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Vargas-Sánchez M, Alcocer J, Puche E, Sánchez-Carrillo S. Abiotic processes control carbon dioxide dynamics in temperate karst lakes. PeerJ 2024; 12:e17393. [PMID: 38799067 PMCID: PMC11127641 DOI: 10.7717/peerj.17393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/25/2024] [Indexed: 05/29/2024] Open
Abstract
Inland waters are crucial in the carbon cycle, contributing significantly to the global CO2 fluxes. Carbonate lakes may act as both sources and sinks of CO2 depending on the interactions between the amount of dissolved inorganic carbon (DIC) inputs, lake metabolisms, and geochemical processes. It is often difficult to distinguish the dominant mechanisms driving CO2 dynamics and their effects on CO2 emissions. This study was undertaken in three groundwater-fed carbonate-rich lakes in central Spain (Ruidera Lakes), severely polluted with nitrates from agricultural overfertilization. Diel and seasonal (summer and winter) changes in CO2 concentration (CCO2) DIC, and CO2 emissions-(FCO2)-, as well as physical and chemical variables, including primary production and phytoplanktonic chlorophyll-a were measured. In addition, δ13C-DIC, δ13C-CO2 in lake waters, and δ13C of the sedimentary organic matter were measured seasonally to identify the primary CO2 sources and processes. While the lakes were consistently CCO2 supersaturated and FCO2 was released to the atmosphere during both seasons, the highest CCO2 and DIC were in summer (0.36-2.26 µmol L-1). Our results support a strong phosphorus limitation for primary production in these lakes, which impinges on CO2 dynamics. External DIC inputs to the lake waters primarily drive the CCO2 and, therefore, the FCO2. The δ13C-DIC signatures below -12‰ confirmed the primary geogenic influence on DIC. As also suggested by the high values on the calcite saturation index, the Miller-Tans plot revealed that the CO2 source in the lakes was close to the signature provided by the fractionation of δ13C-CO2 from calcite precipitation. Therefore, the main contribution behind the CCO2 values found in these karst lakes should be attributed to the calcite precipitation process, which is temperature-dependent according to the seasonal change observed in δ13C-DIC values. Finally, co-precipitation of phosphate with calcite could partly explain the observed low phytoplankton production in these lakes and the impact on the contribution to increasing greenhouse gas emissions. However, as eutrophication increases and the soluble reactive phosphorus (SRP) content increases, the co-precipitation of phosphate is expected to be progressively inhibited. These thresholds must be assessed to understand how the CO32- ions drive lake co-precipitation dynamics. Carbonate regions extend over 15% of the Earth's surface but seem essential in the CO2 dynamics at a global scale.
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Affiliation(s)
- Mariana Vargas-Sánchez
- Graduate Program in Marine Sciences and Limnology, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Javier Alcocer
- Tropical Limnology Group, FES-Iztacala, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Eric Puche
- Biogeochemistry and Microbial Ecology Dep., Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
- Cavanilles Insitute of Biodiversity and Evolutionary Biology, Universidad de Valencia, Paterna, Valencia, Spain
| | - Salvador Sánchez-Carrillo
- Biogeochemistry and Microbial Ecology Dep., Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
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2
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Grasso G. THE USE OF MASS SPECTROMETRY TO STUDY ZN-METALLOPROTEASE-SUBSTRATE INTERACTIONS. MASS SPECTROMETRY REVIEWS 2020; 39:574-585. [PMID: 31898821 DOI: 10.1002/mas.21621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023]
Abstract
Zinc metalloproteases (ZnMPs) participate in diverse biological reactions, encompassing the synthesis and degradation of all the major metabolites in living organisms. In particular, ZnMPs have been recognized to play a very important role in controlling the concentration level of several peptides and/or proteins whose homeostasis has to be finely regulated for the correct physiology of cells. Dyshomeostasis of aggregation-prone proteins causes pathological conditions and the development of several different diseases. For this reason, in recent years, many analytical approaches have been applied for studying the interaction between ZnMPs and their substrates and how environmental factors can affect enzyme activities. In this scenario, mass spectrometric methods occupy a very important role in elucidating different aspects of ZnMPs-substrates interaction. These range from identification of cleavage sites to quantitation of kinetic parameters. In this work, an overview of all the main achievements regarding the application of mass spectrometric methods to investigating ZnMPs-substrates interactions is presented. A general experimental protocol is also described which may prove useful to the study of similar interactions. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Giuseppe Grasso
- Department of Chemical Sciences, Università degli Studi di Catania, Viale Andrea Doria 6, Catania, 95125, Italy
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3
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Ruszczycky MW, Liu HW. Measurement of Net Rate Constants from Enzyme Progress Curves without Curve Fitting. Biochemistry 2019; 58:4950-4956. [PMID: 31710808 DOI: 10.1021/acs.biochem.9b00762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A method is described whereby net rate constants can be directly inferred from the progress curves of enzyme intermediates without the need for model specification, numerical analysis, curve fitting, or the steady-state approximation. Specifically, if an enzyme intermediate in an ultimately irreversible serial subsequence is perturbed from and returns back to its equilibrium state as the substrate is consumed, then its net rate constant is given by the ratio of the total substrate consumed and the area under the progress curve for the enzyme intermediate. A rigorous analysis demonstrates this result to hold independent of the complete enzymatic reaction in which the subsequence is embedded, making it broadly applicable to a very wide range of kinetic mechanisms, including those complicated by inhibition. As a theoretical consequence, it is shown that traditionally steady-state parameters such as kcat, kcat/KM, and net rate constants can be expressed as limiting ratios of averages without requiring the steady-state hypothesis. Finally, a mock data set is generated for a system of contemporary interest that can serve as both an example of how the methodology would be used in practice and a proof of concept.
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Affiliation(s)
- Mark W Ruszczycky
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Hung-Wen Liu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States.,Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
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4
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Ushimaru R, Ruszczycky MW, Liu HW. Changes in Regioselectivity of H Atom Abstraction during the Hydroxylation and Cyclization Reactions Catalyzed by Hyoscyamine 6β-Hydroxylase. J Am Chem Soc 2018; 141:1062-1066. [PMID: 30545219 DOI: 10.1021/jacs.8b11585] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Hyoscyamine 6β-hydroxylase (H6H) is an αKG-dependent nonheme iron oxidase that catalyzes the oxidation of hyoscyamine to scopolamine via two separate reactions: hydroxylation followed by oxidative cyclization. Both of these reactions are expected to involve H atom abstraction from each of two adjacent carbon centers (C6 vs C7) in the substrate. During hydroxylation, there is a roughly 85:1 preference for H atom abstraction from C6 versus C7; however, this inverts to a 1:16 preference during cyclization. Furthermore, 18O incorporation experiments in the presence of deuterated substrate are consistent with the catalytic iron(IV)-oxo complex being able to support the coordination of an additional ligand during hydroxylation. These observations suggest that subtle differences in the substrate binding configuration can have significant consequences for the catalytic cycle of H6H.
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Affiliation(s)
- Richiro Ushimaru
- Department of Chemistry , University of Texas at Austin , Austin , TX 78712 , United States
| | - Mark W Ruszczycky
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , University of Texas at Austin , Austin , TX 78712 , United States
| | - Hung-Wen Liu
- Department of Chemistry , University of Texas at Austin , Austin , TX 78712 , United States.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , University of Texas at Austin , Austin , TX 78712 , United States
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5
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Sannikova N, Gerak CAN, Shidmoossavee FS, King DT, Shamsi Kazem Abadi S, Lewis AR, Bennet AJ. Both Chemical and Non-Chemical Steps Limit the Catalytic Efficiency of Family 4 Glycoside Hydrolases. Biochemistry 2018; 57:3378-3386. [PMID: 29630821 DOI: 10.1021/acs.biochem.8b00117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The glycoside hydrolase family 4 (GH4) α-galactosidase from Citrobacter freundii (MelA) catalyzes the hydrolysis of fluoro-substituted phenyl α-d-galactopyranosides by utilizing two cofactors, NAD+ and a metal cation, under reducing conditions. In order to refine the mechanistic understanding of this GH4 enzyme, leaving group effects were measured with various metal cations. The derived βlg value on V/ K for strontium activation is indistinguishable from zero (0.05 ± 0.12). Deuterium kinetic isotope effects (KIEs) were measured for the activated substrates 2-fluorophenyl and 4-fluorophenyl α-d-galactopyranosides in the presence of Sr2+, Y3+, and Mn2+, where the isotopic substitution was on the carbohydrate at C-2 and/or C-3. To determine the contributing factors to the virtual transition state (TS) on which the KIEs report, kinetic isotope effects on isotope effects were measured on these KIEs using doubly deuterated substrates. The measured D V/ K KIEs for MelA-catalyzed hydrolysis of 2-fluorophenyl α-d-galactopyranoside are closer to unity than the measured effects on 4-fluorophenyl α-d-galactopyranoside, irrespective of the site of isotopic substitution and of the metal cation activator. These observations are consistent with hydride transfer at C-3 to the on-board NAD+, deprotonation at C-2, and a non-chemical step contributing to the virtual TS for V/ K.
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6
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Schneider TW, Hren MT, Ertem MZ, Angeles-Boza AM. [RuII(tpy)(bpy)Cl]+-Catalyzed reduction of carbon dioxide. Mechanistic insights by carbon-13 kinetic isotope effects. Chem Commun (Camb) 2018; 54:8518-8521. [DOI: 10.1039/c8cc03009j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
13C kinetic isotope effect determinations combined with DFT calculations provide insight on the CO2 reduction reaction catalyzed by a ruthenium complex.
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Affiliation(s)
| | - M. T. Hren
- Department of Chemistry
- University of Connecticut
- Storrs
- USA
| | - M. Z. Ertem
- Chemistry Division
- Energy & Photon Sciences Directorate
- Brookhaven National Laboratory
- Upton
- USA
| | - A. M. Angeles-Boza
- Department of Chemistry
- University of Connecticut
- Storrs
- USA
- Institute of Materials Science
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7
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Investigation of the mechanism of the SpnF-catalyzed [4+2]-cycloaddition reaction in the biosynthesis of spinosyn A. Proc Natl Acad Sci U S A 2017; 114:10408-10413. [PMID: 28874588 DOI: 10.1073/pnas.1710496114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The Diels-Alder reaction is one of the most common methods to chemically synthesize a six-membered carbocycle. While it has long been speculated that the cyclohexene moiety found in many secondary metabolites is also introduced via similar chemistry, the enzyme SpnF involved in the biosynthesis of the insecticide spinosyn A in Saccharopolyspora spinosa is the first enzyme for which catalysis of an intramolecular [Formula: see text]-cycloaddition has been experimentally verified as its only known function. Since its discovery, a number of additional standalone [Formula: see text]-cyclases have been reported as potential Diels-Alderases; however, whether their catalytic cycles involve a concerted or stepwise cyclization mechanism has not been addressed experimentally. Here, we report direct experimental interrogation of the reaction coordinate for the [Formula: see text]-carbocyclase SpnF via the measurement of [Formula: see text]-secondary deuterium kinetic isotope effects (KIEs) at all sites of [Formula: see text] rehybridization for both the nonenzymatic and enzyme-catalyzed cyclization of the SpnF substrate. The measured KIEs for the nonenzymatic reaction are consistent with previous computational results implicating an intermediary state between formation of the first and second carbon-carbon bonds. The KIEs measured for the enzymatic reaction suggest a similar mechanism of cyclization within the enzyme active site; however, there is evidence that conformational restriction of the substrate may play a role in catalysis.
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8
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Ruszczycky MW, Liu HW. Theory and Application of the Relationship Between Steady-State Isotope Effects on Enzyme Intermediate Concentrations and Net Rate Constants. Methods Enzymol 2017; 596:459-499. [PMID: 28911781 PMCID: PMC5837895 DOI: 10.1016/bs.mie.2017.07.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Steady-state kinetic isotope effects on enzyme-catalyzed reactions are often interpreted in terms of the microscopic rate constants associated with the elementary reactions of interest. Unfortunately, this approach can lead to confusion, especially when more than one elementary reaction is isotopically sensitive, because it forces one to consider the full catalytic cycle one step at a time rather than as a complete whole. Herein we argue that shifting focus from intrinsic effects to net rate constants and enzyme intermediate concentrations provides a more natural and holistic interpretation by which the effects of partial rate limitation are more easily understood. In doing so, we demonstrate how the experimental determination of isotope effects on enzyme intermediate concentrations allows a direct determination of isotope effects on net rate constants. The chapter is divided into three main sections. The first outlines the basic theory and its interpretation. The second discusses an application of the theory in the study of the radical SAM enzyme DesII. The final section then provides the complete mathematical treatment.
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Affiliation(s)
| | - Hung-Wen Liu
- University of Texas at Austin, Austin, TX, United States
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9
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10
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Measurement of Kinetic Isotope Effects by Continuously Monitoring Isotopologue Ratios Using NMR Spectroscopy. Methods Enzymol 2017. [DOI: 10.1016/bs.mie.2017.06.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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11
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Abstract
[4 + 2]-Cycloadditions are increasingly being recognized in the biosynthetic pathways of many structurally complex natural products. A relatively small collection of enzymes from these pathways have been demonstrated to increase rates of cyclization and impose stereochemical constraints on the reactions. While mechanistic investigation of these enzymes is just beginning, recent studies have provided new insights with implications for understanding their biosynthetic roles, mechanisms of catalysis, and evolutionary origin.
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Affiliation(s)
- Byung-Sun Jeon
- Department of Chemistry and ‡Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
| | - Shao-An Wang
- Department of Chemistry and ‡Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
| | - Mark W Ruszczycky
- Department of Chemistry and ‡Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
| | - Hung-Wen Liu
- Department of Chemistry and ‡Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
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12
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Schneider TW, Ertem MZ, Muckerman JT, Angeles-Boza AM. Mechanism of Photocatalytic Reduction of CO2 by Re(bpy)(CO)3Cl from Differences in Carbon Isotope Discrimination. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01208] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Taylor W. Schneider
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - Mehmed Z. Ertem
- Chemistry Division, Energy & Photon Sciences Directorate, Brookhaven National Laboratory, Building 555A, Upton, New York 11973, United States
| | - James T. Muckerman
- Chemistry Division, Energy & Photon Sciences Directorate, Brookhaven National Laboratory, Building 555A, Upton, New York 11973, United States
| | - Alfredo M. Angeles-Boza
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
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13
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Khan S, Yang KR, Ertem MZ, Batista VS, Brudvig GW. Mechanism of Manganese-Catalyzed Oxygen Evolution from Experimental and Theoretical Analyses of 18O Kinetic Isotope Effects. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01976] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sahr Khan
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Ke R. Yang
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Mehmed Z. Ertem
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
- Chemistry
Department, Brookhaven National Laboratory, Building 555A, Upton, New
York 11973, United States
| | - Victor S. Batista
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Gary W. Brudvig
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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14
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Kinetic isotope effects for studying post-translational modifying enzymes. Curr Opin Chem Biol 2012; 16:472-8. [PMID: 23146439 DOI: 10.1016/j.cbpa.2012.10.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/14/2012] [Accepted: 10/15/2012] [Indexed: 11/20/2022]
Abstract
The ongoing development of new experimental approaches for the measurement of isotope effects is improving our understanding of the physical and chemical changes that occur during biological catalysis. Biological catalysis involves numerous steps that include binding, conformational changes, chemical catalysis and product release. The critical points on the free energy surface for biologically catalyzed reactions include all bound intermediates and the intervening transition states. Isotope effects can be used to investigate both intermediate (equilibrium isotope effects) and transition state (kinetic isotope effects) structures along the reaction coordinate. This review details new techniques for measuring isotope effects and provides several examples of their use in solving transition state structures for post-translational modifying enzymes.
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15
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Silva RG, Kipp DR, Schramm VL. Constrained bonding environment in the Michaelis complex of Trypanosoma cruzi uridine phosphorylase. Biochemistry 2012; 51:6715-7. [PMID: 22870934 DOI: 10.1021/bi300914q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The transition state for the Trypanosoma cruzi uridine phosphorylase (TcUP) reaction has an expanded S(N)2 character. We used binding isotope effects (BIE's) to probe uridine distortion in the complex with TcUP and sulfate to mimic the Michaelis complex. Inverse 1'-(3)H and 5'-(3)H BIE's indicate a constrained bonding environment of these groups in the complex. Quantum chemical modeling identified a uridine conformer whose calculated BIE's match the experimental values. This conformer differs in sugar pucker and uracil orientation from the unbound conformer and the transition-state structure. These results support ground-state stabilization in the Michaelis complex.
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Affiliation(s)
- Rafael G Silva
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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16
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Griswold WR, Castro JN, Fisher AJ, Toney MD. Ground-state electronic destabilization via hyperconjugation in aspartate aminotransferase. J Am Chem Soc 2012; 134:8436-8. [PMID: 22551424 DOI: 10.1021/ja302809e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Binding isotope effects for l-aspartate reacting with the inactive K258A mutant of PLP-dependent aspartate aminotransferase to give a stable external aldimine intermediate are reported. They provide direct evidence for electronic ground-state destabilization via hyperconjugation. The smaller equilibrium isotope effect with deazaPLP-reconstituted K258A indicates that the pyridine nitrogen plays an important role in labilizing the Cα-H bond.
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Affiliation(s)
- Wait R Griswold
- Department of Chemistry, University of California - Davis, 95616, United States
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17
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Hoepker AC, Collum DB. Computational studies of lithium diisopropylamide deaggregation. J Org Chem 2011; 76:7985-93. [PMID: 21888365 DOI: 10.1021/jo2015642] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Density functional theory computations [MP2/6-31G(d)//B3LYP/6-31G(d)] on the deaggregation of lithium diisopropylamide (LDA) dimer solvated by two tetrahydrofuran ligands to give the corresponding trisolvated monomer show eight structurally distinct minima. The barriers to exchange are comparable to those expected from experimental studies showing rate-limiting deaggregations. The role of conformational isomerism in deaggregation and the extent that deaggregation rates dictate LDA reactivity under synthetically important conditions are considered.
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Affiliation(s)
- Alexander C Hoepker
- Department of Chemistry and Chemical Biology Baker Laboratory, Cornell University, Ithaca, New York 14853-1301, United States
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18
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Heuts DPHM, Gummadova JO, Pang J, Rigby SEJ, Scrutton NS. Reaction of vascular adhesion protein-1 (VAP-1) with primary amines: mechanistic insights from isotope effects and quantitative structure-activity relationships. J Biol Chem 2011; 286:29584-93. [PMID: 21737458 DOI: 10.1074/jbc.m111.232850] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human vascular adhesion protein-1 (VAP-1) is an endothelial copper-dependent amine oxidase involved in the recruitment and extravasation of leukocytes at sites of inflammation. VAP-1 is an important therapeutic target for several pathological conditions. We expressed soluble VAP-1 in HEK293 EBNA1 cells at levels suitable for detailed mechanistic studies with model substrates. Using the model substrate benzylamine, we analyzed the steady-state kinetic parameters of VAP-1 as a function of solution pH. We found two macroscopic pK(a) values that defined a bell-shaped plot of turnover number k(cat,app) as a function of pH, representing ionizable groups in the enzyme-substrate complex. The dependence of (k(cat)/K(m))(app) on pH revealed a single pK(a) value (∼9) that we assigned to ionization of the amine group in free benzylamine substrate. A kinetic isotope effect (KIE) of 6 to 7.6 on (k(cat)/K(m))(app) over the pH range of 6 to 10 was observed with d(2)-benzylamine. Over the same pH range, the KIE on k(cat) was found to be close to unity. The unusual KIE values on (k(cat)/K(m))(app) were rationalized using a mechanistic scheme that includes the possibility of multiple isotopically sensitive steps. We also report the analysis of quantitative structure-activity relationships (QSAR) using para-substituted protiated and deuterated phenylethylamines. With phenylethylamines we observed a large KIE on k(cat,app) (8.01 ± 0.28 with phenylethylamine), indicating that C-H bond breakage is limiting for 2,4,5-trihydroxyphenylalanine quinone reduction. Poor correlations were observed between steady-state rate constants and QSAR parameters. We show the importance of combining KIE, QSAR, and structural studies to gain insight into the complexity of the VAP-1 steady-state mechanism.
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Affiliation(s)
- Dominic P H M Heuts
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
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19
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Hoepker AC, Gupta L, Ma Y, Faggin MF, Collum DB. Regioselective lithium diisopropylamide-mediated ortholithiation of 1-chloro-3-(trifluoromethyl)benzene: role of autocatalysis, lithium chloride catalysis, and reversibility. J Am Chem Soc 2011; 133:7135-51. [PMID: 21500823 PMCID: PMC3102585 DOI: 10.1021/ja200906z] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ortholithiation of 1-chloro-3-(trifluoromethyl)benzene with lithium diisopropylamide (LDA) in tetrahydrofuran at -78 °C displays characteristics of reactions in which aggregation events are rate limiting. Metalation with lithium-chloride-free LDA involves a rate-limiting deaggregation via dimer-based transition structures. The post-rate-limiting proton transfers are suggested to involve highly solvated triple ions. Autocatalysis by the resulting aryllithiums or catalysis by traces (<100 ppm) of LiCl diverts the reaction through di- and trisolvated monomer-based pathways for metalation at the 2 and 6 positions, respectively. The regiochemistry is dictated by a combination of kinetically controlled metalations overlaid by an equilibration involving diisopropylamine that is shown to occur by the microscopic reverse of the monomer-based metalations.
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Affiliation(s)
- Alexander C. Hoepker
- Department of Chemistry and Chemical Biology Baker Laboratory, Cornell University, Ithaca, New York 14853-1301
| | - Lekha Gupta
- Department of Chemistry and Chemical Biology Baker Laboratory, Cornell University, Ithaca, New York 14853-1301
| | - Yun Ma
- Department of Chemistry and Chemical Biology Baker Laboratory, Cornell University, Ithaca, New York 14853-1301
| | - Marc F. Faggin
- Department of Chemistry and Chemical Biology Baker Laboratory, Cornell University, Ithaca, New York 14853-1301
| | - David B. Collum
- Department of Chemistry and Chemical Biology Baker Laboratory, Cornell University, Ithaca, New York 14853-1301
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21
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Elsner M. Stable isotope fractionation to investigate natural transformation mechanisms of organic contaminants: principles, prospects and limitations. ACTA ACUST UNITED AC 2010; 12:2005-31. [PMID: 21038038 DOI: 10.1039/c0em00277a] [Citation(s) in RCA: 238] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gas chromatography-isotope ratio mass spectrometry (GC-IRMS) has made it possible to analyze natural stable isotope ratios (e.g., (13)C/(12)C, (15)N/(14)N, (2)H/(1)H) of individual organic contaminants in environmental samples. They may be used as fingerprints to infer contamination sources, and may demonstrate, and even quantify, the occurrence of natural contaminant transformation by the enrichment of heavy isotopes that arises from degradation-induced isotope fractionation. This review highlights an additional powerful feature of stable isotope fractionation: the study of environmental transformation mechanisms. Isotope effects reflect the energy difference of isotopologues (i.e., molecules carrying a light versus a heavy isotope in a particular molecular position) when moving from reactant to transition state. Measuring isotope fractionation, therefore, essentially allows a glimpse at transition states! It is shown how such position-specific isotope effects are "diluted out" in the compound average measured by GC-IRMS, and how a careful evaluation in mechanistic scenarios and by dual isotope plots can recover the underlying mechanistic information. The mathematical framework for multistep isotope fractionation in environmental transformations is reviewed. Case studies demonstrate how isotope fractionation changes in the presence of mass transfer, enzymatic commitment to catalysis, multiple chemical reaction steps or limited bioavailability, and how this gives information about the individual process steps. Finally, it is discussed how isotope ratios of individual products evolve in sequential or parallel transformations, and what mechanistic insight they contain. A concluding session gives an outlook on current developments, future research directions and the potential for bridging the gap between laboratory and real world systems.
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Affiliation(s)
- Martin Elsner
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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22
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Schramm VL. Binding isotope effects: boon and bane. Curr Opin Chem Biol 2007; 11:529-36. [PMID: 17869163 PMCID: PMC2066183 DOI: 10.1016/j.cbpa.2007.07.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 07/23/2007] [Accepted: 07/27/2007] [Indexed: 11/19/2022]
Abstract
Kinetic isotope effects are increasingly applied to investigate enzyme reactions and have been used to understand transition state structure, reaction mechanisms, quantum mechanical hydride ion tunneling and to design transition state analogue inhibitors. Binding isotope effects are an inherent part of most isotope effect measurements but are usually assumed to be negligible. More detailed studies have established surprisingly large binding isotope effects with lactate dehydrogenase, hexokinase, thymidine phosphorylase, and purine nucleoside phosphorylase. Binding reactants into catalytic sites immobilizes conformationally flexible groups, polarizes bonds, and distorts bond angle geometry, all of which generate binding isotope effects. Binding isotope effects are easily measured and provide high-resolution and detailed information on the atomic changes resulting from ligand-macromolecular interactions. Although binding isotope effects complicate kinetic isotope effect analysis, they also provide a powerful tool for finding atomic distortion in molecular interactions.
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Affiliation(s)
- Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, United States.
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23
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Murkin AS, Birck MR, Rinaldo-Matthis A, Shi W, Taylor EA, Schramm VL. Neighboring group participation in the transition state of human purine nucleoside phosphorylase. Biochemistry 2007; 46:5038-49. [PMID: 17407325 PMCID: PMC2526054 DOI: 10.1021/bi700147b] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The X-ray crystal structures of human purine nucleoside phosphorylase (PNP) with bound inosine or transition-state analogues show His257 within hydrogen bonding distance of the 5'-hydroxyl. The mutants His257Phe, His257Gly, and His257Asp exhibited greatly decreased affinity for Immucillin-H (ImmH), binding this mimic of an early transition state as much as 370-fold (Km/Ki) less tightly than native PNP. In contrast, these mutants bound DADMe-ImmH, a mimic of a late transition state, nearly as well as the native enzyme. These results indicate that His257 serves an important role in the early stages of transition-state formation. Whereas mutation of His257 resulted in little variation in the PNP x DADMe-ImmH x SO4 structures, His257Phe x ImmH x PO4 showed distortion at the 5'-hydroxyl, indicating the importance of H-bonding in positioning this group during progression to the transition state. Binding isotope effect (BIE) and kinetic isotope effect (KIE) studies of the remote 5'-(3)H for the arsenolysis of inosine with native PNP revealed a BIE of 1.5% and an unexpectedly large intrinsic KIE of 4.6%. This result is interpreted as a moderate electronic distortion toward the transition state in the Michaelis complex with continued development of a similar distortion at the transition state. The mutants His257Phe, His257Gly, and His257Asp altered the 5'-(3)H intrinsic KIE to -3, -14, and 7%, respectively, while the BIEs contributed 2, 2, and -2%, respectively. These surprising results establish that forces in the Michaelis complex, reported by the BIEs, can be reversed or enhanced at the transition state.
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Affiliation(s)
| | | | | | | | | | - Vern L. Schramm
- * To whom correspondence should be addressed. E-mail, ; Telephone, (718) 430-2813; Fax, (718) 430-8565
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