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Substrate Selectivity (substrate + selectivity)
Selected AbstractsAssessing the Substrate Selectivities and Enantioselectivities of Eight Novel Baeyer,Villiger Monooxygenases Toward Alkyl-Substituted Cyclohexanones.CHEMINFORM, Issue 17 2004Brian G. Kyte No abstract is available for this article. [source] One-Armed Artificial Receptors for the Binding of Polar Tetrapeptides in Water: Probing the Substrate Selectivity of a Combinatorial Receptor LibraryCHEMISTRY - A EUROPEAN JOURNAL, Issue 5 2006Carsten Schmuck Prof. Dr. Abstract We have recently developed a new class of one-armed artificial receptors 1 for the binding of the polar tetrapeptide N -Ac- D -Glu- L -Lys- D -Ala- D -Ala-OH (EKAA) 2 in water using a combined combinatorial and statistical approach. We have now further probed the substrate selectivity of this receptor library 1 by screening a second tetrapeptide substrate (3) with the inverse sequence N -Ac- D -Ala- D -Ala- L -Lys- D -Glu-OH (AAKE). This "inverse" substrate is also efficiently bound by our receptors, with Kass ,6000,m,1 for the best receptors, as determined both by a quantitative on-bead binding assay and by UV and fluorescence titration studies in free solution. Hence, the inverse tetrapeptide 3 is in general bound two to three times less efficiently than the "normal" peptide 2 (Kass ,17,000,m,1), even though the complexation mainly involves long-range electrostatic interactions and both the receptor and substrate are rather flexible. Molecular modeling and ab initio calculations have been used to rationalize the observed substrate selectivity and to analyze the various binding interactions within the complex. [source] Proprotein convertase genes in Xenopus developmentDEVELOPMENTAL DYNAMICS, Issue 3 2005Sylvia Nelsen Abstract Proprotein convertases (PCs) are a family of serine endoproteases that proteolytically activate many precursor proteins within various secretory pathway compartments. Loss-of-function studies have demonstrated a critical role for these proteases in embryonic patterning and adult homeostasis, yet little is known about how substrate selectivity is achieved. We have identified Xenopus orthologs of three PCs: furin, PC6, and PC4. In addition to previously described isoforms of PC6 and furin, four novel splice isoforms of PC6, which are predicted to encode constitutively secreted proteases, and a putative transmembrane isoform of PC4 were identified. Furin and PC6 are expressed in dynamic, tissue-specific patterns throughout embryogenesis, whereas PC4 transcripts are restricted primarily to germ cells and brain in adult frogs. Developmental Dynamics 233:1038,1044, 2005. © 2005 Wiley-Liss, Inc. [source] Novel and Efficient Chemoenzymatic Synthesis of D -Glucose 6-Phosphate and Molecular Modeling Studies on the Selective BiocatalysisEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 17 2007Tatiana Rodríguez-Pérez Abstract A concise chemoenzymatic synthesis of glucose 6-phosphate is described. Candida rugosa lipase was found to be an efficient catalyst for both regio- and stereoselective deacetylation of the primary hydroxy group in the peracetylated D -glucose. In addition, we report an improved synthesis of 1,2,3,4,6-penta- O -acetyl-,- D -glucopyranose providing a large-scale procedure for the acetylation of ,- D -glucose without isomerization at the anomeric center. The high overall yield and the easy scalability makes this chemoenzymatic strategy attractive for industrial application. Furthermore, molecular modeling of phosphonate transition-state analog for the enzymatic hydrolysis step supports the substrate selectivity observed with Candida rugosa lipase.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] Donor and acceptor substrate selectivity among plant glycoside hydrolase family 32 enzymesFEBS JOURNAL, Issue 20 2009Wim Van den Ende Plant family 32 glycoside hydrolase enzymes include hydrolases (cell wall invertases, fructan exohydrolases, vacuolar invertases) and fructosyltransferases. These enzymes are very similar at the molecular and structural levels but are functionally different. Understanding the basis of the functional diversity in this family is a challenging task. By combining structural and site-directed mutagenesis data, Asp239 in AtcwINV1 was identified as an amino acid critical for binding and stabilizing sucrose. Plant fructan exohydrolases lack such an Asp239 equivalent. Substitution of Asp239 led to the loss of invertase activity, while its introduction in fructan exohydrolases increased invertase activity. Some fructan exohydrolases are inhibited by sucrose. The difference between the inhibitor (fructan exohydrolase) and the substrate (invertase) binding configurations of sucrose can be explained by the different orientation of Trp82. Furthermore, the evolutionary hydrolase/transferase transition could be mimicked and the difference between S-type fructosyltransferases (sucrose as donor) and F-type fructosyltransferases (fructan as donor) could be unravelled. [source] Combined use of selective inhibitors and fluorogenic substrates to study the specificity of somatic wild-type angiotensin-converting enzymeFEBS JOURNAL, Issue 8 2006Nicolas D. Jullien Somatic angiotensin-converting enzyme (ACE) contains two homologous domains, each bearing a functional active site. Studies on the selectivity of these ACE domains towards either substrates or inhibitors have mostly relied on the use of mutants or isolated domains of ACE. To determine directly the selectivity properties of each ACE domain, working with wild-type enzyme, we developed an approach based on the combined use of N-domain-selective and C-domain-selective ACE inhibitors and fluorogenic substrates. With this approach, marked differences in substrate selectivity were revealed between rat, mouse and human somatic ACE. In particular, the fluorogenic substrate Mca-Ala-Ser-Asp-Lys-DpaOH was shown to be a strict N-domain-selective substrate of mouse ACE, whereas with rat ACE it displayed marked C-domain selectivity. Similar differences in selectivity between these ACE species were also observed with a new fluorogenic substrate of ACE, Mca-Arg-Pro-Pro-Gly-Phe-Ser-Pro-DpaOH. In support of these results, changes in amino-acid composition in the binding site of these three ACE species were pinpointed. Together these data demonstrate that the substrate selectivity of the N-domain and C-domain depends on the ACE species. These results raise concerns about the interpretation of functional studies performed in animals using N-domain and C-domain substrate selectivity data derived only from human ACE. [source] Inhibition of the D -alanine:D -alanyl carrier protein ligase from Bacillus subtilis increases the bacterium's susceptibility to antibiotics that target the cell wallFEBS JOURNAL, Issue 12 2005Juergen J. May The surface charge as well as the electrochemical properties and ligand binding abilities of the Gram-positive cell wall is controlled by the d -alanylation of the lipoteichoic acid. The incorporation of d -Ala into lipoteichoic acid requires the d -alanine:d -alanyl carrier protein ligase (DltA) and the carrier protein (DltC). We have heterologously expressed, purified, and assayed the substrate selectivity of the recombinant proteins DltA with its substrate DltC. We found that apo-DltC is recognized by both endogenous 4,-phosphopantetheinyl transferases AcpS and Sfp. After the biochemical characterization of DltA and DltC, we designed an inhibitor (d -alanylacyl-sulfamoyl-adenosine), which is able to block the d -Ala adenylation by DltA at a Ki value of 232 nmin vitro. We also performed in vivo studies and determined a significant inhibition of growth for different Bacillus subtilis strains when the inhibitor is used in combination with vancomycin. [source] A Highly Selective, Polymer-Supported Organocatalyst for Michael Additions with Enzyme-Like BehaviorADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 18 2009Esther Alza Abstract A polymer-supported ,,,-diarylprolinol silyl ether displays catalytic activity and enantioselectivity comparable to the best homogeneous catalysts in the Michael addition of aldehydes to nitroolefins. Above all, the combination of polymer backbone, triazole linker, and catalytic unit confers to it an unprecedented substrate selectivity in favor of linear, short-chain aldehydes. [source] Key Issues Concerning Biolog Use for Aerobic and Anaerobic Freshwater Bacterial Community-Level Physiological ProfilingINTERNATIONAL REVIEW OF HYDROBIOLOGY, Issue 3 2006Bradley W. Christian Abstract Bacterial heterotrophy in aquatic ecosystems is important in the overall carbon cycle. Biolog MicroPlates provide information into the metabolic potential of bacteria involved in carbon cycling. Specifically, Biolog EcoPlatesÔ were developed with ecologically relevant carbon substrates to allow investigators to measure carbon substrate utilization patterns and develop community-level physiological profiles from natural bacterial assemblages. However, understanding of the functionality of these plates in freshwater research is limited. We explored several issues of EcoPlate use for freshwater bacterial assemblages including inoculum density, incubation temperature, non-bacterial color development, and substrate selectivity. Each of these has various effects on plate interpretation. We offer suggestions and techniques to resolve these interpretation issues. Lastly we propose a technique to allow EcoPlate use in anaerobic freshwater bacterial studies. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Catalytic mechanism and substrate selectivity of aldo-keto reductases: Insights from structure-function studies of Candida tenuis xylose reductaseIUBMB LIFE, Issue 9 2006Regina Kratzer Abstract Aldo-keto reductases (AKRs) constitute a large protein superfamily of mainly NAD(P)-dependent oxidoreductases involved in carbonyl metabolism. Catalysis is promoted by a conserved tetrad of active site residues (Tyr, Lys, Asp and His). Recent results of structure-function relationship studies for xylose reductase (AKR2B5) require an update of the proposed catalytic mechanism. Electrostatic stabilization by the ,-NH3+ group of Lys is a key source of catalytic power of xylose reductase. A molecular-level analysis of the substrate binding pocket of xylose reductase provides a case of how a very broadly specific AKR achieves the requisite selectivity for its physiological substrate and could serve as the basis for the design of novel reductases with improved specificities for biocatalytic applications. iubmb Life, 58: 499-507, 2006 [source] The ubiquitin ligase ability of IAPs regulates apoptosisIUBMB LIFE, Issue 12 2005Ting Ni Abstract Accumulating evidence indicates that there is a critical role of the ubiquitin/proteasome pathway in the regulation of apoptosis. Among the important molecules that couple these two fundamental cellular activities are members of the inhibitor of apoptosis (IAP) protein family. In addition to their well-studied ability to directly bind and inhibit caspases, many IAPs contain RING domains that are necessary and sufficient to cause ubiquitylation and subsequent proteasome-mediated proteolysis. This review summarizes recent findings about the ubiquitin protein ligase activity of IAPs, and considers possible mechanisms for substrate selectivity. [source] Ligand effects upon deuterium exchange in arenes mediated by [Ir(PR3)2(cod)]+.BF4,JOURNAL OF LABELLED COMPOUNDS AND RADIOPHARMACEUTICALS, Issue 1 2004George J. Ellames Abstract A series of complexes of general form [Ir(PR3)2(cod)]+ has been prepared and used, without isolation, to mediate deuteration of a range of model substrates. The data suggest that, with many substrates, basicity of the phosphine ligands bound to iridium is an important factor influencing substrate selectivity and the efficiency of deuteration. In addition, the spectrum of activity of iridium complexes bearing pure donor ligands is different in many cases to that of complexes where the ligands are known to be ,-acids. Copyright © 2003 John Wiley & Sons, Ltd. [source] Biochemical aspects of the neuroprotective mechanism of PTEN-induced kinase-1 (PINK1)JOURNAL OF NEUROCHEMISTRY, Issue 1 2008Ryan D. Mills Abstract Mutations in PTEN-induced kinase 1 (PINK1) gene cause PARK6 familial Parkinsonism. To decipher the role of PINK1 in pathogenesis of Parkinson's disease (PD), researchers need to identify protein substrates of PINK1 kinase activity that govern neuronal survival, and establish whether aberrant regulation and inactivation of PINK1 contribute to both familial Parkinsonism and idiopathic PD. These studies should take into account the several unique structural and functional features of PINK1. First PINK1 is a rare example of a protein kinase with a predicted mitochondrial-targeting sequence and a possible resident mitochondrial function. Second, bioinformatic analysis reveals unique insert regions within the kinase domain that are potentially involved in regulation of kinase activity, substrate selectivity and stability of PINK1. Third, the C-terminal region contains functional motifs governing kinase activity and substrate selectivity. Fourth, accumulating evidence suggests that PINK1 interacts with other signaling proteins implicated in PD pathogenesis and mitochondrial dysfunction. The most prominent examples are the E3 ubiquitin ligase Parkin, the mitochondrial protease high temperature requirement serine protease 2 and the mitochondrial chaperone tumor necrosis factor receptor-associated protein 1. How PINK1 may regulate these proteins to maintain neuronal survival is unclear. This review describes the unique structural features of PINK1 and their possible roles in governing mitochondrial import, processing, kinase activity, substrate selectivity and stability of PINK1. Based upon the findings of previous studies of PINK1 function in cell lines and animal models, we propose a model on the neuroprotective mechanism of PINK1. This model may serve as a conceptual framework for future investigation into the molecular basis of PD pathogenesis. [source] Insights into the anthrax lethal factor,substrate interaction and selectivity using docking and molecular dynamics simulationsPROTEIN SCIENCE, Issue 8 2009Georgios A. Dalkas Abstract The anthrax toxin of the bacterium Bacillus anthracis consists of three distinct proteins, one of which is the anthrax lethal factor (LF). LF is a gluzincin Zn-dependent, highly specific metalloprotease with a molecular mass of ,90 kDa that cleaves most isoforms of the family of mitogen-activated protein kinase kinases (MEKs/MKKs) close to their amino termini, resulting in the inhibition of one or more signaling pathways. Previous studies on the crystal structures of uncomplexed LF and LF complexed with the substrate MEK2 or a MKK-based synthetic peptide provided structure-activity correlations and the basis for the rational design of efficient inhibitors. However, in the crystallographic structures, the substrate peptide was not properly oriented in the active site because of the absence of the catalytic zinc atom. In the current study, docking and molecular dynamics calculations were employed to examine the LF-MEK/MKK interaction along the catalytic channel up to a distance of 20 Ĺ from the zinc atom. This residue-specific view of the enzyme-substrate interaction provides valuable information about: (i) the substrate selectivity of LF and its inactivation of MEKs/MKKs (an issue highly important not only to anthrax infection but also to the pathogenesis of cancer), and (ii) the discovery of new, previously unexploited, hot-spots of the LF catalytic channel that are important in the enzyme/substrate binding and interaction. [source] The 1.9,Ĺ structure of the branched-chain amino-acid transaminase (IlvE) from Mycobacterium tuberculosisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2009L. W. Tremblay Unlike mammals, bacteria encode enzymes that synthesize branched-chain amino acids. The pyridoxal 5,-phosphate-dependent transaminase performs the final biosynthetic step in these pathways, converting keto acid precursors into ,-amino acids. The branched-chain amino-acid transaminase from Mycobacterium tuberculosis (MtIlvE) has been crystallized and its structure has been solved at 1.9,Ĺ resolution. The MtIlvE monomer is composed of two domains that interact to form the active site. The biologically active form of IlvE is a homodimer in which each monomer contributes a substrate-specificity loop to the partner molecule. Additional substrate selectivity may be imparted by a conserved N-terminal Phe30 residue, which has previously been observed to shield the active site in the type IV fold homodimer. The active site of MtIlvE contains density corresponding to bound PMP, which is likely to be a consequence of the presence of tryptone in the crystallization medium. Additionally, two cysteine residues are positioned at the dimer interface for disulfide-bond formation under oxidative conditions. It is unknown whether they are involved in any regulatory activities analogous to those of the human mitochondrial branched-chain amino-acid transaminase. [source] Deciphering interactions of the aminoglycoside phosphotransferase(3,)-IIIa with its ligandsBIOPOLYMERS, Issue 9 2009Lingzhi Wu Abstract Aminoglycoside phosphotransferase(3,)-IIIa (APH) is the enzyme with broadest substrate range among the phosphotransferases that cause resistance to aminoglycoside antibiotics. In this study, the thermodynamic characterization of interactions of APH with its ligands are done by determining dissociation constants of enzyme,substrate complexes using electron paramagnetic resonance and fluorescence spectroscopy. Metal binding studies showed that three divalent cations bind to the apo-enzyme with low affinity. In the presence of AMPPCP, binding of the divalent cations occurs with 7-to-37-fold higher affinity to three additional sites dependent on the presence and absence of different aminoglycosides. Surprisingly, when both ligands, AMPPCP and aminoglycoside, are present, the number of high affinity metal binding sites is reduced to two with a 2-fold increase in binding affinity. The presence of divalent cations, with or without aminoglycoside present, shows only a small effect (<3-fold) on binding affinity of the nucleotide to the enzyme. The presence of metal,nucleotide, but not nucleotide alone, increases the binding affinity of aminoglycosides to APH. Replacement of magnesium (II) with manganese (II) lowered the catalytic rates significantly while affecting the substrate selectivity of the enzyme such that the aminoglycosides with 2,-NH2 become better substrates (higher Vmax) than those with 2,-OH. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 801,809, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] A thermostable triple mutant of pyranose 2-oxidase from Trametes multicolor with improved properties for biotechnological applicationsBIOTECHNOLOGY JOURNAL, Issue 4 2009Oliver Spadiut Abstract In order to increase the thermal stability and the catalytic properties of pyranose oxidase (P2Ox) from Trametes multicolor toward its poor substrate D-galactose and the alternative electron acceptor 1,4-benzoquinone (1,4-BQ), we designed the triple-mutant T169G/E542K/V546C. Whereas the wild-type enzyme clearly favors D-glucose as its substrate over D-galactose [substrate selectivity (kcat/KM)Glc/(kcat/KM)Gal = 172], the variant oxidizes both sugars equally well [(kcat/KM)Glc/(kcat/KM)Gal = 0.69], which is of interest for food biotechnology. Furthermore, the variant showed lower KM values and approximately ten-fold higher kcat values for 1,4-BQ when D-galactose was used as the saturating sugar substrate, which makes this enzyme particularly attractive for use in biofuel cells and enzyme-based biosensors. In addition to the altered substrate specificity and reactivity, this mutant also shows significantly improved thermal stability. The half life time at 60°C was approximately 10 h, compared to 7.6 min for the wild-type enzyme. We performed successfully small-scale bioreactor pilot conversion experiments of D -glucose/D -galactose mixtures at both 30 and 50°C, showing the usefulness of this P2Ox variant in biocatalysis as well as the enhanced thermal stability of the enzyme. Moreover, we determined the crystal structure of the mutant in its unligated form at 1.55 Ĺ resolution. Modeling D-galactose in position for oxidation at C2 into the mutant active site shows that substituting Thr for Gly at position 169 favorably accommodates the axial C4 hydroxyl group that would otherwise clash with Thr169 in the wild-type. [source] Endo- and exo-inulinases: Enzyme-substrate interaction and rational immobilizationBIOTECHNOLOGY PROGRESS, Issue 2 2010Alessandra Basso Abstract Three-dimensional models of exoinulinase from Bacillus stearothermophilus and endoinulinase from Aspergillus niger were built up by means of homology modeling. The crystal structure of exoinulinase from Aspergillus awamori was used as a template, which is the sole structure of inulinase resolved so far. Docking and molecular dynamics simulations were performed to investigate the differences between the two inulinases in terms of substrate selectivity. The analysis of the structural differences between the two inulinases provided the basis for the explanation of their different regio-selectivity and for the understanding of enzyme-substrate interactions. Surface analysis was performed to point out structural features that can affect the efficiency of enzymes also after immobilization. The computational analysis of the three-dimensional models proved to be an effective tool for acquiring information and allowed to formulate an optimal immobilized biocatalyst even more active that the native one, thus enabling the full exploitation of the catalytic potential of these enzymes. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010 [source] One-Armed Artificial Receptors for the Binding of Polar Tetrapeptides in Water: Probing the Substrate Selectivity of a Combinatorial Receptor LibraryCHEMISTRY - A EUROPEAN JOURNAL, Issue 5 2006Carsten Schmuck Prof. Dr. Abstract We have recently developed a new class of one-armed artificial receptors 1 for the binding of the polar tetrapeptide N -Ac- D -Glu- L -Lys- D -Ala- D -Ala-OH (EKAA) 2 in water using a combined combinatorial and statistical approach. We have now further probed the substrate selectivity of this receptor library 1 by screening a second tetrapeptide substrate (3) with the inverse sequence N -Ac- D -Ala- D -Ala- L -Lys- D -Glu-OH (AAKE). This "inverse" substrate is also efficiently bound by our receptors, with Kass ,6000,m,1 for the best receptors, as determined both by a quantitative on-bead binding assay and by UV and fluorescence titration studies in free solution. Hence, the inverse tetrapeptide 3 is in general bound two to three times less efficiently than the "normal" peptide 2 (Kass ,17,000,m,1), even though the complexation mainly involves long-range electrostatic interactions and both the receptor and substrate are rather flexible. Molecular modeling and ab initio calculations have been used to rationalize the observed substrate selectivity and to analyze the various binding interactions within the complex. [source] Structure,Activity Relationships of SSAO/VAP-1 Arylalkylamine-Based SubstratesCHEMMEDCHEM, Issue 4 2009Francesc Yraola Dr. Abstract SSAO/VAP-1 substrates may be valuable for the treatment or prevention of diabetes mellitus, as they show insulin-mimetic properties. This review highlights the importance of studying the relevant steric and electronic features in the development of new ligands with better SSAO/VAP-1 recognition, enhanced selectivity over other amine oxidases, and improved metabolic behavior. Semicarbazide-sensitive amine oxidase/vascular adhesion protein-1 (SSAO/VAP-1) substrates show insulin-mimetic effects and are therefore potentially valuable molecules for the treatment of diabetes mellitus. Herein we review several structural and electronic aspects of SSAO arylalkylamine-based substrates. Two main modifications directly affect amine oxidase (AO) activity: 1),variation in ring substitution modulates the biological activity of the arylalkylamine ligand by converting a substrate into a substrate-like inhibitor, and 2),variation in the number of methylene units between the aromatic ring and the ammonium groups of the arylalkylamine substrates dramatically alters the oxidation rate between species. Furthermore, we review relevant information about mammalian SSAO/VAP-1 substrate selectivity and specificity over monoamine oxidases (MAOs). [source] |