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Catalytic Site (catalytic + site)
Selected AbstractsIncreased Efficacies of an Individual Catalytic Site in Clustered Multivalent Dendritic CatalystsADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 14-15 2009Govindasamy Jayamurugan Abstract In the studies reported so far on dendrimer-mediated catalysis, the efficacies of the catalytic units were studied and compared primarily across the generations. In order to identify the efficacy of an individual catalytic unit with respect to the number of such units present within a given generation, a series of catalysts were prepared within a generation. Dendrimers incorporated with phosphine-metal complexes were chosen for the study and as many as 11 catalysts within three generations were synthesized. The CC bond-forming reactions, namely, the Heck and the Suzuki coupling reactions, were then selected to study the catalytic efficiencies of the series of partially and fully phosphine-metal complex functionalized dendrimers. The efficacies of the formation of cinnamate and biphenyl, catalyzed by the dendritic catalysts, were compared. The comparative analyses show that an individual catalytic site is far more effective in its catalytic activity when presented in multiple numbers, i.e., in a multivalent dendritic system, than as a single unit within the same generation, i.e., in a monovalent dendritic system. The study identifies the beneficial effects of the multivalent presentation of the catalytic moieties, both within and across the dendrimer generations. [source] ChemInform Abstract: The Structure and Possible Catalytic Sites of Mo3S9 as a Model of Amorphous Molybdenum Trisulfide: A Computational Study.CHEMINFORM, Issue 45 2001Haijun Jiao Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Regulation of monomeric dynein activity by ATP and ADP concentrationsCYTOSKELETON, Issue 4 2001Katsuyuki Shiroguchi Abstract Axonemal dyneins are force-generating ATPases that produce ciliary and flagellar movement. A dynein has large heavy chain(s) in which there are multiple (4,6) ATP-binding consensus sequences (P-loops) as well as intermediate and light chains, constituting a very large complex. We purified a monomeric form of dynein (dynein- a) that has at least three light chains from 14S dyneins of Tetrahymena thermophila and characterized it. In in vitro motility assays, dynein- a rotated microtubules around their longitudinal axis as well as translocated them with their plus-ends leading. ATPase activity at 1 mM ATP was doubled in the presence of a low level of ADP (, 20 ,M). Both ATPase activity and translocational velocities in the presence of ADP (, 20 ,M) fit the Michaelis-Menten equation well. However, in the absence of ADP (< 0.1 ,M), neither of the activities followed the Michaelis-Menten-type kinetics, probably due to the effect of two ATP-binding sites. Our results also indicate that dynein- a has an ATP-binding site that is very sensitive to ADP and affects ATP hydrolysis at the catalytic site. This study shows that a monomeric form of a dynein molecule regulates its activity by direct binding of ATP and ADP to itself, and thus the dynein molecule has an intramolecular regulating system. Cell Motil. Cytoskeleton 49:189,199, 2001. © 2001 Wiley-Liss, Inc. [source] In the Search of Glycogen Phosphorylase Inhibitors: Synthesis of C- D -Glycopyranosylbenzo(hydro)quinones , Inhibition of and Binding to Glycogen Phosphorylase in the Crystal,EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 4 2007Li He Abstract Penta- O -acetyl-,- D -glycopyranoses and 1,4-dimethoxybenzene led selectively by electrophilic substitution to C-,- D -glycopyranosyl-1,4-dimethoxybenzenes which were converted by simple and efficient reactions (oxidation, reduction and deacetylation) to the corresponding C-glycosylhydro- and C-glycosylbenzoquinones, with either an acetylated or deprotected sugar moiety. C-,- D -Glucosylbenzoquinone 19 and C-,- D -Glucosylhydroquinone 23 were found to be competitive inhibitors of rabbit muscle glycogen phosphorylase b (GPb), with respect to the substrate ,- D -glucose-1-phosphate, with Ki values of 1.3 and 0.9 mM, respectively, whereas C-,- D -glucosylhydroquinone 17 was not effective up to a concentration of 8 mM. In order to elucidate the structural basis of inhibition, we determined the crystal structures of 19 and 23 in complex with GPb at a 2.03,2.05 Å resolution. The complex structures reveal that the inhibitors can be accommodated at the catalytic site at approximately the same position as ,- D -glucose and stabilise the transition state conformation of the 280s loop by making several favourable contacts to Asp283 and Asn284 of this loop. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] Stereoselective Hydrolysis of Quaternary Quinuclidinium Benzoates Catalyzed by ButyrylcholinesteraseEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 2 2003Ines Primoz Abstract Four chiral, quaternary, N -methyl and N -benzyl derivatives of (R)- and (S)-quinuclidin-3-yl benzoates were synthesized and studied as substrates of horse serum butyrylcholinesterase (BChE). The kcat for the substrates decreased in the order (R)- N -methyl > (R)- N -benzyl (2.3-fold slower) >> (S)- N -methyl (70.5-fold slower reaction), while for the (S)- N -benzyl ester inhibition of the enzyme was observed. The kinetics of inhibition (Ka = 3.3 ,M) indicated that binding to the catalytic site of BChE occurred. From the ratio of the kcat/KM values of both enantiomers an enantiomeric excess of 95% was calculated for N -methyl derivatives. Thus, BChE is suitable as a biocatalyst for the resolution of racemic quaternary quinuclidinium esters. In order to explain the experimental data, combined quantum chemical (HF/3,21G*) and semiempirical (PM3) calculations within the ONIOM scheme of the stable species in the acylation step were performed. Geometry optimizations were carried out for all benzoate esters for an assumed active site model of BChE. It was confirmed that hydrolysis is affected to an appreciable extent by a proper geometrical orientation of substrates at the choline subsite. The energies of the optimized systems were in good agreement with the experimental data. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] A mutagenic analysis of the RNase mechanism of the bacterial Kid toxin by mass spectrometryFEBS JOURNAL, Issue 17 2009Elizabeth Diago-Navarro Kid, the toxin of the parD (kis, kid) maintenance system of plasmid R1, is an endoribonuclease that preferentially cleaves RNA at the 5, of A in the core sequence 5,-UA(A/C)-3,. A model of the Kid toxin interacting with the uncleavable mimetic 5,-AdUACA-3, is available. To evaluate this model, a significant collection of mutants in some of the key residues proposed to be involved in RNA binding (T46, A55, T69 and R85) or RNA cleavage (R73, D75 and H17) were analysed by mass spectrometry in RNA binding and cleavage assays. A pair of substrates, 5,-AUACA-3,, and its uncleavable mimetic 5,-AdUACA-3,, used to establish the model and structure of the Kid,RNA complex, were used in both the RNA cleavage and binding assays. A second RNA substrate, 5,-UUACU-3, efficiently cleaved by Kid both in vivo and in vitro, was also used in the cleavage assays. Compared with the wild-type protein, mutations in the residues of the catalytic site abolished RNA cleavage without substantially altering RNA binding. Mutations in residues proposed to be involved in RNA binding show reduced binding efficiency and a corresponding decrease in RNA cleavage efficiency. The cleavage profiles of the different mutants were similar with the two substrates used, but RNA cleavage required much lower protein concentrations when the 5,-UUACU-3, substrate was used. Protein synthesis and growth assays are consistent with there being a correlation between the RNase activity of Kid and its inhibitory potential. These results give important support to the available models of Kid RNase and the Kid,RNA complex. [source] The Vps4 C-terminal helix is a critical determinant for assembly and ATPase activity and has elements conserved in other members of the meiotic clade of AAA ATPasesFEBS JOURNAL, Issue 7 2008Parimala R. Vajjhala Sorting of membrane proteins into intralumenal endosomal vesicles, multivesicular body (MVB) sorting, is critical for receptor down regulation, antigen presentation and enveloped virus budding. Vps4 is an AAA ATPase that functions in MVB sorting. Although AAA ATPases are oligomeric, mechanisms that govern Vps4 oligomerization and activity remain elusive. Vps4 has an N-terminal microtubule interacting and trafficking domain required for endosome recruitment, an AAA domain containing the ATPase catalytic site and a , domain, and a C-terminal , helix positioned close to the catalytic site in the 3D structure. Previous attempts to identify the role of the C-terminal helix have been unsuccessful. Here, we show that the C-terminal helix is important for Vps4 assembly and ATPase activity in vitro and function in vivo, but not endosome recruitment or interactions with Vta1 or ESCRT-III. Unlike the , domain, which is also important for Vps4 assembly, the C-terminal helix is not required in vivo for Vps4 homotypic interaction or dominant-negative effects of Vps4,E233Q, carrying a mutation in the ATP hydrolysis site. Vta1 promotes assembly of hybrid complexes comprising Vps4,E233Q and Vps4 lacking an intact C-terminal helix in vitro. Formation of catalytically active hybrid complexes demonstrates an intersubunit catalytic mechanism for Vps4. One end of the C-terminal helix lies in close proximity to the second region of homology (SRH), which is important for assembly and intersubunit catalysis in AAA ATPases. We propose that Vps4 SRH function requires an intact C-terminal helix. Co-evolution of a distinct Vps4 SRH and C-terminal helix in meiotic clade AAA ATPases supports this possibility. [source] Protein farnesyltransferase inhibitors interfere with farnesyl diphosphate binding by rubber transferaseFEBS JOURNAL, Issue 19 2003Christopher J. D. Mau Rubber transferase, a cis -prenyltransferase, catalyzes the addition of thousands of isopentenyl diphosphate (IPP) molecules to an allylic diphosphate initiator, such as farnesyl diphosphate (FPP, 1), in the presence of a divalent metal cofactor. In an effort to characterize the catalytic site of rubber transferase, the effects of two types of protein farnesyltransferase inhibitors, several chaetomellic acid A analogs (2, 4,7) and ,-hydroxyfarnesylphosphonic acid (3), on the ability of rubber transferase to add IPP to the allylic diphosphate initiator were determined. Both types of compounds inhibited the activity of rubber transferases from Hevea brasiliensis and Parthenium argentatum, but there were species,specific differences in the inhibition of rubber transferases by these compounds. Several shorter analogs of chaetomellic acid A did not inhibit rubber transferase activity, even though the analogs contained chemical features that are present in an elongating rubber molecule. These results indicate that the initiator-binding site in rubber transferase shares similar features to FPP binding sites in other enzymes. [source] Molecular modeling of the dimeric structure of human lipoprotein lipase and functional studies of the carboxyl-terminal domainFEBS JOURNAL, Issue 18 2002Yoko Kobayashi Lipoprotein lipase (LPL) plays a key role in lipid metabolism. Molecular modeling of dimeric LPL was carried out using insight ii based upon the crystal structures of human, porcine, and horse pancreatic lipase. The dimeric model reveals a saddle-shaped structure and the key heparin-binding residues in the amino-terminal domain located on the top of this saddle. The models of two dimeric conformations , a closed, inactive form and an open, active form , differ with respect to how surface-loop positions affect substrate access to the catalytic site. In the closed form, the surface loop covers the catalytic site, which becomes inaccessible to solvent. Large conformational changes in the open form, especially in the loop and carboxyl-terminal domain, allow substrate access to the active site. To dissect the structure,function relationships of the LPL carboxyl-terminal domain, several residues predicted by the model structure to be essential for the functions of heparin binding and substrate recognition were mutagenized. Arg405 plays an important role in heparin binding in the active dimer. Lys413/Lys414 or Lys414 regulates heparin affinity in both monomeric and dimeric forms. To evaluate the prediction that LPL forms a homodimer in a ,head-to-tail' orientation, two inactive LPL mutants , a catalytic site mutant (S132T) and a substrate-recognition mutant (W390A/W393A/W394A) , were cotransfected into COS7 cells. Lipase activity could be recovered only when heterodimerization occurred in a head-to-tail orientation. After cotransfection, 50% of the wild-type lipase activity was recovered, indicating that lipase activity is determined by the interaction between the catalytic site on one subunit and the substrate-recognition site on the other. [source] The presence of phosphate at a catalytic site suppresses the formation of the MgADP-inhibited form of F1 -ATPaseFEBS JOURNAL, Issue 1 2002Noriyo Mitome F1 -ATPase is inactivated by entrapment of MgADP in catalytic sites and reactivated by MgATP or Pi. Here, using a mutant ,3,3, complex of thermophilic F1 -ATPase (,W463F/,Y341W) and monitoring nucleotide binding by fluorescence quenching of an introduced tryptophan, we found that Pi interfered with the binding of MgATP to F1 -ATPase, but binding of MgADP was interfered with to a lesser extent. Hydrolysis of MgATP by F1 -ATPase during the experiments did not obscure the interpretation because another mutant, which was able to bind nucleotide but not hydrolyse ATP (,W463F/,E190Q/,Y341W), also gave the same results. The half-maximal concentrations of Pi that suppressed the MgADP-inhibited form and interfered with MgATP binding were both ,,20 mm. It is likely that the presence of Pi at a catalytic site shifts the equilibrium from the MgADP-inhibited form to the enzyme,MgADP,Pi complex, an active intermediate in the catalytic cycle. [source] Engineering the properties of a cold active enzyme through rational redesign of the active siteFEBS JOURNAL, Issue 19 2001Iason Tsigos ,In an effort to explore the effects of local flexibility on the cold adaptation of enzymes, we designed point mutations aiming to modify side-chain flexibility at the active site of the psychrophilic alkaline phosphatase from the Antarctic strain TAB5. The mutagenesis targets were residues Trp260 and Ala219 of the catalytic site and His135 of the Mg2+ binding site. The replacement of Trp260 by Lys in mutant W260K, resulted in an enzyme less active than the wild-type in the temperature range 5,25 °C. The additional replacement of Ala219 by Asn in the double mutant W260K/A219N, resulted in a drastic increase in the energy of activation, which was reflected in a considerably decreased activity at temperatures of 5,15 °C and a significantly increased activity at 20,25 °C. Further substitution of His135 by Asp in the triple mutant W260K/A219N/H135D restored a low energy of activation. In addition, the His135,Asp replacement in mutants H135D and W260K/A219N/H135D resulted in considerable stabilization. These results suggest that the psychrophilic character of mutants can be established or masked by very slight variations of the wild-type sequence, which may affect active site flexibility through changes in various conformational constraints. [source] Phosphorylation of phosphodiesterase-5 by cyclic nucleotide-dependent protein kinase alters its catalytic and allosteric cGMP-binding activitiesFEBS JOURNAL, Issue 9 2000Jackie D. Corbin In addition to its cGMP-selective catalytic site, cGMP-binding cGMP-specific phosphodiesterase (PDE5) contains two allosteric cGMP-binding sites and at least one phosphorylation site (Ser92) on each subunit [Thomas, M.K., Francis, S.H. & Corbin, J.D. (1990) J. Biol. Chem.265, 14971,14978]. In the present study, prior incubation of recombinant bovine PDE5 with a phosphorylation reaction mixture [cGMP-dependent protein kinase (PKG) or catalytic subunit of cAMP-dependent protein kinase (PKA), MgATP, cGMP, 3-isobutyl-1-methylxanthine], shown earlier to produce Ser92 phosphorylation, caused a 50,70% increase in enzyme activity and also increased the affinity of cGMP binding to the allosteric cGMP-binding sites. Both effects were associated with increases in its phosphate content up to 0.6 mol per PDE5 subunit. Omission of any one of the preincubation components caused loss of stimulation of catalytic activity. Addition of the phosphorylation reaction mixture to a crude bovine lung extract, which contains PDE5, also produced a significant increase in cGMP PDE catalytic activity. The increase in recombinant PDE5 catalytic activity brought about by phosphorylation was time-dependent and was obtained with 0.2,0.5 ,m PKG subunit, which is approximately the cellular level of this enzyme in vascular smooth muscle. Significantly greater stimulation was observed using cGMP substrate concentrations below the Km value for PDE5, although stimulation was also seen at high cGMP concentrations. Considerably higher concentration of the catalytic subunit of PKA than of PKG was required for activation. There was no detectable difference between phosphorylated and unphosphorylated PDE5 in median inhibitory concentration for the PDE5 inhibitors, sildenafil, or zaprinast 3-isobutyl-1-methylxanthine. Phosphorylation reduced the cGMP concentration required for half-maximum binding to the allosteric cGMP-binding sites from 0.13 to 0.03 ,m. The mechanism by which phosphorylation of PDE5 by PKG could be involved in physiological negative-feedback regulation of cGMP levels is discussed. [source] Hev b 9, an enolase and a new cross-reactive allergen from Hevea latex and moldsFEBS JOURNAL, Issue 24 2000Purification, characterization, cloning, expression Natural rubber latex allergy is an IgE-mediated disease that is caused by proteins that elute from commercial latex products. A complementary DNA (cDNA) coding for Hev b 9, an enolase (2-phospho- d -glycerate hydrolyase) and allergen from latex of the rubber tree Hevea brasiliensis, was amplified by PCR. The PCR primers were designed according to conserved regions of enolases from plants. The obtained cDNA amplification product consisted of 1651 bp and encoded a protein of 445 amino-acid residues with a calculated molecular mass of 47.6 kDa. Sequence comparisons revealed high similarities of the Hevea latex enolase to mold enolases that have been identified as important allergens. In addition, the crucial amino-acid residues that participate in the formation of the catalytic site and the Mg2+ binding site of enolases were also conserved. Hevea latex enolase was produced as a recombinant protein in Escherichia coli with an N-terminal hexahistidyl tag, and purified by affinity chromatography. The yield amounted to 110 mg of purified Hev b 9 per litre of bacterial culture. The recombinant allergen bound IgE from latex, as well as mold-allergic patients, in immunoblot and ELISA experiments. The natural enolase was isolated from Hevea latex by (NH4)2SO4 precipitation and ion exchange chromatography. The natural and the recombinant (r)Hev b 9 showed equivalent enzymatic activity. Patients' IgE-antibodies preincubated with rHev b 9 lost their ability to bind to natural (n) Hev b 9, indicating the identity of the B-cell epitopes on both molecules. Cross-reactivity with two enolases from Cladosporium herbarum and Alternaria alternata was determined by inhibition of IgE-binding to these enolases by rHev b 9. Therefore, enolases may represent another class of highly conserved enzymes with allergenic potentials. [source] Bacterial cell death induced by human pro-apoptotic Bax is blocked by an RNase E mutant that functions in an anti-oxidant pathwayGENES TO CELLS, Issue 3 2000Rika Nanbu-Wakao Background Bax is a member of the Bcl-2 family and induces apoptosis of mammalian cells. We have shown that a trace amount of human Bax induces the cell death of Escherichia coli, accompanied by damage to DNA, and that the region of Bax which is lethal to E. coli is also responsible for apoptosis-inducing activity in the mammalian cells. Results We isolated a Bax-resistant mutant from E. coli cells that survive in the presence of paraquat, a generator of superoxide, by screening a library constructed from the random insertion of a transposon. Psb1 (paraquat-resistant, suppressor of Bax-1) mutant had a Tn 10 transposon inserted in the rne gene of E. coli, splitting the RNase E gene (rne) into N- and C-terminal halves. The introduction of the truncated 5, end of rne specifically enhanced resistance to paraquat, prevented cell death induced by Bax and decreased the intracellular H2O2 concentration. The region responsible for the paraquat- and Bax-resistance was not the catalytic site for the endoribonuclease activity of RNase E. Conclusions The N-terminal region of the RNase E protein inhibits bacterial death induced by human Bax as well as paraquat through a unique mechanism that is distinct from RNA digestion. This study implies that the protection of bacterial death induced by Bax is associated with an anti-oxidant pathway and that a mutant RNase E has a novel function as an anti-oxidant. [source] Cover Picture: Functionalized Gold Nanoparticles Mimic Catalytic Activity of a Polysiloxane-Synthesizing Enzyme (Adv. Mater.ADVANCED MATERIALS, Issue 10 200510/2005) Abstract A system that acts as a biomimetic of the silica-synthesizing enzyme found in a marine sponge is reported by Morse and co-workers on p.,1234. Gold nanoparticles (GNPs) are functionalized with the same organic moieties that are found in the enzyme's catalytic site. Interaction between the nucleophilic (OH-terminated) and hydrogen-bonding (imidazole-terminated) GNPs, as shown on the cover, is required for the hydrolysis of a silicon alkoxide precursor and subsequent polycondensation to form silica at a low temperature and near-neutral pH. Replacement of either of the required functional groups by a non-reactive methyl group abolishes catalysis in this synthetic system, as it does in the biological enzyme. Cover art provided by Peter Allen. [source] [Fe-Fe]-hydrogenase reactivated by residue mutations as bridging carbonyl rearranges: A QM/MM studyINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 14 2010Stefan Motiu Abstract In this work, we found aqueous enzyme phase reaction pathways for the reactivation of the exogenously inhibited [Fe-Fe]-hydrogenases by O2, or OH,, which metabolizes to H2O (Dogaru et al., Int J Quantum Chem 2008, 108; Motiu et al., Int J Quantum Chem 2007, 107, 1248). We used the hybrid quantum mechanics/molecular mechanics (QM/MM) method to study the reactivation pathways of the exogenously inhibited enzyme matrix. The ONIOM calculations performed on the enzyme agree with experimental results (Liu et al., J Am Chem Soc 2002, 124, 5175), that is, wild-type [Fe-Fe]-hydrogenase H-cluster is inhibited by oxygen metabolites. An enzyme spherical region with a radius of 8 Å (from the distal iron, Fed) has been screened for residues that prevent H2O from leaving the catalytic site and reactivate the [Fe-Fe]-hydrogenase H-cluster. In the screening process, polar residues were removed, one at a time, and frequency calculations provided the change in the Gibbs' energy for the dissociation of water (due to their deletion). When residue deletion resulted in significant Gibbs' energy decrease, further residue substitutions have been carried out. Following each substitution, geometry optimization and frequency calculations have been performed to assess the change in the Gibbs' energy for the elimination of H2O. Favorable thermodynamic results have been obtained for both single residue removal (,G,Glu374 = ,1.6 kcal/mol), single substitution (,GGlu374His = ,3.1 kcal/mol), and combined residue substitutions (,GArg111Glu;Thr145Val;Glu374His;Tyr375Phe = ,7.5 kcal/mol). Because the wild-type enzyme has only an endergonic step to overcome, that is, for H2O removal, by eliminating several residues, one at a time, the endergonic step was made to proceed spontaneously. Thus, the most promising residue deletions which enhance H2O elimination are ,Arg111, ,Thr145, ,Ser177, ,Glu240, ,Glu374, and ,Tyr375. The thermodynamics and electronic structure analyses show that the bridging carbonyl (COb) of the H-cluster plays a concomitant role in the enzyme inhibition/reactivation. In gas phase, COb shifts towards Fed to compensate for the electron density donated to oxygen upon the elimination of H2O. However, this is not possible in the wild-type enzyme because the protein matrix hinders the displacement of COb towards Fed, which leads to enzyme inhibition. Nevertheless, enzyme reactivation can be achieved by means of appropriate amino acid substitutions. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Increased Efficacies of an Individual Catalytic Site in Clustered Multivalent Dendritic CatalystsADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 14-15 2009Govindasamy Jayamurugan Abstract In the studies reported so far on dendrimer-mediated catalysis, the efficacies of the catalytic units were studied and compared primarily across the generations. In order to identify the efficacy of an individual catalytic unit with respect to the number of such units present within a given generation, a series of catalysts were prepared within a generation. Dendrimers incorporated with phosphine-metal complexes were chosen for the study and as many as 11 catalysts within three generations were synthesized. The CC bond-forming reactions, namely, the Heck and the Suzuki coupling reactions, were then selected to study the catalytic efficiencies of the series of partially and fully phosphine-metal complex functionalized dendrimers. The efficacies of the formation of cinnamate and biphenyl, catalyzed by the dendritic catalysts, were compared. The comparative analyses show that an individual catalytic site is far more effective in its catalytic activity when presented in multiple numbers, i.e., in a multivalent dendritic system, than as a single unit within the same generation, i.e., in a monovalent dendritic system. The study identifies the beneficial effects of the multivalent presentation of the catalytic moieties, both within and across the dendrimer generations. [source] Structure,Activity Relationship Studies in Single-Site Esterase Peptide DendrimersISRAEL JOURNAL OF CHEMISTRY, Issue 1 2009Sacha Javor We recently reported on peptide dendrimers with a single catalytic site at the dendrimer core catalyzing the hydrolysis of acetoxy- and butyryloxy-pyrene trisulfonate 1a/b in aqueous buffer with Michaelis,Menten kinetics. Substrate binding is mediated by a pair of protonated arginine or histidine residues in the first generation branch, and esterolysis is performed by the imidazole side-chain of a histidine residue in the core acting as a general base or nucleophile. Herein we report on a structure,activity relationship study searching for an optimal combination between amino acid sequence and catalytic machinery. Installation of histidine residues onto the aromatic dendrimer framework "R" leads to 10-fold higher rate acceleration up to kcat/kuncat = 1.5 * 103 at pH 5.5 with dendrimers RG3H (AcYT)8 (BWG)4 (BHS)2BHS and RMG3H (AcYT)8(BWG)4(BHSG)2BHS (one-letter codes for L -amino acids; Ac = acetyl, B = L -2,3-diaminopropionic acid branching point, C-terminus is amide -CONH2). These dendrimers reach the compactness of a native folded protein. [source] Deamination of adenosine by extracts of Penicillium politans NRC-510JOURNAL OF BASIC MICROBIOLOGY, Issue 2 2005Ali M. Elshafei Prof. Cell-free extracts of nitrate-grown Penicillium politans NRC-510 could catalyze the hydrolytic deamination of adenosine to inosine maximally at pH 6.0 and 45 °C. However the same extracts could not catalyze the N-glycosidic bond cleavage of adenosine at pH 4.0, 6.0 and 8.0. Incubation of the extracts at 55 °C for 30 minutes caused about 31% loss in activity whereas incubation of the extracts at 60 °C for 15 minutes caused a complete loss of enzyme activity. Results indicated the absence of the involvement of sulfhydryl groups in the catalytic site of adenosine deaminase. The enzyme is inhibited by ethylene diamine tetraacetate indicating that adenosine deaminase is a metalloenzyme. MnCl2 and MgCl2 had a remarkable activating effect, whereas HgCl2, CaCl2 and ZnSO4 showed an inhibitory effect on enzyme activity. Dialyzing the extracts for 24 hours significantly increase deaminase activity by about 33%. The apparent Km value was calculated for adenosine and found to be 3.63 × 10,3M, which indicates high affinity of adenosine deaminase for its substrate adenosine. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] K vitamins, PTP antagonism, and cell growth arrestJOURNAL OF CELLULAR PHYSIOLOGY, Issue 3 2002Brian I. Carr The main function of K vitamins is to act as co-factors for ,-glutamyl carboxylase. However, they have also recently been shown to inhibit cell growth. We have chemically synthesized a series of K vitamin analogs with various side chains at the 2 or 3 position of the core naphthoquinone structure. The analogs with short thio-ethanol side chains are found to be more potent growth inhibitors in vitro of various tumor cell lines. Cpd 5 or [2-(2-mercaptoethanol)-3-methyl-1,4-naphthoquinone] is one of the most potent. The anti-proliferation activity of these compounds is antagonized by exogenous thiols but not by non-thiol antioxidants. This suggests that the growth inhibition is mediated by sulfhydryl arylation of cellular glutathione and cysteine-containing proteins and not by oxidative stress. The protein tyrosine phosphatases (PTP) are an important group of proteins that contain cysteine at their catalytic site. PTPs regulate mitogenic signal transduction and cell cycle progression. PTP inhibition by Cpd 5 results in prolonged tyrosine phosphorylation and activation of several kinases and transcription factors including EGFR, ERK1/2, and Elk1. Cpd 5 could activate ERK1/2 either by signaling from an activated EGFR, which is upstream in the signaling cascade, or by direct inhibition of ERK1/2 phosphatase(s). Prolonged ERK1/2 phosphorylation strongly correlates with Cpd 5-mediated growth inhibition. Cpd 5 can also bind to and inhibit the Cdc25 family of dual specific phosphatases. As a result, several Cdc25 substrates (Cdk1, Cdk2, Cdk4) involved in cell cycle progression are tyrosine phosphorylated and thereby inhibited by its action. Cpd 5 could also inhibit both normal liver regeneration and hepatoma growth in vivo. DNA synthesis during rat liver regeneration following partial hepatectomy, transplantable rat hepatoma cell growth, and glutathione-S-transferase-pi expressing hepatocytes after administration of the chemical carcinogen diethylnitrosamine, are all inhibited by Cpd 5 administration. The growth inhibitory effect during liver regeneration and transplantable tumor growth is also correlated with ERK1/2 phosphorylation induced by Cpd 5. Thus, Cpd 5-mediated inhibition of PTPs, such as Cdc25 leads to cell growth arrest due to altered activity of key cellular kinases involved in signal transduction and cell cycle progression. This prototype K vitamin analog represents a novel class of growth inhibitor based upon its action as a selective PTP antagonist. It is clearly associated with prolonged ERK1/2 phosphorylation, which is in contrast with the transient ERK1/2 phosphorylation induced by growth stimulatory mitogens. © 2002 Wiley-Liss, Inc. [source] Purification and characterization of a 630 kDa bacterial killing metalloprotease (KilC) isolated from plaice Pleuronectes platessa (L.), epidermal mucusJOURNAL OF FISH DISEASES, Issue 5 2008T Tvete Abstract Antibacterial chemicals in the mucus of fish such as lysozyme, lectins, peptides and proteases provide an efficient first line of defence against pathogens. This study shows that there are at least three antibacterial proteins in plaice skin mucus in addition to lysozyme. One of these proteins is responsible for approximately 74% of the antibacterial activity and is a 630 kDa protease complex designated KilC (bacterial killing metalloprotease C). Purified KilC kills the bacteria Staphylococcus aureus, Escherichia coli, Bacillus subtilis and Pseudomonas aeruginosa efficiently. The protease activity of KilC is dependent upon the divalent cation Mg2+ and shows pH dual optima of 5.0 and 8.0. The enzyme has a temperature optimum of 25 °C and is made up of at least five different sized peptides. Studies with protease inhibitors show that the catalytic site of KilC may be cysteine- or serine protease-like. KilC may kill bacterial cells by acting directly upon the bacteria or by producing low molecular weight bioactive compounds such as peptides. [source] Studies on the molecular recognition between bioactive peptides and angiotensin-converting enzymeJOURNAL OF MOLECULAR RECOGNITION, Issue 2 2009A.S. Pina Abstract High blood pressure or hypertension is a condition affecting many individuals and represents a controllable risk factor for cardiovascular diseases such as coronary heart disease and stroke. A non-pharmacological approach to manage these includes the application of food components with antihypertensive activity. Milk protein-derived peptides have been exploited as natural hypotensive agents, namely the peptides Val-Pro-Pro (VPP) and Ile-Pro-Pro (IPP), already commercialized in functional foods as a potential alternative to synthetic drugs. These bioactive peptides inhibit in vitro and in vivo the Angiotensin I-converting enzyme (ACE), a protein with an important role in blood pressure regulation. In this work, we attempted to elucidate the possible mode of interaction between the peptides and ACE, including mechanisms of binding to the cofactor Zn2+, and further contrast this with the known mode of inhibition exerted by synthetic drugs (Captopril, Enalaprilat and Lisinopril). The bioactive peptide Ala-Leu-Pro-Met-His-Ile-Arg (ALPMHIR), also known to inhibit the enzyme ACE but with a lower efficiency than VPP and IPP, was utilized in the docking studies for comparison. It was observed that the best docking poses obtained for VPP and IPP were located at the ACE catalytic site with very high resemblance to the drugs mode of interaction, including the coordination with Zn2+. As for ALPMHIR, the best docking poses were located in the narrow ACE channel outside the catalytic site, representing higher affinity energies and fewer resemblances with the interaction established by drugs. Copyright © 2008 John Wiley & Sons, Ltd. [source] Mutations on N -terminal region of Taiwan cobra phospholipase A2 result in structurally distorted effectsJOURNAL OF PEPTIDE SCIENCE, Issue 8 2008Yi-Ling Chiou Abstract In the present study, three Taiwan cobra PLA2 variants were prepared by adding an extra N -terminal Met, substituting Asn-1 by Met or deleting the N -terminal heptapeptide. Recombinant PLA2 mutants were expressed in Escherichia coli (E. coli), and purified to homogeneity by reverse phase HPLC. Fluorescence measurement showed that the hydrophobic character of the catalytic site, the microenvironment of Trp residues and energy transfer from excited Trp to 8-anilinonaphthalene sulfonate (ANS) were affected by N -terminal mutations. An alteration in the structural flexibility of the active site was noted with the mutants lacking the N -terminal heptapeptide or with an extra N -terminal Met added as evidenced by the inability of the two variants to bind with Ba2+. Moreover, modification of Lys residues and energy transfer within the protein-ANS complex revealed that the Ca2+ -induced change in the global structure of PLA2 was different from that in N -terminal variants. Together with the fact that an ,activation network' connects the N -terminus with the active site, our data suggest that mutagenesis on the N -terminal region affects directly the fine structure of the catalytic site, which subsequently transmits its influence in altering the structure outside the active site of PLA2. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd. [source] Dynamical view of membrane binding and complex formation of human factor VIIa and tissue factorJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 5 2010Y. Z. OHKUBO Summary.,Background:,The molecular mechanism of enhancement of the enzymatic activity of factor VIIa by tissue factor (TF) is not fully understood, primarily because of the lack of atomic models for the membrane-bound form of the TF,FVIIa complex. Objectives:,To construct the first membrane-bound model of the TF,FVIIa complex, and to investigate the dynamics of the complex in solution and on the surface of anionic membranes by using large-scale molecular dynamics (MD) simulations in full atomic detail. Methods:,Membrane-bound models of the TF,FVIIa complex and the individual factors were constructed and subjected to MD simulations, in order to characterize protein,protein and protein,lipid interactions, and to investigate the dynamics of TF and FVIIa. Results:,The MD trajectories reveal that isolated FVIIa undergoes large structural fluctuation, primarily due to the hinge motions between its domains, whereas soluble TF (sTF) is structurally stable. Upon complex formation, sTF restricts the motion of FVIIa significantly. The results also show that, in the membrane-bound form, sTF directly interacts with the lipid headgroups, even in the absence of FVIIa. Conclusion:,The first atomic models of membrane-bound sTF,FVIIa, FVIIa and sTF are presented, revealing that sTF forms direct contacts with the lipids, both in the isolated form and in complex with FVIIa. The main effect of sTF binding to FVIIa is spatial stabilization of the catalytic site of FVIIa, which ensures optimal interaction with the substrate, FX. [source] Cell transformation induced by hepatitis C virus NS3 serine proteaseJOURNAL OF VIRAL HEPATITIS, Issue 2 2001R. Zemel Persistent infection with hepatitis C virus (HCV) may lead to hepatocellular carcinoma (HCC). It has been suggested that HCV-encoded proteins are directly involved in the tumorigenic process. The HCV nonstructural protein NS3 has been identified as a virus-encoded serine protease. To study whether HCV NS3 has oncogenic activity, nontumorigenic rat fibroblast (RF) cells were stably transfected with an expression vector containing cDNA for the NS3 serine protease (nucleotides 3356,4080). The NS3 serine protease activity was determined in the transfected cells. The transfected cells grew rapidly and proliferated serum independently, lost contact inhibition, grew anchorage independently in soft agar and induced significant tumour formation in nude mice. Cells transfected with an expression vector containing a mutated NS3 serine protease (serine 139 to alanine at the catalytic site) showed no transforming abilities; their growth was dependent on serum and they did not grow anchorage independently in soft agar. Moreover, cells transfected with the NS3 serine protease and treated with the chymotrypsin inhibitors TPCK and PMSF (a serine protease inhibitor) lost their transforming feature. These results suggest that the NS3 serine protease of HCV is involved in cell transformation and that the ability to transform requires an active enzyme. [source] Analysis of a dextran-binding domain of the dextranase of Streptococcus mutansLETTERS IN APPLIED MICROBIOLOGY, Issue 3 2002H. Morisaki Aims: To examine the dextran-binding domain of the dextranase (Dex) of Streptococcus mutans. Methods and Results: Deletion mutants of the Dex gene of Strep. mutans were prepared by polymerase chain reaction and expressed in Escherichia coli cells. Binding of the truncated Dexs to dextran was measured with a Sephadex G-150 gel. Although the Dexs which lacked the N-terminal variable region lost enzyme activity, they still retained dextran-binding ability. In addition, further deletion into the conserved region from the N-terminal did not influence the dextran-binding ability. However, the Dex which carried a deletion in the C-terminus still possessed both enzyme activity and dextran-binding ability. Further deletion into the conserved region from the C-terminal resulted in complete disappearance of both enzyme and dextran-binding activities. Conclusions: Deletion analysis of the Dex gene of Strep. mutans showed that the C-terminal side (about 120 amino acid residues) of the conserved region of the Dex was essential for dextran-binding ability. Significance and Impact of the Study: The dextran-binding domain was present in a different area from the catalytic site in the conserved region of the Dex molecule. The amino acid sequence of the dextran-binding domain of the Dex differed from those of glucan-binding regions of other glucan-binding proteins reported. [source] Mutations in the signature motif in MutS affect ATP-induced clamp formation and mismatch repairMOLECULAR MICROBIOLOGY, Issue 6 2008Samir Acharya Summary MutS protein dimer recognizes and co-ordinates repair of DNA mismatches. Mismatch recognition by the N-terminal mismatch recognition domain and subsequent downstream signalling by MutS appear coupled to the C-terminal ATP catalytic site, Walker box, through nucleotide-mediated conformational transitions. Details of this co-ordination are not understood. The focus of this study is a conserved loop in Escherichia coli MutS that is predicted to mediate cross-talk between the two ATP catalytic sites in MutS homodimer. Mutagenesis was employed to assess the role of this loop in regulating MutS function. All mutants displayed mismatch repair defects in vivo. Biochemical characterization further revealed defects in ATP binding, ATP hydrolysis as well as effective mismatch recognition. The kinetics of initial burst of ATP hydrolysis was similar to wild type but the magnitude of the burst was reduced for the mutants. Given its proximity to the ATP bound in the opposing monomer in the crystal and its potential analogy with signature motif of ABC transporters, the results strongly suggest that the loop co-ordinates ATP binding/hydrolysis in trans by the two catalytic sites. Importantly, our data reveal that the loop plays a direct role in co-ordinating conformational changes involved in long-range communication between Walker box and mismatch recognition domains. [source] A cloning and expression analysis of pregnancy-associated glycoproteins expressed in trophoblasts of the white-tail deer placenta,MOLECULAR REPRODUCTION & DEVELOPMENT, Issue 11 2007Gretchen A. Brandt Abstract The pregnancy-associated glycoproteins (PAGs) are placental proteins that have been cloned from swine, sheep, goats, and cattle, but never from animals within the Cervidae family. The goal of this work was to characterize PAGs in white-tailed deer. Placenta and uterine tissues were collected from pregnant does at days 85 and 90 of pregnancy. RNA from cotyledons was used to amplify deer PAGs by RT-PCR. Ten distinct cDNAs were cloned and sequenced. Some normally conserved amino acids comprising the catalytic site were found to be altered in deer PAGs 4, 5, and 8; another PAG, (PAG-9) was a splice variant that lacked exon 7. In each case, these mutations would likely preclude proteolytic activity for these proteins. A phylogenetic analysis revealed that most of the deer PAGs fell within the ancient PAG grouping. The remainder fell within the more modern (BNC-specific) PAG group. Western blotting was performed with anti-PAG antibodies and this analysis revealed that deer PAGs comprise a heterogeneous group based on different antigenicities and electrophoretic mobilities. Immunohistochemistry and in situ hybridization revealed some unique localization patterns of PAGs in the deer placentome compared to those in other ruminants. Most notably, deer PAGs 4 and 5, which according to the phylogeny, are "ancient PAGs," were expected to be present in all trophoblasts; instead, they were localized to the BNC. Although many of the PAGs identified here are very similar to those in Bovidae, some are clearly distinct in their expression pattern and probably possess functional roles unique to cervid reproduction. Mol. Reprod. Dev. 74: 1355,1362, 2007. © 2007 Wiley-Liss, Inc. [source] Gene for porcine pregnancy-associated glycoprotein 2 (poPAG2): Its structural organization and analysis of its promoter,MOLECULAR REPRODUCTION & DEVELOPMENT, Issue 2 2001Bozena Szafranska Abstract The pregnancy-associated glycoproteins (PAG) are abundant secretory products of the placental trophectoderm of ungulate species. They are structurally related to pepsin, having the capability to bind peptides. However, many cannot function as enzymes due to amino acid substitutions in and around the catalytic site. Here, we demonstrate that pigs, like cattle and sheep, but unlike equids, have multiple PAG genes. One of the transcribed porcine PAG (poPAG) genes, the one for poPAG2, was cloned. It had a nine-exon organization similar to that of other mammalian aspartic proteinase genes with an atypical TATA sequence. A total of 1.2 kbp upstream from exon 1 was sequenced. This region shared identity (>,65%) with the promoter regions of the bovine (bo) PAG1, boPAG2 and equine (eq) PAG genes, but not with other aspartyl proteinase genes, including that of pepsinogen A. Nor were there clear similarities to the promoters of other genes with trophoblast-specific expression. Of the different poPAG2 promoter constructs tested in transfection experiments in two human (JAr and JEG3) and one rat (Rcho) choriocarcinoma cell lines, only the shortest (,149 bp) was required to provide full expression of a luciferase reporter. Although this short promoter was not active in Cos-1 and L-929 cells, it was active in CHO cells, a transformed non-trophoblast hamster ovarian cell line. Co-transfection of Ets2 elevated the activity of this short promoter approximately six-fold in JAr cells, but, disruption of the two putative Ets sites did not alter the ability of Ets2 to transactivate the promoter. In the non-trophoblast cell lines, Ets2 failed to elicit any response. Ets2 responsiveness may be a common feature of most or all trophoblast-expressed genes, although in the case of poPAG2, the effect may be indirect. Mol. Reprod. Dev. 60: 137,146, 2001. © 2001 Wiley-Liss, Inc. [source] Dimer,monomer equilibrium of human thymidylate synthase monitored by fluorescence resonance energy transferPROTEIN SCIENCE, Issue 5 2010Filippo Genovese Abstract An ad hoc bioconjugation/fluorescence resonance energy transfer (FRET) assay has been designed to spectroscopically monitor the quaternary state of human thymidylate synthase dimeric protein. The approach enables the chemoselective engineering of allosteric residues while preserving the native protein functions through reversible masking of residues within the catalytic site, and is therefore suitable for activity/oligomerization dual assay screenings. It is applied to tag the two subunits of human thymidylate synthase at cysteines 43 and 43, with an excitation energy donor/acceptor pair. The dimer,monomer equilibrium of the enzyme is then characterized through steady-state fluorescence determination of the intersubunit resonance energy transfer efficiency. [source] | ||||||||||||||||||||||||||||||||||||||||