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Periplasmic Binding ProteinsPeriplasmic ProteinsPeriplasmMaltose-Binding ProteinsEscherichia coli ProteinsBacterial ProteinsATP-Binding Cassette TransportersEscherichia coliMaltoseCarrier ProteinsEnterobactinBiological TransportThermotoga maritimaMembrane Transport ProteinsGenes, BacterialMolecular Sequence DataOperonAmino Acid SequenceCrystallography, X-RayLigandsBiological Transport, ActiveModels, MolecularGene Expression Regulation, BacterialMonosaccharide Transport ProteinsMutationProtein ConformationProtein BindingProtein Structure, TertiaryMembrane ProteinsIronBase SequenceCloning, MolecularBinding SitesSequence Homology, Amino AcidBacterial Outer Membrane ProteinsKineticsNitrate ReductaseNitrate ReductasesSpheroplastsProtein Disulfide-IsomerasesCell MembraneAlkaline PhosphatasePeptidylprolyl IsomerasePlasmidsProtein Sorting SignalsPorinsCytoplasmSalmonella typhimuriumSpirochaetaBrachyspira hyodysenteriaeFlagellaProtein Structure, SecondaryParacoccusMolecular ChaperonesMutagenesis, InsertionalProtein FoldingOxidoreductasesDisulfidesRecombinant Fusion ProteinsHydrogenaseGlucansCytochrome c GroupMutagenesis, Site-DirectedDNA, BacterialEndopeptidase KParacoccus denitrificansOxidation-ReductionCysteineAmino Acid Transport Systems, BasicElectrophoresis, Polyacrylamide Gel
ProteinsExtracellularBacterialEscherichiaCytoplasmicTransporterPutativeReceptorsMaltoseTransmembraneAntigenSequenceMoleculesStructuralPeptideColiCationOuterConcentrationsHigh-affinityAffinityLigandCarbohydratePolypeptidesCrystalDomainUptakeSiteCellularTargetsProtein-protein intePathwayTranscriptionAntibioticsStructuresFamilySurface
Proteins15
  • Nickel ABC transporter, substrate-binding protein NikA / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. (pdbj.org)
  • Periplasmic LptC and LptA proteins of the LPS transport system (Lpt) are responsible for LPS transfer between the Lpt inner and outer membrane complexes. (nih.gov)
  • The fusion protein binds to amylose columns while all other proteins flow through. (wikipedia.org)
  • Chemotaxis is triggered by the binding of ligands (chemoeffectors) to chemoreceptors called methyl-accepting chemotaxis proteins (MCPs) and transducer-like proteins (Tlps). (nature.com)
  • The sizable extracellular N-terminal domain is homologous to bacterial periplasmic binding proteins and serves as the glutamate binding site. (bdbiosciences.com)
  • The Tat pathway ensures that only soluble, well-folded proteins are transported out of the cytoplasm and displayed on the inner membrane, thereby eliminating poorly folded scFvs prior to interrogation for antigen-binding. (jove.com)
  • These methods are powerful and effective for identifying antibodies that bind to targets, yet they depend on the secretory pathway to transport proteins that will be displayed 14-16 . (jove.com)
  • The proteins then fold under oxidizing conditions and are displayed on the cell surface or packaged into phage particles to screen for binding affinity 17,18 . (jove.com)
  • 3) Mutations of Q12, A53, and Y54 of GFKAR beta indicate that these three residues are important for ligand binding (particularly L-glutamate), which is consistent with the sequence homology to bacterial periplasmic binding proteins. (aspetjournals.org)
  • These results are consistent with the notion that the ligand-binding domain has close structural similarities to bacterial periplasmic binding proteins. (aspetjournals.org)
  • Periplasmic proteins such as Maltose Binding Protein can penetrate into the periplasm when added in solution to E.coli cells permeabilized with calcium . (asmblog.org)
  • Tail-specific protease (Tsp) is a periplasmic enzyme that selectively degrades proteins bearing a nonpolar C-terminus. (embl.de)
  • Its substrate specificity suggests that Tsp may contain a substrate recognition domain, which selectively binds to the nonpolar C-termini of substrate proteins, separate from its catalytic site. (embl.de)
  • In this work, we show that substrate recognition of Tsp is mediated by a PDZ domain, a small protein module that promotes protein-protein interactions by binding to internal or C-terminal sequences of their partner proteins. (embl.de)
  • The pH-responsive one-component signaling system CadC in Escherichia coli belongs to the family of ToxR-like proteins, whose members share a conserved modular structure, with an N-terminal cytoplasmic winged helix-turn-helix DNA-binding domain being followed by a single transmembrane helix and a C-terminal periplasmic pH-sensing domain. (cipsm.de)
Extracellular2
  • These data lend further evidence in support of a model of glutamate receptor topology with three transmembrane segments and reveal several general structural features of the extracellular ligand-binding domain of the kainate receptors. (aspetjournals.org)
  • The extracellular loops of CmeC visit the open and closed states freely suggesting the absence of a gating mechanism on this side, while the narrow periplasmic entrance remains tightly closed, regulated via coordination to solvated cations. (soton.ac.uk)
Bacterial3
  • Cefiderocol binds to ferric iron and is actively transported into bacterial cells through the outer membrane via the bacterial iron transporters, which function to incorporate this essential nutrient for bacteria. (drugdiscoverynews.com)
  • This mechanism allows cefiderocol to achieve higher concentrations in the periplasmic space where it can then bind to receptors and inhibit cell wall synthesis in the bacterial cells. (drugdiscoverynews.com)
  • Mutants functionally deficient in vivo show no binding to K30 polymer in vitro.Apparently, Wzi is a novel outer-membrane lectin that assists in the formation of the bacterial capsule via direct interaction with capsular polysaccharides. (tcdb.org)
Escherichia2
  • Maltose-binding protein (MBP) is a part of the maltose/maltodextrin system of Escherichia coli, which is responsible for the uptake and efficient catabolism of maltodextrins. (wikipedia.org)
  • We provide a method to simultaneously screen a library of antibody fragments for binding affinity and cytoplasmic solubility by using the Escherichia coli twin-arginine translocation pathway, which has an inherent quality control mechanism for intracellular protein folding, to display the antibody fragments on the inner membrane. (jove.com)
Cytoplasmic5
  • Commonly used methods for the display and screening of recombinant antibody libraries do not incorporate intracellular protein folding quality control, and, thus, the antigen-binding capability and cytoplasmic folding and solubility of antibodies engineered using these methods often must be engineered separately. (jove.com)
  • Here, we describe a protocol to screen a recombinant library of single-chain variable fragment (scFv) antibodies for antigen-binding and proper cytoplasmic folding simultaneously. (jove.com)
  • Antigen-binding and cytoplasmic solubility can be improved with subsequent rounds of mutagenesis and screening to engineer antibodies with high affinity and high cytoplasmic solubility for intracellular applications. (jove.com)
  • In E. coli CadC, a cytoplasmic linker comprising approximately 50 amino acids is essential for transmission of the signal from the sensor to the DNA-binding domain. (cipsm.de)
  • Thus, we propose that the disordered CadC linker is required for transducing the pH-dependent response of the periplasmic sensor into a structural rearrangement that facilitates dimerization of the cytoplasmic CadC DNA-binding domain. (cipsm.de)
Transporter1
  • With ATP bound, the transporter forms a large transmembrane channel with openings toward the membrane and periplasm. (tcdb.org)
Putative2
  • Systematic deletion mutagenesis of Tsp localized the binding site to amino acids 206-307, a region that completely encompasses the putative PDZ domain (217-301). (embl.de)
  • Computer analysis showed that the MauG polypeptide contains two putative heme binding sites and that the MauM and MauN polypeptides have four and two FeS cluster signatures, respectively. (caltech.edu)
Receptors3
  • Ligand-binding characteristics and related structural features of the expressed goldfish kainate receptors: identification of a conserved disulfide bond and three residues important for ligand binding. (aspetjournals.org)
  • Structural analysis of the DNA-binding domain of alternatively spliced steroid receptors. (mpg.de)
  • We are mutating periplasmic receptors normally linked to gene transcription. (igem.org)
Maltose3
  • The two domains are separated by a deep groove that contains the maltose/maltodextrin binding site. (wikipedia.org)
  • Comparison of the structures of the liganded and unliganded forms of MBP has shown that the binding of maltose induces a major conformational change that closes the groove by a rigid motion of the two domains around the linking polypeptide hinge. (wikipedia.org)
  • Both precursor and mature forms of MBP are functional for the binding of maltose. (wikipedia.org)
Transmembrane2
  • Upon ATP binding, large structural changes within the nucleotide-binding and transmembrane regions push conserved hydrophobic residues at the substrate entry site towards the periplasm and provide a model for polysaccharide translocation. (tcdb.org)
  • 2) A deletion mutant lacking the originally proposed second-transmembrane domain was efficiently expressed and retains the overall ligand-binding properties of wild-type GFKAR alpha, strongly indicating that this region is not a transmembrane domain. (aspetjournals.org)
Antigen2
  • Following removal of the outer membrane, the scFvs displayed on the inner membrane are panned against a target antigen immobilized on magnetic beads to isolate scFvs that bind to the target antigen. (jove.com)
  • Although antibodies have much potential for intracellular applications, engineering them for proper folding and solubility in the intracellular environment while maintaining the ability to bind to a target antigen is challenging. (jove.com)
Sequence1
  • Sato K, Li C, Salard I, Thompson AJ, Banfield MJ, Dennison C. Metal-binding loop length and not sequence dictates structure . (ncl.ac.uk)
Molecules2
  • ABC (ATP binding cassette) transporters catalyze the transport of a wide variety of molecules across lipid bilayers into or out of cells and organelles. (rug.nl)
  • The channel's periplasmic exit is sealed by detergent molecules that block solvent permeation. (tcdb.org)
Structural1
  • In this study, two previously cloned goldfish kainate receptor subunits (GFKAR alpha and GFKAR beta) were transiently expressed in human embryonic kidney 293 cells, and their ligand-binding properties and some associated structural features were characterized, resulting in the following findings. (aspetjournals.org)
Peptide4
  • Peptide binding of the ligand takes place in an elongated surface groove as an anti-parallel beta-strand interacts with the beta-B strand and the B helix. (embl.de)
  • The structure of PDZ domains allows binding to a free carboxylate group at the end of a peptide through a carboxylate-binding loop between the beta-A and beta-B strands. (embl.de)
  • The isolated PDZ domain (amino acids 206-334) is capable of folding into a well-behaved structure and binds to a nonpolar peptide with a dissociation constant (K(D)) of 1.9 microM, similar to that of the intact Tsp protein. (embl.de)
  • Site-directed mutagenesis of a surface residue at the peptide binding site of the PDZ domain, valine 229, to Glu or Gln resulted in an increase in the K(M) value but had no effect on the k(cat) value. (embl.de)
Coli1
  • MBP is exported into the periplasmic space of E. coli. (wikipedia.org)
Cation1
Outer2
  • Periplasmic stress, also known as envelope stress, is triggered by several factors that influence the ability of the bacteria to communicate with other cells through quorum sensing, pathological pathway, pili formation, outer membrane protein formation which plays a role in adhesion of the cells allowing them to form proper colonies and survive. (igem.org)
  • Many stresses in the periplasmic region are triggered by improper formation of outer protein structures such as pili and lipoprotein disruption that reduces pathogenicity of the bacteria. (igem.org)
Concentrations1
  • The 2009 Brown iGEM Team aims to treat allergic rhinitis by engineering "Staphylococcus epidermidis" to secrete a histamine binding protein in response to elevated histamine concentrations during an allergic attack. (igem.org)
High-affinity2
  • TMS IV of the high-affinity sodium-glucose cotransporter participates in sugar binding ( Liu et al . (tcdb.org)
  • rEV131 binds histamine with an extreme high affinity, and normally functions to prevent the inflammatory response while the tick sucks blood. (igem.org)
Affinity2
  • Analysis of [3H]kainate binding to wild-type and cysteine mutations of GFKAR beta indicate that in the absence of the disulfide bond, the affinity for kainate is increased 3-fold. (aspetjournals.org)
  • In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 microns. (embl.de)
Ligand1
  • Li C, Sato K, Monari S, Salard I, Sola M, Banfield MJ, Dennison C. Metal-Binding Loop Length Is a Determinant of the pK(a) of a Histidine Ligand at a Type 1 Copper Site . (ncl.ac.uk)
Carbohydrate1
  • Wzi is a lectin that binds the K30 carbohydrate polymer. (tcdb.org)
Polypeptides2
  • others appear to bind internal (non-C-terminal) polypeptides. (embl.de)
  • The mauB, mauA, and mauC genes encode the periplasmic methylamine dehydrogenase (MADH) large and small subunit polypeptides and amicyanin, respectively. (caltech.edu)
Crystal1
  • 4MIJ: Crystal structure of a Trap periplasmic solute binding protein from Polaromonas sp. (rcsb.org)
Domain2
  • 3 The tandem CBS domain 4 , which is linked to the nucleotide binding protein, plays a pivotal role in the regulation. (rug.nl)
  • CadC dimerizes via its periplasmic domain, but light-scattering analysis provided no evidence for dimerization of the isolated DNA-binding domain, with or without the linker region. (cipsm.de)
Uptake1
  • D. & E. Uptake systems with two or four covalently linked substrate-binding domains (SBDs). (rug.nl)
Site1
Cellular1
  • Cpx pathway is involved in maintaining cellular adhesion and keeping periplasmic environment in check. (igem.org)
Targets1
  • Known drug targets of putrescine include putrescine-binding periplasmic protein, ornithine decarboxylase, and S-adenosylmethionine decarboxylase proenzyme. (drugbank.com)
Protein-protein inte1
  • They have the ability to modulate protein activity by binding to a target protein inside cells to prevent protein-protein interactions, disrupt protein-nucleic acid interactions, or prevent substrate access to enzymes 1-5 . (jove.com)
Pathway2
  • Fqo can be hypothesized to be operative during sulfate reduction with CO. The Fqo complex receives electrons from the reduced coenzyme F 420 (F 420 H 2 ), generated from the oxidative acetyl-CoA pathway, and transfers electrons to the membrane-bound respiratory chain by the reduction of menaquinone [ 16 - 18 ]. (hindawi.com)
  • Cpx also acts as a periplasmic heat shock pathway. (igem.org)
Transcription1
  • Transcription activation requires the binding of adenosine triphosphate (ATP) and maltotriose to MalT and the binding of cyclic AMP to the dimer of CRP. (wikipedia.org)
Antibiotics1
  • Methicillin is of a class of antibiotics known as β-lactams which bind to the penicillin binding protein (PBP) of the bacteria. (randox.com)
Structures1
  • El Ghazouani A, Basle A, Firbank SJ, Knapp CW, Gray J, Graham DW, Dennison C. Copper-Binding Properties and Structures of Methanobactins from Methylosinus trichosporium OB3b . (ncl.ac.uk)
Family1
  • 47904) TATA-box binding family protein CP001857 CDS Arcpr_0059 47991. (go.jp)
Surface1
  • The selectivity of LPS for this intermolecular surface and the observation of such cavities at homo- or heteromolecular interfaces in LptC and LptA suggests that intermolecular sites are essential for binding LPS during its transport. (nih.gov)