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Xu Y, Harris ME, York DM, Wong KY. Altered Mechanisms for Acid-Catalyzed RNA Cleavage and Isomerization Reactions Models. J Chem Theory Comput 2023; 19:1322-1332. [PMID: 36753428 PMCID: PMC10069163 DOI: 10.1021/acs.jctc.2c01277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
RNA strand cleavage by 2'-O-transphosphorylation is catalyzed not only by numerous nucleolytic RNA enzymes (ribozymes) but also by hydroxide or hydronium ions. In experiments, both cleavage of the 5'-linked nucleoside and isomerization between 3',5'- and 2',5'-phosphodiesters occur under acidic conditions, while only the cleavage reaction is observed under basic conditions. An ab initio path-integral approach for simulating kinetic isotope effects is used to reveal the reaction mechanisms for RNA cleavage and isomerization reactions under acidic conditions. Moreover, the proposed mechanisms can also be combined through the experimental pH-rate profiles.
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Affiliation(s)
- Yuqing Xu
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Darrin M York
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Kin-Yiu Wong
- Department of Physics, High Performance Cluster Computing Centre, Institute of Advanced Materials, Institute of Computational and Theoretical Studies, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong
- Institute of Research and Continuing Education, Hong Kong Baptist University (Shenzhen), Shenzhen 518057, China
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2
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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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3
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Harris ME, York DM, Piccirilli JA, Anderson VE. Kinetic Isotope Effect Analysis of RNA 2′- O -Transphosphorylation. Methods Enzymol 2017; 596:433-457. [DOI: 10.1016/bs.mie.2017.07.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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4
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Niedenführ S, ten Pierick A, van Dam PTN, Suarez-Mendez CA, Nöh K, Wahl SA. Natural isotope correction of MS/MS measurements for metabolomics and (13)C fluxomics. Biotechnol Bioeng 2015; 113:1137-47. [PMID: 26479486 DOI: 10.1002/bit.25859] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/08/2015] [Accepted: 10/12/2015] [Indexed: 11/09/2022]
Abstract
Fluxomics and metabolomics are crucial tools for metabolic engineering and biomedical analysis to determine the in vivo cellular state. Especially, the application of (13)C isotopes allows comprehensive insights into the functional operation of cellular metabolism. Compared to single MS, tandem mass spectrometry (MS/MS) provides more detailed and accurate measurements of the metabolite enrichment patterns (tandem mass isotopomers), increasing the accuracy of metabolite concentration measurements and metabolic flux estimation. MS-type data from isotope labeling experiments is biased by naturally occurring stable isotopes (C, H, N, O, etc.). In particular, GC-MS(/MS) requires derivatization for the usually non-volatile intracellular metabolites introducing additional natural isotopes leading to measurements that do not directly represent the carbon labeling distribution. To make full use of LC- and GC-MS/MS mass isotopomer measurements, the influence of natural isotopes has to be eliminated (corrected). Our correction approach is analyzed for the two most common applications; (13)C fluxomics and isotope dilution mass spectrometry (IDMS) based metabolomics. Natural isotopes can have an impact on the calculated flux distribution which strongly depends on the substrate labeling and the actual flux distribution. Second, we show that in IDMS based metabolomics natural isotopes lead to underestimated concentrations that can and should be corrected with a nonlinear calibration. Our simulations indicate that the correction for natural abundance in isotope based fluxomics and quantitative metabolomics is essential for correct data interpretation.
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Affiliation(s)
- Sebastian Niedenführ
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Angela ten Pierick
- Department of Biotechnology, Delft University of Technology, 2628BC Delft, The Netherlands
| | - Patricia T N van Dam
- Department of Biotechnology, Delft University of Technology, 2628BC Delft, The Netherlands
| | - Camilo A Suarez-Mendez
- Department of Biotechnology, Delft University of Technology, 2628BC Delft, The Netherlands. .,Departamento de Procesos y Energia, Universidad Nacional de Colombia, Carrera 80 No. 65-223, Blq. M3, Medellin, Colombia.
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
| | - S Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, 2628BC Delft, The Netherlands.
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Lin HC, Yandek LE, Gjermeni I, Harris ME. Determination of relative rate constants for in vitro RNA processing reactions by internal competition. Anal Biochem 2014; 467:54-61. [PMID: 25173512 DOI: 10.1016/j.ab.2014.08.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/08/2014] [Accepted: 08/20/2014] [Indexed: 12/21/2022]
Abstract
Studies of RNA recognition and catalysis typically involve measurement of rate constants for reactions of individual RNA sequence variants by fitting changes in substrate or product concentration to exponential or linear functions. A complementary approach is determination of relative rate constants by internal competition, which involves quantifying the time-dependent changes in substrate or product ratios in reactions containing multiple substrates. Here, we review approaches for determining relative rate constants by analysis of both substrate and product ratios and illustrate their application using the in vitro processing of precursor transfer RNA (tRNA) by ribonuclease P as a model system. The presence of inactive substrate populations is a common complicating factor in analysis of reactions involving RNA substrates, and approaches for quantitative correction of observed rate constants for these effects are illustrated. These results, together with recent applications in the literature, indicate that internal competition offers an alternate method for analyzing RNA processing kinetics using standard molecular biology methods that directly quantifies substrate specificity and may be extended to a range of applications.
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Affiliation(s)
- Hsuan-Chun Lin
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Lindsay E Yandek
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ino Gjermeni
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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6
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Wong KY, Xu Y, York DM. Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models. J Comput Chem 2014; 35:1302-16. [PMID: 24841935 PMCID: PMC4096342 DOI: 10.1002/jcc.23628] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 04/06/2014] [Indexed: 12/16/2022]
Abstract
Detailed understandings of the reaction mechanisms of RNA catalysis in various environments can have profound importance for many applications, ranging from the design of new biotechnologies to the unraveling of the evolutionary origin of life. An integral step in the nucleolytic RNA catalysis is self-cleavage of RNA strands by 2'-O-transphosphorylation. Key to elucidating a reaction mechanism is determining the molecular structure and bonding characteristics of transition state. A direct and powerful probe of transition state is measuring isotope effects on biochemical reactions, particularly if we can reproduce isotope effect values from quantum calculations. This article significantly extends the scope of our previous joint experimental and theoretical work in examining isotope effects on enzymatic and nonenzymatic 2'-O-transphosphorylation reaction models that mimic reactions catalyzed by RNA enzymes (ribozymes), and protein enzymes such as ribonuclease A (RNase A). Native reactions are studied, as well as reactions with thio substitutions representing chemical modifications often used in experiments to probe mechanism. Here, we report and compare results from eight levels of electronic-structure calculations for constructing the potential energy surfaces in kinetic and equilibrium isotope effects (KIE and EIE) computations, including a "gold-standard" coupled-cluster level of theory [CCSD(T)]. In addition to the widely used Bigeleisen equation for estimating KIE and EIE values, internuclear anharmonicity and quantum tunneling effects were also computed using our recently developed ab initio path-integral method, that is, automated integration-free path-integral method. The results of this work establish an important set of benchmarks that serve to guide calculations of KIE and EIE for RNA catalysis.
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Affiliation(s)
- Kin-Yiu Wong
- Department of Physics, High Performance Cluster Computing Centre, Institute of Computational and Theoretical Studies, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong; Institute of Research and Continuing Education, Hong Kong Baptist University (Shenzhen), Shenzhen, China
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7
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Advances in kinetic isotope effect measurement techniques for enzyme mechanism study. Molecules 2013; 18:9278-92. [PMID: 23917115 PMCID: PMC6270257 DOI: 10.3390/molecules18089278] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 07/22/2013] [Accepted: 07/29/2013] [Indexed: 11/17/2022] Open
Abstract
Kinetic isotope effects (KIEs) are a very powerful tool for investigating enzyme mechanisms. Precision of measurement is the most important factor for KIE determinations, especially for small heavy atom KIEs. Internal competition is commonly used to measure small KIEs on V/K. Several methods, including such as liquid scintillation counting, mass spectrometry, nuclear magnetic resonance spectroscopy and polarimetry have been used to determine KIEs. In this paper, which does not aspire to be an exhaustive review, we briefly review different experimental approaches for the measurement of KIEs on enzymatic reaction with an emphasis on newer techniques employing mass spectrometry and nuclear magnetic resonance spectrometry as well as some corresponding examples.
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8
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Conway JP, Johns DG, Wang SP, Walker ND, McAvoy TA, Zhou H, Zhao X, Previs SF, Roddy TP, Hubbard BK, Yates NA, Hendrickson RC. Measuring H218O Tracer Incorporation on a QQQ-MS Platform Provides a Rapid, Transferable Screening Tool for Relative Protein Synthesis. J Proteome Res 2012; 11:1591-7. [DOI: 10.1021/pr2007494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- James P. Conway
- Merck Research Laboratories, 126 East Lincoln Avenue, Rahway, New Jersey
07065, United States
| | - Douglas G. Johns
- Merck Research Laboratories, 126 East Lincoln Avenue, Rahway, New Jersey
07065, United States
| | - Sheng-Ping Wang
- Merck Research Laboratories, 126 East Lincoln Avenue, Rahway, New Jersey
07065, United States
| | - Nykia D. Walker
- Merck Research Laboratories, 126 East Lincoln Avenue, Rahway, New Jersey
07065, United States
| | - Thomas A. McAvoy
- Merck Research Laboratories, 126 East Lincoln Avenue, Rahway, New Jersey
07065, United States
| | - Haihong Zhou
- Merck Research Laboratories, 126 East Lincoln Avenue, Rahway, New Jersey
07065, United States
| | - Xuemei Zhao
- Merck Research Laboratories, 126 East Lincoln Avenue, Rahway, New Jersey
07065, United States
| | - Stephen F. Previs
- Merck Research Laboratories, 126 East Lincoln Avenue, Rahway, New Jersey
07065, United States
| | - Thomas P. Roddy
- Merck Research Laboratories, 126 East Lincoln Avenue, Rahway, New Jersey
07065, United States
| | - Brian K. Hubbard
- Merck Research Laboratories, 126 East Lincoln Avenue, Rahway, New Jersey
07065, United States
| | - Nathan A. Yates
- Merck Research Laboratories, 126 East Lincoln Avenue, Rahway, New Jersey
07065, United States
| | - Ronald C. Hendrickson
- Merck Research Laboratories, 126 East Lincoln Avenue, Rahway, New Jersey
07065, United States
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9
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Kasumov T, Ilchenko S, Li L, Rachdaoui N, Sadygov RG, Willard B, McCullough AJ, Previs S. Measuring protein synthesis using metabolic ²H labeling, high-resolution mass spectrometry, and an algorithm. Anal Biochem 2011; 412:47-55. [PMID: 21256107 DOI: 10.1016/j.ab.2011.01.021] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 01/14/2011] [Indexed: 10/18/2022]
Abstract
We recently developed a method for estimating protein dynamics in vivo with heavy water ((2)H(2)O) using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) [16], and we confirmed that (2)H labeling of many hepatic free amino acids rapidly equilibrated with body water. Although this is a reliable method, it required modest sample purification and necessitated the determination of tissue-specific amino acid labeling. Another approach for quantifying protein kinetics is to measure the (2)H enrichments of body water (precursor) and protein-bound amino acid or proteolytic peptide (product) and to estimate how many copies of deuterium are incorporated into a product. In the current study, we used nanospray linear trap Fourier transform ion cyclotron resonance mass spectrometry (LTQ FT-ICR MS) to simultaneously measure the isotopic enrichment of peptides and protein-bound amino acids. A mathematical algorithm was developed to aid the data processing. The most notable improvement centers on the fact that the precursor/product labeling ratio can be obtained by measuring the labeling of water and a protein (or peptide) of interest, thereby minimizing the need to measure the amino acid labeling. As a proof of principle, we demonstrate that this approach can detect the effect of nutritional status on albumin synthesis in rats given (2)H(2)O.
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Affiliation(s)
- Takhar Kasumov
- Department of Gastroenterology, Cleveland Clinic, Cleveland, OH 44195, USA.
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10
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Harris ME, Dai Q, Gu H, Kellerman DL, Piccirilli JA, Anderson VE. Kinetic isotope effects for RNA cleavage by 2'-O- transphosphorylation: nucleophilic activation by specific base. J Am Chem Soc 2010; 132:11613-21. [PMID: 20669950 DOI: 10.1021/ja103550e] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To better understand the interactions between catalysts and transition states during RNA strand cleavage, primary (18)O kinetic isotope effects (KIEs) and solvent D(2)O isotope effects were measured to probe the mechanism of base-catalyzed 2'-O-transphosphorylation of the RNA dinucleotide 5'-UpG-3'. The observed (18)O KIEs for the nucleophilic 2'-O and in the 5'-O leaving group at pH 14 are both large relative to reactions of phosphodiesters with good leaving groups, indicating that the reaction catalyzed by hydroxide has a transition state (TS) with advanced phosphorus-oxygen bond fission to the leaving group ((18)k(LG) = 1.034 +/- 0.004) and phosphorus-nucleophile bond formation ((18)k(NUC) = 0.984 +/- 0.004). A breakpoint in the pH dependence of the 2'-O-transphosphorylation rate to a pH independent phase above pH 13 has been attributed to the pK(a) of the 2'-OH nucleophile. A smaller nucleophile KIE is observed at pH 12 ((18)k(NUC) = 0.995 +/- 0.004) that is interpreted as the combined effect of the equilibrium isotope effect (ca. 1.02) on deprotonation of the 2'-hydroxyl nucleophile and the intrinsic KIE on the nucleophilic addition step (ca. 0.981). An alternative mechanism in which the hydroxide ion acts as a general base is considered unlikely given the lack of a solvent deuterium isotope effect above the breakpoint in the pH versus rate profile. These results represent the first direct analysis of the transition state for RNA strand cleavage. The primary (18)O KIE results and the lack of a kinetic solvent deuterium isotope effect together provide strong evidence for a late transition state and 2'-O nucleophile activation by specific base catalysis.
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Affiliation(s)
- Michael E Harris
- RNA Center and Departmet of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44118, USA.
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11
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Rachdaoui N, Austin L, Kramer E, Previs MJ, Anderson VE, Kasumov T, Previs SF. Measuring proteome dynamics in vivo: as easy as adding water? Mol Cell Proteomics 2009; 8:2653-63. [PMID: 19724074 DOI: 10.1074/mcp.m900026-mcp200] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteomics investigations typically yield information regarding static gene expression profiles. The central issues that limit the study of proteome dynamics include how to (i) administer a labeled amino acid in vivo, (ii) measure the isotopic labeling of a protein(s) (which may be low), and (iii) reliably interpret the precursor/product labeling relationships. In this study, we demonstrate the potential of quantifying proteome dynamics by coupling the administration of stable isotopes with mass spectrometric assays. Although the direct administration of a labeled amino acid(s) is typically used to measure protein synthesis, we explain the application of labeled water, comparing (2)H(2)O versus H(2)(18)O for measuring albumin biosynthesis in vivo. This application emphasizes two distinct advantages of using labeled water over a labeled amino acid(s). First, in long term studies (e.g. days or weeks), it is not practical to continuously administer a labeled amino acid(s); however, in the presence of labeled water, organisms will generate labeled amino acids. Second, to calculate rates of protein synthesis in short term studies (e.g. hours), one must utilize a precursor/product labeling ratio; when using labeled water it is possible to reliably identify and easily measure the precursor labeling (i.e. water). We demonstrate that labeled water permits studies of protein synthesis (e.g. albumin synthesis in mice) during metabolic "steady-state" or "non-steady-state" conditions, i.e. integrating transitions between the fed and fasted state or during an acute perturbation (e.g. following a meal), respectively. We expect that the use of labeled water is applicable to wide scale investigations of proteome dynamics and can therein be used to obtain a functional image of gene expression in vivo.
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Affiliation(s)
- Nadia Rachdaoui
- Department Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
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Griffin JL, Des Rosiers C. Applications of metabolomics and proteomics to the mdx mouse model of Duchenne muscular dystrophy: lessons from downstream of the transcriptome. Genome Med 2009; 1:32. [PMID: 19341503 PMCID: PMC2664943 DOI: 10.1186/gm32] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Functional genomic studies are dominated by transcriptomic approaches, in part reflecting the vast amount of information that can be obtained, the ability to amplify mRNA and the availability of commercially standardized functional genomic DNA microarrays and related techniques. This can be contrasted with proteomics, metabolomics and metabolic flux analysis (fluxomics), which have all been much slower in development, despite these techniques each providing a unique viewpoint of what is happening in the overall biological system. Here, we give an overview of developments in these fields 'downstream' of the transcriptome by considering the characterization of one particular, but widely used, mouse model of human disease. The mdx mouse is a model of Duchenne muscular dystrophy (DMD) and has been widely used to understand the progressive skeletal muscle wasting that accompanies DMD, and more recently the associated cardiomyopathy, as well as to unravel the roles of the other isoforms of dystrophin, such as those found in the brain. Studies using proteomics, metabolomics and fluxomics have characterized perturbations in calcium homeostasis in dystrophic skeletal muscle, provided an understanding of the role of dystrophin in skeletal muscle regeneration, and defined the changes in substrate energy metabolism in the working heart. More importantly, they all point to perturbations in proteins, metabolites and metabolic fluxes reflecting mitochondrial energetic alterations, even in the early stage of the dystrophic pathology. Philosophically, these studies also illustrate an important lesson relevant to both functional genomics and the mouse phenotyping in that the knowledge generated has advanced our understanding of cell biology and physiological organization as much as it has advanced our understanding of the disease.
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Affiliation(s)
- Julian L Griffin
- Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QW, UK
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Harris ME, Cassano AG. Experimental analyses of the chemical dynamics of ribozyme catalysis. Curr Opin Chem Biol 2008; 12:626-39. [PMID: 18952193 DOI: 10.1016/j.cbpa.2008.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 10/13/2008] [Accepted: 10/13/2008] [Indexed: 11/30/2022]
Abstract
Most ribozymes in Nature catalyze alcoholysis or hydrolysis of RNA phosphodiester bonds. Studies of the corresponding non-enzymatic reactions reveal a complex mechanistic landscape allowing for a variety of transition states and both concerted and stepwise mechanisms. High-resolution structures, incisive biochemical studies and computer simulations are providing glimpses into how ribozyme catalyzed reactions traverse this landscape. However, direct experimental tests of mechanistic detail at the chemical level are not easily achieved. Kinetic isotope effects (KIEs) probe directly the differences in the vibrational 'environment' of the atoms undergoing chemical transformation on going from the ground state to the transition state. Thus, KIEs can in principle provide direct information about transition state bonding and so may be instrumental in evaluating possible transition states for ribozyme catalyzed reactions. Understanding charge distribution in the transition state may help resolve how rate acceleration is accomplished and perhaps the similarities and differences in how RNA and protein active sites operate. Several barriers to successful application of KIE analysis to ribozymes have recently been overcome, and new chemical details are beginning to emerge.
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Affiliation(s)
- Michael E Harris
- RNA Center and Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44118, USA.
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Wang B, Sun G, Anderson DR, Jia M, Previs S, Anderson VE. Isotopologue distributions of peptide product ions by tandem mass spectrometry: quantitation of low levels of deuterium incorporation. Anal Biochem 2007; 367:40-8. [PMID: 17559791 PMCID: PMC2153461 DOI: 10.1016/j.ab.2007.03.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 03/26/2007] [Accepted: 03/28/2007] [Indexed: 11/20/2022]
Abstract
Protonated molecular peptide ions and their product ions generated by tandem mass spectrometry appear as isotopologue clusters due to the natural isotopic variations of carbon, hydrogen, nitrogen, oxygen, and sulfur. Quantitation of the isotopic composition of peptides can be employed in experiments involving isotope effects, isotope exchange, and isotopic labeling by chemical reactions and in studies of metabolism by stable isotope incorporation. Both ion trap and quadrupole-time of flight mass spectrometry are shown to be capable of determining the isotopic composition of peptide product ions obtained by tandem mass spectrometry with both precision and accuracy. Tandem mass spectra of clusters of isotopologue ions obtained in profile mode are fit by nonlinear least squares to a series of Gaussian peaks which quantify the Mn/M0 values which define the isotopologue distribution (ID). To determine the isotopic composition of product ions from their ID, a new algorithm that predicts the Mn/M0 ratios and obviates the need to determine the intensity of all of the ions of an ID is developed. Consequently a precise and accurate determination of the isotopic composition of a product ion may be obtained from only the initial values of the ID, however, the entire isotopologue cluster must be isolated prior to fragmentation. Following optimization of the molecular ion isolation width, fragmentation energy, and detector sensitivity, the presence of isotopic excess (2H, 13C, 15N, 18O) is readily determined within 1%. The ability to determine the isotopic composition of sequential product ions permits the isotopic composition of individual amino acid residues in the precursor ion to be determined.
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Affiliation(s)
- Benlian Wang
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | - Gang Sun
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | - David R. Anderson
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | - Minghong Jia
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | - Stephen Previs
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | - Vernon E. Anderson
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106
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