• It implies that some enzymes will work on substrates they are not perfectly specific to (and hence can recognize multiple substrates), but that the reaction will be slower. (getrevising.co.uk)
  • Different enzymes show a different degree of specificity. (getrevising.co.uk)
  • Protease-substrate interactions are governed by a variety of structural features. (ox.ac.uk)
  • Overall these results suggest that topological specificity may be a guiding principle for protease behavior and can be utilized to design specific substrates and inhibitors. (ox.ac.uk)
  • Employing the Jerini pepSTAR method in combination with kinetic analysis of phosphorylation of variant peptides, we establish the key substrate specificity determinants for NEK6. (jpt.com)
  • In the present study, the topological substrate specificity of ADAMTS-4 (aggrecanase-1) was examined using triple-helical or single-stranded poly(Pro) II helical peptides. (ox.ac.uk)
  • The triple-helical and single-stranded poly(Pro) II helical peptides represent the first synthetic substrates successfully designed for aggrecanases. (ox.ac.uk)
  • Its mutation to either Ile or Val severely reduced the efficacy with which NEK6-phosphorylated peptide substrates, and moreover, mutation of the equivalent Leu residue in S6K1 or SGK1 prevented phosphorylation of their hydrophobic motifs by NEK6 in vitro. (jpt.com)
  • Several candidate neuropeptides such as endothelin, galanin, calcitonin, bradykinin, met- and leu-enkephalins, and somatostatin were considered as potential substrates for XCE activity. (biomedcentral.com)
  • Suggestion of a common topological specificity for functionally diverse proteases. (ox.ac.uk)
  • Although the substrate sequence specificities of numerous proteases have been established, "topological specificities," whereby proteases may be classified based on recognition of distinct three-dimensional structural motifs, have not. (ox.ac.uk)
  • Unfolding of the α-helix comprising the S2' subsite residues in aECE-1 correlate well with its endopeptidase activity while their compact folding in aXCE may account for the inactivity of the enzyme towards large C-terminal containing substrates. (biomedcentral.com)
  • Enzyme kinetics and modeling studies of these EntE variants demonstrated that the NRPS code residues at positions 236, 240, and 339 collectively regulate the substrate specificity toward DHB and Sal. (figshare.com)
  • In turn, non-catalytic ADAMTS-4 domains were critical for hydrolysis of triple-helical and poly(Pro) II helical substrates. (ox.ac.uk)
  • Substrate conformation modulates aggrecanase (ADAMTS-4) affinity and sequence specificity. (ox.ac.uk)
  • Substrate topology modulated the affinity and sequence specificity of ADAMTS-4 with K(m) values indicating a preference for triple-helical structure. (ox.ac.uk)
  • The results evaluated are in good agreement with available experimental data, thus providing detailed molecular models which can explain the structural and specificities differences between both zinc peptidases. (biomedcentral.com)
  • flexible interaction between ligand and active site induces a conformational change -enzyme is in an open state and as it binds to substrate it is pushed towards transition state. (getrevising.co.uk)
  • the reaction path, not the selectivity for substrates or products. (getrevising.co.uk)
  • The aggrecanase members of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) family cleave a variety of proteins but do not seem to possess distinct sequence specificities. (ox.ac.uk)
  • Large collections of peptidic enzyme substrates in microtiter plates or displayed on microarrays for screening and enyzme profiling. (jpt.com)
  • In what two ways does the substrate tend to be specific to the active site? (getrevising.co.uk)
  • Some are specific to one substrate, whilst others aren't. (getrevising.co.uk)
  • Based on comparison of known prenylated proteins, both FTase and GGTase-I have been proposed to recognize protein or peptide substrates containing a C-terminal "Ca 1 a 2 X" sequence 11-17 . (sigmaaldrich.com)
  • 1992) "Synthetic Peptide Libraries in the Determination of T Cell Epitopes and Peptide Binding Specificity of Class I Molecules" Eur. (patentgenius.com)
  • 1991) "Peptide-Binding Specificity of the Molecular Chaperone BiP" Nature 353:726-730. (patentgenius.com)
  • In the method of the invention, a protein kinase is contacted with an oriented degenerate peptide library, peptides within the library which are substrates for the kinase are converted to phosphopeptides and the phosphopeptides are separated from non-phosphorylated peptides. (patentgenius.com)
  • The invention also provides peptide substrates for protein kinase A, cell cycle control kinases, src family kinases, the EGF receptor and p92.sup.c-fps/fes based upon amino acid sequence motifs for the phosphorylation sites of these kinases. (patentgenius.com)
  • When coupled with high-throughput quantitative proteomics technique, this simplified model enabled the accurate determination of catalytic efficiencies for 2369 peptide substrates of a protease by using only one enzymatic reaction experiment. (mcponline.org)
  • Highly complex substrate libraries including the synthetic oligonucleotide or peptide mixture ( 9 , 10 ), the peptide library derived from the digestion of proteins in total cell lysate ( 11 , 12 ) and the proteins in total cell lysate ( 13 , 14 ) were used for substrate screening. (mcponline.org)
  • This requirement for arginine in peptide substrates could not be substituted with the similarly charged lysine. (caltech.edu)
  • This specificity determined for peptide substrates was also evident in many of the proteins phosphorylated by Dbf2-Mob1 in a proteome chip analysis. (caltech.edu)
  • Conclusion: We have determined by peptide library selection and phosphosite array screening that the protein kinase Dbf2-Mob1 preferentially phosphorylated substrates that contain an RXXS motif. (caltech.edu)
  • Direct insights into substrate binding and catalytic mechanism of an intramembrane protease now come from X‐ray structures of the bacterial rhomboid protease GlpG complexed to substrate‐derived peptide inhibitors. (embopress.org)
  • To address these interesting observations, we have synthesized a library of substrates containing different peptide scaffolds functionalized with a number of N - ε -acyl moieties. (dtu.dk)
  • We report a systematic analysis of the P1 and P2 substrate specificity of TNF-α converting enzyme (TACE) using a peptide library and a novel analytical method, and we use the substrate specificity information to design novel reverse hydroxamate inhibitors. (eurekaselect.com)
  • Based on this result, 1000 different peptide substrates of the form Biotin-LAQA-P1-P2- SSK(DNP)-NH2 were prepared, with 50 different natural and unnatural amino acids at P1 in combination with 20 different amino acids at P2. (eurekaselect.com)
  • Because of the well-developed enzyme kinetics theories and assay methods, the screening for optimal substrates is often performed by using the in vitro enzymatic reaction system involving an enzyme and a substrate ( 5 ⇓ ⇓ - 8 ). (mcponline.org)
  • Additionally, we have characterized the kinetics governing the specificity and discrimination of several widely administered Nucleotide Reverse Transcriptase Inhibitors (NRTI's) used to combat HIV infection including 3TC (Lamivudine), FTC (Emtricitabine), and AZT (Zidovudine) for the wild-type polymerase and mutants with clinical resistance to these compounds. (utexas.edu)
  • To investigate the fundamental differences in substrate specificity between BMO and MMO, single amino acid substitutions were made to the hydroxylase α-subunit of BMO (BMOH-α). (oregonstate.edu)
  • The pyrophosphorylases can be divided into three families: UDP-Glc pyrophosphorylase (UGPase), UDP-sugar pyrophosphorylase (USPase), and UDP- N -acetyl glucosamine pyrophosphorylase (UAGPase), which can be distinguished both by their amino acid sequences and by differences in substrate specificity. (frontiersin.org)
  • We have analyzed the substrate specificity of OmpT by two complementary substrate filamentous phage display methods: (i) in situ cleavage of phage that display protease-susceptible peptides by Escherichia coli expressing OmpT and (ii) in vitro cleavage of phage-displayed peptides using purified enzyme. (asm.org)
  • To assess the origin of specificity of Escherichia coli leucyl-tRNA synthetase (LeuRS) against the cognate aminoacylation product in editing, we followed binding and catalysis independently using cognate leucyl- and non-cognate norvalyl-tRNA Leu and their non-hydrolyzable analogues. (elsevier.com)
  • We describe a rapid genome-scale approach, MORE (mapping by overexpression of an RNase in Escherichia coli) RNA-seq, for defining the cleavage specificity of endoribonucleolytic toxins. (uniprot.org)
  • To gain insight into substrate binding by rhomboid proteases, we have synthesised a series of novel peptidyl‐chloromethylketone (CMK) inhibitors and analysed their interactions with Escherichia coli rhomboid GlpG enzymologically and structurally. (embopress.org)
  • HeLa cells expressing double- and triple-haplotype mutants also revealed results similar to those for the single mutants ( Fig. 1, A to C ). However, the P-gp inhibitors cyclosporin A (CsA) and verapamil (fig. S1) were less effective against all the substrates in cells expressing the double or triple haplotypes carrying C3435T relative to the wild type, the SNPs, or the haplotype that does not carry C3435T. (sciencemag.org)
  • 1976) "Synthetic Hexapeptide Substrates and Inhibitors of 3':5'-Cyclic AMP-Dependent Protein Kinase" Proc. (patentgenius.com)
  • Taken together, these results provide a structural basis for understanding FTO substrate-specificity, and serve as a foundation for the rational design of FTO inhibitors. (sigmaaldrich.com)
  • Other putative human CYP1A xenobiotic substrates and inhibitors, including caffeine, 5- and 8-methoxypsoralen, nifedipine, paraxanthine, propranolol and theophylline similarly inhibited CYP1A1- and 1A2-catalyzed phenacetin O-deethylation and the high-affinity human liver phenacetin O-deethylase. (aspetjournals.org)
  • 1. Substrate-specificity of the main protease of SARS coronavirus was systematically profiled at P5 to P3' positions, which provided insights into a rational design of peptidomimetic inhibitors. (hkmj.org)
  • Peptidyl chloromethylketones are substrate‐mimicking, mechanism‐based inhibitors of rhomboid protease. (embopress.org)
  • In GH32 members, some of the sugar substrates can also function as inhibitors, this regulatory aspect further adding to the complexity in enzyme functionalities within this family. (kuleuven.be)
  • These substrate preferences were used in the design of novel reverse hydroxamate TACE inhibitors with phenethyl and 5-methyl-thiophene-methyl side-chains at P1, and threonine and nitro-arginine at P2. (eurekaselect.com)
  • The results show that CYP2D6.17 exhibits altered substrate specificity compared with CYP2D6.1 and CYP2D6.2. (pubfacts.com)
  • Mechanistic insight into the substrate specificity of 1,2-β-oligoglucan phosphorylase from Lachnoclostridium phytofermentans. (nii.ac.jp)
  • The essential role of hemopexin carboxyl-domain exosites in the cleavage of noncollagenous substrates such as chemokines has also been recently revealed. (springer.com)
  • The potential role of collagen binding in regulating MMP-2 (gelatinase A) activation at the cell surface reveals unexpected consequences of substrate interactions that can lead to collagen cleavage and regulation of the activation and activity of downstream proteinases necessary to complete the collagenolytic cascade. (springer.com)
  • More advanced bioinformatics techniques were used recently to identify the substrate specificities of calpains and to develop a predictor for calpain cleavage sites, demonstrating the potential of combining empirical data acquisition and machine learning. (nih.gov)
  • An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3. (uniprot.org)
  • Defining the physiological targets of a MazF toxin first requires the identification of its cleavage specificity, yet the current toolkit is antiquated and limited. (uniprot.org)
  • This work included chemical relaxation of specificities towards very frequent cleavage of DNA by Tsp GWI (Zylicz-Stachula et al. (springer.com)
  • While the relaxed cleavage was not as intense as in the previous cases, we discovered and characterised the inherent Secondary-Cognate-Specificity (SCS) of Tso I, which is further highly stimulated by the presence of SAC-an analogue, which is not a methyl group donor, thus can be considered both an analogue of the reaction product-S-adenosyl-homocysteine (SAH) and the cofactor SAM. (springer.com)
  • Acquired mutations in the MXR/BCRP/ABCP gene alter substrate specificity in MXR/BCRP/ABCP-overexpressing cells. (semanticscholar.org)
  • In light of the fact that mutations in Pgp derived from drug selection have been shown to alter substrate specificity (11) , the MXR/BCRP/ABCP mRNA from 11 cell lines was sequenced to determine whether mutations could explain the differing substrate specificities. (aacrjournals.org)
  • This extreme substrate specificity of EaDAcT distinguishes it from all other MBOATs which typically catalyze the transfer of much longer acyl groups. (k-state.edu)
  • These results suggest that amino acid 482 has a crucial role in MXR/BCRP/ABCP function and that mutation of a single amino acid residue significantly changes substrate specificity, thus altering the drug resistance phenotype. (aacrjournals.org)
  • Binding sites that have been designed to interact quite strongly with specific substrates are unlikely to bind nonspecifically to other substrates. (uu.nl)
  • Kinetic characterization with both aldehydes and the in vivo primary substrate acetaldehyde also enabled to correlate the alterations in substrate affinity with the different amino acid substitutions. (diva-portal.org)
  • Vascular peroxidase 1 catalyzes the formation of hypohalous acids: characterization of its substrate specificity and enzymatic properties. (biomedsearch.com)
  • Molecular Characterization and Substrate Specificity of Nitrobenzene Dioxygenase from Comamonas sp. (asm.org)
  • Surprisingly, of the remaining peptides, 67 % were farnesylated under single-turnover conditions, suggesting that there are two classes of substrates for FTase with distinct reactivity profiles. (sigmaaldrich.com)
  • Analysis of the sequence preferences for these two classes of substrates illustrates a significant difference in FTase selectivity for the multiple- and single-turnover substrates, with the multiple-turnover substrates adhering closely to the current Ca 1 a 2 X model for FTase selectivity while the singleturnover substrates show distinct sequence preferences. (sigmaaldrich.com)
  • Neuronal palmitoyl acyl transferases exhibit distinct substrate specificity. (semanticscholar.org)
  • Human paraoxonases (PON1, PON2, and PON3) are lactonases with overlapping and distinct substrate specificities. (semanticscholar.org)
  • We have previously speculated that this architecture might enable the Firmicutes BY-kinases to interact with alternative activators, and thus account for the observed ability of these kinases to phosphorylate several distinct classes of protein substrates. (frontiersin.org)
  • The relatively low degree of sequence restriction at the site of phosphorylation suggests that Dbf2 achieves specificity by docking its substrates at a site that is distinct from the phosphorylation site. (caltech.edu)
  • The target of rapamycin (TOR) protein kinase forms multi-subunit TOR complex 1 (TORC1) and TOR complex 2 (TORC2), which exhibit distinct substrate specificities. (elifesciences.org)
  • G262V, S121G, F218Y, and F218I improve conversion of type I substrates, whereas G262A and IMP-1 improve conversion of type II substrates, indicating two distinct evolutionary adaptations from IMP-6. (caltech.edu)
  • Although these substrates resemble each other structurally, they are transported by distinct coupling mechanisms. (embopress.org)
  • Mutations affecting substrate specificity of the Bacillus subtilis multidrug transporter Bmr. (asm.org)
  • The X-ray structure of N-methyltryptophan oxidase reveals the structural determinants of substrate specificity. (uniprot.org)
  • The analysis of the substrate binding site highlights the structural determinants that favour the accommodation of the bulky N-methyltryptophan residue in MTOX. (uniprot.org)
  • Nevertheless, the enzyme's high thermostability and broad acceptor specificity makes it a valuable candidate for industrial disaccharide synthesis. (ugent.be)
  • As the size of the ('3)H-oligosaccharide acceptor increases, the maximum velocity of the enzyme increases for chondroitin-6-sulfate and chondroitin substrates. (illinois.edu)
  • The contributions of side chains that provide key interactions with the acceptor substrate, defining its specificity, have also been quantitated. (ubc.ca)
  • Critical issues examined include the function of water molecules in providing strength and specificity of binding, the extent to which binding subsites are interdependent, and the roles of polypeptide chain flexibility and distal structural elements in contributing to specificity profiles. (nih.gov)
  • Porcine liver carboxylesterase 1 specificity for amino acid esters of three nucleoside analogs [floxuridine, gemcitabine, and 2-bromo-5,6-dichloro-1-(β- d -ribofuranosyl) benzimidazole] was evaluated to assess optimal structural preferences for prodrug design. (aspetjournals.org)
  • The mechanisms of intramembrane proteases are incompletely understood due to the lack of structural data on substrate complexes. (embopress.org)
  • Kinetic analyses of mutants of ST3Gal-I, in conjunction with structural studies, have confirmed the mechanistic roles of His302 and His319 as general acid and base catalysts, respectively, and have quantitated other interactions with the cytosine monophosphate-N-acetyl beta-neuraminic acid donor substrate. (ubc.ca)
  • Here, we show that the closely related cytochrome c peroxidase enzyme can duplicate the substrate binding properties of ascorbate peroxidase through the introduction of relatively modest structural changes at Tyr36 and Asn184. (le.ac.uk)
  • The enzyme oxidizes a wide range of substrates, and relative reaction rates with partially purified Oxygenase NBZ revealed a preference for 3-nitrotoluene, which was shown to be a growth substrate for JS765. (asm.org)
  • In addition, we have extended preliminary studies that showed that NBDO can oxidize a wide range of substrates ( 18 ). (asm.org)
  • The betaine-choline-carnitine (BCC) transporter family comprises secondary carriers that facilitate the transport of a wide range of substrates that bear trimethylammonium groups ([‐N + (CH 3 ) 3 ]), such as betaine, choline, l ‐carnitine and γ‐butyrobetaine ( Ziegler et al , 2010 ). (embopress.org)
  • It will also efficiently ligate many undesirable structures, including substrates containing gaps of one or more nucleotides and nicked substrates that contain DNA base pair mismatches (12-15). (neb.com)
  • Moreover, a single amino acid substitution enlarged the active-site cavity enough to accommodate the larger farnesyl pyrophosphate substrate and led to the efficient synthesis of sesquiterpenes, while alternate single substitutions of this critical amino acid yielded five additional terpene synthases. (plantcell.org)
  • Studies of the substrate specificity, enzyme-substrate interactions, and the function of lipid. (semanticscholar.org)
  • Our results suggest that the respective interactions of SalA and TkmA with PtkA favor phosphorylation of different protein substrates in vivo and in vitro . (frontiersin.org)
  • These results were rationalized based on the enzyme-substrate interactions observed in a homology model with a docked ligand. (ugent.be)
  • By exploiting the fact that the conformational stabilization of a protein is altered upon ligand binding due to specific interactions, and using an array of selectively chosen ligand analogs, one can quantify the contribution individual interactions have on specificity. (diva-portal.org)
  • In contrast, the absence of these stabilizing interactions with type II substrates may result in poor conversion. (caltech.edu)
  • The substrate specificity was investigated in detail by measuring the relative activity on a range of alternative acceptors, applied in the reverse synthetic reaction, and determination of the kinetic parameters for the best acceptors. (ugent.be)
  • Substrate specificity of Ca(2+)/calmodulin-dependent protein kinase phosphatase: kinetic studies using synthetic phosphopeptides as model substrates. (semanticscholar.org)
  • In doing so, we define the role of induced-fit in nucleotide specificity and mismatch discrimination. (utexas.edu)
  • Computer graphic analysis suggested that these substitutions would differentially affect arginine and lysine substrate binding of the enzyme. (nih.gov)
  • The novel human protein arginine N-methyltransferase PRMT6 is a nuclear enzyme displaying unique substrate specificity. (semanticscholar.org)
  • In most cases the results show flexibility in the P4 position, very high specificity for arginine in the P3 position and glycine in the P2 position, in accord with the sequence of the natural substrate, ubiquitin. (portlandpress.com)
  • Moreover, besides the effect of substrate entrance on its own, we strongly suggest that a highly conserved arginine residue (in the RDP motif) rather than the previously proposed Tyr motif (not conserved) provides the proton to increase the pKa of the acid-base catalyst. (kuleuven.be)
  • Here, we present the development of a screening assay for the substrate specificity of para -phenol oxidases based on the detection of hydrogen peroxide using the ferric-xylenol orange complex method. (mdpi.com)
  • The assay was used to screen the activity of VAO and EUGO towards a set of twenty-four potential substrates. (mdpi.com)
  • The state of art high throughput assay approaches like mass spectrometry-based proteomics are able to monitor the changing of substrates or products during the course of this type of complex enzymatic reactions. (mcponline.org)
  • In the present study, site-directed mutagenesis of both native and mutated ADH1 genes was performed in order to identify the key amino acids involved in this substrate shift, resulting in Adh1p-variants with different substrate specificities. (diva-portal.org)
  • Overall, the results presented in this work indicate that in addition to the P1 and P1′ positions, additional amino acids within a six-residue window (between P4 and P2′) contribute to the binding of substrate polypeptides to the OmpT binding site. (asm.org)
  • The result is a polymerase that is kinetically indistinguishable from the wild-type enzyme, but provides a signal to monitor changes in enzyme structure that result from conformational changes induced by substrate binding. (utexas.edu)
  • Super-reactive' substrate sequences were engineered, with more than a 2-fold increase in activity, by combining the best residue choices at P5 to P3 positions. (hkmj.org)
  • This change in specificity occurs even though residue 262 is remote from the active site. (caltech.edu)
  • We investigated the substrate specificities of five other point mutants resulting from single-nucleotide substitutions at positions near residue 262: G262A, G262V, S121G, F218Y, and F218I. (caltech.edu)
  • The full spectrum of this substrate specificity, however, has not been clarified using standard sequence analysis algorithms, e.g., the position-specific scoring-matrix method. (nih.gov)
  • The components of MEN that act upstream of Dbf2-Mob1 have been characterized, but physiological substrates for Dbf2-Mob1 have yet to be identified. (caltech.edu)
  • The d-myo-inositol in the physiological substrate was successfully replaced by cyclohexanediol and is still a substrate for T. brucei GlcNAc-PI de-N-acetylase. (lancs.ac.uk)
  • This improved understanding of EaDAcT specificity confirms that the enzyme preferentially utilizes acetyl-CoA to acetylate sn-1,2-DAGs and will be helpful in engineering the production of acetyl-TAG with improved functionality in transgenic plants. (k-state.edu)
  • Herein, we demonstrate that the microenvironment from which Ras signals emanate determines which substrates will be preferentially phosphorylated by the activated ERK1/2. (hud.ac.uk)
  • Probing the substrate specificity of Trypanosom. (lancs.ac.uk)
  • Alteration of a single amino acid changes the substrate specificity of dihydroflavonol 4-reductase. (semanticscholar.org)