Biology subjects

Shukla, A. K.

Publications and source records attributed to Shukla, A. K..

At least 19 recordsLinked to original sources

bioRxiv2026

Integrated Pangenomic and Systems Biology Analyses Reveal the Genomic Basis of Virulence and Adaptation in Bipolaris sorokiniana

Bipolaris sorokiniana is a hemibiotrophic fungal pathogen responsible for foliar and root diseases of cereals, causing annual yield losses of 10-50%. The recurrent breakdown of host resistance and the emergence of fungicide-resistant pathogen populations underscore the urgent need to understand the genomic mechanisms underpinning pathogen adaptation and virulence. Here, we present the first comprehensive species-wide pangenomic and systems-level analyses of B. sorokiniana based on 19 genomes of globally distributed strains. Orthology-based analyses revealed an open pangenome comprising 16,981 orthogroups, partitioned into a conserved core genome (60.8%) and a highly dynamic accessory genome (39.2%), consisting of soft-core (8.5%), shell (19.7%), and cloud (11.0%) compartments. The core genes were predominantly associated with essential cellular and metabolic functions, while the accessory fractions were enriched in regulatory, stress-responsive, and adaptive processes. Secondary metabolite profiling identified 39-54 biosynthetic gene clusters per genome and revealed a largely conserved metabolic repertoire. Gene family evolution analyses revealed an excess of gene loss over expansion, indicating ongoing genome streamlining and lineage-specific adaptation. The core interactome comprised four densely connected functional communities governing genome maintenance, ribosome biogenesis, cellular bioenergetics, and protein translation. Collectively, this study elevates B. sorokiniana research from single-genome analyses to a population-scale analysis, providing vital insights into the evolutionary architecture of pathogenicity, adaptation, and genome diversification. These findings provide a valuable genomic resource for disease surveillance and functional characterization of virulence determinants, as well as the development of durable resistance strategies and next-generation antifungals for sustainable disease management in cereals.

bioinformatics↗

bioRxiv2026

Molecular basis of promiscuous chemokine-engagement by the Duffy antigen receptor

The Duffy blood group antigen, encoded by a seven transmembrane protein known as Duffy Antigen Receptor for Chemokines (DARC), or Atypical Chemokine Receptor 1 (ACKR1), serves as a key receptor for the malarial parasite, Plasmodium vivax, on erythrocytes. DARC exhibits remarkable functional divergence compared to prototypical chemokine receptors and other G protein-coupled receptors (GPCRs) as it does not engage canonical signal-transducers such as G-proteins, GPCR regulatory kinases (GRKs), and {beta}-arrestins. DARC is a highly promiscuous receptor interacting with several homeostatic and inflammatory C-C and C-X-C subtype chemokines, and similar to other chemokine receptors, these interactions are modulated by post-translational tyrosine sulfation in the N-terminus. A single nucleotide polymorphism in DARC leading to Gly42Asp substitution forms the basis for Fya vs. Fyb Duffy blood group antigen classification with differential impact on Plasmodium vivax infection and cancer progression. However, the molecular basis of promiscuous chemokine-binding by DARC and the modulation by receptor sulfation and Fya/Fyb allelic variation remains unclear. Here, we design a sortase-mediated chemical-ligation strategy to generate purified DARC with naturally-occurring tyrosine sulfation at the N-terminus, and determine high-resolution cryo-EM structures in complex with a C-C type chemokine, CCL7, and a C-X-C type chemokine, CXCL8. We observe that similar to CCL7, CXCL8 engages with DARC primarily through the N-terminus of the receptor, which is in stark contrast with the two-site binding mechanism displayed by other chemokine receptors. Interestingly, the E-L-R motif in CXCL8 engages a pseudo-R-D motif in DARC leading to superficial engagement unlike CXCR2, a prototypical chemokine receptor sharing the same agonist. Moreover, tyrosine sulfation and Fyb allelic variation leads to a repositioning of the receptor N-terminus on the core domain of CXCL8, resulting in distinct interaction network imparting greater binding affinity. Taken together, our study presents novel insights into promiscuous chemokine-binding to DARC, tyrosine sulfation-mediated fine-tuning of chemokine engagement, and a generalizable sortase-mediated chemical-ligation platform applicable to other chemokine receptors.

biochemistry↗

bioRxiv2026

Genome-wide, evolutionary, and stress-responsive landscape of the Pectin methylesterase gene family in cucumber and muskmelon

Pectin methylesterases (PMEs) are key regulators of plant cell wall remodeling; however, their evolutionary dynamics and stress-responsive roles remain poorly understood in cucurbit crops. This study aimed to systematically characterize the PME gene family in cucumber (Cucumis sativus) and muskmelon (Cucumis melo), addressing how PME diversification, duplication, and regulatory architecture underpin their responses to biotic and abiotic stresses. Using a Hidden Markov Model-based genome-wide screening approach, we identified 52 PME genes in cucumber and 56 in muskmelon, which were classified into Type I and Type II PMEs based on their domain composition. Comparative structural and phylogenetic analyses revealed conserved domain organization but substantial intron-driven structural diversification, resolving PMEs into two major evolutionary lineages with lineage-specific expansion patterns. Duplication and synteny analyses demonstrated that dispersed duplication was the primary driver of PME family expansion, while Ka/Ks estimates indicated strong purifying selection, highlighting functional conservation across cucurbits. Promoter cis-element profiling and protein-protein interaction network analyses revealed extensive enrichment of stress- and hormone-responsive regulatory features, identifying central PME hub genes. Meta-transcriptomic analyses across diverse biotic and abiotic stresses revealed dynamic, condition-specific PME regulation, with Type I PMEs predominantly associated with stress responses in cucumber, whereas both PME types contributed substantially in muskmelon. Several PMEs exhibited conserved stress-induced expression, while others displayed species-, tissue-, or pathogen-specific patterns. Collectively, this study establishes an integrative evolutionary and stress-responsive framework for PME genes in cucurbits, providing mechanistic insights into cell wall plasticity and identifying candidate PME targets for improving multi-stress resilience in crop breeding.

bioinformatics↗

bioRxiv2025

Multilayered Transcriptomic Reprogramming and Spliceosomal Divergence Shape Bipolaris sorokiniana Pathogenicity

Bipolaris sorokiniana, the causative agent of spot blotch of wheat, significantly limits wheat productivity. Despite the pathogens widespread impact, the in planta molecular mechanisms underpinning its virulence remain poorly characterized. We performed a comprehensive RNA-sequencing analysis of B. sorokiniana during attack on spot-blotch-resistant and susceptible wheat genotypes, integrating differentially expressed genes (DEGs), alternative splicing (AS) events, and identification of long non-coding RNAs (lncRNAs). The pathogen exhibited extensive host-genotype-dependent transcriptomic reprogramming, with 128 pathogen genes upregulated in the susceptible host. These genes were associated with ribosome biogenesis, RNA processing, and primary metabolic functions, supporting aggressive colonization. In contrast, pathogen attack on the resistant genotype triggered the upregulation of 58 pathogen genes associated with stress-responsive pathways, including sphingolipid and ceramide metabolism. This suggests a shift toward defensive metabolic reprogramming in the resistant host that restricted its proliferation. Our investigation uncovered five classes of AS events and 14 differentially expressed lncRNAs, revealing substantial post-transcriptional complexity. Notably, a subunit of the H/ACA small nucleolar ribonucleoprotein (snoRNP) complex emerged as a rare "triple-hit" candidate simultaneously identified as a DEG, differentially alternatively spliced gene, and target of a differentially expressed lncRNA, highlighting its potential as a central regulatory node in host-responsive stress adaptation. This study reveals a multilayered regulatory landscape involving transcriptional plasticity, alternative splicing, and lncRNA-mediated control, enabling B. sorokiniana to fine-tune its infection strategy in response to host resistance. This work advances the understanding of fungal pathogenesis and identifies molecular vulnerabilities that could be exploited for targeted, host-specific disease control.

bioinformatics↗

bioRxiv2025

Molecular fingerprints of a convergent mechanism orchestrating diverse ligand recognition and species-specific pharmacology at the complement anaphylatoxin receptors

Complement anaphylatoxin receptors (C3aR and C5aR1) are prototypical G protein-coupled receptors (GPCRs) playing crucial physiological roles in innate immunity by combating pathogenic infections and orchestrating inflammatory responses. They continue to be important therapeutic targets for multiple disorders including autoimmune diseases, acute and chronic inflammation, and allergy-related conditions. Recent structural coverage has provided important insights into their activation and signaling, however, confounding observations in the literature related to ligand efficacy and functional responses, especially in different model systems, present a major challenge for drug discovery efforts. Here, we systematically and comprehensively profile a broad set of natural and synthetic ligands at C3aR and C5aR1 and discover a previously unanticipated level of functional specialization in terms of species-specific pharmacology and receptor activation. Taking a lead from this, we determine seventeen cryo-EM structures of different ligand-receptor-G-protein complexes and uncover distinct orientation of agonists between the human and mouse receptors despite an overlapping positioning in the orthosteric binding pocket. Combined with extensive mutagenesis and functional assays, these structural snapshots allow us to decode and validate a convergent molecular mechanism involving a "Five-Point-Switch" in these receptors that orchestrates the recognition and efficacy of diverse agonists. We also identify species-specific differences at the level of phosphorylation patterns encoded in the carboxyl-terminus of these receptors and directly visualize their impact on {beta}arr binding and activation using cryo-EM structures. Interestingly, we observe that {beta}arrs engage with the mouse C5aR1 using a variation of previously discovered P-X-P-P phosphorylation motif via a "Sliding-Mechanism" and also exhibit distinct oligomeric state for the human vs. mouse receptors. Taken together, this study elucidates functional specialization at the complement anaphylatoxin receptors and underlying molecular mechanisms, offering a previously lacking framework with direct and immediate implications for the development of novel therapeutics.

biochemistry↗

bioRxiv2023

Structure of the human Duffy antigen receptor

The Duffy antigen receptor, also known as FY glycoprotein or CD234, is a seven transmembrane protein expressed primarily at the surface of red blood cells, which displays promiscuous binding to multiple chemokines. Not only does it serve as the basis of the Duffy blood group system but it also acts as the primary attachment site for malarial parasite Plasmodium vivax on erythrocytes and as one of the nucleating receptors for the pore forming toxins secreted by Staphylococcus aureus. Despite a predicted 7TM architecture and efficient binding to a spectrum of chemokines, it fails to exhibit canonical second messenger response such as calcium release, likely due to a lack of G protein coupling. Unlike prototypical GPCRs and {beta}-arrestin-biased atypical chemokine receptors, the Duffy antigen receptor also appears to lack {beta}-arrestin binding, making it an enigmatic 7TM chemokine receptor. In order to decipher the molecular mechanism of this intriguing functional divergence exhibited by the Duffy antigen receptor, we have determined its cryo-EM structure in complex with a C-C type chemokine, CCL7. The structure reveals a relatively superficial binding mode of CCL7, with the N-terminus of the receptor serving as the key interaction interface, and a partially formed orthosteric binding pocket lacking the second site for chemokine recognition compared to prototypical chemokine receptors. The structural framework allows us to employ HDX-MS approach to uncover ligand-induced structural changes in the receptor and draw important insights into the promiscuous nature of chemokine binding. Interestingly, we also observe a dramatic shortening of TM5 and 6 on the intracellular side, compared to prototypical GPCRs, which precludes the coupling of canonical signal-transducers namely G proteins, GRKs and {beta}-arrestins, as demonstrated through extensive cellular assays. Taken together, our study uncovers a previously unknown structural mechanism that imparts unique functional divergence on the 7TM fold encoded in the Duffy antigen receptor while maintaining its scavenging function and should facilitate the designing of novel therapeutics targeting this receptor.

biochemistry↗

bioRxiv2023

Molecular insights into atypical modes of beta-arrestin interaction with seven transmembrane receptors

{beta}-arrestins are multifunctional proteins that are critically involved in regulating spatio-temporal aspects of GPCR signaling. The interaction of {beta}-arrestins with GPCRs is typically conceptualized in terms of receptor activation and phosphorylation primarily in the carboxyl-terminus. Interestingly however, there are several GPCRs that harbor majority of phosphorylation sites in their 3rd intracellular loop (ICL3) instead of carboxyl-terminus but still robustly engage {beta}-arrestins. Moreover, there are several 7TMRs that are now characterized as intrinsically-biased, {beta}-arrestin-coupled receptors (ACRs) due to lack of functional G-protein-coupling but robust {beta}-arrestin binding leading to functional outcomes. The molecular basis of {beta}-arrestin interaction and activation upon binding to these types of 7TMRs is currently elusive, and it represents a major knowledge gap in our current understanding of this signaling system. Here, we present seven cryo-EM structures of {beta}-arrestins in basal state, activated by the muscarinic M2 receptor (M2R) through its ICL3, and a {beta}-arrestin-coupled receptor known as decoy D6 receptor (D6R). These structural snapshots combined with biochemical, cellular, and biophysical experiments including HDX-MS and MD simulation provide novel insights into the ability of {beta}-arrestins to preferentially select specific phosphorylation patterns in the receptors, and also illuminate the structural diversity in 7TMR-{beta}-arrestin interaction. Surprisingly, we also observe that the carboxyl-terminus of {beta}-arrestin2 but not {beta}-arrestin1 undergoes structural transition from a {beta}-strand to -helix upon activation by D6R, which may preclude the core-interaction with the activated receptor. Taken together, our study elucidates previously unappreciated aspects of 7TMR-{beta}-arrestin interaction, and provides important mechanistic clues about how the two isoforms of {beta}-arrestins can recognize and regulate a large repertoire of GPCRs.

biochemistry↗

bioRxiv2023

Structure-guided engineering of biased-agonism in the human niacin receptor via single amino acid substitution

The Hydroxycarboxylic acid receptor 2 (HCA2), also known as the niacin receptor or GPR109A, is a prototypical G protein-coupled receptor that plays a central role in the inhibition of lipolytic and atherogenic activities in our body. Interestingly, GPR109A activation also results in vasodilation that is linked to the side-effect of flushing associated with dyslipidemia drugs such as niacin. This receptor continues to be a key target for developing novel pharmacophores and lead compounds as potential therapeutics in dyslipidemia with minimized flushing response, however, the lack of structural insights into agonist-binding and receptor activation has limited the efforts. Here, we present five different cryo-EM structures of the GPR109A-G-protein complexes with the receptor bound to dyslipidemia drugs, niacin or acipimox, non-flushing agonists, MK6892 or GSK256073, and recently approved psoriasis drug, monomethyl fumarate (MMF). These structures allow us to visualize the binding mechanism of agonists with a conserved molecular interaction network, and elucidate the previously lacking molecular basis of receptor activation and transducer-coupling. Importantly, cellular pharmacology experiments, guided by the structural framework determined here, elucidate pathway-selective biased signaling elicited by the non-flushing agonists. Finally, taking lead from the structural insights, we successfully engineered receptor mutants via single amino acid substitutions that either fail to elicit agonist-induced transducer-coupling or exhibits G-protein signaling bias. Taken together, our study provides previously lacking structural framework to understand the agonist-binding and activation of GPR109A, and opens up the possibilities of structure-guided novel drug discovery targeting this therapeutically important receptor.

biochemistry↗

bioRxiv2023

Structural insights into agonist-binding and activation of the human complement C3a receptor

The complement cascade is an integral part of innate immunity, and it plays a crucial role in our bodys innate immune response including combating microbial infections. Activation of the complement cascade results in the generation of multiple peptide fragments, of which complement C3a and C5a are potent anaphylatoxins. The complement C3a binds and activates a G protein-coupled receptor (GPCR) known as C3aR while C5a activates two distinct receptors namely C5aR1 and C5aR2. Our current understanding of complement peptide recognition by their corresponding receptors is limited primarily to biochemical studies, and direct structural visualization of ligand-receptor complexes is still elusive. Here, we present structural snapshots of C3aR in complex with heterotrimeric G-proteins, with the receptor in ligand-free state, activated by full-length complement C3a, and a peptide agonist EP54, derived based on the carboxyl-terminal sequence of C5a. A comprehensive analysis of these structures uncovers the critical residues involved in C3a-C3aR interaction, and also provides molecular insights to rationally design carboxyl-terminal fragments of C3a and C5a to act as potent agonists of the receptor. Surprisingly, a comparison of C3a-C3aR structure with C5a-C5aR1 structure reveals diagonally opposite placement of these two complement peptides on their respective receptors, which helps explain the subtype selectivity of these complement peptides. Finally, taking lead from the structural insights, we also identify EP141, a peptide derived from the carboxyl-terminus of C3a, as a G-protein-biased agonist at C3aR. Taken together, our study illuminates the structural mechanism of complement C3a recognition by C3aR, and it also offers the first structural template for designing novel C3aR ligands with therapeutic potential for inflammatory disorders.

biochemistry↗

bioRxiv2023

Structural insights into ligand-recognition, activation, and signaling-bias at the complement C5a receptor, C5aR1

Activation of the complement cascade is a critical part of our innate immune response against invading pathogens, and it operates in a concerted fashion with the antibodies and phagocytic cells towards the clearance of pathogens. The complement peptide C5a, generated during the activation of complement cascade, is a potent inflammatory molecule, and increased levels of C5a are implicated in multiple inflammatory disorders including the advanced stages of COVID-19 pathophysiology. The proximal step in C5a-mediated cellular and physiological responses is its interaction with two different seven transmembrane receptors (7TMRs) known as C5aR1 and C5aR2. Despite a large body of functional data on C5a-C5aR1 interaction, direct visualization of their interaction at high-resolution is still lacking, and it represents a significant knowledge gap in our current understanding of complement receptor activation and signaling. Here, we present cryo-EM structures of C5aR1 activated by its natural agonist C5a, and a G-protein-biased synthetic peptide ligand C5apep, in complex with heterotrimeric G-proteins. The C5a-C5aR1 structure reveals the ligand binding interface involving the N-terminus and extracellular loops of the receptor, and we observe that C5a exhibits a significant conformational change upon its interaction with the receptor compared to the basal conformation. On the other hand, the structural details of C5apep-C5aR1 complex provide a molecular basis to rationalize the ability of peptides, designed based on the carboxyl-terminus sequence of C5a, to act as potent agonists of the receptor, and also the mechanism underlying their biased agonism. In addition, these structural snapshots also reveal activation-associated conformational changes in C5aR1 including outward movement of TM6 and a dramatic rotation of helix 8, and the interaction interface for G-protein-coupling. In summary, this study provides previously lacking molecular basis for the complement C5a recognition and activation of C5aR1, and it should facilitate structure-based discovery of novel lead molecules to target C5aR1 in inflammatory disorders.

biophysics↗

bioRxiv2022

pH - responsive, reversible A-motif based DNA hydrogels: synthesis and biosensing applications

Functional DNA hydrogels using various motifs and functional groups require perfect sequence designing to avoid cross-bonding interference with self or other structural sequences. The present work reports an A-motif functional DNA hydrogel that does not require any sequence design. A-motif DNA is a non-canonical parallel DNA duplex structure comprises homopolymeric deoxyadenosines (poly-dA) strands that undergo conformational changes from single strands at neutral pH to a parallel duplex DNA helix at acidic pH. Despite many advantages over other DNA motifs like no sequence, design is required and no cross-bonding interference with other structural sequences, A-motif has not been explored much. We successfully synthesized DNA hydrogel utilizing A-motif as a reversible handle to polymerize DNA three-way junction (3WJ). The composed A-motif hydrogel was first characterized by EMSA, & DLS, which shows the formation of higher-order structures. Further, we utilized imaging techniques like atomic force microscopy (AFM) and scanning electron microscope (SEM) validating its hydrogel like highly branched morphology. pH-induced conformational transformation from monomers to gel is quick and reversible, and was analysed for multiple acid-base cycles. The sol-to-gel transitions and gelation properties is further examined using rheological studies. The use of A-motif hydrogel in the visual detection of pathogenic target nucleic acid sequence is demonstrated for the first time using the capillary assay. Moreover, the pH-induced hydrogel formation is observed in-situ as a layer over the mammalian cells. The proposed A-motif DNA scaffold has enormous potential in designing stimuli-responsive nanostructures that can be utilized for many biological applications.

bioengineering↗

bioRxiv2022

Single-molecule analysis of receptor-beta-arrestin interactions in living cells

{beta}-arrestin plays a key role in G protein-coupled receptor (GPCR) signaling and desensitization. Despite recent structural advances, the mechanisms that govern receptor-{beta}-arrestin interactions at the plasma membrane of living cells remain elusive. Here, we combine single-molecule microscopy with molecular dynamics simulations to dissect the complex sequence of events involved in {beta}-arrestin interactions with both receptors and the lipid bilayer. In contrast to the currently widely accepted model, we show that {beta}-arrestin spontaneously inserts into the lipid bilayer and transiently interacts with receptors via lateral diffusion on the plasma membrane. Moreover, we show that following receptor interaction, the plasma membrane stabilizes {beta}-arrestin in a membrane-bound, active-like conformation, allowing it to diffuse to clathrin coated pits separately from the activating receptor. These results challenge our current understanding of {beta}-arrestin function at the plasma membrane, revealing a new critical role for {beta}-arrestin pre-association with the lipid bilayer in facilitating its interactions with receptors and subsequent activation.

cell biology↗

bioRxiv2022

A key GPCR phosphorylation motif discovered in arrestin2-CCR5 phosphopeptide complexes

The two non-visual arrestin isoforms, arrestin2 and arrestin3 recognize and bind hundreds of G protein-coupled receptors (GPCRs) with different phosphorylation patterns leading to distinct functional outcomes. The impact of phosphorylation on arrestin interactions has been well studied only for very few GPCRs. Here we have characterized the interactions between the phosphorylated CC chemokine receptor 5 (CCR5) and arrestin2. We detected several new CCR5 phosphorylation sites, which are necessary for stable complex formation with arrestin2. Crystal structures of arrestin2 in apo form and in complexes with CCR5 C-terminal phosphopeptides together with NMR spectroscopy, biochemical and functional assays revealed three phosphoresidues in a pXpp motif that are essential for the arrestin2 interactions and activation. The same phosphoresidue cluster is present in other receptors, which form stable complexes with arrestin2. We propose that the identified pXpp motif is responsible for robust arrestin2 recruitment in many GPCRs. An analysis of available sequences, structural and functional information on other GPCR*arrestin interactions suggests that a particular arrangement of phosphoresidues within the GPCR intracellular loop 3 and C-terminal tail determines arrestin2 and 3 isoform specificity. Taken together, our findings demonstrate how multi-site phosphorylation controls GPCR*arrestin interactions and provide a framework to probe the intricate details of arrestin activation and signaling. One-sentence summaryA structural and functional analysis of arrestin2 in apo form and complexes with several CCR5 phosphopeptides reveals key phosphorylation sites responsible for stable GPCR*arrestin interactions and their contributions to CCR5-arrestin2 function.

biophysics↗

bioRxiv2022

Molecular insights into intrinsic transducer-coupling bias in the CXCR4-CXCR7 system

Chemokine receptors constitute an important subfamily of G protein-coupled receptors (GPCRs), and they are critically involved in a broad range of immune response mechanisms. Ligand promiscuity among these receptors makes them an interesting target to explore novel aspects of biased agonism. Here, we comprehensively characterize two chemokine receptors namely, CXCR4 and CXCR7, which share a common chemokine agonist (CXCL12), in terms of their G-protein coupling, {beta}-arrestin ({beta}arr) recruitment, contribution of GRKs, and ERK1/2 MAP kinase activation. We observe that CXCR7 lacks G-protein coupling while maintaining robust {beta}arr recruitment with a major contribution of GRK5/6. On the other hand, CXCR4 displays robust G-protein activation as expected, however, it exhibits significantly reduced {beta}arr-coupling compared to CXCR7 in response to their shared natural agonist, CXCL12. These two receptors induce distinct {beta}arr conformations even when activated by the same agonist, and CXCR7, unlike CXCR4, fails to activate ERK1/2 MAP kinase. We further determine the crystal structure of {beta}arr2 in complex with a carboxyl-terminal phosphopeptide derived from CXCR7, which reveals a smaller interdomain rotation than observed previously for activated {beta}arrs. Importantly, structure-guided cellular experiments reveal a key contribution of a single phosphorylation site in CXCR7 on {beta}arr recruitment and endosomal trafficking. Taken together, our study provides molecular insights into intrinsic bias encoded in the CXCR4-CXCR7 system, and it has broad implications for therapeutically important framework of biased agonism.

biochemistry↗

bioRxiv2022

Allosteric modulation of GPCR-induced β-arrestin trafficking and signaling by a synthetic intrabody

Agonist-induced phosphorylation of G protein-coupled receptors (GPCRs) is a primary determinant of {beta}-arrestin ({beta}arr) recruitment and trafficking. For several GPCRs, such as the vasopressin type II receptor (V2R), which exhibit high affinity for {beta}arrs, agonist-stimulation first drives the translocation of {beta}arrs to the plasma membrane, followed by endosomal trafficking. We previously found that mutation of a single phosphorylation site in V2R (i.e., V2RT360A) results in near-complete loss of {beta}arr translocation to endosomes although {beta}arrs are robustly recruited to the plasma membrane. Here, we show that a synthetic intrabody referred to as intrabody30 (Ib30), which selectively recognizes an active-like {beta}arr1 conformation, rescues endosomal translocation of {beta}arr1 for V2RT360A. In addition, Ib30 also rescues agonist-induced ERK1/2 MAP kinase activation for V2RT360A to levels similar to that of the wild-type V2R. Molecular dynamics simulations reveal that Ib30 binding promotes active-like conformation in {beta}arr1 with respect to the inter-domain rotation. Interestingly, we also observe that Ib30 enhances the interaction of {beta}arr1 with {beta}2-adaptin, which provides a mechanistic basis for the ability of Ib30 to promote endosomal trafficking of {beta}arr1. Taken together, our data provide a novel mechanism to positively modulate the receptor-transducer-effector axis for GPCRs using intrabodies, which can potentially be integrated in the current paradigm of GPCR-targeted drug discovery. SignificanceThe interaction of G protein-coupled receptors (GPCRs) with {beta}-arrestins ({beta}arrs) is a critical step in their regulatory and signaling paradigms. While intrabodies that bind to GPCRs, G proteins and {beta}arrs have been utilized as biosensors and regulators of functional outcomes, allosteric targeting of receptor-transducer complexes to encode gain of function has not been documented so far. Here, we discover that a conformation-specific synthetic intrabody recognizing GPCR-bound {beta}arr1 can allosterically enhance endosomal trafficking of {beta}arr1 and agonist-induced ERK1/2 MAP kinase activation. This intrabody promotes an active-like {beta}arr1 conformation and enhances the interaction of {beta}2-adaptin with {beta}arr1. Our findings establish a conceptual framework to allosterically modulate protein-protein interactions in GPCR signaling cascade to modulate their trafficking and signaling responses.

biochemistry↗

bioRxiv2019

Crystal structure of β-arrestin 2 in complex with an atypical chemokine receptor phosphopeptide reveals an alternative active conformation

{beta}-arrestins ({beta}arrs) critically regulate signaling and trafficking of G protein-coupled receptors (GPCRs), the largest family of drug targets in the human genome, and there are two isoforms of {beta}arrs: {beta}arr1 and {beta}arr2. Most GPCRs interact with both the heterotrimeric G-proteins and {beta}arrs, inducing distinct downstream signal transduction. However, certain chemokine receptors lack functional G-protein coupling, but they can efficiently recruit {beta}arrs upon agonist-stimulation, and they are referred to as atypical chemokine receptors (ACKRs). Receptor phosphorylation is a key determinant for the binding of {beta}arrs, and understanding the intricate details of receptor-{beta}arr interaction is the next frontier in GPCR structural biology. To date, the high-resolution structures of active {beta}arr1 have been revealed, but the activation mechanism of {beta}arr2 by a phosphorylated GPCR remains elusive. Here, we present a 1.95 [A] crystal structure of {beta}arr2 in complex with a phosphopeptide (C7pp) derived from the carboxyl-terminus of ACKR3, also known as CXCR7. The structure of C7pp-bound {beta}arr2 reveals key differences from the previously determined active conformation of {beta}arr1. One of the key differences is that C7pp-bound {beta}arr2 shows a relatively small inter-domain rotation. An antibody-fragment-based conformational sensor and hydrogen/deuterium exchange experiments further corroborate structural features and suggest that the determined structure is an alternative active conformation of {beta}arr2.

biochemistry↗

bioRxiv2019

Purification of native CCL7 and its functional interaction with selected chemokine receptors

Chemokine receptors form a major sub-family of G protein-coupled receptors (GPCRs) and they are involved in a number of cellular and physiological processes related to our immune response and regulation. A better structural understanding of ligand-binding, activation, signaling and regulation of chemokine receptors is very important to design potentially therapeutic interventions for human disorders arising from aberrant chemokine signaling. One of the key limitations in probing the structural details of chemokine receptors is the availability of large amounts of purified, homogenous and fully functional chemokine ligands, and the commercially available products, are not affordable for in-depth structural studies. Moreover, production of uniformly isotope-labeled chemokines, for example, suitable for NMR-based structural investigation, also remains challenging. Here, we have designed a streamlined approach to express and purify the human chemokine CCL7 as well as its 15N-, 15N/13C-, 2H/15N/13C-isotope-labeled derivatives, at milligram levels using E. coli expression system. Purified CCL7 not only maintains a well-folded three-dimensional structure as analyzed using circular dichroism and 1H/15N NMR but it also induces coupling of heterotrimeric G-proteins and {beta}-arrestins for selected chemokine receptors in cellular system. Our strategy presented here may be applicable to other chemokines and therefore, provide a potentially generic and cost-effective approach to produce chemokines in large amounts for functional and structural studies.

biochemistry↗

bioRxiv2019

Conformational sensors and domain-swapping reveal structural and functional differences between β-arrestin isoforms

Desensitization, signaling and trafficking of G protein-coupled receptors (GPCRs) are critically regulated by multifunctional adaptor proteins, {beta}-arrestins ({beta}arrs). The two isoforms of {beta}arrs ({beta}arr1 and 2) share a high degree of sequence and structural similarity, still however, they often mediate distinct functional outcomes in the context of GPCR signaling and regulation. A mechanistic basis for such a functional divergence of {beta}arr isoforms is still lacking. Using a set of complementary approaches including antibody fragment based conformational sensors, we discover structural differences between {beta}arr1 and 2 upon their interaction with activated and phosphorylated receptors. Interestingly, domain swapped chimeras of {beta}arrs display robust complementation in functional assays thereby, linking the structural differences between the receptor-bound {beta}arr1 and 2 with their divergent functional outcomes. Our findings reveal important insights into the ability of {beta}arr isoforms to drive distinct functional outcomes, and underscore the importance of integrating this aspect in the current framework of biased agonism.

biophysics↗