Efficient recovery of high-affinity antibodies from a single-chain Fab yeast display library.

Abstract:

:Yeast display is a powerful technology for the isolation of monoclonal antibodies (mAbs) against a target antigen. Antibody libraries have been displayed on the surface of yeast as both single-chain variable fragment (scFv) and antigen binding fragment (Fab). Here, we combine these two formats to display well-characterized mAbs as single-chain Fabs (scFabs) on the surface of yeast and construct the first scFab yeast display antibody library. When expressed on the surface of yeast, two out of three anti-human immunodeficiency virus (HIV)-1 mAbs bound with higher affinity as scFabs than scFvs. Also, the soluble scFab preparations exhibited binding and neutralization profiles comparable to that of the corresponding Fab fragments. Display of an immune HIV-1 scFab library on the surface of yeast, followed by rounds of sorting against HIV-1 gp120, allowed for the selection of 13 antigen-specific clones. When the same cDNA was used to construct the library in an scFv format, a similar number but a lower affinity set of clones were selected. Based on these results, yeast-displayed scFab libraries can be constructed and selected with high efficiency, characterized without the need for a reformatting step, and used to isolate higher-affinity antibodies than scFv libraries.

journal_name

J Mol Biol

authors

Walker LM,Bowley DR,Burton DR

doi

10.1016/j.jmb.2009.04.019

subject

Has Abstract

pub_date

2009-06-05 00:00:00

pages

365-75

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(09)00449-5

journal_volume

389

pub_type

杂志文章
  • Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide.

    abstract::Approximately one-third of the human proteome is made up of proteins that are entirely disordered or that contain extended disordered regions. Although these disordered proteins are closely linked with many major diseases, their binding mechanisms with small molecules remain poorly understood, and a major concern is w...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2017.07.016

    authors: Heller GT,Aprile FA,Bonomi M,Camilloni C,De Simone A,Vendruscolo M

    更新日期:2017-09-01 00:00:00

  • The changing face of glucagon fibrillation: structural polymorphism and conformational imprinting.

    abstract::We have established a time-resolved fluorescence assay to study fibrillation of the 29 residue peptide hormone glucagon under a variety of different conditions in a high-throughput format. Fibrils formed at pH 2.5 differ in fibrillation kinetics, morphology, thioflavin T staining and FTIR/CD spectra depending on salts...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.09.100

    authors: Pedersen JS,Dikov D,Flink JL,Hjuler HA,Christiansen G,Otzen DE

    更新日期:2006-01-20 00:00:00

  • Crystal structure of a human embryonic haemoglobin: the carbonmonoxy form of gower II (alpha2 epsilon2) haemoglobin at 2.9 A resolution.

    abstract::The production of recombinant embryonic haemoglobins via a yeast expression system has enabled structural and functional studies to be conducted on these proteins. As part of a programme aimed at understanding the properties of the embryonic haemoglobins we have crystallized the human alpha2 epsilon2 (Gower II) embryo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1868

    authors: Sutherland-Smith AJ,Baker HM,Hofmann OM,Brittain T,Baker EN

    更新日期:1998-07-17 00:00:00

  • Multi-scale sequence correlations increase proteome structural disorder and promiscuity.

    abstract::Numerous experiments demonstrate a high level of promiscuity and structural disorder in organismal proteomes. Here, we ask the question what makes a protein promiscuous, that is, prone to nonspecific interactions, and structurally disordered. We predict that multi-scale correlations of amino acid positions within prot...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.03.056

    authors: Afek A,Shakhnovich EI,Lukatsky DB

    更新日期:2011-06-10 00:00:00

  • The Spliceosomal Protein SF3B5 is a Novel Component of Drosophila SAGA that Functions in Gene Expression Independent of Splicing.

    abstract::The interaction between splicing factors and the transcriptional machinery provides an intriguing link between the coupled processes of transcription and splicing. Here, we show that the two components of the SF3B complex, SF3B3 and SF3B5, that form part of the U2 small nuclear ribonucleoprotein particle (snRNP) are a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.05.009

    authors: Stegeman R,Spreacker PJ,Swanson SK,Stephenson R,Florens L,Washburn MP,Weake VM

    更新日期:2016-09-11 00:00:00

  • The conformational properties of the Glc3Man unit suggest conformational biasing within the chaperone-assisted glycoprotein folding pathway.

    abstract::A major puzzle is: are all glycoproteins routed through the ER calnexin pathway irrespective of whether this is required for their correct folding? Calnexin recognizes the terminal Glcalpha1-3Manalpha linkage, formed by trimming of the Glcalpha1-2Glcalpha1-3Glcalpha1-3Manalpha (Glc3Man) unit in Glc3Man9GlcNAc2. Differ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.01.043

    authors: Mackeen MM,Almond A,Deschamps M,Cumpstey I,Fairbanks AJ,Tsang C,Rudd PM,Butters TD,Dwek RA,Wormald MR

    更新日期:2009-03-27 00:00:00

  • Distinct modes of recognition of the lipoyl domain as substrate by the E1 and E3 components of the pyruvate dehydrogenase multienzyme complex.

    abstract::Two-dimensional (15)N-heteronuclear single-quantum coherence (HSQC) NMR studies with a di-domain (lipoyl domain+ linker+ peripheral subunit-binding domain) of the dihydrolipoyl acetyltransferase (E2) component of the pyruvate dehydrogenase complex of Bacillus stearothermophilus allowed a molecular comparison of the ne...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.11.018

    authors: Fries M,Stott KM,Reynolds S,Perham RN

    更新日期:2007-02-09 00:00:00

  • phi29 DNA polymerase active site: role of residue Val250 as metal-dNTP complex ligand and in protein-primed initiation.

    abstract::DNA polymerases require two acidic residues to coordinate metal ions A and B at their polymerisation active site during catalysis of nucleotide incorporation. Crystallographic resolution of varphi29 DNA polymerase ternary complex showed that metal B coordination also depends on the carbonyl group of Val250 that belong...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.10.061

    authors: Pérez-Arnaiz P,Lázaro JM,Salas M,de Vega M

    更新日期:2010-01-15 00:00:00

  • In-vivo degradation pathway of an excised intervening sequence.

    abstract::A study of the distribution in heterogeneous nuclear RNP (hnRNP) of the different forms of the first intervening sequence (IVSI) from the E3 transcription unit of adenovirus serotype 2 suggests a three-step pathway for IVS excision and degradation. First, the lariat IVS is formed in a large RNP of the size of premesse...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90480-3

    authors: Sittler A,Gallinaro H,Kister L,Jacob M

    更新日期:1987-10-20 00:00:00

  • Zinc binding catalytic domain of human tankyrase 1.

    abstract::Tankyrases are recently discovered proteins implicated in many important functions in the cell including telomere homeostasis and mitosis. Tankyrase modulates the activity of target proteins through poly(ADP-ribosyl)ation, and here we report the structure of the catalytic poly(ADP-ribose) polymerase (PARP) domain of h...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.03.058

    authors: Lehtiö L,Collins R,van den Berg S,Johansson A,Dahlgren LG,Hammarström M,Helleday T,Holmberg-Schiavone L,Karlberg T,Weigelt J

    更新日期:2008-05-23 00:00:00

  • The structure of interleukin-23 reveals the molecular basis of p40 subunit sharing with interleukin-12.

    abstract::Interleukin (IL)-23 is a recently identified member of the IL-12 family of heterodimeric cytokines that modulate subpopulations of T helper cells, and both IL-12 and IL-23 are attractive targets for therapy of autoimmune diseases. IL-23 is a binary complex of a four-helix bundle cytokine (p19) and a soluble class I cy...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.07.051

    authors: Lupardus PJ,Garcia KC

    更新日期:2008-10-17 00:00:00

  • Cryo-electron tomography of clathrin-coated vesicles: structural implications for coat assembly.

    abstract::Clathrin-coated vesicles mediate vesicular traffic in cells. Three-dimensional image reconstructions of homogenous populations of in vitro assembled clathrin coats have yielded a molecular model for clathrin and its interactions with some of its partners. The intrinsic averaging required for those calculations has pre...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.10.036

    authors: Cheng Y,Boll W,Kirchhausen T,Harrison SC,Walz T

    更新日期:2007-01-19 00:00:00

  • Divergent genetic control of protein solubility and conformational quality in Escherichia coli.

    abstract::In bacteria, protein overproduction results in the formation of inclusion bodies, sized protein aggregates showing amyloid-like properties such as seeding-driven formation, amyloid-tropic dye binding, intermolecular beta-sheet architecture and cytotoxicity on mammalian cells. During protein deposition, exposed hydroph...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.09.004

    authors: García-Fruitós E,Martínez-Alonso M,Gonzàlez-Montalbán N,Valli M,Mattanovich D,Villaverde A

    更新日期:2007-11-16 00:00:00

  • Conserved patterns in the Cu,Zn superoxide dismutase family.

    abstract::Conserved structural and functional features of Cu,Zn superoxide dismutase enzymes have been studied by comparison of known three-dimensional structures and analysis of the currently available amino acid sequences. For this purpose, the three-dimensional structures of the bovine, spinach and yeast enzymes have been su...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1298

    authors: Bordo D,Djinović K,Bolognesi M

    更新日期:1994-05-06 00:00:00

  • tRNA 3' end maturation in archaea has eukaryotic features: the RNase Z from Haloferax volcanii.

    abstract::Here, we report the first characterization and partial purification of an archaeal tRNA 3' processing activity, the RNase Z from Haloferax volcanii. The activity identified here is an endonuclease, which cleaves tRNA precursors 3' to the discriminator. Thus tRNA 3' processing in archaea resembles the eukaryotic 3' pro...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5395

    authors: Schierling K,Rösch S,Rupprecht R,Schiffer S,Marchfelder A

    更新日期:2002-03-01 00:00:00

  • Partially folded conformation of the (30-51) intermediate in the disulphide folding pathway of bovine pancreatic trypsin inhibitor. 1H and 15N resonance assignments and determination of backbone dynamics from 15N relaxation measurements.

    abstract::An analogue of the important folding intermediate of BPTI with only the disulphide bond between Cys30 and Cys51 has been characterized by 1H and 15N NMR techniques. In particular, the dynamics of the polypeptide backbone were characterized using (1H)-15N NOE and 15N T1 and T2 relaxation data. The intermediate is parti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1108

    authors: van Mierlo CP,Darby NJ,Keeler J,Neuhaus D,Creighton TE

    更新日期:1993-02-20 00:00:00

  • Regulation of IS1 transposition by the insA gene product.

    abstract::The IS1 element contains two adjacent genes called insA and insB, both required for IS1 transposition and IS1-mediated plasmid cointegration. These two genes are transcribed polycistronically from the promoter in the left terminal inverted repeat of IS1 (insL). We constructed overexpression systems of these genes with...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90148-4

    authors: Machida C,Machida Y

    更新日期:1989-08-20 00:00:00

  • How thioredoxin can reduce a buried disulphide bond.

    abstract::We present a study of the interaction between thioredoxin and the model enzyme pI258 arsenate reductase (ArsC) from Staphylococcus aureus. ArsC catalyses the reduction of arsenate to arsenite. Three redox active cysteine residues (Cys10, Cys82 and Cys89) are involved. After a single catalytic arsenate reduction event,...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.04.016

    authors: Messens J,Van Molle I,Vanhaesebrouck P,Limbourg M,Van Belle K,Wahni K,Martins JC,Loris R,Wyns L

    更新日期:2004-06-04 00:00:00

  • Arrangement of photosystem II supercomplexes in crystalline macrodomains within the thylakoid membrane of green plant chloroplasts.

    abstract::The chloroplast thylakoid membrane of green plants is organized in stacked grana membranes and unstacked stroma membranes. We investigated the structural organization of Photosystem II (PSII) in paired grana membrane fragments by transmission electron microscopy. The membrane fragments were obtained by a short treatme...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4037

    authors: Boekema EJ,van Breemen JF,van Roon H,Dekker JP

    更新日期:2000-09-01 00:00:00

  • Isolation and characterization of sarcomeric actin genes expressed in Xenopus laevis embryos.

    abstract::A Xenopus laevis complementary DNA (cDNA) library prepared from messenger RNAs extracted from embryos has been screened for actin-coding sequences. Two cDNA clones corresponding to an alpha cardiac and an alpha skeletal muscle actin mRNA have been identified and characterized. From a genomic library, we have furthermo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(86)90438-9

    authors: Stutz F,Spohr G

    更新日期:1986-02-05 00:00:00

  • Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution.

    abstract::The crystal structure of Thermoactinomyces vulgaris R-47 alpha-Amylase II (TVAII) has been determined by multiple isomorphous replacement at 2.6 A resolution. TVAII was crystallized in an orthorhombic system with the space group P212121 and the cell dimensions a=118.5 A, b=119.5 A, c=114.5 A. There are two molecules i...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2647

    authors: Kamitori S,Kondo S,Okuyama K,Yokota T,Shimura Y,Tonozuka T,Sakano Y

    更新日期:1999-04-16 00:00:00

  • Crystal structure of Leishmania mexicana glycosomal glyceraldehyde-3-phosphate dehydrogenase in a new crystal form confirms the putative physiological active site structure.

    abstract::The structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the trypanosomatid parasite Leishmania mexicana in a new crystal form has been determined by X-ray crystallography. The protein crystallizes in space group P21 with one 156 kDa tetramer per asymmetric unit. The model of the protein with ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1661

    authors: Kim H,Hol WG

    更新日期:1998-04-24 00:00:00

  • Modulation of K11-linkage formation by variable loop residues within UbcH5A.

    abstract::Ubiquitination refers to the covalent addition of ubiquitin (Ub) to substrate proteins or other Ub molecules via the sequential action of three enzymes (E1, E2, and E3). Recent advances in mass spectrometry proteomics have made it possible to identify and quantify Ub linkages in biochemical and cellular systems. We us...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.03.011

    authors: Bosanac I,Phu L,Pan B,Zilberleyb I,Maurer B,Dixit VM,Hymowitz SG,Kirkpatrick DS

    更新日期:2011-05-06 00:00:00

  • Control of ColE1 plasmid replication. Intermediates in the binding of RNA I and RNA II.

    abstract::Replication of plasmid ColE1 is regulated by a plasmid-specified small RNA (RNA I). RNA I binds to the precursor (RNA II) of the primer for DNA synthesis and inhibits primer formation. The process of binding of RNA I to RNA II that results in formation of a stably bound complex consists of a series of reactions formin...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(90)90230-j

    authors: Tomizawa J

    更新日期:1990-04-20 00:00:00

  • Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae.

    abstract::Riboswitches are complex folded RNA domains found in noncoding regions of mRNA that regulate gene expression upon small molecule binding. Recently, Breaker and coworkers reported a tandem aptamer riboswitch (VCI-II) that binds glycine cooperatively. Here, we use hydroxyl radical footprinting and small-angle X-ray scat...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.10.022

    authors: Lipfert J,Das R,Chu VB,Kudaravalli M,Boyd N,Herschlag D,Doniach S

    更新日期:2007-02-02 00:00:00

  • Identification of a specific motif of the DSS1 protein required for proteasome interaction and p53 protein degradation.

    abstract::Deleted in Split hand/Split foot 1 (DSS1) was previously identified as a novel 12-O-tetradecanoylphorbol-13-acetate (TPA)-inducible gene with possible involvement in early event of mouse skin carcinogenesis. The mechanisms by which human DSS1 (HsDSS1) exerts its biological effects via regulation of the ubiquitin-prote...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.08.044

    authors: Wei SJ,Williams JG,Dang H,Darden TA,Betz BL,Humble MM,Chang FM,Trempus CS,Johnson K,Cannon RE,Tennant RW

    更新日期:2008-11-14 00:00:00

  • Conformational changes in phosphoglucose isomerase induced by ligand binding.

    abstract::Phosphoglucose isomerase (PGI; EC 5.3.1.9) is the second enzyme in glycolysis, where it catalyzes the isomerization of D-glucose-6-phosphate to D-fructose-6-phosphate. It is the same protein as autocrine motility factor, differentiation and maturation mediator, and neuroleukin. Here, we report a new X-ray crystal stru...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)00892-6

    authors: Arsenieva D,Jeffery CJ

    更新日期:2002-10-11 00:00:00

  • The funnel approach to the precrystallization production of membrane proteins.

    abstract::Challenges in the production of integral membrane proteins for structural studies include low expression levels, incorrect membrane insertion, aggregation and instability. In this report, we describe a "funnel approach" to overcoming these difficulties and demonstrate its efficacy in a case study of 36 prokaryotic P-t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.12.059

    authors: Lewinson O,Lee AT,Rees DC

    更新日期:2008-03-14 00:00:00

  • Conformational dynamics of the molecular chaperone Hsp90 in complexes with a co-chaperone and anticancer drugs.

    abstract::The molecular chaperone Hsp90 is essential for the correct folding, maturation and activation of a diverse array of client proteins, including several key constituents of oncogenic processes. Hsp90 has become a focus of cancer research, since it represents a target for direct prophylaxis against multistep malignancy. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.04.059

    authors: Phillips JJ,Yao ZP,Zhang W,McLaughlin S,Laue ED,Robinson CV,Jackson SE

    更新日期:2007-10-05 00:00:00

  • Role of domains 4 and 5 in elongation factor G functions on the ribosome.

    abstract::Elongation factor G (EF-G) is a large, five domain GTPase that catalyses the translocation of the tRNAs on the bacterial ribosome at the expense of GTP. In the crystal structure of GDP-bound EF-G, domain 1 (G domain) makes direct contacts with domains 2 and 5, whereas domain 4 protrudes from the body of the molecule. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3886

    authors: Savelsbergh A,Matassova NB,Rodnina MV,Wintermeyer W

    更新日期:2000-07-21 00:00:00