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Jiang Y, Zhang X, Nie H, Fan J, Di S, Fu H, Zhang X, Wang L, Tang C. Dissecting diazirine photo-reaction mechanism for protein residue-specific cross-linking and distance mapping. Nat Commun 2024; 15:6060. [PMID: 39025860 PMCID: PMC11258254 DOI: 10.1038/s41467-024-50315-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024] Open
Abstract
While photo-cross-linking (PXL) with alkyl diazirines can provide stringent distance restraints and offer insights into protein structures, unambiguous identification of cross-linked residues hinders data interpretation to the same level that has been achieved with chemical cross-linking (CXL). We address this challenge by developing an in-line system with systematic modulation of light intensity and irradiation time, which allows for a quantitative evaluation of diazirine photolysis and photo-reaction mechanism. Our results reveal a two-step pathway with mainly sequential generation of diazo and carbene intermediates. Diazo intermediate preferentially targets buried polar residues, many of which are inaccessible with known CXL probes for their limited reactivity. Moreover, we demonstrate that tuning light intensity and duration enhances selectivity towards polar residues by biasing diazo-mediated cross-linking reactions over carbene ones. This mechanistic dissection unlocks the full potential of PXL, paving the way for accurate distance mapping against protein structures and ultimately, unveiling protein dynamic behaviors.
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Affiliation(s)
- Yida Jiang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xinghe Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Honggang Nie
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jianxiong Fan
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Shuangshuang Di
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Hui Fu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xiu Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Lijuan Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Chun Tang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Center for Quantitative Biology, PKU-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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3
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Marchand A, Czar MF, Eggel EN, Kaeslin J, Zenobi R. Studying biomolecular folding and binding using temperature-jump mass spectrometry. Nat Commun 2020; 11:566. [PMID: 31992698 PMCID: PMC6987177 DOI: 10.1038/s41467-019-14179-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/19/2019] [Indexed: 01/14/2023] Open
Abstract
Characterizing folding and complex formation of biomolecules provides a view into their thermodynamics, kinetics and folding pathways. Deciphering kinetic intermediates is particularly important because they can often be targeted by drugs. The key advantage of native mass spectrometry over conventional methods that monitor a single observable is its ability to identify and quantify coexisting species. Here, we show the design of a temperature-jump electrospray source for mass spectrometry that allows one to perform fast kinetics experiments (0.16-32 s) at different temperatures (10-90 °C). The setup allows recording of both folding and unfolding kinetics by using temperature jumps from high to low, and low to high, temperatures. Six biological systems, ranging from peptides to proteins to DNA complexes, exemplify the use of this device. Using temperature-dependent experiments, the folding and unfolding of a DNA triplex are studied, providing detailed information on its thermodynamics and kinetics.
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Affiliation(s)
- Adrien Marchand
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093, Zurich, Switzerland
| | - Martin F Czar
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093, Zurich, Switzerland
| | - Elija N Eggel
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093, Zurich, Switzerland
| | - Jérôme Kaeslin
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093, Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093, Zurich, Switzerland.
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4
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Cheng S, Wu Q, Xiao H, Chen H. Online Monitoring of Enzymatic Reactions Using Time-Resolved Desorption Electrospray Ionization Mass Spectrometry. Anal Chem 2017; 89:2338-2344. [DOI: 10.1021/acs.analchem.6b03975] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Si Cheng
- Center
for Intelligent Chemical Instrumentation, Department of Chemistry
and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, Ohio 45701, United States,
| | - Qiuhua Wu
- Center
for Intelligent Chemical Instrumentation, Department of Chemistry
and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, Ohio 45701, United States,
- Department
of Chemistry, College of Science, Agricultural University of Hebei, Baoding 071001, China
| | - He Xiao
- Center
for Intelligent Chemical Instrumentation, Department of Chemistry
and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, Ohio 45701, United States,
| | - Hao Chen
- Center
for Intelligent Chemical Instrumentation, Department of Chemistry
and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, Ohio 45701, United States,
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5
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Cong Y, Katipamula S, Trader CD, Orton DJ, Geng T, Baker ES, Kelly RT. Mass spectrometry-based monitoring of millisecond protein-ligand binding dynamics using an automated microfluidic platform. LAB ON A CHIP 2016; 16:1544-8. [PMID: 27009517 PMCID: PMC4846533 DOI: 10.1039/c6lc00183a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Characterizing protein-ligand binding dynamics is crucial for understanding protein function and for developing new therapeutic agents. We present a novel microfluidic platform that features rapid mixing of protein and ligand solutions, variable incubation times, and an integrated electrospray ionization source for mass spectrometry-based monitoring of protein-ligand binding dynamics. This platform offers many advantages, including solution-based binding, label-free detection, automated operation, rapid mixing, and low sample consumption.
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Affiliation(s)
- Yongzheng Cong
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA.
| | - Shanta Katipamula
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA.
| | - Cameron D Trader
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA.
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Tao Geng
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA.
| | - Erin S Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA.
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6
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Su X, Zhang J, Guo Y, Zhang Q. Study of Effects of Cigarette Smoke Condensates on Acetylcholinesterase Activity in Human Lung Epithelial Cells by Matrix-Assisted Laser Desorption/Ionization-Fourier Transform Mass Spectrometry. ANAL LETT 2012. [DOI: 10.1080/00032719.2012.700467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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7
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Chevreux G, Atmanene C, Lopez P, Ouazzani J, Van Dorsselaer A, Badet B, Badet-Denisot MA, Sanglier-Cianférani S. Monitoring the dynamics of monomer exchange using electrospray mass spectrometry: the case of the dimeric glucosamine-6-phosphate synthase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:431-439. [PMID: 21472562 DOI: 10.1007/s13361-010-0054-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2010] [Revised: 11/28/2010] [Accepted: 12/10/2010] [Indexed: 05/30/2023]
Abstract
Escherichia coli glucosamine-6-phosphate synthase (GlmS) is a dimeric enzyme from the glutamine-dependent amidotransferases family, which catalyses the conversion of D-fructose-6-phosphate (Fru6P) and glutamine (Gln) into D-glucosamine-6-phosphate (GlcN6P) and glutamate, respectively. Extensive X-ray crystallography investigations have been reported, highlighting the importance of the dimeric association to form the sugar active site as well as significant conformational changes of the protein upon substrate and product binding. In the present work, an approach based on time-resolved noncovalent mass spectrometry has been developed to study the dynamics of GlmS subunit exchange. Using (14)N versus (15)N labeled proteins, the kinetics of GlmS subunit exchange was monitored with the wild-type enzyme in the presence of different substrates and products as well as with the protein bearing a key amino acid mutation specially designed to weaken the dimer interface. Determination of rate constants of subunit exchange revealed important modifications of the protein dynamics: while glutamine, glutamate, and K603A mutation accelerates subunit exchange, Fru6P and GlcN6P totally prevent it. These results are described in light of the available structural information, providing additional useful data for both the characterization of GlmS catalytic process and the design of new GlmS inhibitors. Finally, time-resolved noncovalent MS can be proposed as an additional biophysical technique for real-time monitoring of protein dynamics.
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Affiliation(s)
- Guillaume Chevreux
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel 67087, Strasbourg, France
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8
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Robbins MD, Yoon OK, Barbula GK, Zare RN. Stopped-flow kinetic analysis using Hadamard transform time-of-flight mass spectrometry. Anal Chem 2010; 82:8650-7. [PMID: 20843011 DOI: 10.1021/ac101899n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A home-built stopped-flow apparatus is interfaced to a Hadamard transform time-of-flight mass spectrometer, which permits study of reaction kinetics with a time between reaction initiation and observation as short as about 100 ms and a sampling rate of chemical change that can approach 1 ms. This technique is applied to the trypsin-catalyzed hydrolysis of several peptides and is validated by comparing the results with literature values as well as to optical data obtained with the present stopped-flow apparatus. In addition, we report a kinetic study of the action of trypsin on a peptide having more than one cleavage site.
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Affiliation(s)
- Matthew D Robbins
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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9
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Roberts A, Furdui C, Anderson KS. Observation of a chemically labile, noncovalent enzyme intermediate in the reaction of metal-dependent Aquifex pyrophilus KDO8PS by time-resolved mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:1919-1924. [PMID: 20533322 PMCID: PMC3381509 DOI: 10.1002/rcm.4594] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The direct detection of intermediates in enzymatic reactions can yield important mechanistic insights but may be difficult due to short intermediate lifetimes and chemical instability. Using a rapid-mixing device coupled with electrospray ionization time-of-flight mass spectrometry, the noncovalent hemiketal intermediate in the reaction of metal-dependent 3-deoxy-D-manno-octulosonate-8-phosphate (KDO8P) synthase from Aquifex pyrophilus was observed in the millisecond time range. Using single turnover conditions, the noncovalent complexes of enzyme with Cd(2+):phosphoenolpyruvate, Cd(2+):phosphate, Cd(2+):KDO8P, and Cd(2+):intermediate complexes were resolved. The intermediate complex is present during times ranging from 50-630 ms, indicating that the intermediate builds up at the ambient temperatures of the experiment. This represents the first direct detection of the intermediate with a native metal-dependent KDO8PS, and further demonstrates that time-resolved mass spectrometry is a useful tool in mechanistic studies of enzymatic reactions.
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Affiliation(s)
- Anne Roberts
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Cristina Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157
| | - Karen S. Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA
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10
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Clarke DJ, Stokes AA, Langridge-Smith P, Mackay CL. Online quench-flow electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for elucidating kinetic and chemical enzymatic reaction mechanisms. Anal Chem 2010; 82:1897-904. [PMID: 20112916 DOI: 10.1021/ac9026302] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have developed an automated quench-flow microreactor which interfaces directly to an electrospray ionization (ESI) mass spectrometer. We have used this device in conjunction with ESI Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) to demonstrate the potential of this approach for studying the mechanistic details of enzyme reactions. For the model system chosen to test this device, namely, the pre-steady-state hydrolysis of p-nitrophenyl acetate by the enzyme chymotrypsin, the kinetic parameters obtained are in good agreement with those in the literature. To our knowledge, this is the first reported use of online quench-flow coupled with FTICR MS. Furthermore, we have exploited the power of FTICR MS to interrogate the quenched covalently bound enzyme intermediate using top-down fragmentation. The accurate mass capabilities of FTICR MS permitted the nature of the intermediate to be assigned with high confidence. Electron capture dissociation (ECD) fragmentation allowed us to locate the intermediate to a five amino acid section of the protein--which includes the known catalytic residue, Ser(195). This experimental approach, which uniquely can provide both kinetic and chemical details of enzyme mechanisms, is a potentially powerful tool for studies of enzyme catalysis.
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Affiliation(s)
- David J Clarke
- SIRCAMS, School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JJ, UK.
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11
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Ngu TT, Lee JA, Rushton MK, Stillman MJ. Arsenic metalation of seaweed Fucus vesiculosus metallothionein: the importance of the interdomain linker in metallothionein. Biochemistry 2009; 48:8806-16. [PMID: 19655782 DOI: 10.1021/bi9007462] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The presence of metallothionein in seaweed Fucus vesiculosus has been suggested as the protecting agent against toxic metals in the contaminated waters it can grow in. We report the first kinetic pathway data for A3+ binding to an algal metallothionein, F. vesiculosus metallothionein (rfMT). The time and temperature dependence of the relative concentrations of apo-rfMT and the five As-containing species have been determined following mixing of As3+ and apo-rfMT using electrospray ionization mass spectrometry (ESI MS). Kinetic analysis of the detailed time-resolved mass spectral data for As3+ metalation allows the simulation of the metalation reactions showing the consumption of apo-rfMT, the formation and consumption of As1- to As4-rfMT, and subsequent, final formation of As5-rfMT. The kinetic model proposed here provides a stepwise analysis of the metalation reaction showing time-resolved occupancy of the Cys7 and the Cys9 domain. The rate constants (M(-1) s(-1)) calculated from the fits for the 7-cysteine gamma domain are k1gamma, 19.8, and k2gamma, 1.4, and for the 9-cysteine beta domain are k1beta, 16.3, k2beta, 9.1, and k3beta, 2.2. The activation energies and Arrhenius factors for each of the reaction steps are also reported. rfMT has a long 14 residue linker, which as we show from analysis of the ESI MS data, allows each of its two domains to bind As3+ independently of each other. The analysis provides for the first time an explanation of the differing metal-binding properties of two-domain MTs with linkers of varying lengths, suggesting further comparison between plant (with long linkers) and mammalian (with short linkers) metallothioneins will shed light on the role of the interdomain linker.
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Affiliation(s)
- Thanh T Ngu
- Department of Chemistry, University of Western Ontario, London, Ontario, Canada N6A 5B7
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12
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Abstract
Metallothionein are small, cysteine-rich, metal-binding proteins that are found ubiquitously in nature. Most metallothioneins bind multiple metals in two well-defined metal-thiolate clusters. This perspective discusses the use of optical spectroscopy to study the metalation of metallothioneins and the emergence of electrospray ionization mass spectrometry as a means of studying the mechanism of metalation for metallothioneins. A brief history of past kinetic studies of cadmium metallothioneins and recent kinetic study advances for the arsenic metalation of metallothionein will be presented. Lastly, a possible functional role for the two-domain structure of metallothionein will be briefly discussed.
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Affiliation(s)
- Thanh T Ngu
- Department of Chemistry, The University of Western Ontario, London, CanadaN6A 5B7
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13
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Ngu TT, Easton A, Stillman MJ. Kinetic analysis of arsenic-metalation of human metallothionein: significance of the two-domain structure. J Am Chem Soc 2009; 130:17016-28. [PMID: 19053406 DOI: 10.1021/ja8060326] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metallothionein (MT) is ubiquitous in Nature, underlying MT's importance in the cellular chemistry of metals. Mammalian MT consists of two metal-binding domains while microorganisms like cyanobacteria consist of a single metal-binding domain MT. The evolution of a two-domain protein has been speculated on for some time; however, no conclusive evidence explaining the evolutionary necessity of the two-domain structure has been reported. The results presented in this report provide the complete kinetic analysis and subsequent mechanism of the As(3+)-metalation of the two-domain beta alpha hMT and the isolated single domain fragments using time- and temperature-resolved electrospray ionization mass spectrometry. The mechanism for beta alpha hMT binding As(3+) is noncooperative and involves six sequential bimolecular reactions in which the alpha domain binds As(3+) first followed by the beta domain. At room temperature (295 K) and pH 3.5, the sequential individual rate constants, k(n) (n = 1-6) for the As(3+)-metalation of beta alpha hMT starting at k(1beta alpha) are 25, 24, 19, 14, 8.7, and 3.7 M(-1)s(-1). The six rate constants follow an almost linear trend directly dependent on the number of unoccupied sites for the incoming metal. Analysis of the temperature-dependent kinetic electrospray ionization mass spectra data allowed determination of the activation energy for the formation of As(1)-H(17)-beta alpha hMT (14 kJ mol(-1)) and As(2-6)-beta alpha hMT (22 kJ mol(-1)). On the basis of the increased rate of metalation for the two-domain protein when compared with the isolated single-domain, we propose that there is an evolutionary advantage for the two-domain MT structures in higher organism, which allows MT to bind metals faster and, therefore, be a more efficient metal scavenger.
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Affiliation(s)
- Thanh T Ngu
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, N6A 5B7
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14
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Xu Z, Yao S, Wei Y, Zhou J, Zhang L, Wang C, Guo Y. Monitoring enzyme reaction and screening of inhibitors of acetylcholinesterase by quantitative matrix-assisted laser desorption/ionization Fourier transform mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:1849-55. [PMID: 18789720 DOI: 10.1016/j.jasms.2008.07.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Revised: 07/05/2008] [Accepted: 07/30/2008] [Indexed: 05/09/2023]
Abstract
A matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS)-based assay was developed for kinetic measurements and inhibitor screening of acetylcholinesterase. Here, FTMS coupled to MALDI was applied to quantitative analysis of choline using the ratio of choline/acetylcholine without the use of additional internal standard, which simplified the experiment. The Michaelis constant (K(m)) of acetylcholinesterase (AChE) was determined to be 73.9 micromol L(-1) by this approach. For Huperzine A, the linear mixed inhibition of AChE reflected the presence of competitive and noncompetitive components. The half maximal inhibitory concentration (IC(50)) value of galantamine obtained for AChE was 2.39 micromol L(-1). Inhibitory potentials of Rhizoma Coptidis extracts were identified with the present method. In light of the results the referred extracts as a whole showed inhibitory action against AChE. The use of high-resolution FTMS largely eliminated the interference with the determination of ACh and Ch, produced by the low-mass compounds of chemical libraries for inhibitor screening. The excellent correlation with the reported kinetic parameters confirms that the MS-based assay is both accurate and precise for determining kinetic constants and for identifying enzyme inhibitors. The obvious advantages were demonstrated for quantitative analysis and also high-throughput characterization. This study offers a perspective into the utility of MALDI-FTMS as an alternate quantitative tool for inhibitor screening of AChE.
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Affiliation(s)
- Zhe Xu
- Shanghai Mass Spectrometry Center, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, Shanghai, China
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15
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Abstract
The number of reported cases of chronic arsenic poisoning is on the rise throughout the world, making the study of the long-term effects of arsenic critical. As(3+) binds readily to biological thiols, including mammalian metallothionein (MT), which is an ubiquitous sulfur-rich metalloprotein known to coordinate a wide range of metals. The two-domain mammalian protein binds divalent metals (M) into two metal-thiolate clusters with stoichiometries of M(3)S(cys9) (beta) and M(4)S(cys11) (alpha). We report that As(3+) binds with stoichiometries of As(3)S(cys9) (beta) and As(3)S(cys11) (alpha) to the recombinant human metallothionein (rhMT) isoform 1a protein. Further, we report the complete kinetic analysis of the saturation reactions of the separate alpha and beta domains of rhMT with As(3+). Speciation in the metalation reactions was determined using time- and temperature-resolved electrospray ionization mass spectrometry. The binding reaction of As(3+) to the alpha and beta MT domains is shown to be noncooperative and involves three sequential, bimolecular metalation steps. The analyses allow for the first time the complete simulation of the experimental data for the stepwise metalation reaction of MT showing the relative concentrations of the metal-free, apo MT and each of the As-MT intermediate species as a function of time and temperature. At room temperature (298 K) and pH 3.5, the individual rate constants for the first, second, and third As(3+) binding to apo-alphaMT are 5.5, 6.3, and 3.9 M(-)(1) s(-)(1) and for apo-betaMT the constants are 3.6, 2.0, and 0.6 M(-)(1) s(-)(1). The activation energy for formation of As(1)-H(6)-betaMT is 32 kJ mol(-)(1), for As(2)-H(3)-betaMT it is 35 kJ mol(-)(1), for As(3)-betaMT it is 29 kJ mol(-)(1), for As(1)-H(8)-alphaMT it is 33 kJ mol(-)(1), for As(2)-H(5)-alphaMT it is 29 kJ mol(-)(1), and for As(3)-H(2)-alphaMT it is 23 kJ mol(-)(1).
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Affiliation(s)
- Thanh T Ngu
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7
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16
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Shipovskov S, Reimann CT. Electrospray ionization mass spectrometry in enzymology: uncovering the mechanisms of two-substrate reactions. Analyst 2007; 132:397-402. [PMID: 17471382 DOI: 10.1039/b615394c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The purpose of this review is to draw attention to the use of electrospray ionization mass spectrometry (ESI-MS) for monitoring the course of enzyme-substrate interactions, in the particular case of complex systems in which two substrates participate. The determination and characterization of intra-molecular reactions, especially those that occur in the enzyme active site, is not a trivial task in chemical kinetics, typically requiring long measurement times and relatively expensive techniques such as nuclear magnetic resonance (NMR), X-ray crystallography or electron microscopy (EM). However, nowadays almost all laboratories are equipped with or else have access to the ESI-MS technique. The aim of this review is to focus on the possibilities of employing even quite simple MS equipment to tackle different applications in studies of complex enzymatic systems.
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Affiliation(s)
- Stepan Shipovskov
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UKM1 7DN.
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17
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Tagore R, Chen H, Crabtree RH, Brudvig GW. Determination of μ-Oxo Exchange Rates in Di-μ-Oxo Dimanganese Complexes by Electrospray Ionization Mass Spectrometry. J Am Chem Soc 2006; 128:9457-65. [PMID: 16848483 DOI: 10.1021/ja061348i] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A time-resolved mass spectrometric technique has been used for the determination of rates of exchange of mu-O atoms with water for the complexes [(mes-terpy)2Mn2(III/IV)(mu-O)2(H2O)2](NO3)3 (1, mes-terpy = 4'-mesityl-2,2':6',2' '-terpyridine), [(bpy)4Mn2(III/IV)(mu-O)2](ClO4)3 (2, bpy = 2,2'-bipyridine), [(phen)4Mn2(III/IV)(mu-O)2](ClO4)3 (3, phen = 1,10-phenanthroline), [(bpea)2Mn2(III/IV)(mu-O)2(mu-OAc)](ClO4)2 (4, bpea = bis(2-pyridyl)ethylamine), [(bpea)2Mn2(IV/IV)(mu-O)2(mu-OAc)](ClO4)3 (4ox), [(terpy)4Mn4(IV/IV/IV/IV)(mu-O)5(H2O)2](ClO4)6 (5, terpy = 2,2':6',2''-terpyridine), and [(tacn)4Mn4(IV/IV/IV/IV)(mu-O)6]Br(3.5)(OH)0.5.6H2O (6, tacn = 1,4,7-triazacyclononane). The rate of exchange of mu-OAc bridges with free acetate in solution has been measured for complexes 4 and 4ox. These are the first measurements of rates of ligand exchange on biologically relevant high-valent Mn complexes. The data analysis method developed here is of general utility in the quantitation of isotope exchange processes by mass spectrometry. We find that the presence of labile coordination sites on Mn increases mu-O exchange rates, and that all-Mn(IV) states are more inert toward exchange than mixed Mn(III)-Mn(IV) states. The rates of mu-O exchange obtained in this work for a di-mu-oxo Mn2(III/IV) dimer with labile coordination sites are compared with the oxygen isotope incorporation rates from substrate water to evolved dioxygen measured in different S states of the oxygen evolving complex (OEC) of photosystem II (PSII). On the basis of this comparison, we propose that both substrate waters are not bound as mu-O bridges between Mn atoms in the S2 and S3 states of the OEC.
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Affiliation(s)
- Ranitendranath Tagore
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, USA
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Li Z, Sau AK, Furdui CM, Anderson KS. Probing the role of tightly bound phosphoenolpyruvate in Escherichia coli 3-deoxy-d-manno-octulosonate 8-phosphate synthase catalysis using quantitative time-resolved electrospray ionization mass spectrometry in the millisecond time range. Anal Biochem 2005; 343:35-47. [PMID: 15979047 DOI: 10.1016/j.ab.2005.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2005] [Accepted: 04/14/2005] [Indexed: 10/25/2022]
Abstract
Escherichia coli 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase catalyzes the condensation of phosphoenolpyruvate (PEP) and D-arabinose 5-phosphate (A5P) to produce KDO8P and inorganic phosphate. The enzyme is often isolated with varying amounts of tightly bound PEP substrate. To better understand the role of tightly bound PEP in E. coli KDO8P synthase catalysis, a combination of transient kinetic methodologies including rapid chemical quench and mass spectrometry techniques such as time-resolved electrospray ionization mass spectrometry (ESI-TOF MS) were used to study the enzyme purified both in the PEP-bound state and in the unbound state. Pre-steady state burst and single-turnover experiments using radiolabeled [1-(14)C] and [(32)P]A5P revealed significant kinetic differences between these enzyme preparations. The active sites concentrations for the bound and unbound states of the enzyme were almost the same (approximately 100%) and the product release for both states of the enzyme was rate limiting. However, the rate constant of product formation for the PEP-bound enzyme (125 s(-1)) was higher than that of the unbound enzyme (46 s(-1)). This was further confirmed by single-turnover experiments using radiolabeled [(32)P]A5P. Interestingly, when PEP was removed from the PEP-bound enzyme and external PEP was added before the kinetic experiments, both the pre-steady state burst and the single-turnover kinetic parameters were similar to those of the enzyme purified in the unbound state. The rate constants of product formation were determined as 44 s(-1) (burst experiment) and 48 s(-1) (single-turnover experiment). The reaction kinetics of the E. coli KDO8P synthase was also followed by time-resolved ESI mass spectrometry. To validate the suitability of this technique for conducting enzyme kinetics, the standard reaction of p-nitrophenyl acetate hydrolysis by chymotrypsin was analyzed by stopped-flow and time-resolved ESI-TOF MS. The rate constant of p-nitrophenol formation followed by stopped-flow spectrophotometry matched perfectly the rate constant of acetyl-chymotrypsin intermediate formation followed by time-resolved ESI-TOF MS (0.1 s(-1)). The catalytic properties of the PEP-bound and unbound states of the E. coli KDO8P synthase were then studied on a millisecond time scale. The changes in the intensity of E*PEP, E*KDO8P, and E*intermediate complexes as a function of time were quantified and the reaction kinetics were modeled using KinTekSim simulation software. An analysis of the reaction kinetics established the kinetic competence of the intermediate based upon the rate constants for substrate decay and product formation. The ability of time-resolved ESI-TOF MS to detect and monitor the kinetics for the reaction intermediate constitutes a significant advantage over the traditional rapid chemical quench technique. For all three states of the enzyme (PEP-bound, unbound, and PEP removed from the PEP-bound state) the rate constants obtained by time-resolved ESI-TOF MS matched the pre-steady state rates determined by rapid chemical quench. A comparison of reaction time courses for each state of the enzyme revealed that, in the case of PEP-bound enzyme, the enzymatic reaction reached completion faster than that for the unbound state. In summary, these studies led to the conclusion that bound PEP has an important role in catalysis, maintaining the enzyme in a conformational state optimal for catalytic activity, and established the kinetic competence of the reaction intermediate. This technique has broad applicability for the kinetic analysis of any enzyme system where the substrates, products, or intermediates are eluding the common detection techniques or as a method alternative to the widely used radioactivity assays.
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Affiliation(s)
- Zhili Li
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
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Liesener A, Karst U. Monitoring enzymatic conversions by mass spectrometry: a critical review. Anal Bioanal Chem 2005; 382:1451-64. [PMID: 16007447 DOI: 10.1007/s00216-005-3305-2] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Revised: 05/11/2005] [Accepted: 05/13/2005] [Indexed: 10/25/2022]
Abstract
This review highlights recent advances in the application of electrospray ionisation and matrix-assisted laser desorption/ionisation mass spectrometry (MS) to study enzymatic reactions. Several assay schemes for different fields of application are presented. The employment of MS as a means of detection in pre-steady-state kinetic studies by rapid-mixing direct analysis and rapid-mixing quench flow techniques is discussed. Several steady-state kinetic studies of a broad range of different enzymatic systems are presented as well as enzyme inhibition studies for various target enzymes. As a promising new development multiplex assays, which monitor the conversion of several substrates simultaneously in one experiment, are described. This assay type has been used for competition studies, enzymatic activity screenings and for diagnostic purposes in clinical chemistry. Generally, it can be concluded that mass spectrometry offers an intriguing alternative as detection methodology in enzymatic bioassays. Its applicability for the monitoring the conversion of naturally occurring substrates and its overall versatility make MS an especially promising tool for the study of enzyme-catalysed processes.
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Affiliation(s)
- André Liesener
- Chemical Analysis Group and MESA+ Institute for Nanotechnology, University of Twente, PO Box 217, 7500, AE Enschede, The Netherlands
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:693-704. [PMID: 15880598 DOI: 10.1002/jms.806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
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