The Experts below are selected from a list of 12156 Experts worldwide ranked by ideXlab platform
Hee-myong Ro - One of the best experts on this subject based on the ideXlab platform.
-
factors modifying the structural configuration of Oxyanions and organic acids adsorbed on iron hydr oxides in soils a review
Environmental Chemistry Letters, 2020Co-Authors: Hee-myong RoAbstract:Oxyanions are ubiquitous in soils, organisms and the environment. Due to their unique chemical structure, Oxyanions can be easily transferred into other systems. Carbonate (CO32−), nitrate (NO3−), phosphate (PO43−), silicate (SiO42−) and sulfate (SO42−) are the major Oxyanions in organisms and the soil environment, whereas arsenate (AsO43−), antimonate (SbO43−), borate (BO33−), selenate (SeO42−), and tellurate (TeO42−) are generally reported as toxic chemicals found at trace levels. Excessive Oxyanions leached from soils into water have caused severe environmental problems. Here, we review the factors affecting the structural configuration of Oxyanions and organic acids adsorbed on iron oxides and hydroxides. The configuration of Oxyanions on iron (hydr)oxides is controlled by surface loading, pH, sample phase, competing ions and organic acids. Under conditions of low surface loading and low pH at the interface in the absence of competing ions, Oxyanions with high affinity possibly form a complex with higher denticity. But an increase in pH decreases the number of sorption sites; thus, a transition from a tri- or bidentate complex to monodentate and outer-sphere complexes occurs.
-
Factors modifying the structural configuration of Oxyanions and organic acids adsorbed on iron (hydr)oxides in soils. A review
Environmental Chemistry Letters, 2020Co-Authors: Junho Han, Minhee Kim, Hee-myong RoAbstract:Oxyanions are ubiquitous in soils, organisms and the environment. Due to their unique chemical structure, Oxyanions can be easily transferred into other systems. Carbonate (CO_3^2−), nitrate (NO_3^−), phosphate (PO_4^3−), silicate (SiO_4^2−) and sulfate (SO_4^2−) are the major Oxyanions in organisms and the soil environment, whereas arsenate (AsO_4^3−), antimonate (SbO_4^3−), borate (BO_3^3−), selenate (SeO_4^2−), and tellurate (TeO_4^2−) are generally reported as toxic chemicals found at trace levels. Excessive Oxyanions leached from soils into water have caused severe environmental problems. Here, we review the factors affecting the structural configuration of Oxyanions and organic acids adsorbed on iron oxides and hydroxides. The configuration of Oxyanions on iron (hydr)oxides is controlled by surface loading, pH, sample phase, competing ions and organic acids. Under conditions of low surface loading and low pH at the interface in the absence of competing ions, Oxyanions with high affinity possibly form a complex with higher denticity. But an increase in pH decreases the number of sorption sites; thus, a transition from a tri- or bidentate complex to monodentate and outer-sphere complexes occurs.
Chrislaine Martinez - One of the best experts on this subject based on the ideXlab platform.
-
contribution of cutinase serine 42 side chain to the stabilization of the Oxyanion transition state
Biochemistry, 1996Co-Authors: Aurelie Nicolas, Maarten R Egmond, Cornelis Theodorus Verrips, J De Vlieg, Sonia Longhi, Christian Cambillau, Chrislaine MartinezAbstract:: Cutinase from the fungus Fusarium solani pisi is a lipolytic enzyme able to hydrolyze both aggregated and soluble substrates. It therefore provides a powerful tool for probing the mechanisms underlying lipid hydrolysis. Lipolytic enzymes have a catalytic machinery similar to those present in serine proteinases. It is characterized by the triad Ser, His, and Asp (Glu) residues, by an Oxyanion binding site that stabilizes the transition state via hydrogen bonds with two main chain amide groups, and possibly by other determinants. It has been suggested on the basis of a covalently bond inhibitor that the cutinase Oxyanion hole may consist not only of two main chain amide groups but also of the Ser42 O gamma side chain. Among the esterases and the serine and the cysteine proteases, only Streptomyces scabies esterase, subtilisin, and papain, respectively, have a side chain residue which is involved in the Oxyanion hole formation. The position of the cutinase Ser42 side chain is structurally conserved in Rhizomucor miehei lipase with Ser82 O gamma, in Rhizopus delemar lipase with Thr83 O gamma 1, and in Candida antartica B lipase with Thr40 O gamma 1. To evaluate the increase in the tetrahedral intermediate stability provided by Ser42 O gamma, we mutated Ser42 into Ala. Furthermore, since the proper orientation of Ser42 O gamma is directed by Asn84, we mutated Asn84 into Ala, Leu, Asp, and Trp, respectively, to investigate the contribution of this indirect interaction to the stabilization of the Oxyanion hole. The S42A mutation resulted in a drastic decrease in the activity (450-fold) without significantly perturbing the three-dimensional structure. The N84A and N84L mutations had milder kinetic effects and did not disrupt the structure of the active site, whereas the N84W and N84D mutations abolished the enzymatic activity due to drastic steric and electrostatic effects, respectively.
Petri Kursula - One of the best experts on this subject based on the ideXlab platform.
-
the thiolase reaction mechanism the importance of asn316 and his348 for stabilizing the enolate intermediate of the claisen condensation
Biochemistry, 2009Co-Authors: Gitte Merilainen, Petri Kursula, Visa Poikela, Rikkert K WierengaAbstract:The biosynthetic thiolase catalyzes a Claisen condensation reaction between acetyl-CoA and the enzyme acetylated at Cys89. Two Oxyanion holes facilitate this catalysis: Oxyanion hole I stabilizes the enolate intermediate generated from acetyl-CoA, whereas Oxyanion hole II stabilizes the tetrahedral intermediate of the acetylated enzyme. The latter intermediate is formed when the α-carbanion of acetyl-CoA enolate reacts with the carbonyl carbon of acetyl-Cys89, after which C−C bond formation is completed. Oxyanion hole II is made of two main chain peptide NH groups, whereas Oxyanion hole I is formed by a water molecule (Wat82) and NE2(His348). Wat82 is anchored in the active site by an optimal set of hydrogen bonding interactions, including a hydrogen bond to ND2(Asn316). Here, the importance of Asn316 and His348 for catalysis has been studied; in particular, the properties of the N316D, N316A, N316H, H348A, and H348N variants have been determined. For the N316D variant, no activity could be detected. For ...
-
high resolution crystal structures of human cytosolic thiolase ct a comparison of the active sites of human ct bacterial thiolase and bacterial kas i
Journal of Molecular Biology, 2005Co-Authors: Toshiyuki Fukao, Herkko Sikkila, Naomi Kondo, Petri Kursula, Rikkert K WierengaAbstract:Thiolases belong to a superfamily of condensing enzymes that includes also β-ketoacyl acyl carrier protein synthases (KAS enzymes), involved in fatty acid synthesis. Here, we describe the high resolution structure of human cytosolic acetoacetyl-CoA thiolase (CT), both unliganded (at 2.3 A resolution) and in complex with CoA (at 1.6 A resolution). CT catalyses the condensation of two molecules of acetyl-CoA to acetoacetyl-CoA, which is the first reaction of the metabolic pathway leading to the synthesis of cholesterol. CT is a homotetramer of exact 222 symmetry. There is an excess of positively charged residues at the interdimer surface leading towards the CoA-binding pocket, possibly important for the efficient capture of substrates. The geometry of the catalytic site, including the three catalytic residues Cys92, His 353, Cys383, and the two Oxyanion holes, is highly conserved between the human and bacterial Zoogloea ramigera thiolase. In human CT, the first Oxyanion hole is formed by Wat38 (stabilised by Asn321) and NE2(His353), and the second by N(Cys92) and N(Gly385). The active site of this superfamily is constructed on top of four active site loops, near Cys92, Asn321, His353, and Cys383, respectively. These loops were used for the superpositioning of CT on the bacterial thiolase and on the Escherichia coli KAS I. This comparison indicates that the two thiolase Oxyanion holes also exist in KAS I at topologically equivalent positions. Interestingly, the hydrogen bonding interactions at the first Oxyanion hole are different in thiolase and KAS I. In KAS I, the hydrogen bonding partners are two histidine NE2 atoms, instead of a water and a NE2 side-chain atom in thiolase. The second Oxyanion hole is in both structures shaped by corresponding main chain peptide NH-groups. The possible importance of bound water molecules at the catalytic site of thiolase for the reaction mechanism is discussed.
Rikkert K Wierenga - One of the best experts on this subject based on the ideXlab platform.
-
the thiolase reaction mechanism the importance of asn316 and his348 for stabilizing the enolate intermediate of the claisen condensation
Biochemistry, 2009Co-Authors: Gitte Merilainen, Petri Kursula, Visa Poikela, Rikkert K WierengaAbstract:The biosynthetic thiolase catalyzes a Claisen condensation reaction between acetyl-CoA and the enzyme acetylated at Cys89. Two Oxyanion holes facilitate this catalysis: Oxyanion hole I stabilizes the enolate intermediate generated from acetyl-CoA, whereas Oxyanion hole II stabilizes the tetrahedral intermediate of the acetylated enzyme. The latter intermediate is formed when the α-carbanion of acetyl-CoA enolate reacts with the carbonyl carbon of acetyl-Cys89, after which C−C bond formation is completed. Oxyanion hole II is made of two main chain peptide NH groups, whereas Oxyanion hole I is formed by a water molecule (Wat82) and NE2(His348). Wat82 is anchored in the active site by an optimal set of hydrogen bonding interactions, including a hydrogen bond to ND2(Asn316). Here, the importance of Asn316 and His348 for catalysis has been studied; in particular, the properties of the N316D, N316A, N316H, H348A, and H348N variants have been determined. For the N316D variant, no activity could be detected. For ...
-
high resolution crystal structures of human cytosolic thiolase ct a comparison of the active sites of human ct bacterial thiolase and bacterial kas i
Journal of Molecular Biology, 2005Co-Authors: Toshiyuki Fukao, Herkko Sikkila, Naomi Kondo, Petri Kursula, Rikkert K WierengaAbstract:Thiolases belong to a superfamily of condensing enzymes that includes also β-ketoacyl acyl carrier protein synthases (KAS enzymes), involved in fatty acid synthesis. Here, we describe the high resolution structure of human cytosolic acetoacetyl-CoA thiolase (CT), both unliganded (at 2.3 A resolution) and in complex with CoA (at 1.6 A resolution). CT catalyses the condensation of two molecules of acetyl-CoA to acetoacetyl-CoA, which is the first reaction of the metabolic pathway leading to the synthesis of cholesterol. CT is a homotetramer of exact 222 symmetry. There is an excess of positively charged residues at the interdimer surface leading towards the CoA-binding pocket, possibly important for the efficient capture of substrates. The geometry of the catalytic site, including the three catalytic residues Cys92, His 353, Cys383, and the two Oxyanion holes, is highly conserved between the human and bacterial Zoogloea ramigera thiolase. In human CT, the first Oxyanion hole is formed by Wat38 (stabilised by Asn321) and NE2(His353), and the second by N(Cys92) and N(Gly385). The active site of this superfamily is constructed on top of four active site loops, near Cys92, Asn321, His353, and Cys383, respectively. These loops were used for the superpositioning of CT on the bacterial thiolase and on the Escherichia coli KAS I. This comparison indicates that the two thiolase Oxyanion holes also exist in KAS I at topologically equivalent positions. Interestingly, the hydrogen bonding interactions at the first Oxyanion hole are different in thiolase and KAS I. In KAS I, the hydrogen bonding partners are two histidine NE2 atoms, instead of a water and a NE2 side-chain atom in thiolase. The second Oxyanion hole is in both structures shaped by corresponding main chain peptide NH-groups. The possible importance of bound water molecules at the catalytic site of thiolase for the reaction mechanism is discussed.
A C Storer - One of the best experts on this subject based on the ideXlab platform.
-
contribution of the glutamine 19 side chain to transition state stabilization in the Oxyanion hole of papain
Biochemistry, 1991Co-Authors: Robert Ménard, Céline Plouffe, Pierre Laflamme, Thierry Vernet, Daniel C. Tessier, David Y. Thomas, Julie Carriere, Henri E Khouri, A C StorerAbstract:: The existence of an Oxyanion hole in cysteine proteases able to stabilize a transition-state complex in a manner analogous to that found with serine proteases has been the object of controversy for many years. In papain, the side chain of Gln19 forms one of the hydrogen-bond donors in the putative Oxyanion hole, and its contribution to transition-state stabilization has been evaluated by site-directed mutagenesis. Mutation of Gln19 to Ala caused a decrease in kcat/KM for hydrolysis of CBZ-Phe-Arg-MCA, which is 7700 M-1 s-1 in the mutant enzyme as compared to 464,000 M-1 s-1 in wild-type papain. With a Gln19Ser variant, the activity is even lower, with a kcat/KM value of 760 M-1 s-1. The 60- and 600-fold decreases in kcat/KM correspond to changes in free energy of catalysis of 2.4 and 3.8 kcal/mol for Gln19Ala and Gln19Ser, respectively. In both cases, the decrease in activity is in large part attributable to a decrease in kcat, while KM values are only slightly affected. These results indicate that the Oxyanion hole is operational in the papain-catalyzed hydrolysis of CBZ-Phe-Arg-MCA and constitute the first direct evidence of a mechanistic requirement for Oxyanion stabilization in the transition state of reactions catalyzed by cysteine proteases. The equilibrium constants Ki for inhibition of the papain mutants by the aldehyde Ac-Phe-Gly-CHO have also been determined. Contrary to the results with the substrate, mutation at position 19 of papain has a very small effect on binding of the inhibitor.(ABSTRACT TRUNCATED AT 250 WORDS)
