural stimulation relative to the standard epidural approaches. (Some figures in this article are in colour only in the electronic version)

biophysics↗

bioRxiv2018

The Folding Pathway of an Ig Domain is Conserved On and Off the Ribosome

Proteins that fold cotranslationally may do so in a restricted configurational space, due to the volume occupied by the ribosome. How does this environment, coupled with the close proximity of the ribosome, affect the folding pathway of a protein? Previous studies have shown that the cotranslational folding process for many proteins, including small, single domains, is directly affected by the ribosome. Here, we investigate the cotranslational folding of an all-b immunoglobulin domain, titin I27. Using an arrest peptide-based assay and structural studies by cryo-EM, we show that I27 folds in the mouth of the ribosome exit tunnel. Simulations that use a kinetic model for the force-dependence of escape from arrest, accurately predict the fraction of folded protein as a function of length. We used these simulations to probe the folding pathway on and off the ribosome. Our simulations - which also reproduce experiments on mutant forms of I27 - show that I27 folds, while still sequestered in the mouth of the ribosome exit tunnel, by essentially the same pathway as free I27, with only subtle shifts of critical contacts from the C to the N terminus.\n\nSignificance StatementMost proteins need to fold into a specific three-dimensional structure in order to function. The mechanism by which isolated proteins fold has been thoroughly studied by experiment and theory. However, in the cell proteins do not fold in isolation, but are synthesized as linear chains by the ribosome during translation. It is therefore natural to ask at which point during synthesis proteins fold, and whether this differs from the folding of isolated protein molecules. By studying folding of a well characterized protein domain, titin I27, stalled at different points during translation, we show that it already folds in the mouth of the ribosome exit tunnel, and that the mechanism is almost identical to that of the isolated protein.

biophysics↗

bioRxiv2018

qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps

Proteins and ligands sample a conformational ensemble that governs molecular recognition, activity, and dissociation. In structure-based drug design, access to this conformational ensemble is critical to understand the balance between entropy and enthalpy in lead optimization. However, ligand conformational heterogeneity is currently severely underreported in crystal structures in the Protein Data Bank, owing in part to a lack of automated and unbiased procedures to model an ensemble of protein-ligand states into X-ray data. Here, we designed a computational method, qFit-ligand, to automatically resolve conformationally averaged ligand heterogeneity in crystal structures, and applied it to a large set of protein receptor-ligand complexes. We found that up to 29 % of a dataset of protein crystal structures bound with drug-like molecules present evidence of unmodeled, averaged, relatively isoenergetic conformations in ligand-receptor interactions. In many retrospective cases, these alternate conformations were adventitiously exploited to guide compound design, resulting in improved potency or selectivity. Combining qFit-ligand with high-throughput screening or multi-temperature crystallography could therefore augment the structure-based drug design toolbox.

biophysics↗

bioRxiv2018

The yeast GRASP Grh1 displays a high polypeptide backbone mobility along with an amyloidogenic behavior

GRASPs are proteins involved in cell processes that seem paradoxical, such as being responsible for shaping the Golgi cisternae and also involved in unconventional secretion mechanisms that bypass the Golgi, among other functions in the cell. Despite its involvement in several relevant cell processes, there is still a considerable lack of studies on full-length GRASPs. Our group has previously reported an unexpected behavior of the full-length GRASP from the fungus C. neoformans: its intrinsically-disordered characteristic. Here, we generalize this finding by showing that is also observed in the GRASP from the yeast S. cerevisae (Grh1), which strongly suggests it may be a general property within the GRASP family. Furthermore, Grh1 is also able to form amyloid fibrils either upon heating or when submitted to changes in the dielectric constant of its surroundings, a condition that is experienced by the protein when in close contact with membranes of cell compartments, such as the Golgi apparatus. Intrinsic disorder and amyloid fibril formation can thus be two structural properties exploited by GRASP during its functional cycle.

biophysics↗

bioRxiv2018

Mechanical evolution of DNA double-strand breaks in the nucleosome

Double strand breaks in the DNA backbone are the most lethal type of defect that can be induced in the cell nucleus by chemical and radiation treatments of cancer. However, little is known about the potentially large differences in the outcomes of damage between free and nucleosomal DNA, leading to corresponding differences in damage repair capability. We performed microsecond-length molecular dynamics computer simulations of nucleosomes including double-strand breaks (DSB) at various sites, to characterize the early stages of the evolution of this important DNA lesion right after its formation. We find that all DSB configurations tend to remain compact, with only the terminal bases interacting with histone proteins; the interacting molecular structures are studied by looking at the essential dynamics of the relevant DNA and histone fragments, and compared to the intact nucleosome, thus exposing key features of the interactions. Moreover, we show that the broken DNA ends at the DSB must overcome a free-energy barrier to detach from the nucleosome core, as measured by means of umbrella sampling of the potential of mean force. Finally, by using state-of-the-art calculation of the covariant mechanical stress at the molecular scale, we demonstrate that, depending on the DNA-core separation distance, the coupled bending and torsional stress stored in the detached DNA can force the free end to either stick back to the nucleosome core surface, or to open up straight, thus making it accessible to damage signalization proteins.

biophysics↗

bioRxiv2018

An Adaptive Flagellar Photoresponse Determines the Dynamics of Accurate Phototactic Steering in Chlamydomonas

Our understanding of phototaxis of biflagellates stems almost exclusively from the model alga Chlamydomonas reinhardtii, via studies of its flagella, light-sensor and steering. However, no comprehensive model linking all these aspects of its physiology and behavior has been constructed and tested experimentally. Here, we develop such a mathematical model by coupling an adaptive flagellar photoresponse to rigid-body dynamics tailored to details of flagellar beating, and corroborate it with experimental data - at the flagellar and tactic levels - to explain the accurate phototactic steering of this alga. We experimentally validate the hypothesized adaptive flagellar photoresponse using high spatio-temporal resolution methodology on immobilized cells, and corroborate the predicted reorientation dynamics of phototactic swimmers using 3D-tracking of free-swimming cells. Finally, we reconfirm, both theoretically and experimentally, that the adaptive nature of the response has peak fidelity at a frequency of about 1.6 Hz, corresponding to the rotation frequency of the cell body.

biophysics↗

bioRxiv2018

Exposure of zebra mussels to extracorporeal shock waves demonstrates formation of new mineralized tissue inside and outside the focus zone

A substantial body of evidence supports the use of extracorporeal shock wave therapy (ESWT) for fracture nonunions in human medicine. However, the success rate (i.e., radiographic union at six months after ESWT) is only approximately 75%. Detailed knowledge regarding the underlying mechanisms that induce bio-calcification after ESWT is limited. The aim of the present study was to analyze the biological response within mineralized tissue of a new invertebrate model organism, the zebra mussel Dreissena polymorpha, after exposure with extracorporeal shock waves (ESWs). Mussels were exposed to ESWs with positive energy density of 0.4 mJ/mm2 or were sham exposed. Detection of newly calcified tissue was performed by concomitantly exposing the mussels to fluorescent markers. Two weeks later, the fluorescence signal intensity of the valves was measured. Mussels exposed to ESWs showed a statistically significantly higher mean fluorescence signal intensity within the shell zone than mussels that were sham exposed. Additional acoustic measurements revealed that the increased mean fluorescence signal intensity within the shell of those mussels that were exposed to ESWs was independent of the size and position of the focal point of the ESWs. These data demonstrate that induction of bio-calcification after ESWT may not be restricted to the region of direct energy transfer of ESWs into calcified tissue. The results of the present study are of relevance for better understanding of the molecular and cellular mechanisms that induce formation of new mineralized tissue after ESWT. Specifically, bio-calcification following ESWT may extend beyond the direct area of treatment.\n\nSummary statementThe use of zebra mussels in research on extracorporeal shock wave (ESW) therapy for fracture nonunions allows new insights into the complex process of induction of biomineralization by ESWs.

biophysics↗

bioRxiv2018

Automatic error control during forward flux sampling of rare events in master equation models

Enhanced sampling methods, such as forward flux sampling (FFS), have great capacity for accelerating stochastic simulations of nonequilibrium biochemical systems involving rare events. However, the description of the tradeoffs between simulation efficiency and error in FFS remains incomplete. We present a novel and mathematically rigorous analysis of the errors in FFS that, for the first time, covers the contribution of every phase of the simulation. We derive a closed form expression for the optimally efficient count of samples to take in each FFS phase in terms of a fixed constraint on sampling error. We introduce a new method, forward flux pilot sampling (FFPilot), that is designed to take full advantage of our optimizing equation without prior information or assumptions about the phase weights and costs along the transition path. In simulations of both single- and multi-dimensional gene regulatory networks, FFPilot is able to completely control sampling error. Higher dimensional systems have additional sources of error and we show that this extra error can be traced to correlations between phases due to roughness on the probability landscape. Finally, we show that in sets of simulations with matched error, FFPilot is on the order of tens-to-hundreds of times faster than direct sampling, in a fashion that scales with the rarity of the events.

biophysics↗

bioRxiv2018

From 1D sequence to 3D chromatin dynamics and cellular functions: a phase separation perspective

The high-order chromatin structure plays a non-negligible role in gene regulation. However, the mechanism for the formation of different chromatin structures in different cells and the sequence dependence of this process remain to be elucidated. As the nucleotide distributions in human and mouse genomes are highly uneven, we identified CGI forest and prairie genomic domains based on CGI density, which better segregates genomic elements along the genome than GC content. The genome is then divided into two sequentially, epigenetically, and transcriptionally distinct regions. These two types of megabase-sized domains spatially segregate, but to a different extent in different cell types. Overall, the forests and prairies gradually segregate from each other in development, differentiation, and senescence. The multi-scale forest-prairie spatial intermingling is cell-type specific and increases in differentiation, thus helps define the cell identity. We propose that the phase separation of the 1D mosaic sequence in space, serving as a potential driving force, together with cell type specific epigenetic marks and transcription factors, shapes the chromatin structure in different cell types and renders them distinct genomic properties. The mosaicity of the genome manifested in terms of alternative forests and prairies of a species could be related to its biological processes such as differentiation, aging and body temperature control.

biophysics↗

bioRxiv2018

Physiological motion of the carotid atherosclerotic plaque quantified using ultrasound B-Mode image analysis

BackgroundPhysical motion throughout the cardiac cycle may contribute to the rupture of the atherosclerotic carotid plaque, resulting in ischaemic stroke. The purpose of this study was to quantify the physiological motion of the atherosclerotic carotid plaque and to investigate any relationship between the quantified motion parameters and the degree of stenosis, greyscale plaque characteristics, and the presence of cerebrovascular symptoms.\n\nMethodsDisplacement, velocity and acceleration of 81 plaques (51% symptomatic, stenosis range 10%-95%) from 51 patients were measured using an automated system employing a block matching algorithm relative to the ultrasound probe and relative to the periadventitial tissues, over a mean duration of 5 cardiac cycles.\n\nResultsAveraged across all plaques, the displacement amplitude was 1.2 mm relative to the probe, and 0.35 mm relative to the periadventitial tissues. Maximum and mean plaque velocities were 4.7 and 1.3 mm/s relative to the ultrasound probe, and 2.4 and 0.70 mm/s relative to the periadventitial tissues. The corresponding acceleration magnitudes were 69 and 22 mm/s2 relative to the probe, and 57 and 18 mm/s2 relative to the periadventitial tissues. There were no significant differences in any of the motion parameters, with respect to the presence of cerebrovascular symptoms, and none of the parameters showed a statistically significant relationship to the degree of stenosis, and the greyscale plaque characteristics (p[≤]0.05). The technique used was able to detect plaque motion amplitudes above 50m.\n\nConclusionsThis study provides quantitative data on the physiological motion of the atherosclerotic carotid plaque in-vivo. No significant relationship was found between the measured motion parameters and the presence of cerebrovascular symptoms, the degree of stenosis, and the greyscale plaque characteristics.

biophysics↗

bioRxiv2018

Membrane bending energy and tension govern mitochondrial division

During mitochondrial fission, key molecular and cellular factors assemble on the outer mitochondrial membrane, where they coordinate to generate constriction. Constriction sites can eventually divide, or reverse upon disassembly of the machinery. However, a role for membrane tension in mitochondrial fission, although speculated, has remained undefined. We captured the dynamics of constricting mitochondria in mammalian cells using live-cell structured illumination microscopy (SIM). By analyzing the diameters of tubules that emerge from mitochondria and implementing a fluorescence lifetime-based mitochondrial membrane tension sensor, we discovered that mitochondria are indeed under tension. Under perturbations that reduce mitochondrial tension, constrictions initiate at the same rate, but are less likely to divide. We propose a model based on our estimates of mitochondrial membrane tension and bending energy in living cells which accounts for the observed probability distribution for mitochondrial constrictions to divide.

biophysics↗

bioRxiv2018

Halogen-aromatic π-interactions modulate inhibitor residence time

Prolonged drug residence times may result in longer lasting drug efficacy, improved pharmacodynamic properties and \"kinetic selectivity\" over off-targets with fast drug dissociation rates. However, few strategies have been elaborated to rationally modulate drug residence time and thereby to integrate this key property into the drug development process. Here, we show that the interaction between a halogen moiety on an inhibitor and an aromatic residue in the target protein can significantly increase inhibitor residence time. By using the interaction of the serine/threonine kinase haspin with 5-iodotubercidin (5-iTU) derivatives as a model for an archetypal active state (type I) kinase-inhibitor binding mode, we demonstrate that inhibitor residence times markedly increase with the size and polarizability of the halogen atom. This key interaction is dependent on the interactions with an aromatic residue in the gate keeper position and we observe this interaction in other kinases with an aromatic gate keeper residue. We provide a detailed mechanistic characterization of the halogen-aromatic {pi} interactions in the haspin-inhibitor complexes by means of kinetic, thermodynamic, and structural measurements along with binding energy calculations. Since halogens are frequently used in drugs and aromatic residues are often present in the binding sites of proteins, our results provide a compelling rationale for introducing aromatic-halogen interactions to prolong drug-target residence times.

biophysics↗

bioRxiv2018

Homeostasis of protein and mRNA concentrations in growing cells

Many experiments show that the numbers of mRNA and protein are proportional to the cell volume in growing cells. However, models of stochastic gene expression often assume constant transcription rate per gene and constant translation rate per mRNA, which are incompatible with these experiments. Here, we construct a minimal gene expression model to fill this gap. Assuming ribosomes and RNA polymerases are limiting in gene expression, we find that (1) because the ribosomes translate all proteins, the concentrations of proteins and mRNAs are regulated in an exponentially growing cell volume; (2) the competition between genes for the RNA polymerases makes the transcription rate independent of the genome number. Furthermore, by extending the model to situations in which DNA (mRNA) can be saturated by RNA polymerases (ribosomes) and becomes limiting, we predict a transition from exponential to linear growth of cell volume as the protein-to-DNA ratio increases.

biophysics↗

bioRxiv2018

Determining a reasonable range of relative numerical tolerance values for simulating deterministic models of biochemical reactions

What values of relative numerical tolerance should be chosen in simulation of a deterministic model of a biochemical reaction is unclear, which impairs the modeling effort since the simulation outcomes of a model may depend on the relative numerical tolerance values. In an attempt to provide a guideline to selecting appropriate numerical tolerance values in simulation of in vivo biochemical reactions, reasonable numerical tolerance values were estimated based on the uncertainty principle and assumptions of related cellular parameters. The calculations indicate that relative numerical tolerance values can be reasonably set at or around 10-4 for the concentrations expressed in ng/L. This work also suggests that further reducing relative numerical values may result in erroneous simulation results.

biophysics↗

bioRxiv2018

Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA

We develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes base-stacking, hydrogen bond, and electrostatic interactions as well as bond-stretching and bond angle potentials that account for the polymeric nature of DNA. The choices of force constants for stretching and the bending potentials were guided by a Boltzmann inversion procedure using a large representative set of DNA structures extracted from the Protein Data Bank. Some of the parameters in the stacking interactions were calculated using a learning procedure, which ensured that the experimentally measured melting temperatures of dimers are faithfully reproduced. Without any further adjustments, the calculations based on the TIS model reproduces the experimentally measured salt and sequence dependence of the size of single stranded DNA (ssDNA), as well as the persistence lengths of poly(dA) and poly(dT) chains. Interestingly, upon application of mechanical force the extension of poly(dA) exhibits a plateau, which we trace to the formation of stacked helical domains. In contrast, the force-extension curve (FEC) of poly(dT) is entropic in origin, and could be described by a standard polymer model. We also show that the persistence length of double stranded DNA, formed from two complementary ssDNAs with one hundred and thirty base pairs, is consistent with the prediction based on the worm-like chain. The persistence length, which decreases with increasing salt concentration, is in accord with the Odijk-Skolnick-Fixman theory intended for stiff polyelectrolyte chains near the rod limit. The range of applications, which did not require adjusting any parameter after the initial construction based solely on PDB structures and melting profiles of dimers, attests to the transferability and robustness of the TIS model for ssDNA and dsDNA.

biophysics↗