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Avvaru BS, Arenas DJ, Tu C, Tanner DB, McKenna R, Silverman DN. Comparison of solution and crystal properties of Co(II)-substituted human carbonic anhydrase II. Arch Biochem Biophys 2010; 502:53-9. [PMID: 20637176 DOI: 10.1016/j.abb.2010.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 07/09/2010] [Accepted: 07/11/2010] [Indexed: 11/24/2022]
Abstract
The visible absorption of crystals of Co(II)-substituted human carbonic anhydrase II (Co(II)-HCA II) were measured over a pH range of 6.0-11.0 giving an estimate of pK(a) 8.4 for the ionization of the metal-bound water in the crystal. This is higher by about 1.2 pK(a) units than the pK(a) near 7.2 for Co(II)-CA II in solution. This effect is attributed to a nonspecific ionic strength effect of 1.4M citrate in the precipitant solution used in the crystal growth. A pK(a) of 8.3 for the aqueous ligand of the cobalt was measured for Co(II)-HCA II in solution containing 0.8M citrate. Citrate is not an inhibitor of the catalytic activity of Co(II)-HCA II and was not observed in crystal structures. The X-ray structures at 1.5-1.6A resolution of Co(II)-HCA II were determined for crystals prepared at pH 6.0, 8.5 and 11.0 and revealed no conformational changes of amino-acid side chains as a result of the use of citrate. However, the studies of Co(II)-HCA II did reveal a change in metal coordination from tetrahedral at pH 11 to a coordination consistent with a mixed population of both tetrahedral and penta-coordinate at pH 8.5 to an octahedral geometry characteristic of the oxidized enzyme Co(III)-HCA II at pH 6.0.
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Tu C, Scafa N, Zhang X, Silverman D. A Comparison of Membrane Inlet Mass Spectrometry and Nitric Oxide (NO) Electrode Techniques to Detect NO in Aqueous Solution. ELECTROANAL 2010. [DOI: 10.1002/elan.200900407] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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78
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Mikulski R, Tu C, Swenson ER, Silverman DN. Reactions of nitrite in erythrocyte suspensions measured by membrane inlet mass spectrometry. Free Radic Biol Med 2010; 48:325-31. [PMID: 19913092 PMCID: PMC2818671 DOI: 10.1016/j.freeradbiomed.2009.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 10/28/2009] [Accepted: 11/05/2009] [Indexed: 10/20/2022]
Abstract
The reactions of nitrite with deoxygenated human erythrocytes were examined using membrane inlet mass spectrometry to detect the accumulation of NO in an extracellular solution. In this method an inlet utilizing a silicon rubber membrane is submerged in cell suspensions and allows NO to pass from the extracellular solution into the mass spectrometer. This provides a direct, continuous, and quantitative determination of nitric oxide concentrations over long periods without the necessity of purging the suspension with inert gas. We have not observed accumulation of NO compared with controls on a physiologically relevant time scale and conclude that, within the limitations of the mass spectrometric method and our experimental conditions, erythrocytes do not generate a net efflux of NO after the addition of millimolar concentrations of nitrite. Moreover, there was no evidence at the mass spectrometer of the accumulation of a peak at mass 76 that would indicate N(2)O(3), an intermediate that decays into NO and NO(2). Inhibition of red cell membrane anion exchangers and aquaporins did not affect these processes.
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Maupin CM, Zheng J, Tu C, McKenna R, Silverman DN, Voth GA. Effect of active-site mutation at Asn67 on the proton transfer mechanism of human carbonic anhydrase II. Biochemistry 2009; 48:7996-8005. [PMID: 19634894 DOI: 10.1021/bi901037u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rate-limiting proton transfer (PT) event in the site-specific mutant N67L of human carbonic anhydrase II (HCA II) has been examined by kinetic, X-ray, and simulation approaches. The X-ray crystallography studies, which were previously reported, and molecular dynamics (MD) simulations indicate that the proton shuttling residue, His64, predominantly resides in the outward orientation with a significant disruption of the ordered water in the active site for the dehydration pathway. While disorder is seen in the active-site water, water cluster analysis indicates that the N67L mutant may form water clusters similar to those seen in the wild-type (WT). For the hydration pathway of the enzyme, the active site water cluster analysis reveals an inability of the N67L mutant to stabilize water clusters when His64 is in the inward orientation, thereby favoring PT when His64 is in the outward orientation. The preference of the N67L mutant to carry out the PT when His64 is in the outward orientation for both the hydration and dehydration pathway is reasoned to be the main cause of the observed reduction in the overall rate. To probe the mechanism of PT, solvent H/D kinetic isotope effects (KIEs) were experimentally studied with catalysis measured by the exchange of (18)O between CO(2) and water. The values obtained from the KIEs were determined as a function of the deuterium content of solvent, using the proton inventory method. No differences were detected in the overarching mechanism of PT between WT and N67L HCA II, despite changes in the active-site water structure and/or the orientation of His64.
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80
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Rowlett RS, Tu C, Lee J, Herman AG, Chapnick DA, Shah SH, Gareiss PC. Allosteric site variants of Haemophilus influenzae beta-carbonic anhydrase. Biochemistry 2009; 48:6146-56. [PMID: 19459702 DOI: 10.1021/bi900663h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Haemophilus influenzae beta-carbonic anhydrase (HICA) is hypothesized to be an allosteric protein that is regulated by the binding of bicarbonate ion to a non-catalytic (inhibitory) site that controls the ligation of Asp44 to the catalytically essential zinc ion. We report here the X-ray crystallographic structures of two variants (W39F and Y181F) involved in the binding of bicarbonate ion in the non-catalytic site and an active-site variant (D44N) that is incapable of forming a strong zinc ligand. The alteration of Trp39 to Phe increases the apparent K(i) for bicarbonate inhibition by 4.8-fold. While the structures of W39F and Y181F are very similar to the wild-type enzyme, the X-ray crystal structure of the D44N variant reveals that it has adopted an active-site conformation nearly identical to that of non-allosteric beta-carbonic anhydrases. We propose that the structure of the D44N variant is likely to be representative of the active conformation of the enzyme. These results lend additional support to the hypothesis that HICA is an allosteric enzyme that can adopt active and inactive conformations, the latter of which is stabilized by bicarbonate ion binding to a non-catalytic site.
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81
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Li Y, Wang H, Oosterwijk E, Tu C, Shiverick KT, Silverman DN, Frost SC. Expression and activity of carbonic anhydrase IX is associated with metabolic dysfunction in MDA-MB-231 breast cancer cells. Cancer Invest 2009; 27:613-23. [PMID: 19367501 DOI: 10.1080/07357900802653464] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The expression of carbonic anhydrase IX (CAIX), a marker for hypoxic tumors, is correlated with poor prognosis in breast cancer patients. We show herein that the MDA-MB-231 cells, a "triple-negative," basal B line, express exclusively CAIX, while a luminal cell line (T47D) expresses carbonic anhydrase XII (CAXII). CAIX expression in the basal B cells is both density- and hypoxia-dependent and is correlated with carbonic anhydrase activity. Evidence is provided that CAIX contributes to extracellular acidification through studies on pH, lactic acid production, and CAIX inhibition. Together, these studies suggest that CAIX expression and activity is associated with metabolic dysfunction in MDA-MB-231 cells.
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Genis C, Sippel KH, Case N, Cao W, Avvaru BS, Tartaglia LJ, Govindasamy L, Tu C, Agbandje-McKenna M, Silverman DN, Rosser CJ, McKenna R. Design of a carbonic anhydrase IX active-site mimic to screen inhibitors for possible anticancer properties. Biochemistry 2009; 48:1322-31. [PMID: 19170619 PMCID: PMC2713499 DOI: 10.1021/bi802035f] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Recently, a convincing body of evidence has accumulated suggesting that the overexpression of carbonic anhydrase isozyme IX (CA IX) in some cancers contributes to the acidification of the extracellular matrix, which in turn promotes the growth and metastasis of the tumor. These observations have made CA IX an attractive drug target for the selective treatment of certain cancers. Currently, there is no available X-ray crystal structure of CA IX, and this lack of availability has hampered the rational design of selective CA IX inhibitors. In light of these observations and on the basis of structural alignment homology, using the crystal structure of carbonic anhydrase II (CA II) and the sequence of CA IX, a double mutant of CA II with Ala65 replaced by Ser and Asn67 replaced by Gln has been constructed to resemble the active site of CA IX. This CA IX mimic has been characterized kinetically using (18)O-exchange and structurally using X-ray crystallography, alone and in complex with five CA sulfonamide-based inhibitors (acetazolamide, benzolamide, chlorzolamide, ethoxzolamide, and methazolamide), and compared to CA II. This structural information has been evaluated by both inhibition studies and in vitro cytotoxicity assays and shows a correlated structure-activity relationship. Kinetic and structural studies of CA II and CA IX mimic reveal chlorzolamide to be a more potent inhibitor of CA IX, inducing an active-site conformational change upon binding. Additionally, chlorzolamide appears to be cytotoxic to prostate cancer cells. This preliminary study demonstrates that the CA IX mimic may provide a useful model to design more isozyme-specific CA IX inhibitors, which may lead to development of new therapeutic treatments of some cancers.
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Tu C, Mikulski R, Swenson ER, Silverman DN. Reactions of nitrite with hemoglobin measured by membrane inlet mass spectrometry. Free Radic Biol Med 2009; 46:14-9. [PMID: 18848984 PMCID: PMC2849169 DOI: 10.1016/j.freeradbiomed.2008.09.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 09/08/2008] [Accepted: 09/09/2008] [Indexed: 11/27/2022]
Abstract
Membrane inlet mass spectrometry was used to observe nitric oxide in the well-studied reaction of nitrite with hemoglobin. The membrane inlet was submerged in the reaction solutions and measured NO in solution via its flux across a semipermeable membrane leading to the mass spectrometer detecting the mass-to-charge ratio m/z 30. This method measures NO directly in solution and is an alternate approach compared with methods that purge solutions to measure NO. Addition to deoxy-Hb(Fe(II)) (near 38 microM heme concentration) of nitrite in a range of 80 microM to 16 mM showed no accumulation of either NO or N(2)O(3) on a physiologically relevant time scale with a sensitivity near 1 nM. The addition of nitrite to oxy-Hb(Fe(II)) and met-Hb(Fe(III)) did not accumulate free NO to appreciable extents. These observations show that for several minutes after mixing nitrite with hemoglogin, free NO does not accumulate to levels exceeding the equilibrium level of NO. The presence of cyanide ions did not alter the appearance of the data; however, the presence of 2 mM mercuric ions at the beginning of the experiment with deoxy-Hb(Fe(II)) shortened the initial phase of NO accumulation and increased the maximal level of free, unbound NO by about twofold. These experiments appear consistent with no role of met-Hb(Fe(III)) in the generation of NO and an increase in nitrite reductase activity caused by the presumed binding of mercuric to cysteine residues. These results raise questions about the ability of reduction of nitrite mediated by deoxy-Hb(Fe(II)) to play a role in vasodilation.
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84
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Zheng J, Avvaru BS, Tu C, McKenna R, Silverman DN. Role of hydrophilic residues in proton transfer during catalysis by human carbonic anhydrase II. Biochemistry 2008; 47:12028-36. [PMID: 18942852 DOI: 10.1021/bi801473w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Catalysis by the zinc metalloenzyme human carbonic anhydrase II (HCA II) is limited in maximal velocity by proton transfer between His64 and the zinc-bound solvent molecule. Asn62 extends into the active site cavity of HCA II adjacent to His64 and has been shown to be one of several hydrophilic residues participating in a hydrogen-bonded solvent network within the active site. We compared several site-specific mutants of HCA II with replacements at position 62 (Ala, Val, Leu, Thr, and Asp). The efficiency of catalysis in the hydration of CO 2 for the resulting mutants has been characterized by (18)O exchange, and the structures of the mutants have been determined by X-ray crystallography to 1.5-1.7 A resolution. Each of these mutants maintained the ordered water structure observed by X-ray crystallography in the active site cavity of wild-type HCA II; hence, this water structure was not a variable in comparing with wild type the activities of mutants at residue 62. Crystal structures of wild-type and N62T HCA II showed both an inward and outward orientation of the side chain of His64; however, other mutants in this study showed predominantly inward (N62A, N62V, N62L) or predominantly outward (N62D) orientations of His64. A significant role of Asn62 in HCA II is to permit two conformations of the side chain of His64, the inward and outward, that contributes to maximal efficiency of proton transfer between the active site and solution. The site-specific mutant N62D had a mainly outward orientation of His64, yet the difference in p K a between the proton donor His64 and zinc-bound hydroxide was near zero, as in wild-type HCA II. The rate of proton transfer in catalysis by N62D HCA II was 5% that of wild type, showing that His64 mainly in the outward orientation is associated with inefficient proton transfer compared with His64 in wild type which shows both inward and outward orientations. These results emphasize the roles of the residues of the hydrophilic side of the active site cavity in maintaining efficient catalysis by carbonic anhydrase.
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Barrese, AA, Genis C, Fisher SZ, Orwenyo JN, Kumara MT, Dutta SK, Phillips E, Kiddle JJ, Tu C, Silverman DN, Govindasamy L, Agbandje-McKenna M, McKenna R, Tripp BC. Inhibition of Carbonic Anhydrase II by Thioxolone: A Mechanistic and Structural Study. Biochemistry 2008; 47:3174-84. [DOI: 10.1021/bi702385k] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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86
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McElhinney LM, Marston DA, Stankov S, Tu C, Black C, Johnson N, Jiang Y, Tordo N, Müller T, Fooks AR. Molecular epidemiology of lyssaviruses in Eurasia. DEVELOPMENTS IN BIOLOGICALS 2008; 131:125-131. [PMID: 18634471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The Lyssavirus genus, a member of the Rhabdoviridae family, consists of seven established related viruses (genotypes 1-7). Rabies cases in Eurasia are principally attributed to three of these genotypes, namely genotype 1 (RABV, classical rabies) and to a lesser extent genotypes 5 and 6 (European bat lyssaviruses type-1 and -2). In addition, four newly identified divergent lyssaviruses have been isolated from insectivorous bats. The molecular diversity of classical rabies viruses (genotype 1, RABV) has been studied at the global level and reference has been made to the existence of a number of European strains in a range of mammalian species. It is accepted that these viruses cluster within a 'Cosmopolitan Lineage' having ancestral roots in Europe in the 17th century before its widespread dispersal to Asia, Africa and the Americas as a result of European exploration and colonization.
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Tu C, Swenson ER, Silverman DN. Membrane inlet for mass spectrometric measurement of nitric oxide. Free Radic Biol Med 2007; 43:1453-7. [PMID: 17936190 DOI: 10.1016/j.freeradbiomed.2007.07.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Revised: 06/07/2007] [Accepted: 07/24/2007] [Indexed: 10/23/2022]
Abstract
We point out the advantages of membrane inlet mass spectrometry for the measurement of nitric oxide in aqueous solution. The membrane inlet probe was a 1.0-cm segment of Silastic tubing attached to the vacuum inlet leading to the ion source. Silastic is a semipermeable silicon rubber that allows flux of uncharged substances including nitric oxide (NO). The use of such an inlet to measure NO has several advantages that we demonstrate in this report. It provides a direct, continuous, and quantitative determination of dissolved nitric oxide concentrations over long periods of real time. The use of such an inlet in our system had a response time of 5 to 7 s and a detection lower limit with the current model of 1.0 nM. This apparatus was used to measure the generation of NO from solutions of nitrite, NONOates, and nitroprusside. The usefulness of such an inlet in measuring NO in physiological systems is discussed.
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Xiao C, Liu Y, Jiang Y, Magoffin DE, Guo H, Xuan H, Wang G, Wang LF, Tu C. Monoclonal antibodies against the nucleocapsid proteins of henipaviruses: production, epitope mapping and application in immunohistochemistry. Arch Virol 2007; 153:273-81. [PMID: 17978885 DOI: 10.1007/s00705-007-1079-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Accepted: 10/14/2007] [Indexed: 11/29/2022]
Abstract
Four monoclonal antibodies (mAbs) were generated by immunizing BALB/C mice with recombinant nucleocapsid protein (N) of Nipah virus (NiV) and Hendra virus (HeV) expressed in E. coli. Two mAbs each were obtained for the HeV N and NiV N, respectively. All four mAbs displayed specific reactivity with the recombinant N proteins of both viruses by western blot, which was further confirmed by immunofluorescent antibody assay using fixed insect cells infected with recombinant baculoviruses expressing either the HeV or NiV N protein. Epitope mapping using a 12-mer random peptide phage display library revealed two linear antigenic sites of the henipavirus N proteins, KLxR (aa 17-20) and FKREM (aa 446-450), which have not been reported previously. Two of the mAbs were able to specifically recognize HeV antigens by immunohistochemical staining of lung tissue sections of a horse experimentally infected with HeV. These reagents will be a useful addition to the collection of tools essential for further research and improvement in diagnosis of henipaviruses.
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89
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Jiang Y, Yu X, Wang L, Lu Z, Liu H, Xuan H, Hu Z, Tu C. An outbreak of pig rabies in Hunan province, China. Epidemiol Infect 2007; 136:504-8. [PMID: 17559696 PMCID: PMC2870836 DOI: 10.1017/s0950268807008874] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The first dog-associated outbreak of rabies in swine in China (Hunan province) has been diagnosed and the related virus isolated. Sequence analysis showed that the pig isolate was a genotype 1 rabies virus with a very high nucleotide identity to local dog isolates.
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90
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Elder I, Fisher Z, Laipis PJ, Tu C, McKenna R, Silverman DN. Structural and kinetic analysis of proton shuttle residues in the active site of human carbonic anhydrase III. Proteins 2007; 68:337-43. [PMID: 17427958 DOI: 10.1002/prot.21403] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We report the X-ray crystal structures and rate constants for proton transfer in site-specific mutants of human carbonic anhydrase III (HCA III) that place a histidine residue in the active-site cavity: K64H, R67H, and K64H-R67N HCA III. Prior evidence from the exchange of 18O between CO2 and water measured by mass spectrometry shows each mutant to have enhanced proton transfer in catalysis compared with wild-type HCA III. However, His64 in K64H and K64H-R67N HCA III have at most a capacity for proton transfer that is only 13% that of His64 in HCA II. This reduced rate in mutants of HCA III is associated with a constrained side-chain conformation of His64, which is oriented outward, away from the active-site zinc in the crystal structures. This conformation appears stabilized by a prominent pi stacking interaction of the imidazole ring of His64 with the indole ring of Trp5 in mutants of HCA III. This single orientation of His64 in K64H HCA III predominates also in a double mutant K64H-R67N HCA III, indicating that the positive charge of Arg67 does not influence the observed conformation of His64 in the crystal structure. Hence, the structures and catalytic activity of these mutants of HCA III containing His64 account only in small part for the lower activity of this isozyme compared with HCA II. His67 in R67H HCA III was also shown to be a proton shuttle residue, having a capacity for proton transfer that was approximately four times that of His64 in K64H HCA III. This is most likely due to its proximity and orientation inward towards the zinc-bound solvent. These results emphasize the significance of side chain orientation and range of available conformational states as characteristics of an efficient proton shuttle in carbonic anhydrase.
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Fisher SZ, Tu C, Bhatt D, Govindasamy L, Agbandje-McKenna M, McKenna R, Silverman DN. Speeding up proton transfer in a fast enzyme: kinetic and crystallographic studies on the effect of hydrophobic amino acid substitutions in the active site of human carbonic anhydrase II. Biochemistry 2007; 46:3803-13. [PMID: 17330962 DOI: 10.1021/bi602620k] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Catalysis of the hydration of CO2 by human carbonic anhydrase isozyme II (HCA II) is sustained at a maximal catalytic turnover of 1 mus-1 by proton transfer between a zinc-bound solvent and bulk solution. This mechanism of proton transfer is facilitated via the side chain of His64, which is located 7.5 A from the zinc, and mediated via intervening water molecules in the active-site cavity. Three hydrophilic residues that have previously been shown to contribute to the stabilization of these intervening waters were replaced with hydrophobic residues (Y7F, N62L, and N67L) to determine their effects on proton transfer. The structures of all three mutants were determined by X-ray crystallography, with crystals equilibrated from pH 6.0 to 10.0. A range of changes were observed in the ordered solvent and the conformation of the side chain of His64. Correlating these structural variants with kinetic studies suggests that the very efficient proton transfer (approximately 7 micros-1) observed for Y7F HCA II in the dehydration direction, compared with the wild type and other mutants of this study, is due to a combination of three features. First, in this mutant, the side chain of His64 showed an appreciable inward orientation pointing toward the active-site zinc. Second, in the structure of Y7F HCA II, there is an unbranched chain of hydrogen-bonded waters linking the proton donor His64 and acceptor zinc-bound hydroxide. Finally, the difference in pKa of the donor and acceptor appears favorable for proton transfer. The data suggest roles for residues 7, 62, and 67 in fine-tuning the properties of His64 for optimal proton transfer in catalysis.
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Fisher SZ, Maupin CM, Budayova-Spano M, Govindasamy L, Tu C, Agbandje-McKenna M, Silverman DN, Voth GA, McKenna R. Atomic Crystal and Molecular Dynamics Simulation Structures of Human Carbonic Anhydrase II: Insights into the Proton Transfer Mechanism†,‡. Biochemistry 2007; 46:2930-7. [PMID: 17319692 DOI: 10.1021/bi062066y] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human carbonic anhydrase II (HCA II) is a zinc-metalloenzyme that catalyzes the reversible interconversion of CO2 and HCO3-. The rate-limiting step of this catalysis is the transfer of a proton between the Zn-bound solvent molecule and residue His64. In order to fully characterize the active site structural features implicated in the proton transfer mechanism, the refined X-ray crystal structure of uncomplexed wild type HCA II to 1.05 A resolution with an Rcryst value of 12.0% and an Rfree value of 15.1% has been elucidated. This structure provides strong clues as to the pathway of the intramolecular proton transfer between the Zn-bound solvent and His64. The structure emphasizes the role of the solvent network, the unique positioning of solvent molecule W2, and the significance of the dual conformation of His64 in the active site. The structure is compared with molecular dynamics (MD) simulation calculations of the Zn-bound hydroxyl/His64+ (charged) and the Zn-bound water/His64 (uncharged) HCA II states. A comparison of the crystallographic anisotropic atomic thermal parameters and MD simulation root-mean-square fluctuation values show excellent agreement in the atomic motion observed between the two methods. It is also interesting that the observed active site solvent positions in the crystal structure are also the most probable positions of the solvent during the MD simulations. On the basis of the comparative study of the MD simulation results, the HCA II crystal structure observed is most likely in the Zn-bound water/His64 state. This conclusion is based on the following observations: His64 is mainly (80%) orientated in an inward conformation; electron density omit maps infer that His64 is not charged in an either inward or outward conformation; and the Zn-bound solvent is most likely a water molecule.
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93
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Hsieh CY, Wu ZB, Tung MC, Tu C, Lo SP, Chang TC, Chang CD, Chen SC, Hsieh YC, Tsai SS. In situ hybridization and RT-PCR detection of Macrobrachium rosenbergii nodavirus in giant freshwater prawn, Macrobrachium rosenbergii (de Man), in Taiwan. JOURNAL OF FISH DISEASES 2006; 29:665-71. [PMID: 17169113 DOI: 10.1111/j.1365-2761.2006.00762.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Between January and March 2006, suspected outbreaks of white tail disease were observed in post-larvae and juveniles of Macrobrachium rosenbergii in hatcheries and nursery ponds at Kaohsiung and Pingtung Counties in southern Taiwan. Pathognomonic lesions showed the presence of large oval and/or irregular basophilic, cytoplasmic inclusion bodies in the infected muscles and hepatopancreas. Reverse transcriptase polymerase chain reaction (RT-PCR) assay and in situ hybridization (ISH) revealed evidence of M. rosenbergii nodavirus (MrNV) infection but did not detect extra small virus. Phylogenetic analysis indicated that there were very high identities between nucleotide sequences among six strains obtained in this study (99.5-100%), moderate identities with Caribbean and Indian strains (98.2-98.6%), but slightly lower identity with a Chinese strain (95.2%). This is the first confirmation of MrNV in giant freshwater prawns, using an RT-PCR and ISH, in Taiwan.
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94
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Bhatt D, Fisher SZ, Tu C, McKenna R, Silverman DN. Location of binding sites in small molecule rescue of human carbonic anhydrase II. Biophys J 2006; 92:562-70. [PMID: 17071654 PMCID: PMC1751391 DOI: 10.1529/biophysj.106.093203] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Small molecule rescue of mutant forms of human carbonic anhydrase II (HCA II) occurs by participation of exogenous donors/acceptors in the proton transfer pathway between the zinc-bound water and solution. To examine more thoroughly the energetics of this activation, we have constructed a mutant, H64W HCA II, which we have shown is activated by 4-methylimidazole (4-MI) by a mechanism involving the binding of 4-MI to the side chain of Trp-64 approximately 8 A from the zinc. A series of experiments are consistent with the activation of H64W HCA II by the interaction of imidazole and pyridine derivatives as exogenous proton donors with the indole ring of Trp-64; these experiments include pH profiles and H/D solvent isotope effects consistent with proton transfer, observation of approximately fourfold greater activation with the mutant containing Trp-64 compared with Gly-64, and the observation by x-ray crystallography of the binding of 4-MI associated with the indole side chain of Trp-64 in W5A-H64W HCA II. Proton donors bound at the less flexible side chain of Trp-64 in W5A-H64W HCA II do not show activation, but such donors bound at the more flexible Trp-64 of H64W HCA II do show activation, supporting suggestions that conformational mobility of the binding site is associated with more efficient proton transfer. Evaluation using Marcus theory showed that the activation of H64W HCA II by these proton donors was reflected in the work functions w(r) and w(p) rather than in the intrinsic Marcus barrier itself, consistent with the role of solvent reorganization in catalysis.
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Fisher SZ, Tariku I, Case NM, Tu C, Seron T, Silverman DN, Linser PJ, McKenna R. Expression, purification, kinetic, and structural characterization of an α-class carbonic anhydrase from Aedes aegypti (AaCA1). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1413-9. [PMID: 16920039 DOI: 10.1016/j.bbapap.2006.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Accepted: 06/22/2006] [Indexed: 11/24/2022]
Abstract
Carbonic anhydrases (CAs) are zinc-containing metalloenzymes that catalyze the interconversion of carbon dioxide and bicarbonate. The alpha-class CAs are found predominantly in vertebrates, but they are also expressed in insects like mosquitoes. Recently, an alpha-CA from the midgut of Aedes aegypti larvae (AaCA1) was identified, cloned, and subsequently shown to share high sequence homologous to human CA I (HCA I). This paper presents the bacterial expression, purification, and kinetic characterization of the soluble CA domain of AaCA1. The data show AaCA1 is a highly active CA that displays inhibition by methazolamide and ethoxzolamide with nM affinity. Additionally, a homology model of AaCA1, based on the crystal structure of HCA I, is presented and the overall structure, active site, and surface charge properties are compared to those of HCA I and II. Measurements of catalysis show that AaCA1 is more like HCA II in terms of proton transfer, but more similar to HCA I in terms of conversion of carbon dioxide to bicarbonate, and these differences are rationalized in terms of structure. These results also indicate that amino acid differences in the active site of AaCA1 compared to human CAs could be used to design specific CA inhibitors for the management of mosquito populations.
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96
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Ren X, Tu C, Bhatt D, Perry JJP, Tainer JA, Cabelli DE, Silverman DN. Kinetic and structural characterization of human manganese superoxide dismutase containing 3-fluorotyrosines. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2005.10.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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97
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Cronk JD, Rowlett RS, Zhang KYJ, Tu C, Endrizzi JA, Lee J, Gareiss PC, Preiss JR. Identification of a Novel Noncatalytic Bicarbonate Binding Site in Eubacterial β-Carbonic Anhydrase. Biochemistry 2006; 45:4351-61. [PMID: 16584170 DOI: 10.1021/bi052272q] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structures of beta class carbonic anhydrases (beta-CAs) determined so far fall into two distinct subclasses based on the observed coordination of the catalytic zinc (Zn2+) ion. The subclass of beta-CAs that coordinate Zn2+ tetrahedrally with four protein-derived ligands is represented by the structures of orthologues from Porphyridium purpureum, Escherichia coli, and Mycobacterium tuberculosis. Here we present the structure of an additional member of that subclass, that from Haemophilus influenzae, as well as detailed kinetic analysis, revealing the correspondence between structural classification and kinetic profile for this subclass. In addition, we identify a unique, noncatalytic binding mode for the substrate bicarbonate that occurs in both the H. influenzae and E. coli enzymes. The kinetic and structural analysis indicates that binding of bicarbonate in this site of the enzyme may modulate its activity by influencing a pH-dependent, cooperative transition between active and inactive forms. We hypothesize that the two structural subclasses of beta-CAs may provide models for the proposed active and inactive forms of the H. influenzae and E. coli enzymes.
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98
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del Pilar Corena M, VanEkeris L, Salazar MI, Bowers D, Fiedler MM, Silverman D, Tu C, Linser PJ. Carbonic anhydrase in the adult mosquito midgut. ACTA ACUST UNITED AC 2006; 208:3263-73. [PMID: 16109888 DOI: 10.1242/jeb.01739] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have previously demonstrated the involvement of carbonic anhydrase (CA) in larval mosquito midgut physiology. In this study, we used Hansson's histochemistry to examine the distribution of the enzyme in the midgut of Aedes aegypti, Aedes albopictus, Culex quinquefasciatus, Culex nigripalpus, Ochlerotatus taeniorhynchus, Anopheles albimanus and Anopheles quadrimaculatus adult mosquitoes. Additionally, we quantitated CA content in the anterior and posterior midgut of adult males and females from these species using the 18O isotope exchange method coupled to mass spectrometry. We also tested the effect of CA inhibitors such as methazolamide and acetazolamide in the alkalization of the midgut in females from these species. Our results indicate that CA is present in the midgut of adults from the species studied and that it appears to be preferentially associated with the posterior midgut in both males and females. CA inhibitors appear to have a profound effect on midgut pH indicating that this enzyme might play a key role in the maintenance of this pH.
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99
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Tao J, Wang Y, Yang Z, Tu C, Xu MG, Wang JM. Circulating endothelial progenitor cell deficiency contributes to impaired arterial elasticity in persons of advancing age. J Hum Hypertens 2006; 20:490-5. [PMID: 16496018 DOI: 10.1038/sj.jhh.1001996] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Reduced arterial elasticity is a hallmark of ageing in healthy humans and appears to occur independently of coexisting disease processes. Endothelial-cell injury and dysfunction may be responsible for this fall in arterial elasticity. We hypothesized that circulating endothelial progenitor cells (EPCs) are involved in endothelial repair and that lack of EPCs contributes to impaired arterial elasticity. A total of 56 healthy male volunteers were divided into young (n=26) and elderly (n=30) groups. Large and small artery elasticity indices were noninvasively assessed using pulse wave analysis. The number of circulating EPCs was measured by using flow cytometry. Cells demonstrating DiI-acLDL and FITC-ulex lectin double-positive fluorescence were identified as EPCs. C1 large artery elasticity and C2 small artery elasticity indices were significantly reduced in the elderly group compared with the young group (11.73+/-1.45 vs 16.88+/-1.69 ml/mm Hg x 10, P<0.001; 8.40+/-1.45 vs 10.58+/-1.18 ml/mm Hg x 100, P<0.001, respectively). In parallel, the number of circulating EPCs was significantly reduced in the elderly group compared with the young group (0.13+/-0.02 vs 0.17+/-0.04%, P<0.05). The number of circulating EPCs correlated with C1 large and C2 small artery elasticity indices (r=0.47, P<0.01; r=0.4, P<0.01). The present findings suggest that the fall in circulating EPCs with subsequently impaired endothelial-cell repair and function contributes to reduced arterial elasticity in humans with ageing. The decrease in circulating EPCs may serve as a surrogate biologic measure of vascular function and human age.
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100
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Fisher SZ, Govindasamy L, Tu C, Agbandje-McKenna M, Silverman DN, Rajaniemi HJ, McKenna R. Structure of human salivary alpha-amylase crystallized in a C-centered monoclinic space group. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:88-93. [PMID: 16511271 PMCID: PMC2150953 DOI: 10.1107/s1744309105042491] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Accepted: 12/19/2005] [Indexed: 11/11/2022]
Abstract
Human salivary alpha-amylase (HSA) is a major secretory protein component of saliva and has important biological functions, including the initial digestion of starch. HSA acts as a monomer and mediates the hydrolysis of alpha-1,4-glucosidic linkages in oligosaccharides. To date, all published crystal structures of HSA have been crystallized as monomers in space group P2(1)2(1)2(1). Here, the serendipitous purification, crystallization and ultimate structure determination of a HSA non-crystallographic symmetry (NCS) dimer, while attempting to purify human carbonic anhydrase VI (HCA VI) from saliva using an affinity resin for alpha-class carbonic anhydrases, is presented. On further investigation, it was shown that HSA could only be copurified using the affinity resin in the presence of HCA VI which is glycosylated and not the non-glycosylated HCA II. The identification of the HSA crystals was carried out by peptide mapping and mass spectrometry. HSA was shown to have crystallized as an NCS dimer in space group C2, with unit-cell parameters a = 150.9, b = 72.3, c = 91.3 A, beta = 102.8 degrees. The NCS dimer crystal structure is reported to 3.0 A resolution, with a refined Rcryst of 0.228. The structure is compared with the previously reported P2(1)2(1)2(1) monomer structures and the crystal packing and dimer interface are discussed.
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