Structural mimicry of O-antigen by a peptide revealed in a complex with an antibody raised against Shigella flexneri serotype 2a.

Abstract:

:The use of carbohydrate-mimicking peptides to induce immune responses against surface polysaccharides of pathogenic bacteria offers a novel approach to vaccine development. Factors governing antigenic and immunogenic mimicry, however, are complex and poorly understood. We have addressed this question using the anti-lipopolysaccharide monoclonal antibody F22-4, which was raised against Shigella flexneri serotype 2a and shown to protect against homologous infection in a mouse model. In a previous crystallographic study, we described F22-4 in complex with two synthetic fragments of the O-antigen, the serotype-specific saccharide moiety of lipopolysaccharide. Here, we present a crystallographic and NMR study of the interaction of F22-4 with a dodecapeptide selected by phage display using the monoclonal antibody. Like the synthetic decasaccharide, the peptide binds to F22-4 with micromolar affinity. Although the peptide and decasaccharide use very similar regions of the antigen-binding site, indicating good antigenic mimicry, immunogenic mimicry by the peptide was not observed. The F22-4-antigen interaction is significantly more hydrophobic with the peptide than with oligosaccharides; nonetheless, all hydrogen bonds formed between the peptide and F22-4 have equivalents in the oligosaccharide complex. Two bridging water molecules are also in common, adding to partial structural mimicry. Whereas the bound peptide is entirely helical, its structure in solution, as shown by NMR, is helical in the central region only. Moreover, docking the NMR structure into the antigen-binding site shows that steric hindrance would occur, revealing poor complementarity between the major solution conformation and the antibody that could contribute to the absence of immunogenic mimicry.

journal_name

J Mol Biol

authors

Theillet FX,Saul FA,Vulliez-Le Normand B,Hoos S,Felici F,Weintraub A,Mulard LA,Phalipon A,Delepierre M,Bentley GA

doi

10.1016/j.jmb.2009.03.057

subject

Has Abstract

pub_date

2009-05-15 00:00:00

pages

839-50

issue

4

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(09)00364-7

journal_volume

388

pub_type

杂志文章
  • Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins.

    abstract::Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small, fast-folding proteins. To investigate the extent of the topological control of the folding process, we studied the folding of simplified models ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3693

    authors: Clementi C,Nymeyer H,Onuchic JN

    更新日期:2000-05-19 00:00:00

  • Decreased thermodynamic stability as a crucial factor for familial amyloidotic polyneuropathy.

    abstract::A single mutation in the wild-type transthyretin (WT TTR) such as V30M causes a familial amyloidotic polyneuropathy disease. Comparison of the three-dimensional crystal structures of WT and V30M does not tell much about the reason. High-pressure NMR revealed that at neutral pH both WT and V30M exist as equilibrium bet...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/S0022-2836(02)00425-4

    authors: Niraula TN,Haraoka K,Ando Y,Li H,Yamada H,Akasaka K

    更新日期:2002-07-05 00:00:00

  • On the mechanism of ribosomal frameshifting at hungry codons.

    abstract::In a few, rather rare cases, frameshift mutant alleles are phenotypically suppressed during limitation for particular aminoacyl-tRNA species. The simplest interpretation is compensatory ribosome frameshifting at a "hungry" codon in the vicinity of the suppressed frameshift mutation. We have now tested this interpretat...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90008-3

    authors: Weiss R,Lindsley D,Falahee B,Gallant J

    更新日期:1988-09-20 00:00:00

  • Cloning, overexpression and purification of the terminase proteins gp16 and gp17 of bacteriophage T4. Construction of a defined in-vitro DNA packaging system using purified terminase proteins.

    abstract::Terminases of double-stranded DNA bacteriophages are required for packaging and generation of terminii in replicated concatemeric DNA molecules. Genetic evidence suggests that these functions in phage T4 are carried out by the products of genes 16 and 17. We cloned these T4 genes into a heat-inducible cI repressor-lam...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90537-2

    authors: Rao VB,Black LW

    更新日期:1988-04-05 00:00:00

  • Crystallization of and preliminary X-ray data for the mouse major urinary protein and rat alpha-2u globulin.

    abstract::Crystals of the mouse major urinary protein (MUP) and rat alpha-2u globulin (AMG) have been grown from solutions of polyethylene glycol 3350 and CdCl2, respectively. The crystals differ both in their morphologies and space groups but have very similar unit cell sizes. AMG crystallized in P2(1) (a = 56.6 A, b = 103.8 A...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90258-8

    authors: Böcskei Z,Findlay JB,North AC,Phillips SE,Somers WS,Wright CE,Lionetti C,Tirindelli R,Cavaggioni A

    更新日期:1991-04-20 00:00:00

  • Structure and assembly of turnip crinkle virus. VI. Identification of coat protein binding sites on the RNA.

    abstract::Structural studies of turnip crinkle virus have been extended to include the identification of high-affinity coat protein binding sites on the RNA genome. Virus was dissociated at elevated pH and ionic strength, and a ribonucleoprotein complex (rp-complex) was isolated by chromatography on Sephacryl S-200. Genomic RNA...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(90)90148-F

    authors: Wei N,Heaton LA,Morris TJ,Harrison SC

    更新日期:1990-07-05 00:00:00

  • Enzymatic catalysis in crystals of Escherichia coli maltodextrin phosphorylase.

    abstract::The bacterial enzyme maltodextrin phosphorylase (MalP) catalyses the phosphorolysis of an alpha-1,4-glycosidic bond in maltodextrins, removing the non-reducing glucosyl residues of linear oligosaccharides as glucose-1-phosphate (Glc1P). In contrast to the well-studied muscle glycogen phosphorylase (GP), MalP exhibits ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)00771-4

    authors: Geremia S,Campagnolo M,Schinzel R,Johnson LN

    更新日期:2002-09-13 00:00:00

  • Mechanisms ensuring rapid and complete DNA replication despite random initiation in Xenopus early embryos.

    abstract::Chromosome replication initiates without sequence specificity at average intervals of approximately 10 kb during the rapid cell cycles of early Xenopus embryos. If the distribution of origins were random, some inter-origin intervals would be too long to be fully replicated before the end of S phase. To investigate wha...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3500

    authors: Lucas I,Chevrier-Miller M,Sogo JM,Hyrien O

    更新日期:2000-02-25 00:00:00

  • Directed evolution of an anti-prion protein scFv fragment to an affinity of 1 pM and its structural interpretation.

    abstract::Bovine spongiform encephalopathy (BSE) is a fatal neurodegenerative prion disease affecting cattle that is transmissible to humans, manifesting as a variant of Creutzfeldt-Jakob disease (vCJD) likely following the consumption of meat contaminated with BSE prions. High-affinity antibodies are a prerequisite for the dev...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.07.027

    authors: Luginbühl B,Kanyo Z,Jones RM,Fletterick RJ,Prusiner SB,Cohen FE,Williamson RA,Burton DR,Plückthun A

    更新日期:2006-10-13 00:00:00

  • β-Structure within the Denatured State of the Helical Protein Domain BBL.

    abstract::Protein denatured states are the origin of both healthy and toxic conformational species. Denatured states of ultrafast folding proteins are of interest in mechanistic studies because they are energetically close to the kinetic bottleneck of folding. However, their transient nature makes them elusive to experiment. He...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2015.08.007

    authors: Thukral L,Schwarze S,Daidone I,Neuweiler H

    更新日期:2015-09-25 00:00:00

  • The 1.3 A crystal structure of a biotin-binding pseudoknot and the basis for RNA molecular recognition.

    abstract::A pseudoknot-containing aptamer isolated from a pool of random sequence molecules has been shown previously to represent an optimal RNA solution to the problem of binding biotin. The affinity of this RNA molecule is nonetheless orders of magnitude weaker than that of its highly evolved protein analogs, avidin and stre...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3539

    authors: Nix J,Sussman D,Wilson C

    更新日期:2000-03-10 00:00:00

  • Robust mechanosensing and tension generation by myosin VI.

    abstract::Myosin VI is a molecular motor that is thought to function both as a transporter and as a cytoskeletal anchor in vivo. Here we use optical tweezers to examine force generation by single molecules of myosin VI under physiological nucleotide concentrations. We find that myosin VI is an efficient transporter at loads of ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.10.010

    authors: Chuan P,Spudich JA,Dunn AR

    更新日期:2011-01-07 00:00:00

  • Contextual constraints on synonymous codon choice.

    abstract::We have studied the statistical constraints on synonymous codon choice to evaluate various proposals regarding the origin of the bias in synonymous codon usage observed by Fiers et al. (1975), Air et al. (1976), Grantham et al. (1980) and others. We have determined the statistical dependence of the degenerate third ba...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(83)90063-3

    authors: Lipman DJ,Wilbur WJ

    更新日期:1983-01-25 00:00:00

  • Crystallization and preliminary crystallographic studies of the decadeoxyoligonucleotide d(CpGpTpApCpGpTpApCpG).

    abstract::Crystals of the self-complementary decadeoxyoligonucleotide d(CpGpTpApCpGpTpApCpG) have been grown from a solution containing [Co(NH3)6]Cl3 and spermine. The amber-colored crystals are hexagonal and belong to the space group P6(5) (or P6(1] with unit cell parameters a = 17.93 A, c = 43.41 A. Precession photography and...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90429-2

    authors: Brennan RG,Sundaralingam M

    更新日期:1985-02-20 00:00:00

  • Genetic analysis of the lytic replicon of bacteriophage P1. II. Organization of replicon elements.

    abstract::The region of bacteriophage P1 DNA containing a lytic (vegetative) replicon has been identified by cloning P1 fragments into a phage lambda vector. We present the sequence of that replicon. Using a novel fusion vector containing two P1 loxP recombination sites, we have developed a transformation assay for replicon fun...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90444-0

    authors: Sternberg N,Cohen G

    更新日期:1989-05-05 00:00:00

  • DNA-directed DNA polymerase and strand displacement activity of the reverse transcriptase encoded by the R2 retrotransposon.

    abstract::R2 elements are non-long terminal repeat (non-LTR) retrotransposons with a single open reading-frame encoding reverse transcriptase, DNA endonuclease and nucleic acid-binding domains. The elements are specialized for insertion into the 28 S rRNA genes of many animal phyla. The R2-encoded activities initiate retrotrans...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.09.047

    authors: Kurzynska-Kokorniak A,Jamburuthugoda VK,Bibillo A,Eickbush TH

    更新日期:2007-11-23 00:00:00

  • Functionally important correlated motions in the single-stranded DNA-binding protein encoded by filamentous phage Pf3.

    abstract::To elucidate the interplay between different parts of dimeric single-stranded DNA-binding proteins we have studied the correlated motions in the protein encoded by filamentous phage Pf3 via the combined use of 15N-NMR relaxation experiments, molecular dynamics simulations and essential dynamics calculations. These stu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2629

    authors: Horstink LM,Abseher R,Nilges M,Hilbers CW

    更新日期:1999-04-02 00:00:00

  • Crystallization and preliminary X-ray data of a phleomycin-binding protein from Streptoalloteichus hindustanus.

    abstract::Large single crystals of a glycopeptide resistance protein encoded by the SH-ble gene from Streptoalloteichus hindustanus have been grown using vapor diffusion techniques with ammonium sulfate as the precipitant. The diffraction pattern extends to 2.0 A resolution. The crystals belong to space group P4(1)2(1)2 or P4(3...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90476-2

    authors: Rondeau JM,Cagnon C,Moras D,Masson JM

    更新日期:1989-06-05 00:00:00

  • Mechanism of action and in vivo efficacy of a human-derived antibody against Staphylococcus aureus α-hemolysin.

    abstract::The emergence and spread of multi-drug-resistant strains of Staphylococcus aureus in hospitals and in the community emphasize the urgency for the development of novel therapeutic interventions. Our approach was to evaluate the potential of harnessing the human immune system to guide the development of novel therapeuti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.02.008

    authors: Foletti D,Strop P,Shaughnessy L,Hasa-Moreno A,Casas MG,Russell M,Bee C,Wu S,Pham A,Zeng Z,Pons J,Rajpal A,Shelton D

    更新日期:2013-05-27 00:00:00

  • Whither Ribosome Structure and Dynamics Research? (A Perspective).

    abstract::As high-resolution cryogenic electron microscopy (cryo-EM) structures of ribosomes proliferate, at resolutions that allow atomic interactions to be visualized, this article attempts to give a perspective on the way research on ribosome structure and dynamics may be headed, and particularly the new opportunities we hav...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2016.04.034

    authors: Frank J

    更新日期:2016-09-11 00:00:00

  • Crystallization and preliminary X-ray analysis of human alpha-galactosidase A complex.

    abstract::Human alpha-galactosidase A (alpha-D-galactoside galactohydrolase; EC 3.2.1.22), the glycosylated lysosomal enzyme deficient in Fabry disease, has been crystallized as a complex with the inhibitor N-6-aminohexanoyl-alpha-D-galactopyranosylamine. The "hanging drop" method of vapor diffusion was used to grow crystals fr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1397

    authors: Murali R,Ioannou YA,Desnick RJ,Burnett RM

    更新日期:1994-06-17 00:00:00

  • All-atom Monte Carlo simulation of GCAA RNA folding.

    abstract::We report a detailed all-atom simulation of the folding of the GCAA RNA tetraloop. The GCAA tetraloop motif is a very common and thermodynamically stable secondary structure in natural RNAs. We use our simulation methods to study the folding behavior of a 12-base GCAA tetraloop structure with a four-base helix adjacen...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.09.041

    authors: Nivón LG,Shakhnovich EI

    更新日期:2004-11-12 00:00:00

  • The eta-globin gene. Its long evolutionary history in the beta-globin gene family of mammals.

    abstract::In phylogenetic reconstructions by the parsimony method, utilizing 62 sequenced globin genes and pseudogenes (including 34 of the beta-globin gene family from eutherian orders Primates, Lagomorpha, Artiodactyla and Rodentia), the branch of primate psi beta pseudogenes and the goat embryonically expressed epsilon II ge...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90258-4

    authors: Goodman M,Koop BF,Czelusniak J,Weiss ML

    更新日期:1984-12-25 00:00:00

  • Energy-optimized structure of antifreeze protein and its binding mechanism.

    abstract::A combination of Monte Carlo simulated annealing and energy minimization was utilized to determine the conformation of the antifreeze protein from the fish winter flounder. It was found from the energy-optimized structure that the hydroxyl groups of its four threonine residues, i.e. Thr2, Thr13, Thr24, Thr35, are alig...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90666-8

    authors: Chou KC

    更新日期:1992-01-20 00:00:00

  • Serpin acceleration of amyloid fibril formation: a role for accessory proteins.

    abstract::Protein aggregation underlies an increasing number of human diseases. Recent experiments have shown that the aggregation reaction is exquisitely specific involving particular interactions between non-native proteins. However, aggregation of certain proteins, for example beta-amyloid, in vivo leads to the recruitment o...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.11.062

    authors: Powers GA,Pham CL,Pearce MC,Howlett GJ,Bottomley SP

    更新日期:2007-02-16 00:00:00

  • Implications of the aquaporin-4 structure on array formation and cell adhesion.

    abstract::Aquaporin-4 (AQP4) is the predominant water channel in the mammalian brain and an important drug target for treatment of cerebral edema, bipolar disorder and mesial temporal lobe epilepsy. We determined the AQP4 structure by electron crystallography of double-layered, two-dimensional (2D) crystals. The structure allow...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.10.081

    authors: Hiroaki Y,Tani K,Kamegawa A,Gyobu N,Nishikawa K,Suzuki H,Walz T,Sasaki S,Mitsuoka K,Kimura K,Mizoguchi A,Fujiyoshi Y

    更新日期:2006-01-27 00:00:00

  • Native and non-native structure in a protein-folding intermediate: spectroscopic studies of partially reduced IGF-I and an engineered alanine model.

    abstract::The structure of a metastable folding intermediate of human insulin-like growth factor I (IGF-I) and an engineered model are investigated by circular dichroism and two-dimensional 1H NMR spectroscopy. The intermediate, which contains two of three native disulfide bonds, was trapped by acid quenching and isolated by re...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0320

    authors: Hua QX,Narhi L,Jia W,Arakawa T,Rosenfeld R,Hawkins N,Miller JA,Weiss MA

    更新日期:1996-06-07 00:00:00

  • Site-specific structural variations accompanying tubular assembly of the HIV-1 capsid protein.

    abstract::The 231-residue capsid (CA) protein of human immunodeficiency virus type 1 (HIV-1) spontaneously self-assembles into tubes with a hexagonal lattice that is believed to mimic the surface lattice of conical capsid cores within intact virions. We report the results of solid-state nuclear magnetic resonance (NMR) measurem...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.12.021

    authors: Bayro MJ,Chen B,Yau WM,Tycko R

    更新日期:2014-03-06 00:00:00

  • Characterization of hnRNP K protein-RNA interactions.

    abstract::The heterogeneous nuclear ribonucleoprotein K protein is an RNA-binding protein found in several subcellular compartments where it is thought to be involved in signaling multiple processes that compose gene expression. K protein contains three K homology (KH) domains that mediate RNA-binding. We used a serial analysis...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.07.099

    authors: Klimek-Tomczak K,Wyrwicz LS,Jain S,Bomsztyk K,Ostrowski J

    更新日期:2004-09-24 00:00:00

  • Detection of Escherichia coli ribosome binding at translation initiation sites in the absence of tRNA.

    abstract::Binary complexes between messenger RNA and E. coli ribosomes were examined. A ribosome-mRNA binary complex on T4 gene 32 mRNA withstood inhibition by antibodies against ribosomal protein S1. Anti-S1 blocks ternary complex formation, as measured by "extension inhibition" or "toeprinting" analysis, only when preincubate...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90876-8

    authors: Hartz D,McPheeters DS,Green L,Gold L

    更新日期:1991-03-05 00:00:00