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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 541 records · Page 30Linked to original sources

bioRxiv2018

Force-profile analysis of the cotranslational folding of HemK and filamin domains: Comparison of biochemical and biophysical folding assays

We have characterized the cotranslational folding of two small protein domains of different folds - the a-helical N-terminal domain of HemK and the {beta}-rich FLN5 filamin domain - by measuring the force that the folding protein exerts on the nascent chain when located in different parts of the ribosome exit tunnel (Force-Profile Analysis - FPA), allowing us to compare FPA to three other techniques currently used to study cotranslational folding: real-time FRET, PET, and NMR. We find that FPA identifies the same cotranslational folding transitions as do the other methods, and that these techniques therefore reflect the same basic process of cotranslational folding in similar ways.

molecular biology↗

bioRxiv2018

Biophysical characterizations of the recognition of the AAUAAA polyadenylation signal

Most eukaryotic messenger RNA precursors must undergo 3-end cleavage and polyadenylation for maturation. We and others recently reported the structure of the AAUAAA polyadenylation signal (PAS) in complex with the protein factors CPSF-30, WDR33 and CPSF-160, revealing the molecular mechanism for this recognition. Here we have characterized in detail the interactions between the PAS RNA and the protein factors using fluorescence polarization experiments. Our studies show that AAUAAA is recognized with ~1 nM affinity by the CPSF-160-WDR33-CPSF-30 ternary complex. Variations in the RNA sequence can greatly reduce the affinity. Similarly, mutations of residues that have van der Waals interactions with the bases of AAUAAA also lead to substantial reductions in affinity. Finally, our studies confirm that both CPSF-30 and WDR33 are required for binding the PAS RNA, and determine a ~7 nM affinity between CPSF-30 and the CPSF-160-WDR33 binary complex.

biochemistry↗

bioRxiv2019

From plasmodesma geometry to effective symplastic permeability through biophysical modelling

Regulation of molecular transport via intercellular channels called plasmodesmata (PDs) is important for both coordinating developmental and environmental responses among neighbouring cells, and isolating (groups of) cells to execute distinct programs. Cell-to-cell mobility of fluorescent molecules and PD dimensions (measured from electron micrographs) are both used as methods to predict PD transport capacity (i.e., effective symplasmic permeability), but often yield very different values. Here, we build a theoretical bridge between both experimental approaches by calculating the effective symplasmic permeability from a geometrical description of individual PDs and considering the flow towards them. We find that a dilated central region has the strongest impact in thick cell walls and that clustering of PDs into pit fields strongly reduces predicted permeabilities. Moreover, our open source multi-level model allows to predict PD dimensions matching measured permeabilities and add a functional interpretation to structural differences observed between PDs in different cell walls.

cell biology↗

bioRxiv2019

Robust emergence of sharply tuned place cell responses in hippocampal neurons with structural and biophysical heterogeneities

Hippocampal pyramidal neurons sustain propagation of fast electrical signals and are electrotonically non-compact structures exhibiting cell-to-cell variability in their complex dendritic arborization. In this study, we demonstrate that sharp place-field tuning and several somato-dendritic functional maps concomitantly emerge despite the presence of geometrical heterogeneities in these neurons. We establish this employing an unbiased stochastic search strategy involving thousands of models that spanned several morphologies and distinct profiles of dispersed synaptic localization and channel expression. Mechanistically, employing virtual knockout models, we explored the impact of bidirectional modulation in dendritic spike prevalence on place-field tuning sharpness. Consistent with prior literature, we found that across all morphologies, virtual knockout of either dendritic fast sodium channels or N-methyl-D-aspartate receptors led to a reduction in dendritic spike prevalence, whereas A-type potassium channel knockouts resulted in a nonspecific increase in dendritic spike prevalence. However, place-field tuning sharpness was critically impaired in all three sets of virtual knockout models, demonstrating that sharpness in feature tuning is maintained by an intricate balance between mechanisms that promote and those that prevent dendritic spike initiation. From the functional standpoint of the emergence of sharp feature tuning and intrinsic functional maps, within this framework, geometric variability was compensated by a combination of synaptic democracy, the ability of randomly dispersed synapses to yield sharp tuning through dendritic spike initiation, and ion-channel degeneracy. Our results suggest electrotonically non-compact neurons to be endowed with several degrees of freedom, encompassing channel expression, synaptic localization and morphological micro-structure, in achieving sharp feature encoding and excitability homeostasis.

neuroscience↗

bioRxiv2019

Biophysical properties of intermediate states of EMT outperform both epithelial and mesenchymal states.

Potential metastatic cells can dissociate from a primary breast tumor by undergoing an epithelial-to-mesenchymal transmission (EMT). Recent work has revealed that cells in intermediate states of EMT acquire an augmented capacity for tumor-cell dissemination. These states have been characterized by molecular markers, but the structural features and the cellular mechanisms that underlie the acquisition of their invasive properties are still unknown. Using human mammary epithelial cells, we generated cells in intermediate states of EMT through the induction of a single EMT-inducing transcription factor, ZEB1, and cells in a mesenchymal state by stimulation with TGF{beta}. In stereotypic and spatially-defined culture conditions, the architecture, internal organization and mechanical properties of cells in the epithelial, intermediate and mesenchymal state were measured and compared. We found that the lack of intercellular cohesiveness in epithelial and mesenchymal cells can be detected early by microtubule destabilization and the repositioning of the centrosome from the cell-cell junction to the cell center. Consistent with their high migration velocities, cells in intermediate states produced low contractile forces compared with epithelial and mesenchymal cells. The high contractile forces in mesenchymal cells powered a retrograde flow pushing the nucleus away from cell adhesion to the extracellular matrix. Therefore, cells in intermediate state had structural and mechanical properties that were distinct but not necessarily intermediate between epithelial and mesenchymal cells. Based on these observations, we found that a panel of triple-negative breast cancer lines had intermediate rather than mesenchymal characteristics suggesting that the structural and mechanical properties of the intermediate state are important for understanding tumor-cell dissemination.

cell biology↗

bioRxiv2019

Brain aging comprises multiple modes of structural and functional change with distinct genetic and biophysical associations

Brain imaging can be used to study how individuals brains are aging, compared against population norms. This can inform on aspects of brain health; for example, smoking and blood pressure can be seen to accelerate brain aging. Typically, a single "brain age" is estimated per subject, whereas here we we identified 62 modes of subject variability, from 21,407 subjects multimodal brain imaging data in UK Biobank. The modes represent different aspects of brain aging, showing distinct patterns of functional and structural brain change, and distinct patterns of association with genetics, lifestyle, cognition, physical measures and disease. While conventional brain-age modelling found no genetic associations, 34 modes had genetic associations. We suggest that it is important not to treat brain aging as a single homogeneous process, and that modelling of distinct patterns of structural and functional change will reveal more biologically meaningful markers of brain aging in health and disease.

neuroscience↗

bioRxiv2019

Biophysical analysis of Plasmodium falciparum Hsp70-Hsp90 organizing protein (PfHop) reveals a monomer that is characterised by folded segments connected by flexible linkers

Plasmodium falciparum causes the most lethal form of malaria. The cooperation of heat shock protein (Hsp) 70 and 90 is important for folding of a select number of cellular proteins that are crucial for cyto-protection and development of the parasites. Hsp70 and Hsp90 are brought into a functional complex that allows substrate exchange by stress inducible protein 1 (STI1), also known as Hsp70-Hsp90 organizing protein (Hop). P. falciparum Hop (PfHop) co-localises and occurs in complex with the parasite cytosolic chaperones, PfHsp70-1 and PfHsp90. Here, we characterised the structure of recombinant PfHop using synchrotron radiation circular dichroism (SRCD) and small-angle X-ray scattering. Structurally, PfHop is a monomeric, elongated but folded protein, in agreement with its predicted TPR domain structure. Using SRCD, we established that PfHop is unstable at temperatures higher than 40 {degrees}C. This suggests that PfHop is less stable at elevated temperatures compared to its functional partner, PfHsp70-1, that is reportedly stable at temperatures as high as 80 {degrees}C. These findings contribute towards our understanding of the role of the Hop-mediated functional partnership between Hsp70 and Hsp90.

biochemistry↗

bioRxiv2025

{Phi}X174 bacteriophage viability predicted by protein biophysical modeling

The relationship between genotype and phenotype underlies our ability to understand and predict evolution. Efforts to build genotype-phenotype (GP) maps have revealed several unifying rules: epistasis is pervasive, fitness effects are not normally distributed, and the GP map is non-linear and complicated for high-level phenotypes. A critical step in developing GP maps is evaluating how well predictive models do in explaining observed phenotypes. We utilize the simplicity of a bacteriophage ({Phi}X174) study system to test if an intermediate phenotype (predicted stability of the G capsid protein) explains more complex phenotypes. In doing so, we compare the predictive performance of free energies of folding and binding obtained using numerous molecular modeling methods as well as phylogenetic and basic biochemical/biophysical properties of amino acid substitutions. By creating a large mutational library, we find that {Phi}X174 tolerates about 50% of the amino acid substitutions we inserted into the G protein and that molecular modeling compliments other substitution models for predicting viability. Mutations predicted to have large destabilizing effects are especially informative and are almost universally detrimental. These large-effect substitutions often coincide with the most conserved residues in the G protein. Apart from large-effect mutations, our ability to predict {Phi}X174 phenotypes is fairly poor and we explore various potential confounding factors (e.g., codon bias) that could be considered to improve viability predictions.

molecular biology↗

bioRxiv2025

Biophysical Modeling Elucidates Mechanistic Principles for Rational Molecular Glue Design

Molecular glues are small molecules that offer a powerful strategy to target previously "undruggable" proteins of interest (POI) by enhancing their interactions with other proteins (effector). Depending on the nature of the effectors, molecular glues can induce stabilizing sequestration or degradation of POI. However, their rational design has been hindered by a poor understanding of how kinetic parameters impact their performance. To address this, we developed a unified mathematical framework that accurately analyzes the dynamics of both glue degraders and stabilizers. Our model reveals that the strong binding affinity of the ternary complex is the key determinant of performance across both modalities, provided that the initial component concentrations and degradation rate constants are fixed. Furthermore, we demonstrate that degrader performance is ultimately limited by its catalytic efficiency and the target proteins natural half-life. We also identify distinct roles for effector abundance, showing that the relative concentrations of the effector and POI are critical for stabilizers but less so for degraders. This quantitative framework provides mechanistic principles for the rationale design and optimization of molecular glues.

molecular biology↗

bioRxiv2025

Structural, biophysical, and virological mechanistic characterization of HIV-1 capsid-targeting antivirals

Due to its significant role in virus replication, the HIV capsid is an attractive antiviral target. This is validated by the recent clinical approval of lenacapavir for both treatment and pre-exposure prophylaxis (PrEP). PF74 is a well-characterized capsid-targeting antiviral that was discontinued in further study due to potency and metabolic issues. We hypothesized that making chemical modifications at certain sites of PF74 could result in capsid-targeting antivirals with improved potency and bioavailability. Our cumulative studies show that making changes at the R1 and R3 positions of PF74 results in compounds with increased antiviral potency, increased stability of wild-type HIV capsid hexamers and virions, tighter binding to wild-type HIV capsid hexamer compared to PF74, and different interactions at the "FG" binding site of capsid compared to PF74. These data provide insights into the design of future capsid-targeting antivirals relevant for clinical use.

biochemistry↗

bioRxiv2026

MyoGen: Unified Biophysical Modeling of Human Neuromotor Activity and Resulting Signals

Understanding human motor control requires integrating cortical and spinal cord activity, muscle mechanics, and electrophysiology, levels that are often studied separately. We present MyoGen, an open-source framework that unifies spinal circuitry, proprioceptive feedback, musculotendon dynamics, cortical activity, and multimodal electromyography (EMG) generation in a single, interoperable platform. Spinal motor neurons and the resulting motor unit (MU) action potentials represent the only neural cells that can be accessed at scale in humans. We used human MU ensembles to validate our model across a wide range of experimental conditions. Using data-driven optimization, we found that MyoGen produces MU population activity that closely matches experimental discharge-rate distributions and discharge variability across human muscles. Moreover, it generates decomposable surface and intramuscular EMG, reproduces beta-band modulation of descending drive and its nonlinear transformation into force, and implements complete sensorimotor loops. Dimensionality reduction of simulated agonist-antagonist EMG reveals low-dimensional control manifolds consistent with experimental recordings from both healthy and spinal cord injured individuals. MyoGen provides physiologically grounded, ground-truth data and integrates seamlessly with analysis pipelines, enabling systematic investigation of motor control principles, validation of signal-processing algorithms, and exploration of sensorimotor interactions that are experimentally inaccessible.

neuroscience↗

bioRxiv2026

Molecular and biophysical requirements for B cell receptor dependent enhancement of dengue virus infection

Dengue virus (DENV) is the causative agent of dengue, a mosquito-borne disease that represents a significant and growing public health burden around the world. A unique pathophysiological feature of dengue is immune-mediated enhancement, wherein preexisting immunity elicited by a primary infection can enhance the severity of a subsequent infection by a heterologous DENV serotype. A leading mechanistic explanation for this phenomenon is antibody dependent enhancement (ADE), where sub-neutralizing concentrations of DENV-specific IgG antibodies facilitate entry of DENV into Fc{gamma}R expressing cells. Accordingly, this model posits that phagocytic mononuclear cells are the primary reservoir of DENV. However, multiple independent groups have shown that B cells are the largest reservoir of virally infected cells in circulation during acute dengue, representing a disconnect in our understanding of immune-mediated DENV tropism. In response to this persistent knowledge gap, our team has previously identified a novel mechanism of immune-mediated enhancement we have termed BCR-dependent enhancement (BDE) of DENV infection. In this study, we show that DENV infection of DENV-reactive B cells is highly sensitive to BCR/DENV envelope (E) protein interactions. DENV entry into this subset of B cells is dynamin-mediated and requires proximal BCR signaling. Finally, we show that DENV-reactive B cells are productively infected by live DENV, capable of supporting active viral replication and dissemination. We propose that BDE provides an additional layer of pathogen-specific immune-mediated infection risk that complements existing models of ADE and offers additional insight into potential mechanisms of DENV immunopathogenesis.

immunology↗

bioRxiv2026

The impact of homeostatic inhibitory plasticity in a generative biophysical model

A main characteristic of biological systems is their capacity to dynamically adapt to environmental changes. In the brain, synaptic plasticity enables the strengthening or weakening of connections between neurons, allowing neural circuits to adapt based on experience, learning, and environmental changes. Yet, it is homeostatically regulated such that it avoids excessive proliferation of synaptic contacts. These mechanisms can be studied with large-scale models of brain activity. Here, we embed a biologically grounded inhibitory-homeostatic plasticity rule into the Dynamic Mean Field (DMF) model, creating a Homeostatic Dynamic Mean Field (HDMF) model that dynamically tunes local excitation-inhibition balance. Convergence of excitatory firing rates is reached by mapping a large range of coupling strength to parameters of inhibitory synapses. The HDMF reproduces statistical observables of brain activity as well as the original DMF, and can sustain neuromodulatory perturbations without overhead computations. The HDMF can generate unprecedented sleep-like slow-wave activity, which can also coexist with wake-like asynchronous dynamics, permitting to model dissociated states of consciousness such as parasomnias. Together, these results show that a single homeostatic rule broadens the stability and expressiveness of the DMF, providing a unified platform for studying how local adaptive processes shape the diverse global dynamics of the human brain.

neuroscience↗

bioRxiv2026

Biophysical properties and phenotypes of cell clusters detached from Staphylococcus epidermidis biofilms after matrix-targeted disruption

Bacterial cells detached from Staphylococcus epidermidis biofilms are found to release predominantly as small oblate clusters ([~]1.9 {micro}m) in both untreated biofilms and biofilms treated with matrix-targeted disruptors. Quantitative image analysis common to colloidal science was applied to quantitatively evaluate the physical properties of 9,147 bacterial clusters detached from S. epidermidis biofilms with and without targeted disruption of individual matrix components (polysaccharides, proteins, extracellular DNA) or solubilization of the extracellular polymeric substances (EPS). Concentrations of S. epidermidis biofilm-detached cells are highest after matrix-targeted disruption of polysaccharides. K-means clustering, an unsupervised machine learning technique, was used to reveal that S. epidermidis biofilm-detached cells are released in five distinct phenotypes: small oblate, mid-sized oblate, large oblate, small spherical, and mid-sized prolate clusters. S. epidermidis biofilm detached cell clusters are predominantly oblate across three size groups (79.5%), with the small oblate phenotype representing 60.1% of cell clusters that have 3.1 {+/-} 1.2 cells per cluster, Euclidean diameters of 1.9 {+/-} 0.4 {micro}m, anisotropy indices of 0.98 {+/-} 0.05, and asphericities of -1.75 {+/-} 0.31 on average. The proportion of S. epidermidis cell clusters within each biofilm-detached cell phenotype differs between matrix-targeted disruptors. There are also variations in the abundance of S. epidermidis biofilm detached cells after matrix-targeted disruption between growth conditions and strains. Evaluating the physical properties of biofilm-detached cells after matrix-targeted disruption is critical to understanding their translocation in fluid flow and susceptibility to the host immune response as well as in evaluating matrix-targeted disruption for biofilm control.

microbiology↗

bioRxiv2026

The biophysical basis of enterocyte homeostasis

We present an approach to analysing cell homeostasis using a bond graph modelling approach that ensures that the conservation laws of physics (conservation of mass, charge, and energy, respectively) are satisfied for the interdependent biochemical, electrical, mechanical, and thermal energy storage mechanisms operating within the cell. We apply the bond graph approach to several cell membrane transport mechanisms and then consider how physics constrains intracellular electrolyte homeostasis for enterocytes (the epithelial absorptive cells of the gut). The model includes the electrogenic sodium-potassium ATPase pump (NKA), the glucose transporter (GLUT2), and an inwardly rectifying potassium channel, all in the basolateral membrane, and the electrogenic sodium-driven glucose transporter (SGLT1) in the apical membrane. Glycolysis converts the imported glucose to ATP to drive NKA. For specified levels of sodium, potassium, and glucose in the blood, the model demonstrates how enterocytes absorb sodium and glucose from the gut and transfer glucose to the blood while maintaining the membrane potential and homeostasis of intracellular sodium and potassium. The Gibbs free energy available from the ATP hydrolysis ensures that the cell operates as a sodium battery with a high external to internal ratio of sodium concentration in order to provide the energy for many other cellular transport processes. We show that the 3:2 stoichiometry of Na+/K+ exchange in NKA, coupled with 2:1 Na+/glucose cotransport in SGLT1, a 1:2:2 ratio between glucose consumption and ATP and water production in glycolysis, and K+ and glucose efflux through Kir and GLUT2, respectively, provides a balanced system that maintains homeostasis of intracellular Na+, K+, glucose, ATP and water, and homeostasis of the membrane potential, under varying levels of transport of glucose from the gut to the blood. We also show how the flux expressions for SLC transporters, ATPase pumps and ion channels can all be expressed in a consistent and thermodynamically valid way.

bioengineering↗

bioRxiv2026

Biophysical Modeling of Thalamocortical Circuit Dynamics: Species-Specific Insights into Neural Synchrony, Sleep Spindles, and Mechanisms of Neuropsychiatric Disorders

Thalamocortical circuits play a fundamental role in cognitive functions, and neural synchronization, with disruptions implicated in disorders. Here, we investigated the neural dynamics of thalamocortical connectivity using computational modeling of rodent and primate thalamocortical loops. We incorporated distinct projections and varying network configurations and examined their impact on circuit synchrony, spiking patterns, and sleep spindle generation. Circuits included distinct core and matrix thalamocortical projections, with core pathways providing focal, driving input to middle cortical layers, while matrix pathways mediate widespread, modulatory signaling across superficial layers, and the presence of thalamic interneurons, which are scarce in rodents but comprise up to a third of the thalamic neurons in primates. In our simulations, these distinctions produced clear species-and loop architecture-dependent effects: rodent circuits were markedly more sensitive to parameter changes in core and matrix thalamocortical connectivity strength, while primate circuits maintained relatively stable spatiotemporal patterns across parameter variations, exhibiting greater stability and synchrony. Sleep spindle analysis likewise revealed species differences. Overall, across all thalamocortical configurations, rodent simulations produced spindles with greater spatiotemporal variability, showing irregular event structure and timing. In contrast, primate spindles were more uniform and coherent, with clearer and more consistent organization across neurons and time. These findings provide insights into species-specific differences in thalamocortical dynamics and have implications for modeling sensory and cognitive disruptions in disorders such as autism and schizophrenia. By incorporating distinct configurations, and interspecies differences, our model contributes to understanding how thalamocortical dysregulation may differentially impact spindle generation, network synchrony, and information processing across species.

neuroscience↗

bioRxiv2026

Improved Protein Semi-Synthesis Enables Biophysical Studies of Thioamide Destabilization of β-Sheet Interactions

Thioamides are natural post-translational modifications of the peptide backbone and can be introduced synthetically to probe protein folding or functionalize peptides for translational applications. In this work, we demonstrate that thioamide-containing peptides with C-terminal thioesters can be efficiently generated using Knorr pyrazole activation and used in subsequent native chemical ligation reactions to generate thioamide containing proteins. We compare this method to acyl azide activation and find that both routes provide similar yields. We also investigate ultrasound-mediated desulfurization of the ligation site cysteine for potential advantages over chemical radical initiators. Scaling up our syntheses allows us to study thioamide perturbations to the {beta}-sheet region of the B1 domain of protein G (GB1) as well as {beta}-strand interactions in amyloid fibrils of the Parkinsons disease protein -synuclein. In both contexts, we observe dramatic destabilization of the {beta}-sheet networks, manifested in decreased GB1 thermal stability and altered folding and slowed aggregation of -synuclein. These findings illustrate the impact that a single atom substitution can have on cooperative hydrogen bonding networks and prompt future study of both systems.

biochemistry↗

bioRxiv2026

Structural and biophysical insights into the unique RNase YicC

RNA cleavage and processing are highly conserved regulatory mechanisms across bacteria. We recently discovered a novel family of RNases called YicC, conserved across all bacteria but unrelated to known RNase families. The cryo-EM structure of RNA bound to Escherichia coli YicC endonuclease suggested a clamshell-like ribonuclease mechanism for cleavage, although its exact mechanism and function remain elusive. Here, we report new cryo-EM structures that provide snapshots of the closing of the complex and also capture a surprising dimeric-RNA:protein complex. We further characterize the RNA cleavage targets in solution using nuclear magnetic resonance (NMR) spectroscopy, and use all-atom molecular dynamics (MD) simulations to study Mg2+ binding. Our findings suggest that the YicC family can bind RNA hairpin structures and dimeric conformations with appropriate sequence and structural constraints, with cleavage driven strongly by Mg2+ ion localization. This study therefore provides overall insight into the novel cleavage mechanism of the highly conserved family of YicC-like endoribonucleases.

biochemistry↗