Home About us Contact
|
Home About us Contact | ||
|
|
||
Metal Binding Site (metal + binding_site)
Selected AbstractsNew 4,-Functionalized 2,2,:6,,2,,-Terpyridines for Applications in Macromolecular Chemistry and NanoscienceEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 19 2003Philip R. Andres Abstract The well-known reaction of 4,-chloro-2,2,:6,,2,,-terpyridine with alkoxide nucleophiles leads to 4,-functionalized 2,2,:6,,2,,-terpyridines. This reaction allows the easy introduction of different functional groups onto the terpyridine at the 4,-position, i.e. opposite to the metal binding site, in one reaction step. Among the functionalized 2,2,:6,,2,,-terpyridines reported here are amines (including chiral examples), carboxylic acids, simple alkoxy-chain terpyridines with different chain lengths, and a stilbene-functionalized terpyridine. Moreover, the synthesis of two important already known substances was significantly improved. One example of a sequential functionalization of the (aminopentoxy)terpyridine with a dithiolane functionality is also reported. For two of the alkyl-chain-functionalized terpyridines, single-crystal X-ray crystallographic data were obtained. Finally, ordered monolayers of alkyl-substituted terpyridines on HOPG were visualized using STM. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Modeling dioxygen binding to the non-heme iron-containing enzymesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2006A. V. Nemukhin Abstract The structures and properties of the complexes formed upon binding the oxygen molecule to the iron sites in non-heme 2-oxoglutarate-dependent enzymes are characterized by QM(CASSCF)/MM and density functional theory (DFT) calculations. Molecular models for the calculations are constructed following the crystal structure of hypoxia-inducible factor asparaginyl hydroxylase (FIH-1). DFT calculations for the 37-atomic cluster have been carried out at the B3LYP(LANL2DZdp) level. The flexible effective fragment potential method is used as a combined quantum mechanical,molecular mechanical (QM/MM) technique to characterize the fragment of the enzymatic system, including 1,758 atoms in the MM part and 27 atoms in the QM part. In these calculations, the CASSCF(LANL2DZdp) approach is applied in the QM subsystem, and AMBER force field parameters are used in the MM subsystem. With both approaches, equilibrium geometry configurations have been located for different spin states of the system. In DFT calculations, the order of the states is as follows: septet, triplet (+7.7 kcal/mol), quintet (+10.7 kcal/mol). Geometry configurations correspond to the end-on structures with no evidences of electron transfer from Fe(II) to molecular oxygen. In contrast, QM(CASSCF)/MM calculations predict the quintet state as the lowest one, while the septet structure has slightly (<2 kcal/mol) higher energy, and the triplet state is considerably more energetic. In QM/MM calculations, in both quintet and septet states, the electronic configurations show considerable electron charge transfer from iron to oxygen, and the oxidation state of iron in the metal binding site can be characterized as Fe(III). © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Efficient recognition of protein fold at low sequence identity by conservative application of Psi-BLAST: application,JOURNAL OF MOLECULAR RECOGNITION, Issue 2 2005F. J. Stevens Abstract Based on a study involving structural comparisons of proteins sharing 25% or less sequence identity, three rounds of Psi-BLAST appear capable of identifying remote evolutionary homologs with greater than 95% confidence provided that more than 50% of the query sequence can be aligned with the target sequence. Since it seems that more than 80% of all homologous protein pairs may be characterized by a lack of significant sequence similarity, the experimental biologist is often confronted with a lack of guidance from conventional homology searches involving pair-wise sequence comparisons. The ability to disregard levels of sequence identity and expect value in Psi-BLAST if at least 50% of the query sequence has been aligned allows for generation of new hypotheses by consideration of matches that are conventionally disregarded. In one example, we suggest a possible evolutionary linkage between the cupredoxin and immunoglobulin fold families. A thermostable hypothetical protein of unknown function may be a circularly permuted homolog to phosphotriesterase, an enzyme capable of detoxifying organophosphate nerve agents. In a third example, the amino acid sequence of another hypothetical protein of unknown function reveals the ATP binding-site, metal binding site, and catalytic sidechain consistent with kinase activity of unknown specificity. This approach significantly expands the utility of existing sequence data to define the primary structure degeneracy of binding sites for substrates, cofactors and other proteins. Copyright © 2004 John Wiley & Sons, Ltd. [source] Structural features of a zinc binding site in the superantigen strepococcal pyrogenic exotoxin A (SpeA1): Implications for MHC class II recognitionPROTEIN SCIENCE, Issue 6 2001Matthew Baker Abstract Streptococcal pyrogenic exotoxin A (SpeA) is produced by Streptococcus pyogenes, and has been associated with severe infections such as scarlet fever and Streptococcal Toxic Shock Syndrome (STSS). In this study, the crystal structure of SpeA1 (the product of speA allele 1) in the presence of 2.5 mM zinc was determined at 2.8 Å resolution. The protein crystallizes in the orthorhombic space group P21212, with four molecules in the crystallographic asymmetric unit. The final structure has a crystallographic R -factor of 21.4% for 7,031 protein atoms, 143 water molecules, and 4 zinc atoms (one zinc atom per molecule). Four protein ligands,Glu 33, Asp 77, His 106, and His 110,form a zinc binding site that is similar to the one observed in a related superantigen, staphylococcoal enterotoxin C2. Mutant toxin forms substituting Ala for each of the zinc binding residues were generated. The affinity of these mutants for zinc ion confirms the composition of this metal binding site. The implications of zinc binding to SpeA1 for MHC class II recognition are explored using a molecular modeling approach. The results indicate that, despite their common overall architecture, superantigens appear to have multiple ways of complex formation with MHC class II molecules. [source] Structure of the endonuclease IV homologue from Thermotoga maritima in the presence of active-site divalent metal ionsACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2010Stephen J. Tomanicek The most frequent lesion in DNA is at apurinic/apyrimidinic (AP) sites resulting from DNA-base losses. These AP-site lesions can stall DNA replication and lead to genome instability if left unrepaired. The AP endonucleases are an important class of enzymes that are involved in the repair of AP-site intermediates during damage-general DNA base-excision repair pathways. These enzymes hydrolytically cleave the 5,-phosphodiester bond at an AP site to generate a free 3,-hydroxyl group and a 5,-terminal sugar phosphate using their AP nuclease activity. Specifically, Thermotoga maritima endonuclease IV is a member of the second conserved AP endonuclease family that includes Escherichia coli endonuclease IV, which is the archetype of the AP endonuclease superfamily. In order to more fully characterize the AP endonuclease family of enzymes, two X-ray crystal structures of the T. maritima endonuclease IV homologue were determined in the presence of divalent metal ions bound in the active-site region. These structures of the T. maritima endonuclease IV homologue further revealed the use of the TIM-barrel fold and the trinuclear metal binding site as important highly conserved structural elements that are involved in DNA-binding and AP-site repair processes in the AP endonuclease superfamily. [source] The effect of the side chain length of Asp and Glu on coordination structure of Cu2+ in a de novo designed proteinBIOPOLYMERS, Issue 11 2009Daigo Shiga Abstract Metal ions in proteins are important not only for the formation of the proper structures but also for various biological activities. For biological functions such as hydrolysis and oxidation, metal ions often adopt unusual coordination structures. We constructed a stable scaffold for metal binding to create distorted metal coordination structures. A stable four stranded ,-helical coiled-coil structure was used as the scaffold, and the metal binding site was in the cavity created at the center of the structure. Two His residues and one Asp or Glu residue were used to coordinate the metal ions, AM2D and AM2E, respectively. Cu2+ bound to AM2D with an equatorial planar coordination structure with two His, one Asp, and H2O as detected by electron spin resonance and UV spectral analyzes. On the other hand, Cu2+ had a slightly distorted square planar structure when it bound two His and Glu in AM2E, due to the longer side-chain of the Glu residue as compared to the Asp residue. Computational analysis also supported the distorted coordination structure of Cu2+ in AM2E. This construct should be useful to create various coordinations of metal ions for catalytic functions. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 907,916, 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] Design of a Functional Nitric Oxide Reductase within a Myoglobin ScaffoldCHEMBIOCHEM, Issue 8 2010Valentin Köhler Dr. One site fits all: Yi Lu and co-workers have reported the conversion of sperm-whale myoglobin into a functional nitric oxide reductase. For this purpose, they designed a second metal binding site in the wild-type holo-protein and demonstrated NO reduction with the structurally characterized model, making thereby a significant contribution to the rapidly developing field of artificial metalloenzymes. [source] Enantioselective Fluorescence Sensing of Amino Acids by Modified Cyclodextrins: Role of the Cavity and Sensing MechanismCHEMISTRY - A EUROPEAN JOURNAL, Issue 11 2004Sara Pagliari Dr. Abstract Two selectors based on modified cyclodextrins containing a metal binding site and a dansyl fluorophore,6-deoxy-6- N -(N, -[(5-dimethylamino-1-naphthalenesulfonyl)aminoethyl]phenylalanylamino-,-cyclodextrin,containing D -Phe (3) and L -Phe (4) moieties were synthesized. The conformations of the two selectors were studied by circular dichroism, two-dimensional NMR spectroscopy and time-resolved fluorescence spectroscopy. Cyclodextrin 4 was found to have a predominant conformation in which the dansyl group is self-included in the cyclodextrin cavity, while 3 showed a larger proportion of the conformation with the dansyl group outside the cavity. As a consequence, the two cyclodextrins were found to bind copper(II) with different affinities, as revealed by fluorescence quenching in competitive binding measurements. Addition of D - or L -amino acids induced increases in fluorescence intensity, which were dependent on the amino acid used and in some cases on its absolute configuration. The cyclodextrin 4 was found to be more enantioselective than 3, suggesting that the self-inclusion in the cyclodextrin cavity strongly increases the chiral discrimination ability of the copper(II) complex. Accordingly, a linear fluorescent ligand N, -[(5-dimethylamino-1-naphthalenesulfonyl)aminoethyl]- N1 -propyl-phenylalaninamide, which has the same binding site and absolute configuration as 4, showed very low chiral discrimination ability. The enantioselectivity in fluorescence response was found to be due to the formation of diastereomeric ternary complexes, which were detected by ESI-MS and by circular dichroism. Time-resolved fluorescence studies showed that the fluorescence of the dansyl group was completely quenched in the ternary complexes formed, and that the residual fluorescence was due to uncomplexed ligand. [source] Structural studies of human alkaline phosphatase in complex with strontium: Implication for its secondary effect in bonesPROTEIN SCIENCE, Issue 7 2006Paola Llinas Abstract Strontium is used in the treatment of osteoporosis as a ranelate compound, and in the treatment of painful scattered bone metastases as isotope. At very high doses and in certain conditions, it can lead to osteomalacia characterized by impairment of bone mineralization. The osteomalacia symptoms resemble those of hypophosphatasia, a rare inherited disorder associated with mutations in the gene encoding for tissue-nonspecific alkaline phosphatase (TNAP). Human alkaline phosphatases have four metal binding sites,two for zinc, one for magnesium, and one for calcium ion,that can be substituted by strontium. Here we present the crystal structure of strontium-substituted human placental alkaline phosphatase (PLAP), a related isozyme of TNAP, in which such replacement can have important physiological implications. The structure shows that strontium substitutes the calcium ion with concomitant modification of the metal coordination. The use of the flexible and polarizable force-field TCPEp (topological and classical polarization effects for proteins) predicts that calcium or strontium has similar interaction energies at the calcium-binding site of PLAP. Since calcium helps stabilize a large area that includes loops 210,228 and 250,297, its substitution by strontium could affect the stability of this region. Energy calculations suggest that only at high doses of strontium, comparable to those found for calcium, can strontium substitute for calcium. Since osteomalacia is observed after ingestion of high doses of strontium, alkaline phosphatase is likely to be one of the targets of strontium, and thus this enzyme might be involved in this disease. [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] | ||||||||||