Rate-equilibria relationships in intramolecular proton transfer in human carbonic anhydrase III

Silverman, David N.; Tu, Cong; Chen, Xian; Tanhauser, Susan M.; Kresge, A. J.; Laipis, Philip J.

doi:10.1021/bi00091a029

Cited by 90 publications

(157 citation statements)

References 41 publications

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“…This lack of curvature is in contrast to the very curved free energy plots for bimolecular proton transfer between nitrogen and oxygen acids and bases occurring non-enzymatically in solution (39) and is also in contrast to the very curved plots and low intrinsic kinetic barrier observed for general acid catalysis in site-specific mutants of carbonic anhydrase (40). The lack of curvature in Fig.…”

Section: Discussionmentioning

confidence: 66%

“…This observation was made both for non-enzymatic proton transfer between electronegative atoms (41,42) and for the enzymatic case of carbonic anhydrase (40,43). An explanation for a maximum in isotope effect near ⌬pK a value of zero in proton transfer reactions is based on a comparison of symmetric and asymmetric transition states by Westheimer (44).…”

Section: And 2) and Solvent Hydrogen Isotope Effects For Activation Omentioning

confidence: 99%

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Activation of the Proton Transfer Pathway in Catalysis by Iron Superoxide Dismutase

Greenleaf

Silverman

2002

Journal of Biological Chemistry

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Catalysis by Escherichia coli and Porphyromonas gingivalis iron superoxide dismutase was activated by addition of primary amines, as measured by pulse radiolysis and stopped-flow spectrophotometry. This activation was saturable for most amines investigated, and a free energy plot of the apparent second-order rate constant of activation was linear as a function of the pK a of the amine, indicating activation by proton transfer. Amines provide an alternate rather than the only pathway for proton transfer, and catalysis was appreciable in the absence of amines. Solvent hydrogen isotope effects were near unity for amine activation, which is consistent with rate-contributing proton transfer if the pK a of the proton acceptor on the enzyme is not in the region of the pK a values of the amines studied, from 7.8 to 10.6. The activation of catalysis by these amines was uncompetitive with respect to superoxide, interpreted as proton transfer in a ternary complex of amine with the enzyme-bound peroxide dianion.The superoxide dismutases (SODs) 1 are cyclic redox enzymes that provide protection against oxidative damage caused by the reactions of the superoxide radical anion O 2 . . SODs have been characterized with manganese, iron, copper/zinc, or nickel as the redox active metal (1-3). The catalysis of the dismutation of superoxide occurs in two stages in which the metal ion, designated M in Reactions 1 and 2, alternates between the M 3ϩ and M 2ϩ forms (2-4),Iron superoxide dismutase (Fe-SOD), found in prokaryotes, and Mn-SOD, found in mitochondria as well as in prokaryotes, are highly similar in sequence (5) and in crystal structure (6, 7). Despite this high degree of structural homology, substitution of one metal for the other generally results in an inactive enzyme (8,9). A subclass of SOD exists that is able to utilize either manganese or iron as catalytic metal ion; these are termed cambialistic SODs and are of significant interest from the perspective of metal specificity as well as catalytic mechanism. A well studied cambialistic SOD is that from Porphyromonas gingivalis, the crystal structure of which is reported for the manganese-and iron-containing forms (10). Although they all share common features of their catalytic pathways, the copper/ zinc-and nickel-containing SODs have structures unrelated to the manganese-and iron-containing SODs (2, 11).The crystal structures of the iron-and manganese-containing superoxide dismutases generally show a trigonal bipyramidal geometry about the oxidized metal with three histidines, one aspartic acid, and one solvent molecule as ligands (6, 7). Major features of the active site appear very similar in each enzyme, including the highly conserved hydrogen-bonded network connecting the metal-coordinated solvent molecule and residues Gln-69 2 (in Fe-SOD) or Gln-143 (in Mn-SOD), Tyr-34, His-30, and Tyr-166 from the adjacent subunit. Although this active site Gln emanates from a different backbone position in Fe-SOD and Mn-SOD, the side chain orientation is very similar in both. Thi...

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Section: Discussionmentioning

confidence: 66%

Section: And 2) and Solvent Hydrogen Isotope Effects For Activation Omentioning

confidence: 99%

Activation of the Proton Transfer Pathway in Catalysis by Iron Superoxide Dismutase

Greenleaf

Silverman

2002

Journal of Biological Chemistry

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“…The exothermicity of the reaction from the present calculations, 4.4 kcal/mol with ZPE, is in reasonable agreement with experimental estimates. The reaction is thought to be nearly thermoneutral in the protein based on the similar pK a values of the zinc-bound water (estimated to be around 6 32 ) and His 64 (pK a ∼ 7 46 ).…”

Section: Resultsmentioning

confidence: 99%

“…30 The measured rate constant for the proton transfer in the wild-type CA is on the order of 10 6 s -1 (the activation free energy for proton transfer in solution is estimated to be 2.4 kcal/mol from NMR relaxation measurement, 31 which corresponds to a rate on the order of 10 s -1 ), and a substantial effort has been made to understand the correlation between the proton transfer rate and the pK a difference between the proton donor and the acceptor in the framework of Marcus theory extended to proton transfer reactions. 25a, 32 It was found that the kinetic data for a series of mutants under different buffer conditions can be fitted by Marcus theory with a very small intrinsic barrier of 1-2 kcal/mol and a large reorganization term (about 10 kcal/mol) for bringing the solvent and protein side chains into the right conformation for proton transfer. 25a The precise origin of this reorganization term is not completely clear, although it was suggested that it involves either orienting the bridging water molecules in the active site or a flip of the His64 side chain from an outward to inward orientation.…”

Section: Introductionmentioning

confidence: 99%

Is a “Proton Wire” Concerted or Stepwise? A Model Study of Proton Transfer in Carbonic Anhydrase

2003

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The energetics of proton transfer reactions in carbonic anhydrase (CA) have been studied with an active site model. Specifically, proton transfer from a zinc-bound water molecule to a histidine residue mediated by a numbers of water molecules was investigated. With two or three bridging water molecules, the proton transfers are fully or nearly fully concerted and only one saddle point exists. With an additional water molecule that forms a ring bridge, an intermediate is formed in which one of the water molecules exists as a hydronium ion. In contrast to previous calculations in which either a low-level of theory was employed or a stepwise mechanism was assumed, the energetics obtained from the current work are approximately consistent with the experimental estimates. In all of the scenarios, the motion of more than one proton is involved in the transition state, which is in agreement with the experimental observation that the reaction rates in H 2 O/D 2 O mixture have an exponential dependence on the fraction of D 2 O in the solvent. For three (W3) or four waters (W4), the proton transfer to the "His 64" model is hardly involved in the transition state, suggesting that the orientation of the proton acceptor is less important than for only two waters (W2). Thus, the W3 and W4 results are consistent with the experimental observation that many kinetic properties of the H64A mutant of CA in well-buffered imidazole solution are similar to the wild type. The barrier height increases, and the barrier frequency (and therefore, the contribution of tunneling) decreases as the number of bridging water molecules increases. Overall, these investigations demonstrate that the proton transfer reaction in CA is sensitive to the nature and structure of the water bridge, which would be influenced by the dynamics of the water molecules and amino acids in the active site of the protein.

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“…where the barrier heights can be read off from left to right in Figure 2 [45][46][47]. Because the transit time from one barrier to the next one a distance of a few angstroms away is less than a picosecond the proton arrives with some kinetic energy that has not been completely thermalized leading to a small reduction in the barrier heights.…”

Section: Discussionmentioning

confidence: 99%

Charge transport along proton wires

Karahka¹,

Kreuzer²

2013

Biointerphases

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Using density functional theory we look at the quantum mechanics of charge transport along water wires both with free ends and donor/acceptor terminated. With the intermediate geometries in the DFT iterations we can follow the charge transfer mechanism and also construct the energy landscape explicitly. It shows activation barriers when a proton is transferred from one water molecule to the next. This, together with snapshots of intermediate geometries, leads to a justification and further elucidation of the Grotthuss mechanism and the Bjerrum effect. The charge transfer times and the conductivity of the proton wire are obtained in agreement with experimental results.

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Rate-equilibria relationships in intramolecular proton transfer in human carbonic anhydrase III

Cited by 90 publications

References 41 publications

Activation of the Proton Transfer Pathway in Catalysis by Iron Superoxide Dismutase

Activation of the Proton Transfer Pathway in Catalysis by Iron Superoxide Dismutase

Is a “Proton Wire” Concerted or Stepwise? A Model Study of Proton Transfer in Carbonic Anhydrase

Charge transport along proton wires

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