AnatomyOrganismsChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesInformation ScienceHealth Care
Protein BindingMolecular Sequence DataCarrier ProteinsBinding SitesPoly(A)-Binding ProteinsBase SequenceAmino Acid SequenceDNA-Binding ProteinsRNA-Binding ProteinsTranscription FactorsProtein Structure, TertiaryTacrolimus Binding ProteinsPromoter Regions, GeneticCell LineNuclear ProteinsRecombinant Fusion ProteinsSequence Homology, Amino AcidPoly(A)-Binding Protein IDNARecombinant ProteinsCloning, MolecularRNA, MessengerMutationInsulin-Like Growth Factor Binding ProteinsBinding, CompetitiveBacterial ProteinsHeLa CellsEscherichia coliModels, MolecularFatty Acid-Binding ProteinsKineticsTranscription, GeneticRepressor ProteinsGene Expression RegulationCalcium-Binding ProteinsMolecular WeightTransfectionSequence AlignmentElectrophoresis, Polyacrylamide GelProtein ConformationPlasmidsTwo-Hybrid System TechniquesRibonucleoproteinsCell NucleusPoly(A)-Binding Protein IIMembrane ProteinsNucleic Acid ConformationHeterogeneous-Nuclear RibonucleoproteinsTrans-ActivatorsPeriplasmic Binding ProteinsRegulatory Sequences, Nucleic AcidDNA PrimersCells, CulturedInsulin-Like Growth Factor Binding Protein 3DNA, ComplementaryBlotting, WesternMutagenesis, Site-DirectedViral ProteinsTATA-Box Binding ProteinElectrophoretic Mobility Shift AssayProteinsSignal TransductionSaccharomyces cerevisiaeDNA, Single-StrandedCCAAT-Enhancer-Binding ProteinsAmino Acid MotifsSaccharomyces cerevisiae ProteinsTacrolimus Binding Protein 1AConsensus SequenceCyclic AMP Response Element-Binding ProteinPhosphorylationLatent TGF-beta Binding ProteinsProtein BiosynthesisNerve Tissue ProteinsMaltose-Binding ProteinsLigandsChromatography, AffinityEscherichia coli ProteinsOligodeoxyribonucleotidesDimerizationPolypyrimidine Tract-Binding ProteinCattleInsulin-Like Growth Factor Binding Protein 2Zinc FingersDNA FootprintingFungal ProteinsReceptors, Cell SurfaceMacromolecular SubstancesConserved SequenceCOS CellsInsulin-Like Growth Factor Binding Protein 1Drosophila ProteinsCrystallography, X-RayEnhancer Elements, GeneticCell MembraneAdaptor Proteins, Signal TransducingRetinol-Binding ProteinsGene ExpressionTumor Cells, CulturedPrecipitin Tests
LigandAffinityLigandsGuanylateAmino AcidsResiduesComputationalInteractionsScaffoldSerumHsp90AffinitiesCharacterizePhysiologicalVitroChemicalsFamily is a familyGenesAntibodyMolecularTranscriptionMethodsDomainBiologicalExpressionConcentrationGrowthSitesDesired structureSmallMajorLargeFusionPlasmaModelAdditionalOrderLibrary
Ligand8
  • Selective microfluidics-based ligand enrichment followed by sequencing, or SMiLE-seq, combines antibody arrays, mechanical trapping, and next-generation sequencing readouts to provide a new platform for characterizing DNA-protein interactions. (genomeweb.com)
  • In the first part of this thesis, the interaction between the rat CD2 (rCD2) adhesion protein and its ligand rat CD48T92A (rCD48T92A), a high-affinity mutant of the wild type rat CD48, was used to establish a new method of obtaining single-cell binding affinities of T cells interacting with SLBs using imidazole titrations. (lu.se)
  • Even though the CD4 co-receptor increases the sensitivity of T cell signalling manyfold, it binds to its ligand, peptide major histocompatibility complex II (pMHCII), with the lowest binding affinity known to this day. (lu.se)
  • We would like to understand the 'driving forces' of protein-ligand binding, which amounts to understanding the statistical thermodynamics of the binding process at atomic resolution. (lu.se)
  • This is perhaps one reason why protein conformational entropy has not received widespread attention in the field of ligand/drug design, while the often dominant role of solvent entropy is generally taken into account, together with the change in ligand entropy. (lu.se)
  • For these reasons, we are interested in the role of the conformational entropy of the target protein in ligand-binding processes. (lu.se)
  • By comparing NMR-derived order parameters between the free and ligand-bound protein, we estimate the contributions from conformational entropy to the free energy of ligand binding. (lu.se)
  • In addition to NMR relaxation methods, we use isothermal titration calorimetry to obtain the thermodynamic fingerprint of ligand binding, including the total (standard) free energy, enthalpy, and entropy of the process. (lu.se)
Affinity12
  • Some GBPs have exhibited the ability to bind not only guanosine triphosphate (GTP) to produce guanosine diphosphate (GDP) but also GDP to produce guanosine monophosphate (GMP) with equimolar affinity and high intrinsic rates of hydrolyzation. (wikipedia.org)
  • That year, the two published a paper in Science describing a method to trap low-affinity DNA-protein interactions, specifically those of transcription factors. (genomeweb.com)
  • Streptococcus pneumoniae and Neisseria meningitidis have is specific to the mechanism of resistance to penicillin G com- very similar mechanisms of resistance to penicillin G, which mon to S. pneumoniae and N. meningitidis and mediated by the are mediated by the decreased affinity of penicillin-binding decrease in affinity of their PBPs. (cdc.gov)
  • In nature, antibodies are the primary affinity proteins and their usefulness has led to a widespread use both in basic and applied research. (avhandlingar.se)
  • In this thesis, a 46 amino acid small albumin-binding domain derived from streptococcal protein G was evaluated as a scaffold for the generation of affinity proteins. (avhandlingar.se)
  • In paper I, a bispecific albumin-binding domain was selected by phage display and utilized as a purification tag for highly efficient affinity purification of fusion proteins. (avhandlingar.se)
  • The results in paper II show how protein engineering, in vitro display and multi-parameter fluorescence-activated cell sorting can be used to accomplish the challenging task of incorporating two high affinity binding-sites, for albumin and tumor necrosis factor-alpha, into this new bispecific protein scaffold. (avhandlingar.se)
  • The new alternative protein scaffold described in this thesis is one of the smallest structured affinity proteins reported. (avhandlingar.se)
  • The prebiotic inulin induced other family 1 binding proteins with affinity for intestinal glycans. (escholarship.org)
  • Understanding how proteins interact entails studying the binding affinity (strength) and the lifetime (duration) of the protein-protein interaction to better decompose how an immune response is initiated and how we can explore this knowledge to treat diseases. (lu.se)
  • The results showed a relatively small spread in the rCD2-rCD48T92A binding affinity values despite the considerable spread of receptor densities within the cell population. (lu.se)
  • Using both these methods, the single-cell binding affinity and lifetime of the cell population can be investigated and their spread can provide information concealed with population-average techniques. (lu.se)
Ligands1
  • We combine NMR relaxation experiments with molecular dynamics (MD) simulations to derive a highly detailed picture of how the conformational entropy changes when the protein binds different ligands. (lu.se)
Guanylate3
  • In molecular biology, the guanylate-binding proteins family is a family of GTPases that is induced by interferon (IFN)-gamma. (wikipedia.org)
  • Guanylate-binding proteins (GBP) fall into the last class. (wikipedia.org)
  • Based on primary sequence comparisons, β subunits are predicted to be modular structures composed of five domains (A-E) that are related to the large family of membrane-associated guanylate kinase proteins. (jneurosci.org)
Amino Acids2
  • The primary structure of these proteins contains an N-terminal hydrophobic leader sequence of 30-40 amino acids, which could represent a signal for translocation of the protein to the ER. (wikipedia.org)
  • Raney nickel desulfunization of Pronase hydrolysates released several HCP metabolites that were apparently bound to sulfur-containing amino acids such as cysteine and homocysteine. (aspetjournals.org)
Residues3
  • The mature protein comprises around 165 residues, and contains a number of potential N-glycosylation sites. (wikipedia.org)
  • VH is derived from a single protein domain of 35 residues [ 9 ]. (hindawi.com)
  • Thin-layer chromatography of dinitrophenyl derivatives prepared from Pronase-digested microsomal protein and sodium dodecyl sulfate-polyacrylamide disc gel electrophoresis of solubilized microsomes indicated that the radiolabeled products were covalently bound to amino acid residues of microsomal protein. (aspetjournals.org)
Computational1
  • Computational design of novel proteins with well-defined functions is an ongoing topic in computational biology. (hindawi.com)
Interactions7
  • CaaX motifs) or additional domains that are thought to operate in protein-protein or protein-membrane interactions. (wikipedia.org)
  • It is suggested that Chip cooperates with different LIM domain proteins and other factors to structurally support remote enhancer-promoter interactions. (nih.gov)
  • Hydrophobicity was one of the most important physicochemical properties, due to the fact that it is involved in protein interactions, for example, by forming hydrophobic cores. (hindawi.com)
  • By physically restraining bound molecules against an antibody array, they capture both transient interactions, which yeast two-hybrid or tandem mass spectrometry methods don't, and weak interactions, which are usually obliterated by the wash in protein-DNA microarrays. (genomeweb.com)
  • The transcription factors bind to any number of DNA motifs in the library, those interactions are trapped, and then the readout matches up each motif with the transcription factor via the barcode. (genomeweb.com)
  • Deplancke also worked in advanced bioinformatics to derive predictive models for binding interactions. (genomeweb.com)
  • Protein-protein interactions are crucial in numerous cellular functions and biological processes that take place inside our body. (lu.se)
Scaffold2
  • Protein design methods use trial and error or more sophisticated methods like directed evolution or inverse folding to generate novel scaffolds or to find novel protein sequences folding into a defined scaffold, respectively. (hindawi.com)
  • The bispecific nature, with an inherent ability of the same domain to bind to serum albumin, is unique for this scaffold. (avhandlingar.se)
Serum3
  • Human serum albumin (HSA) binding of anticancer plant alkaloid ellipticine has been studied in conjunction with assessing its association to serum a1-acid-glycoprotein (AAG). (jascoinc.com)
  • Moreover, the native ability of this domain to bind serum albumin provides a useful characteristic that can be used to extend the plasma half-lives of proteins fused to it or potentially of the domain itself. (avhandlingar.se)
  • At a constant concentration of TCPy (200 microM), levels of protein bound to TCPy in cell culture media (Advanced DMEM:F12 supplemented with 2% fetal bovine serum) decreased as much as 52% with an increasing co-exposure to 2,4-D (0-2300 microM), indicating that these chemicals compete for common binding sites on proteins. (cdc.gov)
Hsp902
  • Functional maturation of steroid hormone receptors requires ordered assembly into a large multichaperone complex consisting of receptor monomer, an Hsp90 dimer, the p23 cochaperone, and an FK506-binding protein (FKBP) family member or alternate peptidylprolyl isomerase-related cochaperone. (unboundmedicine.com)
  • Both proteins consist of three domains: two FKBP12-like domains termed FK1 and FK2 and a tetratricopeptide repeat domain that targets binding to Hsp90. (unboundmedicine.com)
Affinities1
  • In this study we have used the Mammalian Glycan Array to determine the specific affinities of these proteins. (escholarship.org)
Characterize2
  • Taking advantage of the ability of chiral protein environments to induce optical activity, circular dichroism (CD) spectroscopy was employed to characterize the alkaloid-protein non-covalent adducts. (jascoinc.com)
  • In this thesis, total internal fluorescence microscopy (TIRF) and single-molecule imaging were used to observe and characterize protein-functionalized supported lipid bilayers (SLBs) interacting with immune cells to obtain the binding kinetics of various protein-protein pairs. (lu.se)
Physiological2
  • Lastly, CD4 binding studies showed that the co-receptor did not noticeably affect the TCR-MHC II binding at physiological levels of hCD4 in the SLB. (lu.se)
  • Additional protein binding (at physiological conditions) and kinetic cellular transport experiments quantifying chemical transport and binding rates were conducted to further explore implications of chemical mixtures transport. (cdc.gov)
Vitro4
  • Bacteria often can't support over-expression needed to get workable quantities of protein for an assay, and in vitro expression often can't synthesize a fully functional transcription factor. (genomeweb.com)
  • Protein engineering and in vitro selection systems are powerful methods to generate binding proteins. (avhandlingar.se)
  • By using in vitro selection from a combinatorial library, bispecific protein domains with ability to recognize several different target proteins were generated. (avhandlingar.se)
  • Finally, some of these proteins were found to be adherent to intestinal epithelial cells in vitro. (escholarship.org)
Chemicals1
  • The transport of chemicals across the cell layer (via passive diffusion) was influenced by the binding of proteins (i.e. unbound chemicals were able to pass through the cell layer). (cdc.gov)
Family is a family1
  • In molecular biology, the auxin binding protein family is a family of proteins which bind auxin. (wikipedia.org)
Genes1
Antibody1
  • By means of combinatorial protein engineering and protein library technology, smaller antibody fragments or alternative non-immunoglobulin protein scaffolds can be engineered for various functions based on molecular recognition. (avhandlingar.se)
Molecular2
  • However, molecular weight is also important due to potential steric incompatibilities within protein cores. (hindawi.com)
  • In the ideal scenario, we would be able to attribute the contributions from individual molecular groups to the enthalpy and entropy of binding. (lu.se)
Transcription4
  • It is suggested that these proteins act synergistically to enhance transcriptional efficiency by acting as co-factors for LIM homeodomain and Otx class transcription factors both of which have essential roles in development. (nih.gov)
  • In a paper published in Nature Methods this week, a Switzerland-based team of researchers, led by bioengineer Bart Deplancke of the École Polytechnique Fédérale de Lausanne (EPFL), showcased the assay's ability to determine DNA-binding specificities for transcription factors. (genomeweb.com)
  • In terms of predicting where in the genome the transcription factors bind, the models we're able to derive seem to be, in general, actually better than the other assays. (genomeweb.com)
  • The assay could help accelerate efforts to map where transcription factors bind the genomes of humans and model organisms, Deplancke said. (genomeweb.com)
Methods2
  • One of the methods that have been proposed is a multiobjective optimization, in which protein stability and catalytic activity are simultaneously optimized [ 4 , 5 ]. (hindawi.com)
  • Several methods have been proposed to design novel stable proteins, such as multi-objective optimization, in which protein stability and catalytic activity are simultaneously optimized. (hindawi.com)
Domain6
  • Examinations of GBP-related sequences have shown that zebrafish gbp3 and gbp4 contain an additional function to find (FIIND) and a caspase recruitment (CARD) domains that resemble those found within the inflammasome-related proteins: Apoptosis-associated speck-like protein containing a CARD (PYCARD) and NLR Family Pyrin Domain Containing 1 (NLRP1). (wikipedia.org)
  • The LIM-domain binding protein, binds to the LIM domain pfam00412 of LIM homeodomain proteins which are transcriptional regulators of development. (nih.gov)
  • Nuclear LIM interactor (NLI) / LIM domain-binding protein 1 (LDB1) is located in the nuclei of neuronal cells during development, it is co-expressed with Isl1 in early motor neuron differentiation and has a suggested role in the Isl1 dependent development of motor neurons. (nih.gov)
  • We have successfully combined two unrelated naturally occurring binding sites, the immunoglobin Fc-binding site of the Z domain and the DNA-binding motif of MyoD bHLH, into a novel stable protein. (hindawi.com)
  • Using protein engineering, the albumin binding has been complemented with a new binding interface localized to the opposite surface of this three-helical bundle domain. (avhandlingar.se)
  • Small bispecific binding proteins based on the albumin-binding domain could potentially contribute to this field. (avhandlingar.se)
Biological1
  • In convergent evolution, nonhomologous proteins evolve in separate biological contexts to catalyze the same or similar reactions. (hindawi.com)
Expression1
  • Growth on HMO induced the expression of specific binding proteins that import HMO isomers, but also bind blood group and mucin oligosaccharides, suggesting coregulated transport mechanisms. (escholarship.org)
Concentration1
  • For this reason, the influence of an adhesion molecule, rat CD2, on the obtained binding kinetics of the human CD4 co-receptor was initially examined showing that the accumulation of CD4 was influenced when having a high concentration of bound CD2 inside the cell-SLB contacts. (lu.se)
Growth1
  • The engineered binding proteins generated against the epidermal growth factor receptors 2 and 3 in papers III and IV are aimed in this direction. (avhandlingar.se)
Sites1
  • Our recent efforts have focused on aromatic side chains, which often are found in binding sites. (lu.se)
Desired structure1
  • Given the intimate relationship between a protein's structure and function, a way to design proteins with targeted properties is to start from a desired structure and find sequences able to fold into it, imposing additional constraints in the process [ 1 ]. (hindawi.com)
Small1
  • These GTPases are classified into three groups: the small 47-KD immunity-related GTPases (IRGs), the Mx proteins (MX1, MX2), and the large 65- to 67-kd GTPases. (wikipedia.org)
Major1
  • This graph shows the total number of publications written about "Poly(A)-Binding Protein II" by people in Harvard Catalyst Profiles by year, and whether "Poly(A)-Binding Protein II" was a major or minor topic of these publication. (harvard.edu)
Large1
  • Arguably, one of the greatest challenges lies in evaluating the conformational entropy of the target protein, which involves a very large number of degrees of freedom. (lu.se)
Fusion1
  • In this work, we generated and optimized a new synthetic fusion protein using an evolutionary approach. (hindawi.com)
Plasma1
  • After intraperitoneal and oral administration of [ 14 C]HCP (5 mg/kg) to male rats treated with phenobarbital, radiocarbon was covalently bound mainly to proteins of the liver, plasma, and kidney. (aspetjournals.org)
Model1
Additional1
  • Retention within the lumen of the ER correlates with an additional signal located at the C terminus, represented by the sequence Lys-Asp-Glu-Leu, known to be responsible for preventing secretion of proteins from the lumen of the ER in eukaryotic cells. (wikipedia.org)
Order1
  • The protein requires a minimum of ten ADENOSINE nucleotides in order for binding to mRNA. (harvard.edu)
Library1
  • Poly(A)-Binding Protein II" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (harvard.edu)