Scholars@Duke
Mario-Juan Borgnia

Mario-Juan Borgnia

Adjunct Professor in the Department of Biochemistry
Biochemistry
mborgnia@nih.gov
4706 Rollingwood Dr, Durham, NC 27713
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Selected Publications

Characterization of α-synuclein oligomers formed in the presence of lipid vesicles

Journal Article Biochemistry and Biophysics Reports · July 1, 2024 Aggregation of α-synuclein into oligomers and fibrils is associated with numerous neurodegenerative diseases such as Parkinson's disease (PD). Although the identity of the pathogenic species formed during the aggregation process is still under active debat ... Full text Cite

Structural and Functional Analysis of Heparosan Synthase 2 from Pasteurella multocida to Improve the Synthesis of Heparin

Journal Article ACS Catalysis · May 3, 2024 Heparin is a widely used drug to treat thrombotic disorders in hospitals. Heparosan synthase 2 from Pasteurella multocida (PmHS2) is a key enzyme used for the chemoenzymatic synthesis of heparin oligosaccharides. It has both activities: glucosaminyl transf ... Full text Cite

Antiviral drug recognition and elevator-type transport motions of CNT3

Journal Article Nature Chemical Biology · January 1, 2024 Nucleoside analogs have broad clinical utility as antiviral drugs. Key to their systemic distribution and cellular entry are human nucleoside transporters. Here, we establish that the human concentrative nucleoside transporter 3 (CNT3) interacts with antiv ... Full text Cite

Sen1 architecture: RNA-DNA hybrid resolution, autoregulation, and insights into SETX inactivation in AOA2.

Journal Article Mol Cell · October 19, 2023 The senataxin (SETX, Sen1 in yeasts) RNA-DNA hybrid resolving helicase regulates multiple nuclear transactions, including DNA replication, transcription, and DNA repair, but the molecular basis for Sen1 activities is ill defined. Here, Sen1 cryoelectron mi ... Full text Link to item Cite

Molecular basis of polyspecific drug and xenobiotic recognition by OCT1 and OCT2.

Journal Article Nat Struct Mol Biol · July 2023 A wide range of endogenous and xenobiotic organic ions require facilitated transport systems to cross the plasma membrane for their disposition. In mammals, organic cation transporter (OCT) subtypes 1 and 2 (OCT1 and OCT2, also known as SLC22A1 and SLC22A2 ... Full text Link to item Cite

Structural basis for pre-tRNA recognition and processing by the human tRNA splicing endonuclease complex.

Journal Article Nat Struct Mol Biol · June 2023 Throughout bacteria, archaea and eukarya, certain tRNA transcripts contain introns. Pre-tRNAs with introns require splicing to form the mature anticodon stem loop. In eukaryotes, tRNA splicing is initiated by the heterotetrameric tRNA splicing endonuclease ... Full text Link to item Cite

Structure and dynamics of the Arabidopsis O-fucosyltransferase SPINDLY.

Journal Article Nature communications · March 2023 SPINDLY (SPY) in Arabidopsis thaliana is a novel nucleocytoplasmic protein O-fucosyltransferase (POFUT), which regulates diverse developmental processes. Sequence analysis indicates that SPY is distinct from ER-localized POFUTs and contains N-terminal tetr ... Full text Open Access Cite

Cryo-EM reveals the architecture of the PELP1-WDR18 molecular scaffold.

Journal Article Nat Commun · November 9, 2022 PELP1 (Proline-, Glutamic acid-, Leucine-rich protein 1) is a large scaffolding protein that functions in many cellular pathways including steroid receptor (SR) coactivation, heterochromatin maintenance, and ribosome biogenesis. PELP1 is a proto-oncogene w ... Full text Link to item Cite

Activation mechanism of the mouse cold-sensing TRPM8 channel by cooling agonist and PIP2.

Journal Article Science · October 14, 2022 The transient receptor potential melastatin 8 (TRPM8) channel is the primary molecular transducer responsible for the cool sensation elicited by menthol and cold in mammals. TRPM8 activation is controlled by cooling compounds together with the membrane lip ... Full text Link to item Cite

Mechanism by which T7 bacteriophage protein Gp1.2 inhibits Escherichia coli dGTPase.

Journal Article Proc Natl Acad Sci U S A · September 13, 2022 Levels of the cellular dNTPs, the direct precursors for DNA synthesis, are important for DNA replication fidelity, cell cycle control, and resistance against viruses. Escherichia coli encodes a dGTPase (2'-deoxyguanosine-5'-triphosphate [dGTP] triphosphohy ... Full text Link to item Cite

Untwisted α-Synuclein Filaments Formed in the Presence of Lipid Vesicles.

Journal Article Biochemistry · September 6, 2022 Accumulation of filamentous aggregates of α-synuclein is a pathological hallmark of several neurodegenerative diseases, including Parkinson's disease (PD). The interaction between α-synuclein and phospholipids has been shown to play a critical role in the ... Full text Link to item Cite

Method for the structural analysis of Twinkle mitochondrial DNA helicase by cryo-EM.

Journal Article Methods · September 2022 The mitochondrial replisome replicates the 16.6 kb mitochondria DNA (mtDNA). The proper functioning of this multicomponent protein complex is vital for the integrity of the mitochondrial genome. One of the critical protein components of the mitochondrial r ... Full text Link to item Cite

Communication network within the essential AAA-ATPase Rix7 drives ribosome assembly

Journal Article PNAS Nexus · September 1, 2022 Rix7 is an essential AAA+ ATPase that functions during the early stages of ribosome biogenesis. Rix7 is composed of three domains including an N-terminal domain (NTD) and two AAA+ domains (D1 and D2) that assemble into an asymmetric stacked hexamer. It was ... Full text Cite

Automated systematic evaluation of cryo-EM specimens with SmartScope.

Journal Article Elife · August 23, 2022 Finding the conditions to stabilize a macromolecular target for imaging remains the most critical barrier to determining its structure by cryo-electron microscopy (cryo-EM). While automation has significantly increased the speed of data collection, specime ... Full text Link to item Cite

Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease.

Journal Article Nucleic Acids Res · August 12, 2022 Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, coronaviruses employ Nsp15, which is a uridine-specific endorib ... Full text Link to item Cite

Structural insight and characterization of human Twinkle helicase in mitochondrial disease.

Journal Article Proc Natl Acad Sci U S A · August 9, 2022 Twinkle is the mammalian helicase vital for replication and integrity of mitochondrial DNA. Over 90 Twinkle helicase disease variants have been linked to progressive external ophthalmoplegia and ataxia neuropathies among other mitochondrial diseases. Despi ... Full text Link to item Cite

Genetically Engineered Nanoparticles of Asymmetric Triblock Polypeptide with a Platinum(IV) Cargo Outperforms a Platinum(II) Analog and Free Drug in a Murine Cancer Model.

Journal Article Nano Lett · July 27, 2022 The development of platinum(Pt)-drugs for cancer therapy has stalled, as no new Pt-drugs have been approved in over a decade. Packaging small molecule drugs into nanoparticles is a way to enhance their therapeutic efficacy. To date, there has been no direc ... Full text Link to item Cite

Molecular dissection of the glutamine synthetase-GlnR nitrogen regulatory circuitry in Gram-positive bacteria.

Journal Article Nat Commun · July 1, 2022 How bacteria sense and respond to nitrogen levels are central questions in microbial physiology. In Gram-positive bacteria, nitrogen homeostasis is controlled by an operon encoding glutamine synthetase (GS), a dodecameric machine that assimilates ammonium ... Full text Link to item Cite

Characterization of α-synuclein oligomers formed in the presence of lipid vesicles

Journal Article Biochemistry and Biophysics Reports · July 1, 2024 Aggregation of α-synuclein into oligomers and fibrils is associated with numerous neurodegenerative diseases such as Parkinson's disease (PD). Although the identity of the pathogenic species formed during the aggregation process is still under active debat ... Full text Cite

Structural and Functional Analysis of Heparosan Synthase 2 from Pasteurella multocida to Improve the Synthesis of Heparin

Journal Article ACS Catalysis · May 3, 2024 Heparin is a widely used drug to treat thrombotic disorders in hospitals. Heparosan synthase 2 from Pasteurella multocida (PmHS2) is a key enzyme used for the chemoenzymatic synthesis of heparin oligosaccharides. It has both activities: glucosaminyl transf ... Full text Cite

Antiviral drug recognition and elevator-type transport motions of CNT3

Journal Article Nature Chemical Biology · January 1, 2024 Nucleoside analogs have broad clinical utility as antiviral drugs. Key to their systemic distribution and cellular entry are human nucleoside transporters. Here, we establish that the human concentrative nucleoside transporter 3 (CNT3) interacts with antiv ... Full text Cite

Sen1 architecture: RNA-DNA hybrid resolution, autoregulation, and insights into SETX inactivation in AOA2.

Journal Article Mol Cell · October 19, 2023 The senataxin (SETX, Sen1 in yeasts) RNA-DNA hybrid resolving helicase regulates multiple nuclear transactions, including DNA replication, transcription, and DNA repair, but the molecular basis for Sen1 activities is ill defined. Here, Sen1 cryoelectron mi ... Full text Link to item Cite

Molecular basis of polyspecific drug and xenobiotic recognition by OCT1 and OCT2.

Journal Article Nat Struct Mol Biol · July 2023 A wide range of endogenous and xenobiotic organic ions require facilitated transport systems to cross the plasma membrane for their disposition. In mammals, organic cation transporter (OCT) subtypes 1 and 2 (OCT1 and OCT2, also known as SLC22A1 and SLC22A2 ... Full text Link to item Cite

Structural basis for pre-tRNA recognition and processing by the human tRNA splicing endonuclease complex.

Journal Article Nat Struct Mol Biol · June 2023 Throughout bacteria, archaea and eukarya, certain tRNA transcripts contain introns. Pre-tRNAs with introns require splicing to form the mature anticodon stem loop. In eukaryotes, tRNA splicing is initiated by the heterotetrameric tRNA splicing endonuclease ... Full text Link to item Cite

Structure and dynamics of the Arabidopsis O-fucosyltransferase SPINDLY.

Journal Article Nature communications · March 2023 SPINDLY (SPY) in Arabidopsis thaliana is a novel nucleocytoplasmic protein O-fucosyltransferase (POFUT), which regulates diverse developmental processes. Sequence analysis indicates that SPY is distinct from ER-localized POFUTs and contains N-terminal tetr ... Full text Open Access Cite

Cryo-EM reveals the architecture of the PELP1-WDR18 molecular scaffold.

Journal Article Nat Commun · November 9, 2022 PELP1 (Proline-, Glutamic acid-, Leucine-rich protein 1) is a large scaffolding protein that functions in many cellular pathways including steroid receptor (SR) coactivation, heterochromatin maintenance, and ribosome biogenesis. PELP1 is a proto-oncogene w ... Full text Link to item Cite

Activation mechanism of the mouse cold-sensing TRPM8 channel by cooling agonist and PIP2.

Journal Article Science · October 14, 2022 The transient receptor potential melastatin 8 (TRPM8) channel is the primary molecular transducer responsible for the cool sensation elicited by menthol and cold in mammals. TRPM8 activation is controlled by cooling compounds together with the membrane lip ... Full text Link to item Cite

Mechanism by which T7 bacteriophage protein Gp1.2 inhibits Escherichia coli dGTPase.

Journal Article Proc Natl Acad Sci U S A · September 13, 2022 Levels of the cellular dNTPs, the direct precursors for DNA synthesis, are important for DNA replication fidelity, cell cycle control, and resistance against viruses. Escherichia coli encodes a dGTPase (2'-deoxyguanosine-5'-triphosphate [dGTP] triphosphohy ... Full text Link to item Cite

Untwisted α-Synuclein Filaments Formed in the Presence of Lipid Vesicles.

Journal Article Biochemistry · September 6, 2022 Accumulation of filamentous aggregates of α-synuclein is a pathological hallmark of several neurodegenerative diseases, including Parkinson's disease (PD). The interaction between α-synuclein and phospholipids has been shown to play a critical role in the ... Full text Link to item Cite

Method for the structural analysis of Twinkle mitochondrial DNA helicase by cryo-EM.

Journal Article Methods · September 2022 The mitochondrial replisome replicates the 16.6 kb mitochondria DNA (mtDNA). The proper functioning of this multicomponent protein complex is vital for the integrity of the mitochondrial genome. One of the critical protein components of the mitochondrial r ... Full text Link to item Cite

Communication network within the essential AAA-ATPase Rix7 drives ribosome assembly

Journal Article PNAS Nexus · September 1, 2022 Rix7 is an essential AAA+ ATPase that functions during the early stages of ribosome biogenesis. Rix7 is composed of three domains including an N-terminal domain (NTD) and two AAA+ domains (D1 and D2) that assemble into an asymmetric stacked hexamer. It was ... Full text Cite

Automated systematic evaluation of cryo-EM specimens with SmartScope.

Journal Article Elife · August 23, 2022 Finding the conditions to stabilize a macromolecular target for imaging remains the most critical barrier to determining its structure by cryo-electron microscopy (cryo-EM). While automation has significantly increased the speed of data collection, specime ... Full text Link to item Cite

Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease.

Journal Article Nucleic Acids Res · August 12, 2022 Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, coronaviruses employ Nsp15, which is a uridine-specific endorib ... Full text Link to item Cite

Structural insight and characterization of human Twinkle helicase in mitochondrial disease.

Journal Article Proc Natl Acad Sci U S A · August 9, 2022 Twinkle is the mammalian helicase vital for replication and integrity of mitochondrial DNA. Over 90 Twinkle helicase disease variants have been linked to progressive external ophthalmoplegia and ataxia neuropathies among other mitochondrial diseases. Despi ... Full text Link to item Cite

Genetically Engineered Nanoparticles of Asymmetric Triblock Polypeptide with a Platinum(IV) Cargo Outperforms a Platinum(II) Analog and Free Drug in a Murine Cancer Model.

Journal Article Nano Lett · July 27, 2022 The development of platinum(Pt)-drugs for cancer therapy has stalled, as no new Pt-drugs have been approved in over a decade. Packaging small molecule drugs into nanoparticles is a way to enhance their therapeutic efficacy. To date, there has been no direc ... Full text Link to item Cite

Molecular dissection of the glutamine synthetase-GlnR nitrogen regulatory circuitry in Gram-positive bacteria.

Journal Article Nat Commun · July 1, 2022 How bacteria sense and respond to nitrogen levels are central questions in microbial physiology. In Gram-positive bacteria, nitrogen homeostasis is controlled by an operon encoding glutamine synthetase (GS), a dodecameric machine that assimilates ammonium ... Full text Link to item Cite

High-resolution structures of the SAMHD1 dGTPase homolog from Leeuwenhoekiella blandensis reveal a novel mechanism of allosteric activation by dATP.

Journal Article J Biol Chem · July 2022 Deoxynucleoside triphosphate (dNTP) triphosphohydrolases (dNTPases) are important enzymes that may perform multiple functions in the cell, including regulating the dNTP pools and contributing to innate immunity against viruses. Among the homologs that are ... Full text Link to item Cite

Redox-sensitive E2 Rad6 controls cellular response to oxidative stress via K63-linked ubiquitination of ribosomes.

Journal Article Cell Rep · May 24, 2022 Protein ubiquitination is an essential process that rapidly regulates protein synthesis, function, and fate in dynamic environments. Within its non-proteolytic functions, we showed that K63-linked polyubiquitinated conjugates heavily accumulate in yeast ce ... Full text Link to item Cite

Dromedary camel nanobodies broadly neutralize SARS-CoV-2 variants.

Journal Article Proc Natl Acad Sci U S A · May 3, 2022 The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is a trimer of S1/S2 heterodimers with three receptor-binding domains (RBDs) at the S1 subunit for human angiotensin-converting enzyme 2 (hACE2). Due to their small size, nanobodies can ... Full text Link to item Cite

Structural basis of NPR1 in activating plant immunity.

Journal Article Nature · May 2022 NPR1 is a master regulator of the defence transcriptome induced by the plant immune signal salicylic acid1-4. Despite the important role of NPR1 in plant immunity5-7, understanding of its regulatory mechanisms has been hindered by a lack of structural info ... Full text Link to item Cite

A humanized nanobody phage display library yields potent binders of SARS CoV-2 spike.

Journal Article PLoS One · 2022 Neutralizing antibodies targeting the SARS-CoV-2 spike protein have shown a great preventative/therapeutic potential. Here, we report a rapid and efficient strategy for the development and design of SARS-CoV-2 neutralizing humanized nanobody constructs wit ... Full text Link to item Cite

Characterization of SARS2 Nsp15 nuclease activity reveals it's mad about U.

Journal Article Nucleic acids research · September 2021 Nsp15 is a uridine specific endoribonuclease that coronaviruses employ to cleave viral RNA and evade host immune defense systems. Previous structures of Nsp15 from across Coronaviridae revealed that Nsp15 assembles into a homo-hexamer and has a conserved a ... Full text Cite

Heat-dependent opening of TRPV1 in the presence of capsaicin.

Journal Article Nat Struct Mol Biol · July 2021 Transient receptor potential vanilloid member 1 (TRPV1) is a Ca2+-permeable cation channel that serves as the primary heat and capsaicin sensor in humans. Using cryo-EM, we have determined the structures of apo and capsaicin-bound full-length rat TRPV1 rec ... Full text Link to item Cite

Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies.

Journal Article Cell · May 27, 2021 Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (b ... Full text Open Access Link to item Cite

Tau induces formation of α-synuclein filaments with distinct molecular conformations.

Journal Article Biochem Biophys Res Commun · May 21, 2021 Recent structural investigation of amyloid filaments extracted from human patients demonstrated that the ex vivo filaments associated with different disease phenotypes adopt diverse molecular conformations, which are different from those of in vitro amyloi ... Full text Link to item Cite

Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography.

Journal Article Nat Commun · March 30, 2021 Tomographic reconstruction of cryopreserved specimens imaged in an electron microscope followed by extraction and averaging of sub-volumes has been successfully used to derive atomic models of macromolecules in their biological environment. Eliminating bio ... Full text Link to item Cite

Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics.

Journal Article Nat Commun · January 27, 2021 Nsp15, a uridine specific endoribonuclease conserved across coronaviruses, processes viral RNA to evade detection by host defense systems. Crystal structures of Nsp15 from different coronaviruses have shown a common hexameric assembly, yet how the enzyme r ... Full text Link to item Cite

Structural Basis for Virulence Activation of Francisella tularensis.

Journal Article Mol Cell · January 7, 2021 The bacterium Francisella tularensis (Ft) is one of the most infectious agents known. Ft virulence is controlled by a unique combination of transcription regulators: the MglA-SspA heterodimer, PigR, and the stress signal, ppGpp. MglA-SspA assembles with th ... Full text Link to item Cite

Smartscope: AI-driven grid navigation for high-throughput cryo-EM

Conference Proceedings - Applied Imagery Pattern Recognition Workshop · January 1, 2021 Specimen optimization is currently one of the main limiting steps in the cryo-electron microscopy (EM) structure determination pipeline. The ideal specimen is a molecule-thin layer of macromolecules in solution frozen on top of a holey membrane stabilized ... Full text Cite

Controlling the SARS-CoV-2 spike glycoprotein conformation.

Journal Article Nat Struct Mol Biol · October 2020 The coronavirus (CoV) spike (S) protein, involved in viral-host cell fusion, is the primary immunogenic target for virus neutralization and the current focus of many vaccine design efforts. The highly flexible S-protein, with its mobile domains, presents a ... Full text Link to item Cite

Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress.

Journal Article Proc Natl Acad Sci U S A · September 8, 2020 Subpopulations of ribosomes are responsible for fine tuning the control of protein synthesis in dynamic environments. K63 ubiquitination of ribosomes has emerged as a new posttranslational modification that regulates protein synthesis during cellular respo ... Full text Link to item Cite

The structure of helical lipoprotein lipase reveals an unexpected twist in lipase storage.

Journal Article Proc Natl Acad Sci U S A · May 12, 2020 Lipases are enzymes necessary for the proper distribution and utilization of lipids in the human body. Lipoprotein lipase (LPL) is active in capillaries, where it plays a crucial role in preventing dyslipidemia by hydrolyzing triglycerides from packaged li ... Full text Link to item Cite

Structural Insights into Electrophile Irritant Sensing by the Human TRPA1 Channel.

Journal Article Neuron · March 4, 2020 Transient receptor potential channel subfamily A member 1 (TRPA1) is a Ca2+-permeable cation channel that serves as one of the primary sensors of environmental irritants and noxious substances. Many TRPA1 agonists are electrophiles that are recognized by T ... Full text Link to item Cite

Structures of AAA protein translocase Bcs1 suggest translocation mechanism of a folded protein.

Journal Article Nat Struct Mol Biol · February 2020 The mitochondrial membrane-bound AAA protein Bcs1 translocate substrates across the mitochondrial inner membrane without previous unfolding. One substrate of Bcs1 is the iron-sulfur protein (ISP), a subunit of the respiratory Complex III. How Bcs1 transloc ... Full text Link to item Cite

Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements.

Journal Article Nat Commun · January 24, 2020 The trimeric HIV-1 Envelope protein (Env) mediates viral-host cell fusion via a network of conformational transitions, with allosteric elements in each protomer orchestrating host receptor-induced exposure of the co-receptor binding site and fusion element ... Full text Link to item Cite

Targeted selection of HIV-specific antibody mutations by engineering B cell maturation.

Journal Article Science · December 6, 2019 INTRODUCTION: A major goal of HIV-1 vaccine development is the design of immunogens that induce broadly neutralizing antibodies (bnAbs). However, vaccination of humans has not resulted in the induction of affinity-matured and potent HIV-1 bnAbs. To devise ... Full text Link to item Cite

Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies.

Journal Article PLoS Pathog · September 2019 The CD4 binding site (CD4bs) of the HIV-1 envelope glycoprotein is susceptible to multiple lineages of broadly neutralizing antibodies (bnAbs) that are attractive to elicit with vaccines. The CH235 lineage (VH1-46) of CD4bs bnAbs is particularly attractive ... Full text Link to item Cite

Cryo-EM reveals active site coordination within a multienzyme pre-rRNA processing complex.

Journal Article Nat Struct Mol Biol · September 2019 Ribosome assembly is a complex process reliant on the coordination of trans-acting enzymes to produce functional ribosomal subunits and secure the translational capacity of cells. The endoribonuclease (RNase) Las1 and the polynucleotide kinase (PNK) Grc3 a ... Full text Link to item Cite

Visualizing structural transitions of ligand-dependent gating of the TRPM2 channel.

Journal Article Nat Commun · August 20, 2019 The transient receptor potential melastatin 2 (TRPM2) channel plays a key role in redox sensation in many cell types. Channel activation requires binding of both ADP-ribose (ADPR) and Ca2+. The recently published TRPM2 structures from Danio rerio in the li ... Full text Link to item Cite

Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment.

Journal Article Nat Commun · May 24, 2019 Genomic DNA in eukaryotes is organized into chromatin through association with core histones to form nucleosomes, each distinguished by their DNA sequences and histone variants. Here, we used a single-chain antibody fragment (scFv) derived from the anti-nu ... Full text Link to item Cite

Symmetry transitions during gating of the TRPV2 ion channel in lipid membranes.

Journal Article Elife · May 15, 2019 The Transient Receptor Potential Vanilloid 2 (TRPV2) channel is a member of the temperature-sensing thermoTRPV family. Recent advances in cryo-electronmicroscopy (cryo-EM) and X-ray crystallography have provided many important insights into the gating mech ... Full text Open Access Link to item Cite

Regulatory switch at the cytoplasmic interface controls TRPV channel gating.

Journal Article Elife · May 9, 2019 Temperature-sensitive transient receptor potential vanilloid (thermoTRPV) channels are activated by ligands and heat, and are involved in various physiological processes. ThermoTRPV channels possess a large cytoplasmic ring consisting of N-terminal ankyrin ... Full text Open Access Link to item Cite

Structural basis of cooling agent and lipid sensing by the cold-activated TRPM8 channel.

Journal Article Science · March 1, 2019 Transient receptor potential melastatin member 8 (TRPM8) is a calcium ion (Ca2+)-permeable cation channel that serves as the primary cold and menthol sensor in humans. Activation of TRPM8 by cooling compounds relies on allosteric actions of agonist and mem ... Full text Link to item Cite

Structural Basis for Recognition of Ubiquitylated Nucleosome by Dot1L Methyltransferase.

Journal Article Cell Rep · February 12, 2019 Histone H3 lysine 79 (H3K79) methylation is enriched on actively transcribed genes, and its misregulation is a hallmark of leukemia. Methylation of H3K79, which resides on the structured disk face of the nucleosome, is mediated by the Dot1L methyltransfera ... Full text Link to item Cite

Cryo-EM structure of the essential ribosome assembly AAA-ATPase Rix7.

Journal Article Nat Commun · January 31, 2019 Rix7 is an essential type II AAA-ATPase required for the formation of the large ribosomal subunit. Rix7 has been proposed to utilize the power of ATP hydrolysis to drive the removal of assembly factors from pre-60S particles, but the mechanism of release i ... Full text Link to item Cite

Polymer Nanodiscs: Discoidal Amphiphilic Block Copolymer Membranes as a New Platform for Membrane Proteins.

Journal Article Sci Rep · November 9, 2017 Lipid nanodiscs are playing increasingly important roles in studies of the structure and function of membrane proteins. Development of lipid nanodiscs as a membrane-protein-supporting platform, or a drug targeting and delivery vehicle in general, is underm ... Full text Link to item Cite

Grc3 programs the essential endoribonuclease Las1 for specific RNA cleavage.

Journal Article Proc Natl Acad Sci U S A · July 11, 2017 Las1 is a recently discovered endoribonuclease that collaborates with Grc3-Rat1-Rai1 to process precursor ribosomal RNA (rRNA), yet its mechanism of action remains unknown. Disruption of the mammalian Las1 gene has been linked to congenital lethal motor ne ... Full text Link to item Cite

Cryo-EM Analysis of the Conformational Landscape of Human P-glycoprotein (ABCB1) During its Catalytic Cycle.

Journal Article Mol Pharmacol · July 2016 The multidrug transporter P-glycoprotein (P-gp, ABCB1) is an ATP-dependent pump that mediates the efflux of structurally diverse drugs and xenobiotics across cell membranes, affecting drug pharmacokinetics and contributing to the development of multidrug r ... Full text Link to item Cite

Using Cryo-EM to Map Small Ligands on Dynamic Metabolic Enzymes: Studies with Glutamate Dehydrogenase.

Journal Article Mol Pharmacol · June 2016 Cryo-electron microscopy (cryo-EM) methods are now being used to determine structures at near-atomic resolution and have great promise in molecular pharmacology, especially in the context of mapping the binding of small-molecule ligands to protein complexe ... Full text Link to item Cite

Cryo-EM Structures of the Magnesium Channel CorA Reveal Symmetry Break upon Gating.

Journal Article Cell · February 11, 2016 CorA, the major Mg(2+) uptake system in prokaryotes, is gated by intracellular Mg(2+) (KD ∼ 1-2 mM). X-ray crystallographic studies of CorA show similar conformations under Mg(2+)-bound and Mg(2+)-free conditions, but EPR spectroscopic studies reveal large ... Full text Link to item Cite

Prefusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy.

Journal Article Nat Struct Mol Biol · December 2013 The activation of trimeric HIV-1 envelope glycoprotein (Env) by its binding to the cell-surface receptor CD4 and co-receptors (CCR5 or CXCR4) represents the first of a series of events that lead to fusion between viral and target-cell membranes. Here, we p ... Full text Link to item Cite

Glutamate receptor desensitization is mediated by changes in quaternary structure of the ligand binding domain.

Journal Article Proc Natl Acad Sci U S A · April 9, 2013 Glutamate receptor ion channels are membrane proteins that mediate excitatory synaptic transmission in the central nervous system of vertebrates. Insight into molecular mechanisms underlying glutamate receptor gating is limited by lack of structural inform ... Full text Link to item Cite

A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography.

Journal Article J Struct Biol · February 2013 The limitation of using low electron doses in non-destructive cryo-electron tomography of biological specimens can be partially offset via averaging of aligned and structurally homogeneous subsets present in tomograms. This type of sub-volume averaging is ... Full text Link to item Cite

Cryo-electron microscopy--a primer for the non-microscopist.

Journal Article FEBS J · January 2013 Cryo-electron microscopy (cryo-EM) is increasingly becoming a mainstream technology for studying the architecture of cells, viruses and protein assemblies at molecular resolution. Recent developments in microscope design and imaging hardware, paired with e ... Full text Link to item Cite

Computational separation of conformational heterogeneity using cryo-electron tomography and 3D sub-volume averaging.

Journal Article J Struct Biol · May 2012 We have previously used cryo-electron tomography combined with sub-volume averaging and classification to obtain 3D structures of macromolecular assemblies in cases where a single dominant species was present, and applied these methods to the analysis of a ... Full text Link to item Cite

Structural mechanism of trimeric HIV-1 envelope glycoprotein activation.

Journal Article PLoS Pathog · 2012 HIV-1 infection begins with the binding of trimeric viral envelope glycoproteins (Env) to CD4 and a co-receptor on target T-cells. Understanding how these ligands influence the structure of Env is of fundamental interest for HIV vaccine development. Using ... Full text Link to item Cite

Determination of molecular structures of HIV envelope glycoproteins using cryo-electron tomography and automated sub-tomogram averaging.

Journal Article J Vis Exp · December 1, 2011 Since its discovery nearly 30 years ago, more than 60 million people have been infected with the human immunodeficiency virus (HIV) (www.usaid.gov). The virus infects and destroys CD4+ T-cells thereby crippling the immune system, and causing an acquired im ... Full text Link to item Cite

Three-dimensional structures of soluble CD4-bound states of trimeric simian immunodeficiency virus envelope glycoproteins determined by using cryo-electron tomography.

Journal Article J Virol · December 2011 The trimeric envelope glycoprotein (Env) spikes displayed on the surfaces of simian immunodeficiency virus (SIV) and human immunodeficiency virus type 1 (HIV-1) virions are composed of three heterodimers of the viral glycoproteins gp120 and gp41. Although ... Full text Link to item Cite

Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures.

Journal Article Proc Natl Acad Sci U S A · July 12, 2011 The initial step in HIV-1 infection occurs with the binding of cell surface CD4 to trimeric HIV-1 envelope glycoproteins (Env), a heterodimer of a transmembrane glycoprotein (gp41) and a surface glycoprotein (gp120). The design of soluble versions of trime ... Full text Link to item Cite

Lateral density of receptor arrays in the membrane plane influences sensitivity of the E. coli chemotaxis response.

Journal Article EMBO J · May 4, 2011 In chemotactic bacteria, transmembrane chemoreceptors, CheA and CheW form the core signalling complex of the chemotaxis sensory apparatus. These complexes are organized in extended arrays in the cytoplasmic membrane that allow bacteria to respond to change ... Full text Link to item Cite

Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: strain-dependent variation in quaternary structure.

Journal Article PLoS Pathog · December 23, 2010 The initial step in target cell infection by human, and the closely related simian immunodeficiency viruses (HIV and SIV, respectively) occurs with the binding of trimeric envelope glycoproteins (Env), composed of heterodimers of the viral transmembrane gl ... Full text Link to item Cite

Evaluation of denoising algorithms for biological electron tomography.

Journal Article J Struct Biol · October 2008 Tomograms of biological specimens derived using transmission electron microscopy can be intrinsically noisy due to the use of low electron doses, the presence of a "missing wedge" in most data collection schemes, and inaccuracies arising during 3D volume r ... Full text Link to item Cite

Molecular architecture of native HIV-1 gp120 trimers.

Journal Article Nature · September 4, 2008 The envelope glycoproteins (Env) of human and simian immunodeficiency viruses (HIV and SIV, respectively) mediate virus binding to the cell surface receptor CD4 on target cells to initiate infection. Env is a heterodimer of a transmembrane glycoprotein (gp ... Full text Link to item Cite

Molecular Architecture of Native HIV-1 gp 120 Trimers

Journal Article Chemtracts · June 1, 2008 A critical step in human and simian immunodeficiency virus (HIV and SIV, respectively) pathogenesis is entry into the target cell. The process of infection is mediated by envelope glycoproteins, Env, which assemble in a trim- eric form on the surface of th ... Cite

Three-dimensional imaging of the highly bent architecture of Bdellovibrio bacteriovorus by using cryo-electron tomography.

Journal Article J Bacteriol · April 2008 Bdellovibrio bacteriovorus cells are small deltaproteobacterial cells that feed on other gram-negative bacteria, including human pathogens. Using cryo-electron tomography, we demonstrated that B. bacteriovorus cells are capable of substantial flexibility a ... Full text Link to item Cite

From gigabytes to bytes: Automated denoising and feature identification in electron tomograms of intact bacterial cells

Journal Article 2007 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro - Proceedings · November 27, 2007 Advances in automated data acquisition in electron tomography have led to an explosion in the amount of data that can be obtained about the spatial architecture of a variety of biologically and medically relevant objects with resolutions in the "nano" rang ... Full text Cite

Regularization for inverting the radon transform with wedge consideration

Journal Article 2007 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro - Proceedings · November 27, 2007 In limited angle tomography, with applications such as electron microscopy, medical imaging, and industrial testing, the object of interest is scanned over a limited angular range, which is less than the full 180° mathematically required for density recons ... Full text Cite

Structure and function of icosahedral pyruvate dehydrogenase complexes

Conference Microscopy and Microanalysis · August 1, 2006 Full text Cite

Molecular structure of a 9-MDa icosahedral pyruvate dehydrogenase subcomplex containing the E2 and E3 enzymes using cryoelectron microscopy.

Journal Article J Biol Chem · February 17, 2006 The pyruvate dehydrogenase multienzyme complexes are among the largest multifunctional catalytic machines in cells, catalyzing the production of acetyl CoA from pyruvate. We have previously reported the molecular architecture of an 11-MDa subcomplex compri ... Full text Link to item Cite

Visualization of alpha-helical features in a density map constructed using 9 molecular images of the 1.8 MDa icosahedral core of pyruvate dehydrogenase.

Journal Article J Struct Biol · August 2004 Strategies to achieve the highest resolutions in structures of protein complexes determined by cryo-electron microscopy generally involve averaging information from large numbers of individual molecular images. However, significant limitations are posed by ... Full text Link to item Cite

Automated image acquisition and processing using a new generation of 4K x 4K CCD cameras for cryo electron microscopic studies of macromolecular assemblies.

Journal Article J Struct Biol · August 2003 We have previously reported the development of AutoEM, a software package for semi-automated acquisition of data from a transmission electron microscope. In continuing efforts to improve the speed of structure determination of macromolecular assemblies by ... Full text Link to item Cite

A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy.

Journal Article J Struct Biol · January 2003 Cryo-electron microscopy of "single particles" is a powerful method to analyze structures of large macromolecular assemblies that are not amenable to investigation by traditional X-ray crystallographic methods. A key step in these studies is to obtain atom ... Full text Link to item Cite

Highly selective water channel activity measured by voltage clamp: analysis of planar lipid bilayers reconstituted with purified AqpZ.

Journal Article Proc Natl Acad Sci U S A · August 14, 2001 Aquaporins are membrane channels selectively permeated by water or water plus glycerol. Conflicting reports have described ion conductance associated with some water channels, raising the question of whether ion conductance is a general property of the aqu ... Full text Link to item Cite

Reconstitution and functional comparison of purified GlpF and AqpZ, the glycerol and water channels from Escherichia coli.

Journal Article Proc Natl Acad Sci U S A · February 27, 2001 A large family of membrane channel proteins selective for transport of water (aquaporins) or water plus glycerol (aquaglyceroporins) has been found in diverse life forms. Escherichia coli has two members of this family-a water channel, AqpZ, and a glycerol ... Full text Link to item Cite

The 6.9-A structure of GlpF: a basis for homology modeling of the glycerol channel from Escherichia coli.

Journal Article J Struct Biol · November 2000 The three-dimensional structure of GlpF, the glycerol facilitator of Escherichia coli, was determined by cryo-electron microscopy. The 6.9-A density map calculated from images of two-dimensional crystals shows the GlpF helices to be similar to those of AQP ... Full text Link to item Cite

The 3.7 A projection map of the glycerol facilitator GlpF: a variant of the aquaporin tetramer.

Journal Article EMBO Rep · August 2000 GlpF, the glycerol facilitator protein of Escherichia coli, is an archetypal member of the aquaporin superfamily. To assess its structure, recombinant histidine-tagged protein was overexpressed, solubilized in octylglucoside and purified to homogeneity. Ne ... Full text Link to item Cite

The aquaporin sidedness revisited.

Journal Article J Mol Biol · June 23, 2000 Aquaporins are transmembrane water channel proteins, which play important functions in the osmoregulation and water balance of micro-organisms, plants, and animal tissues. All aquaporins studied to date are thought to be tetrameric assemblies of four subun ... Full text Link to item Cite

High resolution AFM topographs of the Escherichia coli water channel aquaporin Z.

Journal Article EMBO J · September 15, 1999 Aquaporins form a large family of membrane channels involved in osmoregulation. Electron crystallography has shown monomers to consist of six membrane spanning alpha-helices confirming sequence based predictions. Surface exposed loops are the least conserv ... Full text Link to item Cite

Functional reconstitution and characterization of AqpZ, the E. coli water channel protein.

Journal Article J Mol Biol · September 3, 1999 Understanding the selectivity of aquaporin water channels will require structural and functional studies of wild-type and modified proteins; however, expression systems have not previously yielded aquaporins in the necessary milligram quantities. Here we r ... Full text Link to item Cite

Structure of the water channel AqpZ from Escherichia coli revealed by electron crystallography.

Journal Article J Mol Biol · September 3, 1999 Molecular water channels (aquaporins) allow living cells to adapt to osmotic variations by rapid and specific diffusion of water molecules. Aquaporins are present in animals, plants, algae, fungi and bacteria. Here we present an electron microscopic analys ... Full text Link to item Cite

Cellular and molecular biology of the aquaporin water channels.

Journal Article Annu Rev Biochem · 1999 The high water permeability characteristic of mammalian red cell membranes is now known to be caused by the protein AQP1. This channel freely permits movement of water across the cell membrane, but it is not permeated by other small, uncharged molecules or ... Full text Link to item Cite

Competition of hydrophobic peptides, cytotoxic drugs, and chemosensitizers on a common P-glycoprotein pharmacophore as revealed by its ATPase activity.

Journal Article J Biol Chem · February 9, 1996 The aim of the present study was to demonstrate that the modulation of P-glycoprotein (Pgp) ATPase activity by peptides, drugs, and chemosensitizers takes place on a common drug pharmacophore. To this end, a highly emetine-resistant Chinese hamster ovary c ... Full text Link to item Cite

Transport of polypeptide ionophores into proteoliposomes reconstituted with rat liver P-glycoprotein.

Journal Article J Biol Chem · October 21, 1994 The aim of this study was to examine the peptide transport activity of a naturally occurring P-glycoprotein such as that present in rat liver canalicular membrane vesicles. The peptide ionophores valinomycin and gramicidin D, which are known substrates of ... Link to item Cite

Probing the interaction of the multidrug-resistance phenotype with the polypeptide ionophore gramicidin D via functional channel formation.

Journal Article Eur J Biochem · June 15, 1994 It has been proposed that the multidrug resistance (MDR) transporter, P-glycoprotein (P-170), may be physiologically involved in the transport of polypeptides. As a step towards understanding the interaction of P-170 with polypeptides, we isolated various ... Full text Link to item Cite

Fura-2 transport in toad urinary bladder epithelium: effects of antidiuretic hormone, colchicine and osmotic gradients.

Journal Article Biochim Biophys Acta · September 5, 1993 Fluorescence is transferred across the toad urinary bladder when fura-2/AM is added to the mucosal or serosal sides of the epithelium. It was now observed that: (1) Oxytocin (20 nM, serosal) increased fluorescence transfer from the mucosal to the serosal b ... Full text Link to item Cite

Differential reversal of lipophilic antifolate resistance in mammalian cells with modulators of the multidrug resistance phenotype.

Journal Article Anticancer Drugs · June 1993 Chinese hamster ovary (CHO) T19 cells express a stable P-glycoprotein (P-170)-dependent multidrug resistance (MDR) phenotype and display a 24- to 29-fold cross-resistance to the lipophilic antifolates piritrexim (PTX) and trimetrexate (TMTX). We have exami ... Full text Link to item Cite