Biology subjects

Shukla, D.

Publications and source records attributed to Shukla, D..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Palmitoleate Protects against Zika virus infection-induced Endoplasmic Reticulum Stress and Apoptosis in Neurons

Zika virus (ZIKV) infection during pregnancy is associated with the development of fetal complications such as microcephaly. We have recently demonstrated that palmitoleate protects against ZIKV-induced apoptosis in placental trophoblasts. In the present study, we hypothesize that palmitoleate prevents ZIKV infection-induced endoplasmic reticulum (ER) stress and apoptosis in neurons. Neurons were infected with 0.1-1 multiplicity of infection of recombinant MR766 or PRVABC59 strains of ZIKV for an hour followed by treatment of palmitoleate (100 {micro}M-200 {micro}M) for different post-infection time points. Apoptosis was measured by nuclear morphological changes, caspase 3/7 activity, and immunoblot analysis of pro-apoptotic mediators. Activation of ER stress markers and viral envelope levels were detected using qRT-PCR and immunoblot analysis. Infectious virus particles were measured by using plaque assay. ZIKV infection to neuronal cells showed increased levels of pro-apoptotic markers like cleaved-PARP, cleaved caspase-3, Bim, and Puma, whereas decreased levels of anti-apoptotic markers such as Mcl-1, Bcl-1, and Bcl-xL. Further, we observed activation of three arms of ER stress namely: inositol requiring enzyme 1 alpha (IRE1), protein kinase-like ER kinase (PERK), and activating transcription factor (ATF6) pathways with ZIKV infection. Treatment of palmitoleate dramatically decreased ZIKV infection-induced increase in percent apoptotic nuclei and caspase 3/7 activity. Further, treatment of palmitoleate decreased cleaved PARP and PUMA protein expressions. Treatment of palmitoleate reduced ZIKV-induced ER stress activation as evidenced by decreased levels of phosphorylated forms of IRE1 and eukaryotic initiation factor 2 alpha; decreased expressions of cleaved ATF6, spliced X-box associated protein 1 and C/EBP homologous protein compared to ZIKV infection alone. Further, treatment of palmitoleate attenuated ZIKV envelope levels and infectious titer in SH-SY5Y and primary fetal cortical neurons isolated from humanized STAT2 knockin mice. These data suggest that palmitoleate supplementation protects against ZIKV-induced neuronal ER stress, apoptosis and decreases Zika viral load thereby mitigates neuronal damage.

microbiology↗

bioRxiv2025

Star-Shaped Glatiramer Acetate Mitigates Pulmonary Dysfunction and Brain Neurodegeneration in a Murine Model of Cryptococcus-Associated IRIS

Cryptococcal-associated immune reconstitution inflammatory syndrome (C-IRIS) is a clinical worsening or new presentation of cryptococcal disease following the initiation of antiretroviral therapy. C-IRIS is primarily driven by an influx of pathological CD4+ T cells, which triggers a hyperinflammatory response. The murine model of C-IRIS is a way to study the disease in mice and understand how the immune system triggers life-threatening outcomes in patients. We previously developed a murine C-IRIS model and demonstrated that C-IRIS is triggered by pathological CD4+ T cells, particularly Th1 cells, in the brain, which triggers neurodegeneration and pulmonary dysfunction. Using this unique mouse model, we tested the therapeutic effect of a star-shaped glatiramer acetate (sGA), which is a more effective isomeric form than linear GA. Here, we observed that sGA suppresses Th1 differentiation in the lung tissues, reducing CD4+ T cell and Th1 cell count. It also reduced microglia populations in the brain. Together, these changes improved respiratory dysfunction caused by C-IRIS, lowered mortality rate, and reduced brain neurodegeneration. These findings suggest that sGA could be an effective therapeutic strategy for managing C-IRIS.

immunology↗

bioRxiv2024

Heparanase, a host gene that potently restricts retrovirus transcription

Heparanase (HPSE) is a heterodimeric {beta}-D-glucoronidase that is critical in mammalian cells for the enzymatic cleavage of membrane associated heparan sulfate moieties. Apart from its enzymatic function, HPSE has important non-enzymatic functions, which include transcriptional regulation, chromatin modification and modulation of various signaling pathways. Interestingly, while HPSE is an interferon stimulated gene, past reports have shown that it has proviral properties for many different viruses, including Herpes Simplex Virus 1, as it assists virus release from infected cells. Yet any antiviral functions associated with HPSE have not been described. Here we show that HPSE utilizes a hitherto unknown mechanism to restrict retroviruses, by targeting the step of proviral transcription. Moreover, we demonstrate that HPSE blocks transcription initiation by targeting the SP1 transcription factor. Finally, we illustrate that the antiretroviral effect of HPSE is independent of its enzymatic activity. This report describes a novel antiviral mechanism utilized by HPSE to inhibit retrovirus infection. ImportanceHeparanase (HPSE) has emerged as an important factor that has proviral functions for a number of viruses including herpes simplex virus and hepatitis C virus, by assisting in virus egress. However, HPSE is an interferon stimulated gene and thus is a part of the host antiviral defense. Nothing is known about the antiviral functions of HPSE. Here, we examine in depth the role of HPSE during retrovirus infection using two retroviruses, human immunodeficiency virus type 1 (HIV-1) and murine leukemia virus (MLV). In this report, we show that mouse, but not human, HPSE blocks retrovirus infection by targeting provirus transcription. HPSE sequesters the SP-1 transcription factor away from the proviral promoter thereby inhibiting transcription inhibition. In conclusion, our findings identify a novel antiviral function of HPSE and its potential role as an inhibitor of zoonotic transmission of retroviruses.

microbiology↗

bioRxiv2024

Energetics of cholesterol perception and translocation in the human Smoothened receptor

Smoothened (SMO), a member of the G Protein-Coupled Receptor superfamily, mediates Hedgehog signaling and is linked to cancer and birth defects. SMO responds to accessible cholesterol in the ciliary membrane, translocating it via a longitudinal tunnel to its extracellular domain. Reaching a complete mechanistic understanding of the cholesterol translocation process would help in the development of cancer therapies. Experimental data suggest two modes of translocation to support entry of cholesterol from outer and inner membrane leaflets, but the exact mechanism of translocation remains unclear. Using atomistic molecular dynamics simulations ([~]2 millisecond simulations) and biochemical assays of SMO mutants, we assess the energetic feasibilities of the two modes. We show that the highest energetic barrier for cholesterol translocation from the outer leaflet is lower than that from the inner leaflet. Mutagenesis experiments and complementary simulations of SMO mutants validate the role of critical amino acid residues along the translocation pathways. Our data suggests that cholesterol can take either pathway to enter SMO, thus explaining experimental observations in the literature. Thus, our results illuminate the energetics and provide a first molecular description of cholesterol translocation in SMO.

biochemistry↗

bioRxiv2024

LassoESM: A tailored language model for enhanced lasso peptide property prediction

Ribosomally synthesized and post-translationally modified peptides (RiPPs) comprise a structurally and functionally diverse group of natural products. Lasso peptides represent one of about 50 known molecular classes of RiPPs, which display a characteristic [1] rotaxane conformation formed by a lasso cyclase. This unique, threaded conformation endows lasso peptides with diverse biological activities and remarkable thermal and proteolytic stability. The prediction of lasso peptide properties, such as substrate compatibility with a particular lasso cyclase or desired biological activity, remains challenging due to limited experimental data and the intricate nature of the substrate fitness landscapes. Protein language models (PLMs) have demonstrated impressive performance in predicting protein structure and function. However, general-purpose PLMs perform poorly in lasso peptide-related predictive tasks. Therefore, there is a need to provide effective representations for lasso peptides to enable enhanced property prediction. In this study, we developed a lasso peptide-specific language model (LassoESM) by leveraging advances in pre-trained PLMs to aid the prediction of lasso peptide related properties and experimentally validate the model predictions. We demonstrate that LassoESM embeddings can accurately predict substrate compatibility for a lasso cyclase of interest when experimental data for model training was scarce. Using a deep learning framework incorporating cross-attention between lasso cyclase and substrate peptide embeddings, we identify non-cognate pairs of lasso cyclases and substrate peptides with predicted compatibility. We further show that LassoESM embeddings improve the prediction of RNA polymerase inhibitory activity, which represents a biological activity of several known lasso peptides. We anticipate that LassoESM and future iterations thereof will be instrumental for the rational design of lasso peptides with desired properties.

biophysics↗

bioRxiv2024

Dynamic Mechanism for Subtype Selectivity of Endocannabinoids

Endocannabinoids are naturally occurring lipid-like molecules that bind to cannabinoid receptors (CB1 and CB2) and regulate many of human bodily functions via the endocannabinoid system. There is a tremendous interest in developing selective drugs that target the CB receptors. However, the biophysical mechanisms responsible for the subtype selectivity for endocannbinoids have not been established. Recent experimental structures of CB receptors show that endocannbinoids potentially bind via membrane using the lipid access channel in the transmembrane region of the receptors. Furthermore, the N-terminus of the receptor could move in and out of the binding pocket thereby modulating both the pocket volume and its residue composition. On the basis of these observations, we propose two hypothesis to explain the selectivity of the endocannabinoid, anandamide for CB1 receptor. First, the selectivity arises from distinct enthalpic ligand-protein interactions along the ligand binding pathway formed due to the movement of N-terminus and subsequent shifts in the binding pocket composition. Second, selectivity arises from the volumetric differences in the binding pocket allowing for differences in ligand conformational entropy. To quantitatively test these hypothesis, we perform extensive molecular dynamics simulations ([~]0.9 milliseconds) along with Markov state modeling and deep learning-based VAMPnets to provide an interpretable characterization of the anandamide binding process to cannabinoid receptors and explain its selectivity for CB1. Our findings reveal that the distinct N-terminus positions along lipid access channels between TM1 and TM7 lead to different binding mechanisms and interactions between anandamide and the binding pocket residues. To validate the critical stabilizing interactions along the binding pathway, relative free energy calculations of anandamide analogs are used. Moreover, the larger CB2 pocket volume increases the entropic effects of ligand binding by allowing higher ligand fluctuations but reduced stable interactions. Therefore, the opposing enthalpy and entropy effects between the receptors shape the endocannabinoid selectivity. Overall, the CB1 selectivity of anandamide is explained by the dominant enthalpy contributions due to ligand-protein interactions in stable binding poses. This study shed lights on potential selectivity mechanisms for endocannabinoids that would aid in the discovery of CB selective drugs.

biophysics↗

bioRxiv2024

Mitochondrial DNA Mutations Linking Leigh Syndrome and Carotid Atherosclerosis: A Study of Shared Genetic Pathways

Mitochondrial DNA encodes the genetic information necessary for mitochondrial function. In humans, mitochondrial DNA spans 16,569 base pairs while representing a small fraction of the genetic material in humans. Due to their higher mutation rates compared to nuclear DNA, Mitochondrial DNA mutations are emerging as promising biomarkers for assessing disease predisposition and progression. This in-silico analyzes the correlation between Mitochondrial DNA mutations and two conditions: Leigh syndrome, a severe neurodegenerative disorder, and carotid atherosclerosis, a major cardiovascular disease. We focus on five single nucleotide variants (SNVs) - m.14459G>A, m.13513G>A, m.12315G>A, m.1555A>G, and m.15059G>A - to explore their roles in both diseases. Our findings suggest that mutations m.14459G>A, m.1555A>G, and m.15059G>A contribute to the pathogenesis of both conditions. In contrast, m.12315G>A is linked to MELAS syndrome and carotid atherosclerosis. Interestingly, the m.13513G>A mutation is associated with Leigh syndrome but negatively correlated with atherosclerosis, suggesting a potential protective effect. These SNVs could serve as targets for diagnostic and therapeutic approaches, enhancing our understanding of the genetic basis of these diseases.

bioinformatics↗

bioRxiv2024

Thermal Adaptation of Cytosolic Malate Dehydrogenase Revealed by Deep Learning and Coevolutionary Analysis

Protein evolution has produced enzymes that maintain stability and function across various thermal environments. While sequence variation, structural dynamics, and intermolecular interactions are known to influence an enzymes thermal adaptation, how these factors collectively govern stability and function across diverse temperatures remains unresolved. Cytosolic malate dehydrogenase (cMDH), a citric acid cycle enzyme, is an ideal model for studying these mechanisms due to its temperature-sensitive flexibility and broad presence in species from diverse thermal environments. In this study, we employ techniques inspired by deep learning and statistical mechanics to uncover how sequence variation and structural dynamics shape patterns of cMDHs thermal adaptation. By integrating coevolutionary models with variational autoencoders (VAE), we generate a latent generative landscape (LGL) of cMDH sequence space, enabling us to explore evolutionary pathways and predict fitness using direct coupling analysis (DCA). Structural predictions via AlphaFold and molecular dynamics simulations further illuminate how variations in hydrophobic interactions and conformational flexibility contribute to the thermal stability of warm- and cold-adapted cMDH orthologs. The integrative computational framework employed in this study provides powerful insights into protein adaptation at both sequence and structural levels, offering new perspectives on the evolution of thermal stability and creating avenues for the rational design of proteins with optimized thermal properties for biotechnological applications.

biophysics↗

bioRxiv2024

Deep mutational scanning reveals sequence to function constraints for SWEET family transporters

Protein science is entering a transformative phase enabled by deep mutational scans that provide an unbiased view of the residue level interactions that mediate function. However, it has yet to be extensively used to characterize the mutational and evolutionary landscapes of plant proteins. Here, we apply the method to explore sequence-function relationships within the sugar transporter AtSWEET13. DMS results describe how mutational interrogation throughout different regions of the protein affects AtSWEET13 abundance and transport function. Our results identify novel transport-enhancing mutations that are validated using the FRET sensor assays. Extending DMS results to phylogenetic analyses reveal the role of transmembrane helix 4 (TM4) which makes the SWEET family transporters distinct from prokaryotic SemiSWEETs. We show that transmembrane helix 4 is intolerant to motif swapping with other clade-specific SWEET TM4 compositions, despite accommodating single point-mutations towards aromatic and charged polar amino acids. We further show that the transfer learning approaches based on physics and ML based In silico variant prediction tools have limited utility for engineering plant proteins as they were unable to reproduce our experimental results. We conclude that DMS can produce datasets which, when combined with the right predictive computational frameworks, can direct plant engineering efforts through derivative phenotype selection and evolutionary insights.

plant biology↗

bioRxiv2024

SWEET family transporters act as water conducting carrier proteins in plants

AbstractDedicated water channels are involved in the facilitated diffusion of water molecules across the cell membrane in plants. Transporter proteins are also known to transport water molecules along with substrates, however the molecular mechanism of water permeation is not well understood in plant transporters. Here, we show plant sugar transporters from the SWEET (Sugar Will Eventually be Exported Transporter) family act as water-conducting carrier proteins via a variety of passive and active mechanisms that allow diffusion of water molecules from one side of the membrane to the other. This study provides a molecular perspective on how plant membrane transporters act as water carrier proteins, a topic that has not been extensively explored in literature. Water permeation in membrane transporters could occur via four distinct mechanisms which form our hypothesis for water transport in SWEETs. These hypothesis are tested using molecular dynamics simulations of the outward-facing, occluded, and inward-facing state of AtSWEET1 to identify the water permeation pathways and the flux associated with them. The hydrophobic gates at the center of the transport tunnel act as a barrier that restricts water permeation. We have performed in silico single and double mutations of the hydrophobic gate residues to examine the changes in the water conductivity. Surprisingly, the double mutant allows the water permeation to the intracellular half of the membrane and forms a continuous water channel. These computational results are validated by experimentally examining the transport of hydrogen peroxide molecules by the AtSWEET family of transporters. We have also shown that the transport of hydrogen peroxide follows the similar mechanism as water transport in AtSWEET1. Finally, we conclude that similar water-conduction states are also present in other SWEET transporters due to the high sequence and structure conservation exhibited by this transporter family.

biophysics↗

bioRxiv2024

Interplay between phosphorylation and oligomerization tunes the conformational ensemble of SWEET transporters

SWEET sugar transporters are desirable biotechnological targets for improving plant growth. One engineering strategy includes modulating how SWEET transporters are regulated. Phosphorylation and oligomerization have been shown to positively regulate SWEET function, leading to increased sugar transport activity. However, constitutive phosphorylation may not be beneficial to plant health under basal conditions. Structural and mechanistic understanding of the interplay between phosphorylation and oligomerization in functional regulation of SWEETs remains limited. Using extensive molecular dynamics simulations coupled with Markov state models, we demonstrate the thermodynamic and kinetic effects of SWEET phosphorylation and oligomerization using OsSWEET2b as a model. We report that the beneficial effects of these SWEET regulatory mechanisms bias outward-facing states and improved extracellular gating, which complement published experimental findings. Our results offer molecular insights to SWEET regulation and may guide engineering strategies throughout the SWEET transport family.

biophysics↗

bioRxiv2024

Energetics of substrate transport in proton-dependent oligopeptide transporters

The PepTSo transporter mediates the transport of peptides across biological membranes. Despite advancements in structural biology, including cryogenic electron microscopy structures resolving PepTSo in different states, the molecular basis of peptide recognition and transport by PepTSo is not fully elucidated. In this study, we employed molecular dynamics simulations, Markov State Models (MSMs), and Transition Path Theory (TPT) to investigate the transport mechanism of an alanine-alanine peptide (Ala-Ala) through the PepTSo transporter. Our simulations revealed conformational changes and key intermediate states involved in peptide translocation. We observed that the presence of the Ala-Ala peptide substrate lowers the free energy barriers associated with transition to the inward-facing state. Furthermore, we elucidated the proton transport model and analyzed the pharmacophore features of intermediate states, providing insights for rational drug design. These findings highlight the significance of substrate binding in modulating the conformational dynamics of PepTSo and identify critical residues that facilitate transport.

biophysics↗

bioRxiv2024

Binding Position Dependent Modulation of Smoothened Activity by Cyclopamine

Cyclopamine is a natural alkaloid that is known to act as an agonist when it binds to the Cysteine Rich Domain (CRD) of the Smoothened receptor and as an antagonist when it binds to the Transmembrane Domain (TMD). To study the effect of cyclopamine binding to each binding site experimentally, mutations in the other site are required. Hence, simulations are critical for understanding the WT activity due to binding at different sites. Additionally, there is a possibility that cyclopamine could bind to both sites simultaneously especially at high concentration, the implications of which remain unknown. We performed three independent sets of simulations to observe the receptor activation with cyclopamine bound to each site independently (CRD, TMD) and bound to both sites simultaneously. Using multi-milliseconds long aggregate MD simulations combined with Markov state models and machine learning, we explored the dynamic behavior of cyclopamines interactions with different domains of WT SMO. A higher population of the active state at equilibrium, a lower activation free energy barrier of[~] 2 kcal/mol, and expansion of the hydrophobic tunnel to facilitate cholesterol transport agrees with the cyclopamines agonistic behavior when bound to the CRD of SMO. A higher population of the inactive state at equilibrium, a higher free energy barrier of[~] 4 kcal/mol and restricted the hydrophobic tunnel to impede cholesterol transport showed cyclopamines antagonistic behavior when bound to TMD. With cyclopamine bound to both sites, there was a slightly larger inactive population at equilibrium and an increased free energy barrier ([~] 3.5 kcal/mol). The tunnel was slightly larger than when solely bound to TMD, and showed a balance between agonism and antagonism with respect to residue movements exhibiting an overall weak antagonistic effect.

biophysics↗

bioRxiv2023

Transition-based reweighting and neural rational inference analysis of effects of new psychoactive substances on cannabinoid receptors

New psychoactive substances (NPS) targeting cannabinoid receptor 1 pose a significant threat to society as recreational abusive drugs that have pronounced physiological side effects. These greater adverse effects compared to classical cannabinoids have been linked to the higher downstream {beta}-arrestin signaling. Thus, understanding the mechanism of differential signaling will reveal important structure-activity relationship essential for identifying and potentially regulating NPS molecules. In this study, we simulate the slow (un)binding process of NPS MDMB-Fubinaca and classical cannabinoid HU-210 from CB1 using multi-ensemble simulation to decipher the effects of ligand binding dynamics on downstream signaling. The transition-based reweighing method is used for the estimation of transition rates and underlying thermodynamics of (un)binding processes of ligands with nanomolar affinities. Our analyses reveal major interaction differences with transmembrane TM7 between NPS and classical cannabinoids. A variational autoencoder-based approach, neural relational inference (NRI), is applied to assess the allosteric effects on intracellular regions attributable to variations in binding pocket interactions. NRI analysis indicate a heightened level of allosteric control of NPxxY motif for NPS-bound receptors, which contributes to the higher probability of formation of a crucial triad interaction (Y7.53-Y5.58-T3.46) necessary for stronger {beta}-arrestin signaling. Hence, in this work, MD simulation, data-driven statistical methods, and deep learning point out the structural basis for the heightened physiological side effects associated with NPS, contributing to efforts aimed at mitigating their public health impact.

biophysics↗

bioRxiv2023

Functional Regulation of Aquaporin Dynamics by Lipid Bilayer Composition

With the diversity of lipid-protein interactions, any observed membrane protein dynamics or functions directly depend on the lipid bilayer selection. However, the implications of lipid bilayer choice are seldom considered unless characteristic lipid-protein interactions have been previously reported. Using molecular dynamics simulation, we characterize the effects of membrane embedding on plant aquaporin SoPIP2;1, which has no reported high-affinity lipid interactions. The regulatory impacts of a realistic lipid bilayer, and nine different homogeneous bilayers, on varying SoPIP2;1 dynamics were examined. We demonstrate that SoPIP2;1s structure, thermodynamics, kinetics, and water transport are altered as a function of each membrane constructs ensemble properties. Notably, the realistic bilayer provides stabilization of non-functional SoPIP2;1 metastable states. Hydrophobic mismatch and lipid order parameter calculations further explain how lipid ensemble properties manipulate SoPIP2;1 behavior. Our results illustrate the importance of careful bilayer selection when studying membrane proteins. To this end, we advise cautionary measures when performing membrane protein molecular dynamics simulations.

biophysics↗

bioRxiv2023

An inimitable proprotein convertase subtilisin kexin-9 (PCSK9) cleavage site VFAQ on Spike protein along with furin cleavage site makes SARS-CoV-2 unique

A novel coronavirus (2019-nCoV) or Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) that affects humans has been discovered in Wuhan, China, in 2019. Its genome has been sequenced, and the genetic data was quickly made public. We discovered a novel proprotein convertase subtilisin kexin-9 (PCSK9) cleavage site in the Spike protein of the 2019-nCoV. The recent research also demonstrates that the previously found proprotein convertase 3 (PC3) or furin cleavage site, which was assumed to be unique, is already present in animal corona viruses. In this article, we suggest that the combination of the both proprotein convertase PC3 cleavage site and the PCSK9 site renders SARS-CoV-2 unique in terms of the pathogenicity, potential functional effects, and implications for the development of antiviral drugs.

evolutionary biology↗

bioRxiv2023

The Sequence Basis for Selectivity of Ephrin-B2 Ligand for Eph Receptors and Pathogenic Henipavirus G Glycoproteins

Ephrin-B2 (EFNB2) is a ligand for six Eph receptors in humans and functions as a cell entry receptor for several henipaviruses including Nipah virus (NiV), a pathogenic zoonotic virus with pandemic potential. To understand the sequence basis of promiscuity for EFNB2 binding to the attachment glycoprotein of NiV (NiV-G) and Eph receptors, we performed deep mutagenesis on EFNB2 to identify mutations that enhance binding to NiV-G over EphB2, one of the highest affinity Eph receptors. The mutations highlight how different EFNB2 conformations are selected by NiV-G versus EphB2. Specificity mutations are enriched at the base of the G-H binding loop of EFNB2, especially surrounding a phenylalanine hinge upon which the G-H loop pivots, and at a phenylalanine hook that rotates away from the EFNB2 core to engage Eph receptors. One EFNB2 mutant, D62Q, possesses pan-specificity to the attachment glycoproteins of closely related henipaviruses and has markedly diminished binding to the six Eph receptors. However, EFNB2-D62Q has high residual binding to EphB3 and EphB4. A second deep mutational scan of EFNB2 identified combinatorial mutations to further enhance specificity to NiV-G. A triple mutant of soluble EFNB2, D62Q-Q130L-V167L, has minimal binding to Eph receptors but maintains binding, albeit reduced, to NiV-G. Soluble EFNB2 decoy receptors carrying the specificity mutations were potent neutralizers of chimeric henipaviruses. These findings demonstrate how specific residue changes at the shared binding interface of a promiscuous ligand (EFNB2) can influence selectivity for multiple receptors, and may also offer insight towards the development of henipavirus therapeutics and diagnostics. IMPORTANCEEphrin-B2 (EFNB2) is a ligand for six Eph receptors in humans and regulates multiple cell developmental and signaling processes. It also functions as the cell entry receptor for Nipah virus and Hendra virus, zoonotic viruses that can cause respiratory and/or neurological symptoms in humans with high mortality. Here, we investigate the sequence basis of EFNB2 specificity for binding the Nipah virus attachment G glycoprotein over Eph receptors. We then use this information to engineer EFNB2 as a soluble decoy receptor that specifically binds the attachment glycoproteins of Nipah virus and other related henipaviruses to neutralize infection. These findings further mechanistic understanding of protein selectivity and may facilitate the development of diagnostics or therapeutics against henipavirus infection.

microbiology↗

bioRxiv2023

Mechanistic Basis for Enhanced Strigolactone Sensitivity in KAI2 Triple Mutant

Striga hermonthica is a parasitic weed that destroys billions of dollars worth of staple crops every year. Its rapid proliferation stems from an enhanced ability to me-tabolize strigolactones (SLs), plant hormones that direct root branching and shoot growth. Strigas SL receptor, ShHTL7, bears more similarity to the staple crop kar-rikin receptor KAI2 than to SL receptor D14, though KAI2 variants in plants like Arabidopsis thaliana show minimal SL sensitivity. Recently, studies have indicated that a small number of point mutations to HTL7 residues can confer SL sensitivity to At KAI2. Here, we analyze both wild-type At KAI2 and SL-sensitive mutant Var64 through all-atom, long-timescale molecular dynamics simulations to determine the ef-fects of these mutations on receptor function at a molecular level. We demonstrate that the mutations stabilize SL binding by about 2 kcal/mol. They also result in a doubling of the average pocket volume, and eliminate the dependence of binding on certain pocket conformational arrangements. While the probability of certain non-binding SL-receptor interactions increases in the mutant compared with the wild-type, the rate of binding also increases by a factor of ten. All these changes account for the increased SL sensitivity in mutant KAI2, and suggest mechanisms for increasing functionality of host crop SL receptors.

plant biology↗