Synthetic antibodies against BRIL as universal fiducial marks for single-particle cryoEM structure determination of membrane proteins.

Abstract:

:We propose the concept of universal fiducials based on a set of pre-made semi-synthetic antibodies (sABs) generated by customized phage display selections against the fusion protein BRIL, an engineered variant of apocytochrome b562a. These sABs can bind to BRIL fused either into the loops or termini of different GPCRs, ion channels, receptors and transporters without disrupting their structure. A crystal structure of BRIL in complex with an affinity-matured sAB (BAG2) that bound to all systems tested delineates the footprint of interaction. Negative stain and cryoEM data of several examples of BRIL-membrane protein chimera highlight the effectiveness of the sABs as universal fiducial marks. Taken together with a cryoEM structure of sAB bound human nicotinic acetylcholine receptor, this work demonstrates that these anti-BRIL sABs can greatly enhance the particle properties leading to improved cryoEM outcomes, especially for challenging membrane proteins.

journal_name

Nat Commun

journal_title

Nature communications

authors

Mukherjee S,Erramilli SK,Ammirati M,Alvarez FJD,Fennell KF,Purdy MD,Skrobek BM,Radziwon K,Coukos J,Kang Y,Dutka P,Gao X,Qiu X,Yeager M,Eric Xu H,Han S,Kossiakoff AA

doi

10.1038/s41467-020-15363-0

subject

Has Abstract

pub_date

2020-03-27 00:00:00

pages

1598

issue

1

issn

2041-1723

pii

10.1038/s41467-020-15363-0

journal_volume

11

pub_type

杂志文章
  • Geologically-inspired strong bulk ceramics made with water at room temperature.

    abstract::Dense ceramic materials can form in nature under mild temperatures in water. By contrast, man-made ceramics often require sintering temperatures in excess of 1,400 °C for densification. Chemical strategies inspired by biomineralization processes have been demonstrated but remain limited to the fabrication of thin film...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms14655

    authors: Bouville F,Studart AR

    更新日期:2017-03-06 00:00:00

  • Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability.

    abstract::DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 5'-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 5'-flap was enigmatic. Here we combine...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15855

    authors: Tsutakawa SE,Thompson MJ,Arvai AS,Neil AJ,Shaw SJ,Algasaier SI,Kim JC,Finger LD,Jardine E,Gotham VJB,Sarker AH,Her MZ,Rashid F,Hamdan SM,Mirkin SM,Grasby JA,Tainer JA

    更新日期:2017-06-27 00:00:00

  • Giant regular polyhedra from calixarene carboxylates and uranyl.

    abstract::Self-assembly of large multi-component systems is a common strategy for the bottom-up construction of discrete, well-defined, nanoscopic-sized cages. Icosahedral or pseudospherical viral capsids, built up from hundreds of identical proteins, constitute typical examples of the complexity attained by biological self-ass...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms1793

    authors: Pasquale S,Sattin S,Escudero-Adán EC,Martínez-Belmonte M,de Mendoza J

    更新日期:2012-04-17 00:00:00

  • Quantitative bounds on morphodynamics and implications for reading the sedimentary record.

    abstract::Sedimentary rocks are the archives of environmental conditions and ancient planetary surface processes that led to their formation. Reconstructions of Earth's past surface behaviour from the physical sedimentary record remain controversial, however, in part because we lack a quantitative framework to deconvolve intern...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4298

    authors: Ganti V,Lamb MP,McElroy B

    更新日期:2014-02-28 00:00:00

  • Dual regulatory switch through interactions of Tcf7l2/Tcf4 with stage-specific partners propels oligodendroglial maturation.

    abstract::Constitutive activation of Wnt/β-catenin inhibits oligodendrocyte myelination. Tcf7l2/Tcf4, a β-catenin transcriptional partner, is required for oligodendrocyte differentiation. How Tcf7l2 modifies β-catenin signalling and controls myelination remains elusive. Here we define a stage-specific Tcf7l2-regulated transcrip...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms10883

    authors: Zhao C,Deng Y,Liu L,Yu K,Zhang L,Wang H,He X,Wang J,Lu C,Wu LN,Weng Q,Mao M,Li J,van Es JH,Xin M,Parry L,Goldman SA,Clevers H,Lu QR

    更新日期:2016-03-09 00:00:00

  • O-GlcNAcylation of SIRT1 enhances its deacetylase activity and promotes cytoprotection under stress.

    abstract::SIRT1 is the most evolutionarily conserved mammalian sirtuin, and it plays a vital role in the regulation of metabolism, stress responses, genome stability, and ageing. As a stress sensor, SIRT1 deacetylase activity is significantly increased during stresses, but the molecular mechanisms are not yet fully clear. Here,...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-01654-6

    authors: Han C,Gu Y,Shan H,Mi W,Sun J,Shi M,Zhang X,Lu X,Han F,Gong Q,Yu W

    更新日期:2017-11-14 00:00:00

  • The energy cost of polypeptide knot formation and its folding consequences.

    abstract::Knots are natural topologies of chains. Yet, little is known about spontaneous knot formation in a polypeptide chain-an event that can potentially impair its folding-and about the effect of a knot on the stability and folding kinetics of a protein. Here we used optical tweezers to show that the free energy cost to for...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-01691-1

    authors: Bustamante A,Sotelo-Campos J,Guerra DG,Floor M,Wilson CAM,Bustamante C,Báez M

    更新日期:2017-11-17 00:00:00

  • Bright monomeric near-infrared fluorescent proteins as tags and biosensors for multiscale imaging.

    abstract::Monomeric near-infrared (NIR) fluorescent proteins (FPs) are in high demand as protein tags and components of biosensors for deep-tissue imaging and multicolour microscopy. We report three bright and spectrally distinct monomeric NIR FPs, termed miRFPs, engineered from bacterial phytochrome, which can be used as easil...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12405

    authors: Shcherbakova DM,Baloban M,Emelyanov AV,Brenowitz M,Guo P,Verkhusha VV

    更新日期:2016-08-19 00:00:00

  • Erratum: Observation of ultrahigh mobility surface states in a topological crystalline insulator by infrared spectroscopy.

    abstract::A correction to this article has been published and is linked from the HTML version of this article. ...

    journal_title:Nature communications

    pub_type: 杂志文章,已发布勘误

    doi:10.1038/s41467-017-01354-1

    authors: Wang Y,Luo G,Liu J,Sankar R,Wang NL,Chou F,Fu L,Li Z

    更新日期:2017-10-12 00:00:00

  • ERG induces taxane resistance in castration-resistant prostate cancer.

    abstract::Taxanes are the only chemotherapies used to treat patients with metastatic castration-resistant prostate cancer (CRPC). Despite the initial efficacy of taxanes in treating CRPC, all patients ultimately fail due to the development of drug resistance. In this study, we show that ERG overexpression in in vitro and in viv...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6548

    authors: Galletti G,Matov A,Beltran H,Fontugne J,Miguel Mosquera J,Cheung C,MacDonald TY,Sung M,O'Toole S,Kench JG,Suk Chae S,Kimovski D,Tagawa ST,Nanus DM,Rubin MA,Horvath LG,Giannakakou P,Rickman DS

    更新日期:2014-11-25 00:00:00

  • CTC1-STN1 terminates telomerase while STN1-TEN1 enables C-strand synthesis during telomere replication in colon cancer cells.

    abstract::Telomerase elongates the telomeric G-strand to prevent telomere shortening through conventional DNA replication. However, synthesis of the complementary C-strand by DNA polymerase α is also required to maintain telomere length. Polymerase α cannot perform this role without the ssDNA binding complex CST (CTC1-STN1-TEN1...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05154-z

    authors: Feng X,Hsu SJ,Bhattacharjee A,Wang Y,Diao J,Price CM

    更新日期:2018-07-19 00:00:00

  • O-GlcNAcylation of PGK1 coordinates glycolysis and TCA cycle to promote tumor growth.

    abstract::Many cancer cells display enhanced glycolysis and suppressed mitochondrial metabolism. This phenomenon, known as the Warburg effect, is critical for tumor development. However, how cancer cells coordinate glucose metabolism through glycolysis and the mitochondrial tricarboxylic acid (TCA) cycle is largely unknown. We ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-13601-8

    authors: Nie H,Ju H,Fan J,Shi X,Cheng Y,Cang X,Zheng Z,Duan X,Yi W

    更新日期:2020-01-07 00:00:00

  • Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy.

    abstract::Theory, simulations and experimental results have suggested an important role of internal friction in the kinetics of protein folding. Recent experiments on spectrin domains provided the first evidence for a pronounced contribution of internal friction in proteins that fold on the millisecond timescale. However, it ha...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2204

    authors: Borgia A,Wensley BG,Soranno A,Nettels D,Borgia MB,Hoffmann A,Pfeil SH,Lipman EA,Clarke J,Schuler B

    更新日期:2012-01-01 00:00:00

  • Structural basis of human PCNA sliding on DNA.

    abstract::Sliding clamps encircle DNA and tether polymerases and other factors to the genomic template. However, the molecular mechanism of clamp sliding on DNA is unknown. Using crystallography, NMR and molecular dynamics simulations, here we show that the human clamp PCNA recognizes DNA through a double patch of basic residue...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms13935

    authors: De March M,Merino N,Barrera-Vilarmau S,Crehuet R,Onesti S,Blanco FJ,De Biasio A

    更新日期:2017-01-10 00:00:00

  • Mutations associated with neuropsychiatric conditions delineate functional brain connectivity dimensions contributing to autism and schizophrenia.

    abstract::16p11.2 and 22q11.2 Copy Number Variants (CNVs) confer high risk for Autism Spectrum Disorder (ASD), schizophrenia (SZ), and Attention-Deficit-Hyperactivity-Disorder (ADHD), but their impact on functional connectivity (FC) remains unclear. Here we report an analysis of resting-state FC using magnetic resonance imaging...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-18997-2

    authors: Moreau CA,Urchs SGW,Kuldeep K,Orban P,Schramm C,Dumas G,Labbe A,Huguet G,Douard E,Quirion PO,Lin A,Kushan L,Grot S,Luck D,Mendrek A,Potvin S,Stip E,Bourgeron T,Evans AC,Bearden CE,Bellec P,Jacquemont S

    更新日期:2020-10-19 00:00:00

  • Voltage-induced spreading and superspreading of liquids.

    abstract::The ability to quickly spread a liquid across a surface and form a film is fundamental for a diverse range of technological processes, including printing, painting and spraying. Here we show that liquid dielectrophoresis or electrowetting can produce wetting on normally non-wetting surfaces, without needing modificati...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2619

    authors: McHale G,Brown CV,Sampara N

    更新日期:2013-01-01 00:00:00

  • Patterned human microvascular grafts enable rapid vascularization and increase perfusion in infarcted rat hearts.

    abstract::Vascularization and efficient perfusion are long-standing challenges in cardiac tissue engineering. Here we report engineered perfusable microvascular constructs, wherein human embryonic stem cell-derived endothelial cells (hESC-ECs) are seeded both into patterned microchannels and the surrounding collagen matrix. In ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-08388-7

    authors: Redd MA,Zeinstra N,Qin W,Wei W,Martinson A,Wang Y,Wang RK,Murry CE,Zheng Y

    更新日期:2019-02-04 00:00:00

  • Superresolution mapping of energy landscape for single charge carriers in plastic semiconductors.

    abstract::The performance of conjugated polymer devices is largely dictated by charge transport processes. However, it is difficult to obtain a clear relationship between conjugated polymer structures and charge transport properties, due to the complexity of the structure and the dispersive nature of charge transport in conjuga...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-06846-2

    authors: Jiang Y,McNeill J

    更新日期:2018-10-17 00:00:00

  • Causal factors for seismicity near Azle, Texas.

    abstract::In November 2013, a series of earthquakes began along a mapped ancient fault system near Azle, Texas. Here we assess whether it is plausible that human activity caused these earthquakes. Analysis of both lake and groundwater variations near Azle shows that no significant stress changes were associated with the shallow...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms7728

    authors: Hornbach MJ,DeShon HR,Ellsworth WL,Stump BW,Hayward C,Frohlich C,Oldham HR,Olson JE,Magnani MB,Brokaw C,Luetgert JH

    更新日期:2015-04-21 00:00:00

  • Sequential growth of long DNA strands with user-defined patterns for nanostructures and scaffolds.

    abstract::DNA strands of well-defined sequence are valuable in synthetic biology and nanostructure assembly. Drawing inspiration from solid-phase synthesis, here we describe a DNA assembly method that uses time, or order of addition, as a parameter to define structural complexity. DNA building blocks are sequentially added with...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms8065

    authors: Hamblin GD,Rahbani JF,Sleiman HF

    更新日期:2015-05-05 00:00:00

  • The essential role of YAP O-GlcNAcylation in high-glucose-stimulated liver tumorigenesis.

    abstract::O-GlcNAcylation has been implicated in the tumorigenesis of various tissue origins, but its function in liver tumorigenesis is not clear. Here, we demonstrate that O-GlcNAcylation can enhance the expression, stability and function of Yes-associated protein (YAP), the downstream transcriptional regulator of the Hippo p...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15280

    authors: Zhang X,Qiao Y,Wu Q,Chen Y,Zou S,Liu X,Zhu G,Zhao Y,Chen Y,Yu Y,Pan Q,Wang J,Sun F

    更新日期:2017-05-05 00:00:00

  • Manipulating Majorana zero modes on atomic rings with an external magnetic field.

    abstract::Non-Abelian quasiparticles have been predicted to exist in a variety of condensed matter systems. Their defining property is that an adiabatic braid between two of them results in a non-trivial change of the quantum state of the system. The simplest non-Abelian quasiparticles--the Majorana bound states--can occur in o...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms10395

    authors: Li J,Neupert T,Bernevig BA,Yazdani A

    更新日期:2016-01-21 00:00:00

  • Subduction of the oceanic Hikurangi Plateau and its impact on the Kermadec arc.

    abstract::Large igneous province subduction is a rare process on Earth. A modern example is the subduction of the oceanic Hikurangi Plateau beneath the southern Kermadec arc, offshore New Zealand. This segment of the arc has the largest total lava volume erupted and the highest volcano density of the entire Kermadec arc. Here w...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms5923

    authors: Timm C,Davy B,Haase K,Hoernle KA,Graham IJ,de Ronde CE,Woodhead J,Bassett D,Hauff F,Mortimer N,Seebeck HC,Wysoczanski RJ,Caratori-Tontini F,Gamble JA

    更新日期:2014-09-17 00:00:00

  • Subsistence strategies in traditional societies distinguish gut microbiomes.

    abstract::Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agricult...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms7505

    authors: Obregon-Tito AJ,Tito RY,Metcalf J,Sankaranarayanan K,Clemente JC,Ursell LK,Zech Xu Z,Van Treuren W,Knight R,Gaffney PM,Spicer P,Lawson P,Marin-Reyes L,Trujillo-Villarroel O,Foster M,Guija-Poma E,Troncoso-Corzo L,Warinne

    更新日期:2015-03-25 00:00:00

  • Odour concentration-dependent olfactory preference change in C. elegans.

    abstract::The same odorant can induce attractive or repulsive responses depending on its concentration in various animals including humans. However, little is understood about the neuronal basis of this behavioural phenomenon. Here we show that Caenorhabditis elegans avoids high concentrations of odorants that are attractive at...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms1750

    authors: Yoshida K,Hirotsu T,Tagawa T,Oda S,Wakabayashi T,Iino Y,Ishihara T

    更新日期:2012-03-13 00:00:00

  • Control of lung vascular permeability and endotoxin-induced pulmonary oedema by changes in extracellular matrix mechanics.

    abstract::Increased vascular permeability contributes to many diseases, including acute respiratory distress syndrome, cancer and inflammation. Most past work on vascular barrier function has focused on soluble regulators, such as tumour-necrosis factor-α. Here we show that lung vascular permeability is controlled mechanically ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2774

    authors: Mammoto A,Mammoto T,Kanapathipillai M,Wing Yung C,Jiang E,Jiang A,Lofgren K,Gee EP,Ingber DE

    更新日期:2013-01-01 00:00:00

  • The atypical chemokine receptor ACKR3/CXCR7 is a broad-spectrum scavenger for opioid peptides.

    abstract::Endogenous opioid peptides and prescription opioid drugs modulate pain, anxiety and stress by activating opioid receptors, currently classified into four subtypes. Here we demonstrate that ACKR3/CXCR7, hitherto known as an atypical scavenger receptor for chemokines, is a broad-spectrum scavenger of opioid peptides. Ph...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-16664-0

    authors: Meyrath M,Szpakowska M,Zeiner J,Massotte L,Merz MP,Benkel T,Simon K,Ohnmacht J,Turner JD,Krüger R,Seutin V,Ollert M,Kostenis E,Chevigné A

    更新日期:2020-06-19 00:00:00

  • Mouse oocytes depend on BubR1 for proper chromosome segregation but not for prophase I arrest.

    abstract::Mammalian female meiosis is error prone, with rates of meiotic chromosome missegregations strongly increasing towards the end of the reproductive lifespan. A strong reduction of BubR1 has been observed in oocytes of women approaching menopause and in ovaries of aged mice, which led to the hypothesis that a gradual dec...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms7946

    authors: Touati SA,Buffin E,Cladière D,Hached K,Rachez C,van Deursen JM,Wassmann K

    更新日期:2015-04-21 00:00:00

  • Structural basis for Ca2+-dependent activation of a plant metacaspase.

    abstract::Plant metacaspases mediate programmed cell death in development, biotic and abiotic stresses, damage-induced immune response, and resistance to pathogen attack. Most metacaspases require Ca2+ for their activation and substrate processing. However, the Ca2+-dependent activation mechanism remains elusive. Here we report...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-15830-8

    authors: Zhu P,Yu XH,Wang C,Zhang Q,Liu W,McSweeney S,Shanklin J,Lam E,Liu Q

    更新日期:2020-05-07 00:00:00

  • Cryptic evolved melts beneath monotonous basaltic shield volcanoes in the Galápagos Archipelago.

    abstract::Many volcanoes erupt compositionally homogeneous magmas over timescales ranging from decades to millennia. This monotonous activity is thought to reflect a high degree of chemical homogeneity in their magmatic systems, leading to predictable eruptive behaviour. We combine petrological analyses of erupted crystals with...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-17590-x

    authors: Stock MJ,Geist D,Neave DA,Gleeson MLM,Bernard B,Howard KA,Buisman I,Maclennan J

    更新日期:2020-07-28 00:00:00