Biology subjects

Chen, J. Z.

Publications and source records attributed to Chen, J. Z..

18 recordsLinked to original sources

bioRxiv2026

Nanobodies against Plasmodium adhesins that block receptor engagement and malaria parasite invasion

Malaria is caused by Plasmodium parasites, and its clinical symptoms are a result of parasite invasion of red blood cells and the subsequent cycles of replication and proliferation. In human populations, Plasmodium vivax is responsible for the most widely distributed recurring malaria infections whereas Plasmodium falciparum inflicts the most mortality and morbidity. One well-characterized family of adhesins involved in red blood cell invasion is the reticulocyte-binding-like protein homolog family, known as the RBL superfamily which includes the PfRh family in P. falciparum and PvRBP family in P. vivax. Here we report a collection of nanobodies against three members of this adhesin family, PfRh5, PfRh4 and PvRBP2b. Nanobodies against these Plasmodium adhesins bind with high affinity across several epitopes and can block receptor engagement and inhibit parasite invasion of red blood cells. Using computational design, we generated stabilized PfRh4 variants that encompass the conserved scaffold present in the PfRh and PvRBP families of adhesins and show that several variants with improved expression retained binding to mouse monoclonal antibodies, nanobodies and Complement Receptor 1, the human receptor for PfRh4. We also observed that most of the inhibitory nanobodies against the three antigens recognized the conserved structural scaffold that define this family of adhesins. These results demonstrate the potential of nanobodies to block malaria parasite invasion into red blood cells.

microbiology↗

bioRxiv2026

The modular evolution of chitinases is governed by coevolution of auxiliary and catalytic domains

The modular architecture of multi-domain enzymes is a key source of functional diversity. GH18 chitinases exemplify this, possessing a variety of auxiliary domains that have been postulated to underpin their role as essential global nutrient cyclers. However, there is no evolutionary framework that accounts for vast the assortment of domain compositions observed across the protein family. Here, we map the sequence space of nearly 40,000 bacterial chitinases, integrating phylogenetics with a quantitative analysis of domain promiscuity to decode their evolutionary history. We reveal that diversification follows distinct trajectories: enzymes necessary for environmental chitin scavenging evolve via high modular plasticity and structural elaboration of the catalytic core, whereas sequences required for specialized, essential developmental roles fix their domain architecture to fulfill lineage-specific physiological roles. By resolving how domain accretion co-evolves with catalytic scaffolds, this work provides a framework for understanding how multi-domain enzymes adapt to complex environments.

evolutionary biology↗

bioRxiv2025

Examining Selection Dynamics and Limitations in Multi-round Protein Selection of High Diversity Libraries

Proteins and peptides underpin essential biological functions and technological applications, from targeting disease-relevant interactions to providing broad enzymatic activities. However, engineering molecules with desired properties remains difficult, owing to complex sequence-structure-function relationships and the lack of data on specific systems. Experimental selection strategies, including directed evolution, phage display, and mRNA display, address this challenge by leveraging high diversity libraries and iterative enrichment under defined selection pressures. This allows for the identification of candidates without requiring extensive prior knowledge, and can generate extensive datasets for use in machine learning. While many selection systems exist, comparisons across different selection approaches are hindered by the lack of a unifying analytical framework. Here, we present a set of broadly applicable analyses for assessing selection dynamics in multi-round or multi-condition experiments, ranging from position level analysis of sequence properties to full sequence space mappings through protein language model embeddings. Using the toolset to analyze a variety of different datasets in parallel, we explore the potential effects of diversity, coverage, and reproducibility, offering generalizable insights to guide experimental design, interpretation, and troubleshooting across protein and peptide discovery platforms.

molecular biology↗

bioRxiv2025

Widespread promiscuous alkaline phosphatases underscore early microbial phosphite utilization

Phosphate is often a limiting resource, directly affecting the availability of key biomolecules such as nucleotides. To cope with phosphate scarcity, bacteria have evolved enzymes that utilize alternative phosphorus compounds, including phosphite (Pt). Although a few enzymes oxidize Pt to produce phosphate, the enzymes responsible for Pt oxidation in many environmental bacteria remain unidentified, and the role of microbial Pt oxidation in the global phosphorus cycle is not yet fully understood. In this study, we performed bioinformatic analyses of three Pt-oxidizing enzymes: the native Pt oxidase phosphite dehydrogenase (PtxD), and two promiscuous Pt oxidases, alkaline phosphatase (AP) and carbon-phosphorus (CP) lyase. Among these, AP was found to be widely distributed across bacteria since the early stages of their evolution. In contrast, PtxD emerged later in a limited number of bacterial lineages that had lost AP. Our biochemical characterizations revealed that most extant and reconstructed ancestral APs tested exhibited Pt oxidation activity. Moreover, disruption of active-site residues diminished Pt oxidase activity in AP, while only partially affecting its native function. This promiscuous function of AP reveals an overlooked mechanism in bacterial phosphate metabolism and underscores the role of Pt in the cycling of bioavailable phosphorus in ecosystems.

biochemistry↗

bioRxiv2025

A Spray Dried Replicon Vaccine Platform for Pandemic Response

The recent COVID-19 pandemic, as well as the threat of a global pandemic caused by H5N1 avian influenza virus, has highlighted the need for the development of thermostable vaccines that can be manufactured and distributed rapidly to combat the next global pandemic. To address this need, we previously developed a replicon vaccine platform that utilizes a nanostructured lipid carrier (NLC) to protect and efficiently deliver antigen-expressing replicon molecules in vivo. The replicon-NLC vaccine platform uses readily sourced components and can be rapidly manufactured at scale with the potential for stockpiling, thus enhancing pandemic preparedness. Spray drying is a promising method of vaccine desiccation with reduced costs and increased scale-up capabilities compared to lyophilization. As proof of concept, we demonstrate for the first time the successful spray drying of a replicon-NLC vaccine complex designed to protect against H5N1 avian influenza A virus to enhance its long-term thermostability while maintaining vaccine immunogenicity in an in vivo mouse model. Several glass-forming disaccharide excipients were screened for formulation and process compatibility under low-temperature spray drying conditions, and it was determined that a suitable shell-forming excipient, L-leucine, was necessary to prevent excessive accumulation of replicon-NLC vaccine complexes on the dry powder surface and a subsequent loss in process yield. The spray dried replicon-NLC vaccine powders were chemically stable for 1 month of storage at 40{degrees}C. Immunogenicity of the spray dried drug product was also well maintained for at least 3 months of storage at 4{degrees}C when administered intramuscularly into C57BL/6 mice as a reconstituted liquid. Finally, we demonstrate the ability to precisely control the aerodynamic particle size of the spray dried vaccine product to generate dry powders that are theoretically suitable for nasal or pulmonary delivery without reconstitution. This work establishes the feasibility of spray drying a thermostable replicon-NLC vaccine for rapid pandemic response.

immunology↗

bioRxiv2024

Exploring large protein sequence space through homology- and representation-based hierarchical clustering

Exploration of protein sequence space can offer insight into protein sequence-function relationships, benefitting both basic science and industrial applications. The use of sequence similarity networks (SSNs) is a standard method for exploring large sequence datasets, but is currently limited when scaling to very large datasets and when viewing more than one level (hierarchy) of homology. Here, we present a sequence analysis pipeline with a number of innovations that address some limitations of traditional SSNs. First, we develop a hierarchical visualization approach that captures the full range of homologies across protein superfamilies. Second, we leverage representations embedded by protein language models as an alternative homology metric to the basic local alignment search tool (BLAST), showing that they produce comparable results when identifying isofunctional protein families. Finally, we demonstrate that unbiased representative sampling of sequences from genetic neighborhoods can be achieved through the use of hidden Markov models (HMMs) or vector representations. The utility of these methods is exemplified by updating the sequence-function analysis of the FMN/F420-binding split barrel superfamily and improving phylogenetic analyses. We provide our sequence exploration pipeline as publicly available code (ProteinClusterTools) and show it to be scalable to large datasets ([~]300k sequences) using desktop computers.

bioinformatics↗

bioRxiv2024

A strong priority effect in the assembly of a specialized insect-microbe symbiosis

Microbial community assembly is determined in part by interactions between taxa that colonize ecological niches available within habitat patches. The outcomes of these interactions, and by extension the trajectory of community assembly, can display priority effects - dependency on the order in which taxa first occupy these niches. The underlying mechanisms of these phenomena vary from system to system and are often not well resolved. Here, we characterize priority effects in colonization of the squash bug (Anasa tristis) by bacterial symbionts from the genus Caballeronia, using pairs of strains that are known to strongly compete during host colonization, as well as strains that are isogenic and thus functionally identical. By introducing symbiont strains into individual bugs in a sequential manner, we show that within-host populations established by the first colonist are extremely resistant to invasion, regardless of strain identity and competitive interactions. By knocking down the population of an initial colonist with antibiotics, we further show that colonization success by the second symbiont is still diminished even when space in the symbiotic organ is available and physically accessible for colonization. We propose a paradigm in which resident symbionts exclude subsequent infections by manipulating the host environment, partially but not exclusively by eliciting tissue remodeling of the symbiont organ. ImportanceHost-associated microbial communities underpin critical ecosystem processes and human health, and their ability to do so is determined in turn by the various processes that shape their composition. While natural selection acts on competing genotypes and species during community assembly, the manner by which selection determines the trajectory of community assembly can differ depending on the sequence by which taxa establish within that community. We document this phenomenon, known as a priority effect, during experimental colonization of a North American insect pest, the squash bug Anasa tristis, by its betaproteobacterial symbionts in the genus Caballeronia. Our study demonstrates how stark, strain-level variation can emerge in specialized host-microbe symbioses simply through differences in the order by which strains colonize the host. Understanding the mechanistic drivers of community structure in host-associated microbiomes can highlight both pitfalls and opportunities for the engineering of these communities and their constituent taxa for societal benefit.

microbiology↗

bioRxiv2023

Understanding epistatic networks in the B1 -lactamases through coevolutionary statistical modeling and deep mutational scanning

Over the course of evolution, proteins families undergo sequence diversification via mutation accumulation, with extant homologs often sharing less than 25% sequence identity. The resulting diversity presents a complex view of sequence-structure-function relationships, as epistasis is prevalent, and deleterious mutations in one protein can be tolerated in homologous sequences through networks of intramolecular, compensatory interactions. Understanding these epistatic networks is crucial for understanding and predicting protein function, yet comprehensive analysis of such networks across protein families is limited. In this study, we combine computational and experimental approaches to examine epistatic networks in the class B1 metallo-{beta}-lactamases, a diverse family of antibiotic-degrading enzymes. Using Direct Coupling Analysis, we assess global coevolutionary signatures across the B1 family. We also obtain detailed experimental data from deep mutational scanning on two distant B1 homologs, NDM-1 and VIM-2. There is good agreement between the two approaches, revealing both family-wide and homolog specific patterns that can be associated with 3D structure. However, specific interactions remain complex, and strong epistasis in evolutionarily entrenched residues are not easily compensated for by changes in nearby interactions.

biochemistry↗

bioRxiv2023

Structural insights into the heterotrimeric alternatively spliced P2X7 receptorsCondensed title: Structures of heterotrimeric P2X7 receptors

AlphaFold2-Multimer was used to generate structures of the heterotrimeric P2X7 receptors composed of wild-type P2X7A subunits and alternatively spliced subunits (P2X7B, P2X7E, P2X7J, and P2X7L) that have been confirmed in humans. The study supports laboratory research by providing insight into the structure and flexibility of the heterotrimeric alternatively spliced receptors in a simulated environment and may thereby aid structure-guided drug design. AbstractP2X7 receptors (P2X7Rs) are membrane-bound ATP-gated ion channels that are composed of three subunits. Different subunit structures may be expressed due to alternative splicing of the P2RX7 gene, altering the receptors function when combined with the wild-type P2X7A subunits. In this study, the application of the deep-learning method, AlphaFold2-Multimer (AF2M), for the generation of trimeric P2X7Rs was first validated by comparing an AF2M-generated rat wild-type P2X7A receptor with a structure determined by cryogenic electron microscopy (Protein Data Bank Identification: 6U9V). The results suggested AF2M could firstly, accurately predict the structures of P2X7Rs and secondly, accurately identify the highest quality model through the ranking system. Subsequently, AF2M was used to generate models of heterotrimeric alternatively spliced P2X7Rs consisting of one or two wild-type P2X7A subunits in combination with one or two P2X7B, P2X7E, P2X7J, and P2X7L splice variant subunits. The top-ranking models were deemed valid based on AF2Ms confidence measures, stability in molecular dynamics simulations, and consistent flexibility of the conserved regions between the models. Visual analysis of the heterotrimeric receptors identified missing residues in the ATP binding sites of the P2X7E, P2X7J, and P2X7L splice variants, likely translating into dysfunctional binding sites. Overall, the models produced in this study (available as supplementary material) unlock the possibility of structure-based studies into the heterotrimeric P2X7Rs.

biophysics↗

bioRxiv2023

Neutral Drift and Threshold Selection Promote Phenotypic Variation

Phenotypic variations within a population exist on different scales of biological organization and play a central role in evolution by providing adaptive capacity at the population-level. Thus, the question of how evolution generates phenotypic variation within an evolving population is fundamental in evolutionary biology. Here we address this question by performing experimental evolution of an antibiotic resistance gene, VIM-2 {beta}-lactamase, combined with diverse biochemical assays and population genetics. We found that neutral drift, i.e., evolution under a static environment, with a low antibiotic concentration can promote and maintain significant phenotypic variation within the population with >100-fold differences in resistance strength. We developed a model based on the phenotype-environment-fitness landscape generated with >5,000 VIM-2 variants, and demonstrated that the combination of "mutation-selection balance" and "threshold-like fitness-phenotype relationship" is sufficient to explain the generation of large phenotypic variation within the evolving population. Importantly, high-resistance conferring variants can emerge during neutral drift, without being a product of adaptation. Our findings provide a novel and simple mechanistic explanation for why most genes in nature, and by extension, systems and organisms, inherently exhibit phenotypic variation, and thus, population-level evolvability.

evolutionary biology↗

bioRxiv2021

Environmental changes dictate selection and nonspecific epistasis in an empirical phenotype-environment-fitness landscape

Fitness landscapes, mappings of genotype/phenotype to their effects on fitness, are invaluable concepts in evolutionary biochemistry. Though widely discussed, measurements of phenotype-fitness landscapes in proteins remain scarce. Here, we quantify all single mutational effects on fitness and phenotype of VIM-2 {beta}-lactamase across a 64-fold range of ampicillin concentrations. We then construct a phenotype-fitness landscape that takes variations in environmental selection pressure into account. We found that a simple, empirical landscape accurately models the ~39,000 mutational data points, suggesting the evolution of VIM-2 can be predicted based on the selection environment. Our landscape provides new quantitative knowledge on the evolution of the {beta}-lactamases and proteins in general, particularly their evolutionary dynamics under sub-inhibitory antibiotic concentrations, as well as the mechanisms and environmental dependence of nonspecific epistasis. One Sentence SummaryAn empirical fitness landscape discloses the environmental dependence of mutational effects in VIM-2 {beta}-lactamase.

evolutionary biology↗

bioRxiv2021

Losartan Increases Survival of the Fbn1mgR/mgR Mouse Model of Marfan Syndrome in and Age-Dependent Manner

Clinical trials investigating angiotensin receptor blockers (ARB) for attenuation of thoracic aortic aneurysm in people with Marfan syndrome have demonstrated variable efficacy. The primary objective of this study was to determine whether the age of mice at the time of losartan initiation affected mortality in fibrillin-1 hypomorphic (Fbn1mgR/mgR) mice. Male (n=40) and female (n=28) Fbn1mgR/mgR mice were randomized to receive losartan in drinking water (0.6 g/L) starting at either 24 or 50 days of age. Controls included Fbn1mgR/mgR mice (20M, 14F) and wild type (15M, 15F) littermates who were not administered the drug. Mortality of Fbn1mgR/mgR males receiving losartan at postnatal day 24 (P24) was not different from wild type controls (p=0.138). Survival of Fbn1mgR/mgR males administered losartan at P50 was not different compared to Fbn1mgR/mgR males receiving no drug (p=0.194) and decreased compared to wild type mice (p=0.002). Survival analysis after P50 demonstrated increased survival of Fbn1mgR/mgR males administered losartan at P50 compared to Fbn1mgR/mgR mice receiving no drug (p=0.017). Age is a critical variable that affects the therapeutic efficacy of losartan in male Fbn1mgR/mgR mice. Since overall mortality in female Fbn1mgR/mgR mice was lower than in male Fbn1mgR/mgR mice, a survival benefit with losartan was not detected in females.

physiology↗

bioRxiv2020

Inhibition of Angiotensin II Dependent AT1a Receptor Stimulation Attenuates Thoracic Aortic Pathology in Fibrillin-1C1041G/+ Mice

Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/127670v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@8e7c32org.highwire.dtl.DTLVardef@7bf57aorg.highwire.dtl.DTLVardef@312d3forg.highwire.dtl.DTLVardef@9198bd_HPS_FORMAT_FIGEXP M_FIG C_FIG ObjectiveA cardinal feature of Marfan syndrome is thoracic aortic aneurysm (TAA). The contribution of ligand-dependent stimulation of angiotensin II receptor type 1a (AT1aR) to TAA progression remains controversial because the beneficial effects of angiotensin receptor blockers have been ascribed to off-target effects. This study used genetic and pharmacologic modes of attenuating angiotensin receptor and ligand, respectively, to determine their roles on TAA in mice with fibrillin-1 haploinsufficiency (Fbn1C1041G/+). Approach and ResultsTAA in Fbn1C1041G/+ mice were determined in both sexes and found to be strikingly sexual dimorphic. Males displayed progressive dilation over 12 months while ascending aortic dilation in Fbn1C1041G/+ females did not differ significantly from wild type mice. To determine the role of AT1aR, Fbn1C1041G/+ mice that were either +/+ or -/- for AT1aR were generated. AT1aR deletion reduced progressive expansion of ascending aorta and aortic root diameter from 1 to 12 months of age in males. Medial thickening and elastin fragmentation were attenuated. An antisense oligonucleotide against angiotensinogen (AGT-ASO) was administered to male Fbn1C1041G/+ mice to determine the effects of angiotensin II depletion. AGT-ASO administration, at doses that markedly reduced plasma AGT concentrations, attenuated progressive dilation of the ascending aorta and aortic root. AGT-ASO also reduced medial thickening and elastin fragmentation. ConclusionsGenetic approaches to delete AT1aR and deplete AngII production exerted similar effects in attenuating pathology in the proximal thoracic aorta of male Fbn1C1041G/+ mice. These data are consistent with ligand (AngII) dependent stimulation of AT1aR being responsible for aortic disease progression. HighlightsO_LIProfound sexual dimorphism of aortic disease occurs in Fbn1C1041G/+ mice, with female mice being more resistant and male mice being more susceptible. C_LIO_LIInhibition of the AngII-AT1aR axis attenuates aortic pathology in male Fbn1C1041G/+ mice. C_LIO_LIAntisense oligonucleotides targeting angiotensinogen deplete plasma angiotensinogen and attenuate thoracic aortic aneurysms. C_LI

physiology↗

bioRxiv2020

Comprehensive exploration of the translocation, stability and substrate recognition requirements in VIM-2 lactamase.

Metallo-{beta}-lactamases (MBLs) degrade a broad spectrum of {beta}-lactam antibiotics, and are a major disseminating source for multidrug resistant bacteria. Despite many biochemical studies in diverse MBLs, molecular understanding of the roles of residues in the enzymes stability and function, and especially substrate specificity, is lacking. Here, we employ deep mutational scanning (DMS) to generate comprehensive single amino acid variant data on a major clinical MBL, VIM-2, by measuring the effect of thousands of VIM-2 mutants on the degradation of three representative classes of {beta}-lactams (ampicillin, cefotaxime, and meropenem) and at two different temperatures (25{degrees}C and 37{degrees}C). We revealed residues responsible for expression and translocation, and mutations that increase resistance and/or alter substrate specificity. The distribution of specificity-altering mutations unveiled distinct molecular recognition of the three substrates. Moreover, these function-altering mutations are frequently observed among naturally occurring variants, suggesting that the enzymes has continuously evolved to become more potent resistance genes.

biochemistry↗

bioRxiv2020

Functional Importance of Second Heart Field-derived Cells During Thoracic Aortic Aneurysm Formation

BackgroundThe ascending aorta is a common location for aneurysm and dissection. This aortic region is populated by a mosaic of medial and adventitial cells that are embryonically derived from either the second heart field (SHF) or the cardiac neural crest. SHF-derived cells populate areas that coincide with the spatial specificity of thoracic aortopathies. The purpose of this study was to determine whether and how SHF-derived cells contribute to ascending aortopathies. MethodsAscending aortic pathologies were examined in patients with sporadic thoracic aortopathies and angiotensin II (AngII)-infused mice. Ascending aortas without overt pathology from AngII-infused mice were subjected to mass spectrometry assisted proteomics, and molecular features of SHF-derived cells were determined by single cell transcriptomic analyses. Genetic deletion of either low-density lipoprotein receptor-related protein 1 (Lrp1) or transforming growth factor-{beta} receptor 2 (Tgfbr2) in SHF- derived cells was conducted to examine the impact of SHF-derived cells on vascular integrity. ResultsPathologies in human ascending aortic aneurysmal tissues were predominant in outer medial layers and adventitia. This gradient was mimicked in mouse aortas following AngII infusion that was coincident with the distribution of SHF-derived cells. Proteomics indicated that brief AngII infusion, prior to overt pathology, evoked downregulation of SMC proteins and differential expression of extracellular matrix proteins, including several LRP1 ligands. LRP1 deletion in SHF-derived cells augmented AngII-induced ascending aortic aneurysm and rupture. Single cell transcriptomic analysis revealed that brief AngII infusion decreased Lrp1 and Tgfbr2 mRNA abundance in SHF-derived cells and induced a unique fibroblast population with low abundance of Tgfbr2 mRNA. SHF-specific Tgfbr2 deletion led to embryonic lethality at E12.5 with dilatation of the outflow tract and retroperitoneal hemorrhage. Integration of proteomic and single cell transcriptomics results identified plasminogen activator inhibitor 1 (PAI1) as the most increased protein in SHF-derived SMCs and fibroblasts during AngII infusion. Immunostaining revealed a transmural gradient of PAI1 in both ascending aortas of AngII-infused mice and human ascending aneurysmal aortas that mimicked the gradient of medial and adventitial pathologies. ConclusionSHF-derived cells exert a critical role in maintaining vascular integrity through LRP1 and TGF-{beta} signaling associated with increases of aortic PAI1. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/930917v6_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@185e3d9org.highwire.dtl.DTLVardef@131d702org.highwire.dtl.DTLVardef@11afa42org.highwire.dtl.DTLVardef@242786_HPS_FORMAT_FIGEXP M_FIG C_FIG Clinical PerspectiveO_ST_ABSWhat is new?C_ST_ABS- SHF-derived SMCs and fibroblasts associate with AngII-induced aortic pathologies. - AngII induces a distinct fibroblast sub-cluster that is less abundant for mRNAs related to major extracellular components and TGF{beta} ligands and receptors, but more abundant for proliferative genes. - TGFBR2 deletion in SHF-derived cells are embryonic lethal with significant dilatation of the outflow tract in mice. - SHF-specific deletion of LRP1 leads to aortic pathologies in mice, supporting the importance of SHF-derived cells in maintaining ascending aortic wall integrity. What are the clinical implications?- Heterogeneity of the embryonic origins of SMCs and fibroblasts contributes to complex mechanisms of vasculopathy formation, which should be considered when investigating the pathogenesis of thoracic aortopathies.

pathology↗

bioRxiv2018

Convergent Allostery in Ribonucleotide Reductase

Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for being largely restricted to bacteria, including many pathogens, and for lacking an evolutionarily mobile ATP-cone domain that allosterically controls overall activity. In this study, we report the emergence of a new and unexpected mechanism of activity regulation in the sole RNR of the model organism Bacillus subtilis. Using a hypothesis-driven structural approach that combines the strengths of small-angle X-ray scattering (SAXS), crystallography, and cryo-electron microscopy (cryo-EM), we describe the reversible interconversion of six unique structures, including a flexible, active tetramer and two novel, inhibited filaments. These structures reveal the conformational gymnastics necessary for RNR activity and the molecular basis for its control via an evolutionarily convergent form of allostery.

biochemistry↗

bioRxiv2018

Cryo-EM visualization of an active high open probability CFTR ion channel

The Cystic fibrosis transmembrane conductance regulator (CFTR) anion channel, crucial to epithelial salt and water homeostasis, and defective due to mutations in its gene in patients with cystic fibrosis is a unique member of the large family of ATP-binding cassette transport proteins. Regulation of CFTR channel activity is stringently controlled by phosphorylation and nucleotide binding. Structural changes that underlie transitions between active and inactive functional states are not yet fully understood. Indeed the first 3D structures of dephosphorylated, ATP-free and phosphorylated ATP-bound states were only recently reported. Here we have determined the structure of inactive and active states of a thermally stabilized CFTR with very high channel open probability, confirmed after reconstitution into proteoliposomes. The unique repositioning of the TMHs and R domain density that we observe provide insights into the structural transition between active and inactive functional states of CFTR.\n\nHighlightsO_LIStructures of thermostabilized avian CFTR in dephosphorylated or phosphorylated forms at 4.3 [A] and 6.6 [A] resolution, respectively.\nC_LIO_LIConformational differences of transmembrane helices 7 & 8 compared to zebra fish and human CFTR structures reveal an extracellular vestibule that may provide anion access to the pore.\nC_LIO_LIR-domain density appears to \"plug\" the intercellular vestibule in the dephosphorylated avian CFTR cryo-EM map.\nC_LI

biophysics↗

bioRxiv2016

Cryo-EM structure of the ATP-sensitive potassium channel illuminates mechanisms of assembly and gating

ATP-sensitive potassium (KATP) channels are metabolic sensors that couple cell energetics to membrane excitability. In pancreatic {beta}-cells, channels formed by SUR1 and Kir6.2 regulate insulin secretion and are the targets of antidiabetic sulfonylureas. Here, we used cryo-EM to elucidate structural basis of channel assembly and gating. The structure, determined in the presence of ATP and the sulfonylurea glibenclamide, at ~6[A] resolution reveals a closed Kir6.2 tetrameric core with four peripheral SUR1s each anchored to a Kir6.2 by its N-terminal transmembrane domain (TMD0). Intricate interactions between TMD0, the loop following TMD0, and Kir6.2 near the proposed PIP2 binding site, and where ATP density is observed, suggest SUR1 may contribute to ATP and PIP2 binding to enhance Kir6.2 sensitivity to both. The SUR1-ABC core is found in an unusual inward-facing conformation whereby the two nucleotide binding domains are misaligned along a two-fold symmetry axis, revealing a possible mechanism by which glibenclamide inhibits channel activity.

biochemistry↗