Biology subjects

Bhattarai, N.

Publications and source records attributed to Bhattarai, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Bioinformatic Characterization of Regulated IRE1a-Dependent Decay (RIDD) in Heart Failure

Inositol-requiring enzyme 1a (IRE1a) is a canonical signaling factor in the unfolded protein response (UPR). In addition to this essential role (which prevents the accumulation of misfolded proteins in the endoplasmic reticulum), the endoribonuclease activity of IRE1a targets multiple mRNAs for degradation through a process called Regulated IRE1a-Dependent Decay (RIDD). The products of over 50 genes have been identified as RIDD targets; however, the biological significance of this process remains underexplored. Using publicly available datasets, we examined the fate of 27 well-characterized RIDD targets in the septal wall of heart failure patients, and in mice subject to pressure overload-induced heart failure. We show that decreased mRNA abundance from these RIDD substrate genes - an outcome consistent with RIDD induction - is commonly observed in heart failure.

cell biology↗

bioRxiv2026

Physical laws predict methane hotspots in global mountain waters

Accurate accounting of aquatic methane emissions is critical for climate change mitigation, yet current global budgets overlook a key driver: the elevation-regulated atmospheric pressure. Here, we present the first large-scale investigation of methane ebullition across 164 shallow waters spanning elevations from sea level to 4886 meters. We demonstrate that ebullition rate increases with elevation-over four times higher at >3000 m a.s.l. than at sea level-due to two synergistic, pressure-dependent physical mechanisms: a degas effect (enhanced bubble formation) and a trigger effect (facilitated bubble ascent). Independent theoretical prediction of the combined effects shows near-perfect agreement with the empirical elevation trend, quantitatively confirming that these physical mechanisms are the primary drivers of enhanced ebullition at high elevations. Our findings reveal that mountain aquatic ecosystems represent unaccounted methane hotspots that have been systematically underestimated in global inventories.We therefore call for urgent integration of these ecosystems into IPCC assessments and targeted mountain mitigation and sustainable management strategies.

ecology↗

bioRxiv2026

A model for PIP2/3 and Rnd1 effects on Plexin-B1 GAP activity on Rap1b GTPase derived from molecular dynamics simulations

Plexin-B1 is a transmembrane receptor that integrates signals from Rho-family and Ras-family (Rap1b) GTPases to regulate cellular processes. While ligand simulated activation of the receptor is largely understood, the role of membrane composition and GTPase allosteric effects on plexin structure, internal protein dynamics, and function is still to be elucidated. Here, we performed multi-replica, 1 s all-atom simulations of Plexin-B1-GTPase complexes on PIP2- and PIP3-containing membranes to investigate the effects of these two signaling lipids, as well as on the GTPases. We found that both Rap1b and Rnd1 stably associate with the membrane, with PIP2 promoting broader lipid engagement and stronger Rap1b-Plexin-B1 interactions, whereas PIP3 enhances Rnd1-Plexin contacts and induces a membrane proximal orientation of Plexins juxtamembrane helix and makes contacts with a previously discovered activation switch loop. Contact map and network analyses revealed lipid-dependent shifts in allosteric communication, with PIP2 favoring Rap1b-centric hotspots and PIP3 favoring Rnd1-centric pathways. These predictions allow us to suggest a model for plexin intracellular region activation where both the identity of phosphoinositides and GTPase context synergistically stabilize Plexin-B1 membrane engagement, alter structural dynamics, and allosteric networks. Thus, we propose that the membrane is an active modulator of plexin receptor signaling.

biophysics↗

bioRxiv2025

From Dimerization to Signaling: Molecular Dynamics Insights into EphA1 and EphA2 Isoform Specificity

Ephrin receptors (Ephs) are receptor tyrosine kinases that regulate cellular growth, differentiation, and motility. EphA2, often overexpressed in cancer, is notable for its ligand-independent activation, which drives pro-oncogenic signaling distinct from the canonical, ligand-dependent pathway that restricts cell movement. While ligand binding induces extracellular clustering, kinase activation depends on dimerization within the transmembrane (TM) region. EphA1 and EphA2 differ substantially in their function, likely due to differences in their TM, but more-so in their juxtamembrane (JM), and membrane-proximal fibronectin type III (FN1/FN2) domains. How these latter two regions modulate dimerization has not yet been investigated. To address this, we performed extensive coarse-grained (CG) simulations using Martini 3 in an anionic POPC/PS/PIP2 model of the plasma membrane. Both receptors formed stable TM dimers, though EphA1 favored a symmetric AXXXGXXXG-centered interface, whereas EphA2 favoured an alternate leucine zipper interface. All protein constructs sampled multiple configurations, reflecting substantial intrinsic variability. AlphaFold3 does not yield reliable predictions and cannot account of effects of the lipid bilayer. In the CG simulations, basic residues in the JM region remained membrane-bound, and the EphA2 FN domain displayed sustained PIP2 interactions, consistent with previous observations. Notably, constructs with the FN2 domain alone restricted TM association in both receptors, whereas inclusion of the second FN1 domain restored dimerization but produced receptor-specific extracellular interfaces. These differences arise from distinct FN1-FN2 linker flexibilities, a different level sequence conservation of EphA1 compared to several other Ephs and FN-domain membrane contacts, which together shape TM geometry and lipid engagement. Our results predict how TM and TM-proximal elements cooperatively tune dimerization in Eph receptors. This work offers a molecular rationale into the divergent activation behaviors of EphA1 and EphA2 and provides testable models relevant to cancer biology and Eph-driven signaling.

biophysics↗

bioRxiv2025

Aer is a bidirectional redox sensor mediating negative chemotaxis to antibiotic-induced ROS in E. coli

The Aer chemoreceptor in E. coli is known to perform oxygen- or aero-taxis by sensing metabolic flux through ETC via an FAD cofactor bound to its PAS domain. We show in this study that Aer also senses oxidative stress and performs FAD-dependent negative chemotaxis in response to the known ROS H2O2. The ability of Aer to detect both oxidizing and reducing intracellular environments redefines its functional range and establishes Aer as a bidirectional redox sensor. We show in addition that the ability of bacterial swarms to move away from bactericidal antibiotics is Aer-dependent and is abolished by expression of the catalase-peroxidase enzyme KatG, which scavenges intracellular ROS. Our study thus provides independent behavioral evidence that certain antibiotics generate intracellular ROS, while also offering a sensitive assay for detecting these reactive species. ImportanceMotile bacteria rely on aerotaxis to seek environments that maximize energy production. We show that in E. coli, Aer mediates not only positive chemotaxis toward favorable redox conditions but also negative chemotaxis in response to oxidative stress. The ability of Aer to detect both oxidizing and reducing cellular environments reveals an unexpected sensory versatility, shared to varying degrees by other E. coli chemoreceptors. We show that E. coli uses Aer to actively move away from ROS-generating antibiotics, revealing a previously unrecognized behavioral mechanism for bacterial survival under oxidative stress.

microbiology↗

bioRxiv2025

Essential Role for Trf2 in Cardiac Development and Function

Telomere Repeat-binding Factor 2 (Trf2) is essential for protecting our telomeres. While Trf2 global deletion is lethal, its role in organ-specific development, particularly in the heart, remains less understood. In this study, we investigated the role of Trf2 in cardiac development and function. Our studies reveal that cardiomyocyte (CM)-specific loss of Trf2 leads to profound defects in heart morphology, including impaired ventricular wall formation and compromised CM proliferation, concurrent with no CM telomere length attrition. Further, in vivo functional assessment and molecular analyses of CM-Trf2 deficient ventricles revealed severe cardiac dysfunction and, interestingly, altered nuclear envelope gene expression, respectively. Our work provides new insights into the essential role of Trf2 in heart development and function, and potential avenues for therapeutic intervention targeting telomere biology.

developmental biology↗

bioRxiv2025

Texas 2-Step: A new Model for YcgR::c-di-GMP Action at the Flagellar Motor

YcgR is a c-di-GMP effector that inhibits chemotaxis and swimming speed in Escherichia coli and Salmonella. Genetic, biochemical, and structural studies suggest that YcgR interacts with both the bidirectional flagellar rotor and the stator to bias rotation toward counterclockwise (CCW) and reduce motor speed, but the underlying mechanism remains unresolved. Recent cryo-EM structures revealing conformational changes in the rotor-stator complex during directional switching suggested to us a mechanism by which YcgR acts. We call this the Texas 2-Step model, after the country dance in which partners move smoothly in a CCW arc with quick steps followed by slow ones. In this model, YcgR first binds a MotA subunit when the rotor adopts the CCW conformation, in which stators are largely displaced from the C-ring. In the next step, the rotating MotA pentamer delivers YcgR to the rotor protein FliG, thereby slowing motor speed. We provide evidence for the first step of this model, offering testable predictions for future work. ImportanceThe mechanism of YcgR action has been investigated by multiple laboratories using diverse approaches, yet no consensus has emerged. Some studies implicate the rotor, others the stator. A key complication is the involvement of four interacting proteins--MotA, FliG, FliM, and YcgR--with multiple contact sites in several of them. Recent rotor-stator cryo-EM structures revealing conformational changes during directional switching suggested a mechanism that we set out to test. Our experiments show that rotor conformation is crucial for YcgR function.

microbiology↗

bioRxiv2025

Adropin protects against cardiac metabolic remodeling and dysfunction in HFpEF

Cardiometabolic heart failure with preserved ejection fraction (HFpEF) is a heterogenous metabolic disease, which in the heart presents as left ventricle diastolic dysfunction, ventricular stiffness, and myocardial structural remodeling. Deleterious changes in cardiac metabolism are central to HFpEF pathophysiology, and proposed treatments for the disease have focused on repairing these defects. In this study, we used a preclinical mouse model that recapitulates cardiometabolic HFpEF to elucidate the molecular mechanisms driving cardiac dysfunction, and tested whether recombinant Adropin (a liver- and brain-derived endogenous peptide hormone) could reverse observed defects. We show that long-term treatment with Adropin reversed multiple markers of HFpEF-related cardiac dysfunction (including fibrosis, diastolic dysfunction, and cardiomyocyte hypertrophy). Using untargeted metabolomics, we found that Adropin treatment reduced hexosamine biosynthesis pathway activity, leading to a reduction in the O-GlcNAcylation of the cardiac fatty acid oxidation enzyme long chain acyl-CoA dehydrogenase (LCAD). Reducing LCAD O-GlcNAcylation increased LCAD activity in vitro, and reduced the accumulation of long-chain acylcarnitines in HFpEF mouse hearts in vivo. Our results suggest that Adropin may restore cardiac metabolic function in HFpEF, and that targeting this pathway may be a novel therapeutic avenue for this disease. CLINICAL PERSPECTIVE- Adropin is a circulating liver- and brain-derived peptide that regulates energy metabolism in the heart and other high metabolic-demand tissues. The plasma abundance of Adropin is decreased in diabetic, hypertensive, and aged individuals; all comorbid risk factors for the development of heart failure with preserved ejection (HFpEF). We therefore examined the potential role of Adropin in HFpEF pathophysiology. - Patients with HFpEF display significant reductions in circulating Adropin levels, matching those seen in comorbid diseases. In a mouse model of HFpEF, treatment with recombinant Adropin reduced diastolic dysfunction, cardiac fibrosis, and cardiomyocyte hypertrophy. - These data suggest that targeting the Adropin pathway may represent a new therapeutic approach in HFpEF.

physiology↗

bioRxiv2025

Computation model predicts Rho GTPase function with the Plexin Transmembrane receptor GAP activity on Rap1b via dynamic allosteric changes

Plexin-semaphorin signaling regulates key processes such as cell migration, neuronal development, angiogenesis, and immune responses. Plexins stand out because they can directly bind with both Rho- and Ras-family small GTPases through their intracellular domains when these GTPases are in their active, GTP-bound states. This binding occurs via intracellular regions which include a Rho-GTPase Binding Domain (RBD) and a GTPase Activating Protein (GAP) segment. Studies have shown that Rho and Ras GTPases play vital roles in plexin signaling and activation. However, the structural dynamics of plexins and GTPases and how these conformational changes affect interactions when plexin is bound with both Ras and Rho-GTPases or bound to only one specific GTPase has remained unclear. In this study, we conducted molecular dynamics (MD) simulations on six distinct plexin-GTPase bound systems to investigate the differences in conformations and dynamics between Plexin-B1 and three GTPases: Rap1b, Rnd1, and Rac1. Our analysis revealed that dynamics with Rac1 are more altered, compared to Rnd1 depending on whether plexins GAP domain is bound or unbound to Rap1b. In addition, we further investigated alterations in network centralities and compared the network dynamics of the Plexin-GTPases complexes, focusing on the differences when Plexin is bound to both Ras (Rap1b) and Rho-GTPases (Rnd1/Rac1) versus when it is bound to only one GTPase. Our study revealed that Rnd1 exhibits stronger and more stable interactions with Plexin-B1 in the absence of Rap1b, while Rac1 shows fewer and less stable connections in comparison. These computational models have features that broadly agree with experimental results from hydrogen-deuterium exchange detected by mass spectrometry (HDX-MS). Such insights provide a better understanding of the molecular mechanisms underlying Plexin-GTPase interactions and the complexities of signaling mechanisms involving GTPases in general.

biophysics↗

bioRxiv2025

Cardiac-specific deletion of GCN5L1 promotes fatty liver disease in HFpEF

The prevalence of cardiometabolic heart failure with preserved ejection fraction (HFpEF) continues to grow, representing over half of heart failure cases in the United States. As no specific medication for HFpEF exists, treatment guidelines focus on the management of comorbidities related to metabolic syndrome (e.g. obesity, diabetes, hypertension) that promote the disease1. These same comorbidities also drive pathology in non-cardiac tissues, and the links between cardiometabolic disease presentations in different organs are increasingly being recognized. Preclinical studies on the potential crosstalk between HFpEF and metabolic disease in the liver (e.g. metabolic dysfunction-associated liver disease; MASLD) have focused on how liver dysfunction may affect the heart, particularly through the release of secreted liver proteins. This may reflect the situation in the clinic, where incident MASLD is a risk factor for future HFpEF development. Here, in contrast to this developing paradigm of liver-initiated cardiac disease, we report for the first time a defect in cardiac metabolism related to the mitochondrial metabolic protein GCN5L1 that drives hepatic steatosis and MASLD in HFpEF.

physiology↗

bioRxiv2025

Cholesterol-Dependent Dimerization and Conformational Dynamics of EphA2 Receptors: Insights from Coarse-Grained and All-Atom Simulations

The EphA2 transmembrane receptor regulates cellular growth, differentiation, and motility, and its overexpression in various cancers makes it a potential biomarker for clinical cancer management. EphA2 signaling occurs through ligand-induced dimerization, where the transmembrane (TM) and juxtamembrane (JM) domains play crucial roles in stabilizing the dimer conformations and thereby facilitating signal transduction. Electrostatic interactions between basic JM residues and signaling lipids (PIP2 and PIP3) regulate phosphorylation while Cholesterols potential role in modulating EphA2 activation remains unclear. To investigate this, we modeled the TM-full JM peptide of EphA2 and employed coarse-grain and all-atom simulations to investigate its dimerization in cholesterol-rich and cholesterol-deficient membranes. Our findings reveal that cholesterol stabilizes specific TM dimers and TM-JM interactions with PIP2, highlighting the importance of membrane composition in EphA2 dimerization, oligomerization, and clustering. These insights enhance our understanding of lipid-mediated regulation of EphA2 and its implications in receptor signaling and cancer progression.

biophysics↗

bioRxiv2024

TCA Cycle Dysfunction and Amino Acid Catabolism Drive Hepatic Steatosis in Mice with HFpEF

The prevalence of cardiometabolic heart failure with preserved ejection fraction (HFpEF) continues to grow worldwide, and now represents over half of current heart failure cases in the United States (1). Due to a lack of specific approved therapies, current treatment guidelines focus on the management of comorbidities related to metabolic syndrome (e.g. obesity, diabetes, hypertension) that promote HFpEF progression (1). The same comorbidities also drive cardiometabolic disease in non-cardiac tissues, and links between disease presentations in different organs are increasingly being recognized in the clinic. However, mechanistic studies examining the underlying pathophysiological connections have not kept pace, particularly in the cardio-hepatic disease axis (2). To address this, we used a recently developed and validated preclinical model of HFpEF (3) to examine how this disease impacts the liver. The development of HFpEF in mice leads to the simultaneous development of widespread hepatic steatosis that is consistent with human non-alcoholic fatty liver disease (NAFLD). Mechanistically, we show that the liver steatosis observed is driven by excess glucogenic amino acid entry into the TCA cycle, which promotes hepatic glucose production and de novo lipogenesis. Our findings suggest that HFpEF development is a multi-organ event, with implications for both preclinical and translational research.

physiology↗

bioRxiv2024

GCN5L1 regulates glucose and ketone body metabolism during cardiac ischemia-reperfusion injury

Myocardial infarction remains one of the leading causes of mortality. Reperfusion of the infarcted myocardium restores blood flow and reduces primary ischemic injury. However, despite its protective function, reperfusion is also associated with several deleterious outcomes that can result in ischemia-reperfusion (I/R) injury to cardiac tissue. While negative outcomes such as reactive oxygen species generation are strongly associated with I/R injury, cardiac energy metabolism is also greatly disrupted. Furthermore, previous studies have shown that the restoration of normal fuel oxidation in the myocardium regulates the extent of contractile recovery. A better understanding of the pathophysiological mechanisms underlying I/R injury may allow us to develop new treatments that limit the negative aspects of the process. In this study, we examined the role played by GCN5L1, a protein implicated in the regulation of energy metabolism, in I/R injury. We demonstrate that cardiac-specific loss of GCN5L1 promotes the inhibitory phosphorylation of pyruvate dehydrogenase in vitro and in vivo, a process likely to inhibit glucose oxidation, and that this corresponds to increased myocardial damage following ischemia-reperfusion (I/R) injury.

physiology↗

bioRxiv2024

Molecular dynamics simulations reveal molecular mechanisms for the gain and loss of function effects of four SCN2A variants

SCN2A gene disorders cover a wide range of medical conditions, from epileptic encephalopathies to neurodevelopmental disorders. The variants of these disorders, studied through electrophysiology, show complex behaviors that go beyond simple classification as either gain or loss of function. In our study, we simulated the biophysical effects of variants (R937C, V208E, S1336Y, and R853Q) to understand their impact. Our findings reveal that all these variants negatively affect the structural stability of the gene, with R937C being the most unstable. Specifically, R937C disrupts important charged interactions affecting sodium ion flow, while S1336Y introduces a new interaction that impacts the channels inactivation gate. Conversely, the variants V208E and R853Q, which are located in the voltage-sensing domains, have opposite effects: R853Q increases compactness and interaction, whereas V208E shows a decrease. Our computer-based method offers a scalable way to gain crucial insights into how genetic variants influence channel dysfunction and contribute to neurodevelopmental disorders. AUTHOR SUMMARYDespite numerous advancements in computational methods for predicting variant pathogenicity in the SCN2A gene, understanding the precise biophysical molecular mechanisms associated with each variant at the atomic level remains a challenge. Presently, variants are predominantly categorized as either gain or loss of function, often overlooking critical structural details associated with these variants. This study focuses on elucidating the molecular mechanisms linked to the four most common SCN2A variants using all-atom molecular dynamics simulations, employing three replicas for each system. Our findings offer insights into the potential mechanisms underlying these four variants, thereby providing explanations for the observed electrophysiological outcomes. This investigation significantly contributes to enhancing our comprehension of how SCN2A variants manifest in various diseases. It underscores the importance of unraveling the biophysical properties underlying potential disease mechanisms, which could potentially enhance diagnostic and therapeutic strategies for patients afflicted with SCN2A-related disorders.

biophysics↗

bioRxiv2023

Iron Memory in E. coli

The importance of memory in bacterial decision-making is relatively unexplored. We show here that a prior experience of swarming is remembered when E. coli encounters a new surface, improving its future swarming efficiency. We conducted >10,000 single-cell swarm assays to discover that cells store memory in the form of cellular iron levels. This memory pre-exists in planktonic cells, but the act of swarming reinforces it. A cell with low iron initiates swarming early and is a better swarmer, while the opposite is true for a cell with high iron. The swarming potential of a mother cell, whether low or high, is passed down to its fourth-generation daughter cells. This memory is naturally lost by the seventh generation, but artificially manipulating iron levels allows it to persist much longer. A mathematical model with a time-delay component faithfully recreates the observed dynamic interconversions between different swarming potentials. We also demonstrate that iron memory can integrate multiple stimuli, impacting other bacterial behaviors such as biofilm formation and antibiotic tolerance.

microbiology↗

bioRxiv2021

Mutation-induced Changes in the Receptor-binding Interface of the SARS-CoV-2 Delta Variant B.1.617.2 and Implications for Immune Evasion

While the vaccination efforts against SARS-CoV-2 infections are ongoing worldwide, new genetic variants of the virus are emerging and spreading. Following the initial surges of the Alpha (B.1.1.7) and the Beta (B.1.351) variants, a more infectious Delta variant (B.1.617.2) is now surging, further deepening the health crises caused by the pandemic. The sharp rise in cases attributed to the Delta variant has made it especially disturbing and is a variant of concern. Fortunately, current vaccines offer protection against known variants of concern, including the Delta variant. However, the Delta variant has exhibited some ability to dodge the immune system as it is found that neutralizing antibodies from prior infections or vaccines are less receptive to binding with the Delta spike protein. Here, we investigated the structural changes caused by the mutations in the Delta variants receptor-binding interface and explored the effects on binding with the ACE2 receptor as well as with neutralizing antibodies. We find that the receptor-binding {beta}-loop-{beta} motif adopts an altered but stable conformation causing separation in some of the antibody binding epitopes. Our study shows reduced binding of neutralizing antibodies and provides a possible mechanism for the immune evasion exhibited by the Delta variant.

biophysics↗

bioRxiv2020

Lipid-specific protein oligomerization is regulated by two interfaces in Marburg virus matrix protein VP40

Marburg virus major matrix protein (mVP40) dimers associate with anionic lipids at the plasma membrane and undergo a dynamic and extensive self-oligomerization into the structural matrix layer which confers the virion shape and stability. Using a myriad of in vitro and cellular techniques, we present a mVP40 assembly model highlighting two distinct oligomerization interfaces (N-terminal domain (NTD) and C-terminal domain (CTD)) in mVP40. Cellular studies of NTD and CTD oligomerization interface mutants demonstrated the importance of each interface in the mVP40 matrix assembly through protein trafficking to the plasma membrane and homo-multimerization that induced protein enrichment, plasma membrane fluidity changes and elongations at the plasma membrane. A novel APEX-TEM method was employed to closely assess the ultrastructural localization of and formation of viral particles for wild type and mutants. Taken together, these studies present a mechanistic model of mVP40 oligomerization and assembly at the plasma membrane during virion assembly.

microbiology↗

bioRxiv2018

PI(4,5)P2 Binding Sites in the Ebola Virus Matrix Protein Modulate Assembly and Budding

Ebola virus (EBOV) causes sever hemorrhagic fever in humans, can cause death in a large percentage of those infected, and still lacks FDA approved treatment options. In this study, we investigated how the essential EBOV protein, VP40, forms stable oligomers to mediate budding and assembly from the host cell plasma membrane. An array of in vitro and cellular assays identified and characterized two lysine rich regions that bind to PI(4,5)P2 and serve distinct functions through the lipid binding and assembly of the viral matrix layer. We found that when VP40 binds PI(4,5)P2, VP40 oligomers become extremely stable and long lived. Together, this work characterizes the molecular basis of PI(4,5)P2 binding by VP40, which stabilizes formation of VP40 oligomers necessary for viral assembly and budding. Quercetin, a natural product that lowers PI(4,5)P2 in the plasma membrane, inhibited budding of VP40 VLPs and may inform future treatment strategies against EBOV.

microbiology↗