1
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Bollinger E, Zubrod JP, Konschak M, Schulz R, Bundschuh M. Tracer or toxicant: Does stable isotope labeling affect central processes in aquatic food webs? AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 259:106542. [PMID: 37084478 DOI: 10.1016/j.aquatox.2023.106542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/03/2023]
Abstract
Stable isotope analysis (SIA) is an elementary technique in food web ecology, but its insights become increasingly ambiguous in complex systems. One approach to elevate the utility of SIA in such systems is the use of heavy isotope tracers (i.e., labeling). However, the fundamental assumption that the addition of such tracers does not affect in situ conditions has been challenged. This study tests if labeling is suitable for autotrophy-based and detritus-based aquatic food webs. For the former, the survival and reproduction of Daphnia magna fed with phytoplankton cultured at different levels of 15N addition were assessed. For the latter, the microbial decomposition of leaf litter was assessed at the same tracer levels. While no significant differences were observed, effect patterns were comparable to a previous study, supporting the isotopic redundancy hypothesis that postulates discrete quantum mechanical states at which the reaction speeds of metabolic processes are altered. Although physiology (reproduction) and activity (microbial decomposition) might not be altered to an ecologically significant level, labeling with heavy stable isotopes could potentially affect isotopic fractionation in biochemical processes and bias conclusions drawn from resulting SI ratios.
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Affiliation(s)
- Eric Bollinger
- iES Landau, Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Germany.
| | - Jochen P Zubrod
- iES Landau, Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Germany; Zubrod Environmental Data Science, Germany
| | - Marco Konschak
- iES Landau, Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Germany
| | - Ralf Schulz
- iES Landau, Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Germany; Eußerthal Ecosystem Research Station, RPTU Kaiserslautern-Landau, Germany
| | - Mirco Bundschuh
- iES Landau, Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Germany; Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Sweden
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2
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Chen BW. Equilibrium and kinetic isotope effects in heterogeneous catalysis: A density functional theory perspective. CATAL COMMUN 2023. [DOI: 10.1016/j.catcom.2023.106654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
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3
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Li X, Xue S, Guo Y, Chang WC. Mechanism of Methyldehydrofosmidomycin Maturation: Use Olefination to Enable Chain Elongation. J Am Chem Soc 2022; 144:8257-8266. [PMID: 35482829 DOI: 10.1021/jacs.2c01924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Utilization of mononuclear iron- and 2-oxoglutarate-dependent (Fe/2OG) enzymes to enable C-H bond functionalization is a widely used strategy to diversify the structural complexity of natural products. Besides those well-studied reactions including hydroxylation, epoxidation, and halogenation, in the biosynthetic pathway of dehydrofosmidomycin, an Fe/2OG enzyme is reported to catalyze desaturation, alkyl chain elongation, along with demethylation in which trimethyl-2-aminoethylphosphonate is converted into methyldehydrofosmidomycin. How this transformation takes place is largely unknown. Herein, we characterized the reactive species, revealed the structure of the reaction intermediate, and used mechanistic probes to investigate the reaction pathway and mechanism. These results led to the elucidation of a two-step process in which the first reaction employs a long-lived Fe(IV)-oxo species to trigger C═C bond installation. During the second reaction, the olefin installed in situ enables C-C bond formation that is accompanied with a C-N bond cleavage and hydroxylation to furnish the alkyl chain elongation and demethylation. This work expands the reaction repertoire of Fe/2OG enzymes by introducing a new pathway to the known C-C bond formation mechanisms utilized by metalloenzymes.
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Affiliation(s)
- Xiaojun Li
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Shan Xue
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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4
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Srinivasan B. A guide to the Michaelis-Menten equation: steady state and beyond. FEBS J 2021; 289:6086-6098. [PMID: 34270860 DOI: 10.1111/febs.16124] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/01/2021] [Accepted: 07/15/2021] [Indexed: 01/25/2023]
Abstract
The modern definition of enzymology is synonymous with the Michaelis-Menten equation instituted by Leonor Michaelis and Maud Menten. Most textbooks, or chapters within, discussing enzymology start with the derivation of the equation under the assumption of rapid equilibrium (as done by Michaelis-Menten) or steady state (as modified by Briggs and Haldane) conditions to highlight the importance of this equation as the bedrock on which interpretation of enzyme kinetic results is dependent. However, few textbooks or monographs take the effort of placing the equation within its right historical context and discuss the assumptions that have gone into its institution. This guide will dwell on these in substantial detail. Further, this guide will attempt to instil a sense of appreciation for the mathematical curve rectangular hyperbola, its unique attributes and how ubiquitous the curve is in biological systems. To conclude, this guide will discuss the limitations of the equation, and the method it embodies, and trace the journey of how investigators are attempting to move beyond the steady-state approach and the Michaelis-Menten equation into full progress curve, pre-steady state and single-turnover kinetic analysis to obtain greater insights into enzyme kinetics and catalysis.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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5
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Vaidyanathan D, Paskaleva E, Vargason T, Ke X, McCallum SA, Linhardt RJ, Dordick JS. Elucidating the unusual reaction kinetics of D-glucuronyl C5-epimerase. Glycobiology 2020; 30:847-858. [PMID: 32304324 PMCID: PMC7581656 DOI: 10.1093/glycob/cwaa035] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 12/11/2022] Open
Abstract
The chemoenzymatic synthesis of heparin, through a multienzyme process, represents a critical challenge in providing a safe and effective substitute for this animal-sourced anticoagulant drug. D-glucuronyl C5-epimerase (C5-epi) is an enzyme acting on a heparin precursor, N-sulfoheparosan, catalyzing the reversible epimerization of D-glucuronic acid (GlcA) to L-iduronic acid (IdoA). The absence of reliable assays for C5-epi has limited elucidation of the enzymatic reaction and kinetic mechanisms. Real time and offline assays are described that rely on 1D 1H NMR to study the activity of C5-epi. Apparent steady-state kinetic parameters for both the forward and the pseudo-reverse reactions of C5-epi are determined for the first time using polysaccharide substrates directly relevant to the chemoenzymatic synthesis and biosynthesis of heparin. The forward reaction shows unusual sigmoidal kinetic behavior, and the pseudo-reverse reaction displays nonsaturating kinetic behavior. The atypical sigmoidal behavior of the forward reaction was probed using a range of buffer additives. Surprisingly, the addition of 25 mM each of CaCl2 and MgCl2 resulted in a forward reaction exhibiting more conventional Michaelis-Menten kinetics. The addition of 2-O-sulfotransferase, the next enzyme involved in heparin synthesis, in the absence of 3'-phosphoadenosine 5'-phosphosulfate, also resulted in C5-epi exhibiting a more conventional Michaelis-Menten kinetic behavior in the forward reaction accompanied by a significant increase in apparent Vmax. This study provides critical information for understanding the reaction kinetics of C5-epi, which may result in improved methods for the chemoenzymatic synthesis of bioengineered heparin.
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Affiliation(s)
- Deepika Vaidyanathan
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Elena Paskaleva
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Troy Vargason
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Xia Ke
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Scott A McCallum
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Robert J Linhardt
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
- Department of Biological Sciences, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
- Department of Biological Sciences, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
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Dependence of Biocatalysis on D/H Ratio: Possible Fundamental Differences for High-Level Biological Taxons. Molecules 2020; 25:molecules25184173. [PMID: 32933093 PMCID: PMC7571008 DOI: 10.3390/molecules25184173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/03/2020] [Accepted: 09/06/2020] [Indexed: 12/16/2022] Open
Abstract
The kinetics of biological reactions depends on the deuterium/protium (D/H) ratio in water. In this work, we describe the kinetic model of biocatalytic reactions in living organisms depending on the D/H ratio. We show that a change in the lifetime or other characteristics of the vital activity of some organisms in response to a decrease or increase in the content of deuterium in the environment can be a sign of a difference in taxons. For animals-this is a curve with saturation according to the Gauss's principle, for plants-it is the Poisson dependence, for bacteria a weakly saturated curve with a slight reaction to the deuterium/protium ratio toward increasing deuterium. The biological activity of the aquatic environment with reduced, elevated, and natural concentrations of deuterium is considered. The results of the study are presented in different vital indicators of some taxons: the bacteria kingdom-the colony forming units (CFU) index (Escherichia coli); animals-the activation energy of the death of ciliates (Spirostomum ambiguum), embryogenesis of fish (Brachydanio rerio); plants-germination and accumulation of trace elements Callisia fragrans L., sprouting of gametophores and peptidomics of moss Physcomitrella patens. It was found that many organisms change their metabolism and activity, responding to both high and low concentrations of deuterium in water.
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7
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Zlatska AV, Vasyliev RG, Gordiienko IM, Rodnichenko AE, Morozova MA, Vulf MA, Zubov DO, Novikova SN, Litvinova LS, Grebennikova TV, Zlatskiy IA, Syroeshkin AV. Effect of the deuterium on efficiency and type of adipogenic differentiation of human adipose-derived stem cells in vitro. Sci Rep 2020; 10:5217. [PMID: 32251307 PMCID: PMC7089999 DOI: 10.1038/s41598-020-61983-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/27/2020] [Indexed: 12/30/2022] Open
Abstract
In this study, we performed an adipogenic differentiation of human adipose-derived stem cells (ADSCs) in vitro with different deuterium content (natural, low and high) in the culture medium during differentiation process with parallel analysis of the gene expression, metabolic activity and cell viability/toxicity. After ADSCs differentiation into adipocytes we have done the analysis of differentiation process efficiency and determined a type of resulting adipocytes (by morphology, gene expression, UCP1 protein detection and adipokine production analysis). We have found that high (5 × 105 ppm) deuterium content significantly inhibit in vitro adipogenic differentiation of human ADSCs compared to the groups with natural (150 ppm) and low (30 ppm) deuterium content. Importantly, protocol of differentiation used in our study leads to white adipocytes development in groups with natural (control) and high deuterium content, whereas deuterium-depleted differentiation medium leads to brown-like (beige) adipocytes formation. We have also remarked the direct impact of deuterium on the cellular survival and metabolic activity. Interesting, in deuterium depleted-medium, the cells had normal survival rate and high metabolic activity, whereas the inhibitory effect of deuterated medium on ADSCs differentiation at least was partly associated with deuterium cytotoxicity and inhibitory effect on metabolic activity. The inhibitory effect of deuterium on metabolic activity and the subsequent decrease in the effectiveness of adipogenic differentiation is probably associated with mitochondrial dysfunction. Thus, deuterium could be considered as an element that affects the substance chirality. These findings may be the basis for the development of new approaches in the treatment of obesity, metabolic syndrome and diabetes through the regulation of adipose-derived stem cell differentiation and adipocyte functions.
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Affiliation(s)
- Alona V Zlatska
- State Institute of Genetic and Regenerative Medicine NAMS of Ukraine, 67 Vyshgorodska Str., Kyiv, 04114, Ukraine.,Biotechnology Laboratory ilaya.regeneration, Medical Company ilaya, 9 I. Kramskogo Str., Kyiv, 03115, Ukraine
| | - Roman G Vasyliev
- State Institute of Genetic and Regenerative Medicine NAMS of Ukraine, 67 Vyshgorodska Str., Kyiv, 04114, Ukraine
| | - Inna M Gordiienko
- Biotechnology Laboratory ilaya.regeneration, Medical Company ilaya, 9 I. Kramskogo Str., Kyiv, 03115, Ukraine.,R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology NAS of Ukraine, 45 Vasylkivska Str., Kyiv, 03022, Ukraine
| | - Anzhela E Rodnichenko
- State Institute of Genetic and Regenerative Medicine NAMS of Ukraine, 67 Vyshgorodska Str., Kyiv, 04114, Ukraine
| | - Maria A Morozova
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow, 117198, Russian Federation
| | - Maria A Vulf
- Immanuel Kant Baltic federal University (IKBFU), 6 Gaidara St, Kaliningrad, 236001, Russian Federation
| | - Dmytro O Zubov
- State Institute of Genetic and Regenerative Medicine NAMS of Ukraine, 67 Vyshgorodska Str., Kyiv, 04114, Ukraine
| | - Svitlana N Novikova
- State Institute of Genetic and Regenerative Medicine NAMS of Ukraine, 67 Vyshgorodska Str., Kyiv, 04114, Ukraine
| | - Larisa S Litvinova
- Immanuel Kant Baltic federal University (IKBFU), 6 Gaidara St, Kaliningrad, 236001, Russian Federation
| | - Tatiana V Grebennikova
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow, 117198, Russian Federation.,Federal Research Center of Epidemiology and Microbiology named Gamalei, Moscow, Russian Federation
| | - Igor A Zlatskiy
- State Institute of Genetic and Regenerative Medicine NAMS of Ukraine, 67 Vyshgorodska Str., Kyiv, 04114, Ukraine. .,Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow, 117198, Russian Federation.
| | - Anton V Syroeshkin
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow, 117198, Russian Federation
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8
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Comparative Analysis of the Different Dyes' Potential to Assess Human Normal and Cancer Cell Viability In Vitro under Different D/ H Ratios in a Culture Medium. ScientificWorldJournal 2020; 2020:2373021. [PMID: 32158363 PMCID: PMC7060866 DOI: 10.1155/2020/2373021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 01/23/2020] [Accepted: 01/25/2020] [Indexed: 01/08/2023] Open
Abstract
In this study, using new approach (laser diffraction + biological dyes), we have demonstrated the decrease of cells viability in vitro in the deuterated growth medium, whereas in the deuterium-depleted medium, there was an increase of cell viability. We have also found that not all dyes are equally sensitive to the D/H ratios in the culture medium (system) as well as to the different cell types (cancer vs normal cells).
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9
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Halenova T, Zlatskiy I, Syroeshkin A, Maximova T, Pleteneva T. Deuterium-Depleted Water as Adjuvant Therapeutic Agent for Treatment of Diet-Induced Obesity in Rats. Molecules 2019; 25:E23. [PMID: 31861678 PMCID: PMC6982901 DOI: 10.3390/molecules25010023] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/03/2019] [Accepted: 12/12/2019] [Indexed: 12/26/2022] Open
Abstract
In this study, we present the potential application of deuterium-depleted water (DDW) for the prevention and adjuvant treatment of obesity in rats. We tested the hypothesis that DDW can alleviate diet-induced obesity (DIO) and its associated metabolic impairments. Rats fed a high-fat diet had an increased body weight index (BWI), glucose concentration, and level of certain proinflammatory cytokines; decreased levels of insulin in the serum; decreased tryptophan and serotonin in the brain, and a decreased concentration of some heavy metals in the liver. Drinking DDW at a concentration of 10 ppm deuterium/protium (D/H) ad libitum for 3 weeks restored the BWI, glucose (serum), tryptophan (brain), and serotonin (brain) levels and concentration of Zn in the liver in the DIO animals to those of the controls. The levels of proinflammatory cytokines (IL-1β, IL-6, IFNγ) and anti-inflammatory TNFα were decreased in DIO rats, while anti-inflammatory cytokine (IL-4, IL-10) levels remained at the control levels, which is indicative of a pathophysiological syndrome. In contrast, in groups of rats treated with DDW, a significant increase in anti-inflammatory (IL-4, IL-10) and proinflammatory cytokines (IFNγ) was observed. This finding indicates a reduction in systemic inflammation in obese animals treated with DDW. Similarly, the high-fat diet caused an increased level of oxidative stress products, which was accompanied by decreased activity of both superoxide dismutase and catalase, whereas the administration of DDW decreased the level of oxidative stress and enhanced antioxidant enzyme activities.
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Affiliation(s)
- Tetiana Halenova
- Taras Shevchenko National University of Kyiv, ESC “Institute of Biology and Medicine”, 64 Volodymyrska Str., 01601 Kyiv, Ukraine;
| | - Igor Zlatskiy
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow 117198, Russian; (A.S.); (T.M.); (T.P.)
- State Institute of Genetic and Regenerative Medicine NAMS of Ukraine, 67 Vyshgorodska Str., 04114 Kyiv, Ukraine
| | - Anton Syroeshkin
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow 117198, Russian; (A.S.); (T.M.); (T.P.)
| | - Tatiana Maximova
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow 117198, Russian; (A.S.); (T.M.); (T.P.)
| | - Tatiana Pleteneva
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow 117198, Russian; (A.S.); (T.M.); (T.P.)
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10
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Lian S, Wu L, Nikolausz M, Lechtenfeld OJ, Richnow HH. 2H and 13C isotope fractionation analysis of organophosphorus compounds for characterizing transformation reactions in biogas slurry: Potential for anaerobic treatment of contaminated biomass. WATER RESEARCH 2019; 163:114882. [PMID: 31352241 DOI: 10.1016/j.watres.2019.114882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/10/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
The ability of anaerobic digestion (AD) to eliminate organophosphorus model compounds (OPs) with structural elements of phosphate, phosphorothioate and phosphorodithioate esters was studied. The enzymatic mechanism of the first irreversible degradation reaction was characterized using metabolite pattern and kinetic 2H/13C-isotope effect in original, cell-free and heat sterilized biogas slurry. The isotope fractionation study suggests different modes of degradation reactions. Representatives for phosphate ester, tris(2-chloroethyl) phosphate and tris(1,3-dichloro-2-propyl) phosphate, were hydrolyzed in biogas slurry without carbon or hydrogen isotope fractionation. Representatives for phosphorodithioate, Dimethoate and Malathion, were degraded in original slurry yielding carbon enrichment factor (εC) of -0.6 ± 0.1‰ and -5.5 ± 0.1‰ (-0.9 ± 0.1‰ and -7.2 ± 0.5‰ in cell-free slurry), without hydrogen isotope fractionation. Phosphorothioate degradation represented by Parathion and Parathion-methyl yielded surprisingly different εC (-0.7 ± 0.2 and -3.6 ± 0.4‰) and εH (-33 ± 5 and -5 ± 1‰) in original slurry compared to cell-free slurry (εC = -2.5 ± 0.5 and -8.6 ± 1.4‰; εH = -61 ± 10 and -10 ± 3‰) suggesting H-C bond cleavage. Degradation of Parathion and Parathion-methyl in sterilized slurry gave carbon but not hydrogen fractionation implying relative thermostable enzymatic activity with different mechanism. The correlation of 2H and 13C stable isotope fractionation of Parathion in biogas slurry showed distinct pattern (Λoriginal = 31 ± 11, Λcell-free = 20 ± 2), indicating different mechanism from chemical hydrolysis. Overall, AD can be a potential treatment for OPs contaminated biomass or contaminated organic waste material.
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Affiliation(s)
- Shujuan Lian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Langping Wu
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Marcell Nikolausz
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Oliver J Lechtenfeld
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
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11
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Li H, Wu H, Zhang H, Su Y, Yang S, Hensen EJM. A Facile Direct Route to N-(Un)substituted Lactams by Cycloamination of Oxocarboxylic Acids without External Hydrogen. CHEMSUSCHEM 2019; 12:3778-3784. [PMID: 31278839 PMCID: PMC6772168 DOI: 10.1002/cssc.201901780] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Indexed: 05/22/2023]
Abstract
Lactams are privileged in bioactive natural products and pharmaceutical agents and widely featured in functional materials. This study presents a novel versatile approach to the direct synthesis of lactams from oxocarboxylic acids without catalyst or external hydrogen. The method involves the in situ release of formic acid from formamides induced by water to facilitate efficient cycloamination. Water also suppresses the formation of byproducts. This unconventional pathway is elucidated by a combination of model experiments and density functional theory calculations, whereby cyclic imines (5-methyl-3,4-dihydro-2-pyrrolone and its tautomeric structures) are found to be favorable intermediates toward lactam formation, in contrast to the conventional approach encompassing cascade reductive amination and cyclization. This sustainable and simple protocol is broadly applicable for the efficient production of various N-unsubstituted and N-substituted lactams.
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Affiliation(s)
- Hu Li
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural BioengineeringKey Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive, Utilization of BiomassCenter for R&D of Fine ChemicalsGuizhou UniversityGuiyangGuizhou550025P.R. China
| | - Hongguo Wu
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural BioengineeringKey Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive, Utilization of BiomassCenter for R&D of Fine ChemicalsGuizhou UniversityGuiyangGuizhou550025P.R. China
| | - Heng Zhang
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural BioengineeringKey Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive, Utilization of BiomassCenter for R&D of Fine ChemicalsGuizhou UniversityGuiyangGuizhou550025P.R. China
| | - Yaqiong Su
- Laboratory of Inorganic Materials & Catalysis, Schuit Institute of CatalysisDepartment of Chemical Engineering and ChemistryEindhoven University of TechnologyP.O. Box 513, 5600MBEindhovenThe Netherlands
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural BioengineeringKey Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive, Utilization of BiomassCenter for R&D of Fine ChemicalsGuizhou UniversityGuiyangGuizhou550025P.R. China
| | - Emiel J. M. Hensen
- Laboratory of Inorganic Materials & Catalysis, Schuit Institute of CatalysisDepartment of Chemical Engineering and ChemistryEindhoven University of TechnologyP.O. Box 513, 5600MBEindhovenThe Netherlands
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12
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Ruiz-Pernía JJ, Tuñón I, Moliner V, Allemann RK. Why are some Enzymes Dimers? Flexibility and Catalysis in Thermotoga Maritima Dihydrofolate Reductase. ACS Catal 2019; 9:5902-5911. [PMID: 31289693 PMCID: PMC6614790 DOI: 10.1021/acscatal.9b01250] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Dihydrofolate
reductase from Thermotoga maritima (TmDFHFR) is a
dimeric thermophilic enzyme that catalyzes the hydride
transfer from the cofactor NADPH to dihydrofolate less efficiently
than other DHFR enzymes, such as the mesophilic analogue Escherichia
coli DHFR (EcDHFR). Using QM/MM potentials, we show that
the reduced catalytic efficiency of TmDHFR is most likely due to differences
in the amino acid sequence that stabilize the M20 loop in an open
conformation, which prevents the formation of some interactions in
the transition state and increases the number of water molecules in
the active site. However, dimerization provides two advantages to
the thermophilic enzyme: it protects its structure against denaturation
by reducing thermal fluctuations and it provides a less negative activation
entropy, toning down the increase of the activation free energy with
temperature. Our molecular picture is confirmed by the analysis of
the temperature dependence of enzyme kinetic isotope effects in different
DHFR enzymes.
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Affiliation(s)
- J. Javier Ruiz-Pernía
- Departamento de Química Física, Universitat de Valencia, 46100 Burjassot, Valencia, Spain
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de Valencia, 46100 Burjassot, Valencia, Spain
| | - Vicent Moliner
- Departamento de Química Física y Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Rudolf K. Allemann
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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13
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Harrison PJ, Gable K, Somashekarappa N, Kelly V, Clarke DJ, Naismith JH, Dunn TM, Campopiano DJ. Use of isotopically labeled substrates reveals kinetic differences between human and bacterial serine palmitoyltransferase. J Lipid Res 2019; 60:953-962. [PMID: 30792183 PMCID: PMC6495160 DOI: 10.1194/jlr.m089367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 02/14/2019] [Indexed: 12/17/2022] Open
Abstract
Isotope labels are frequently used tools to track metabolites through complex biochemical pathways and to discern the mechanisms of enzyme-catalyzed reactions. Isotopically labeled l-serine is often used to monitor the activity of the first enzyme in sphingolipid biosynthesis, serine palmitoyltransferase (SPT), as well as labeling downstream cellular metabolites. Intrigued by the effect that isotope labels may be having on SPT catalysis, we characterized the impact of different l-serine isotopologues on the catalytic activity of recombinant SPT isozymes from humans and the bacterium Sphingomonas paucimobilis Our data show that S. paucimobilis SPT activity displays a clear isotope effect with [2,3,3-D]l-serine, whereas the human SPT isoform does not. This suggests that although both human and S. paucimobilis SPT catalyze the same chemical reaction, there may well be underlying subtle differences in their catalytic mechanisms. Our results suggest that it is the activating small subunits of human SPT that play a key role in these mechanistic variations. This study also highlights that it is important to consider the type and location of isotope labels on a substrate when they are to be used in in vitro and in vivo studies.
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Affiliation(s)
- Peter J Harrison
- EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom; Division of Structural Biology Wellcome Trust Centre for Human Genomics, Oxford OX3 7BN, United Kingdom; Research Complex at Harwell Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Kenneth Gable
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD 20814-4799
| | | | - Van Kelly
- EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
| | - David J Clarke
- EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
| | - James H Naismith
- Division of Structural Biology Wellcome Trust Centre for Human Genomics, Oxford OX3 7BN, United Kingdom; Research Complex at Harwell Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom; The Rosalind Franklin Institute Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, MD 20814-4799
| | - Dominic J Campopiano
- EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom.
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14
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Bhakta S, Nayek A, Roy B, Dey A. Induction of Enzyme-like Peroxidase Activity in an Iron Porphyrin Complex Using Second Sphere Interactions. Inorg Chem 2019; 58:2954-2964. [DOI: 10.1021/acs.inorgchem.8b02707] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Snehadri Bhakta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Abhijit Nayek
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Bijan Roy
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Abhishek Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
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15
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Tokunou Y, Hashimoto K, Okamoto A. Electrochemical Detection of Deuterium Kinetic Isotope Effect on Extracellular Electron Transport in Shewanella oneidensis MR-1. J Vis Exp 2018. [PMID: 29708543 DOI: 10.3791/57584] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Direct electrochemical detection of c-type cytochrome complexes embedded in the bacterial outer membrane (outer membrane c-type cytochrome complexes; OM c-Cyts) has recently emerged as a novel whole-cell analytical method to characterize the bacterial electron transport from the respiratory chain to the cell exterior, referred to as the extracellular electron transport (EET). While the pathway and kinetics of the electron flow during the EET reaction have been investigated, a whole-cell electrochemical method to examine the impact of cation transport associated with EET has not yet been established. In the present study, an example of a biochemical technique to examine the deuterium kinetic isotope effect (KIE) on EET through OM c-Cyts using a model microbe, Shewanella oneidensis MR-1, is described. The KIE on the EET process can be obtained if the EET through OM c-Cyts acts as the rate-limiting step in the microbial current production. To that end, before the addition of D2O, the supernatant solution was replaced with fresh media containing a sufficient amount of the electron donor to support the rate of upstream metabolic reactions, and to remove the planktonic cells from a uniform monolayer biofilm on the working electrode. Alternative methods to confirm the rate-limiting step in microbial current production as EET through OM c-Cyts are also described. Our technique of a whole-cell electrochemical assay for investigating proton transport kinetics can be applied to other electroactive microbial strains.
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Affiliation(s)
| | - Kazuhito Hashimoto
- Global Research Center for Environment and Energy based on Nanomaterials Science, National Institute for Materials Science
| | - Akihiro Okamoto
- Global Research Center for Environment and Energy based on Nanomaterials Science, National Institute for Materials Science;
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16
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Oyugi MA, Bashiri G, Baker EN, Johnson-Winters K. Mechanistic insights into F 420-dependent glucose-6-phosphate dehydrogenase using isotope effects and substrate inhibition studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:387-395. [PMID: 28807886 DOI: 10.1016/j.bbapap.2017.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/24/2017] [Accepted: 08/03/2017] [Indexed: 01/24/2023]
Abstract
F420-dependent glucose-6-phosphate dehydrogenase (FGD) is involved in the committed step of the pentose phosphate pathway within mycobacteria, where it catalyzes the reaction between glucose-6-phosphate (G6P) and the F420 cofactor to yield 6-phosphogluconolactone and the reduced cofactor, F420H2. Here, we aim to probe the FGD reaction mechanism using dead-end inhibition experiments, as well as solvent and substrate deuterium isotope effects studies. The dead-end inhibition studies performed using citrate as the inhibitor revealed competitive and uncompetitive inhibition patterns for G6P and F420 respectively, thus suggesting a mechanism of ordered addition of substrates in which the F420 cofactor must first bind to FGD before G6P binding. The solvent deuterium isotope effects studies yielded normal solvent kinetic isotope effects (SKIE) on kcat and kcat/Km for both G6P and F420. The proton inventory data yielded a fractionation factor of 0.37, suggesting that the single proton responsible for the observed SKIE is likely donated by Glu109 and protonates the cofactor at position N1. The steady state substrate deuterium isotope effects studies using G6P and G6P-d1 yielded KIE of 1.1 for both kcat and kcat/Km, while the pre-steady state KIE on kobs was 1.4. Because the hydride transferred to C5 of F420 was the one targeted for isotopic substitution, these KIE values provide further evidence to support our previous findings that hydride transfer is likely not rate-limiting in the FGD reaction.
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Affiliation(s)
- Mercy A Oyugi
- Department of Chemistry and Biochemistry, University of Texas at Arlington, TX 76019-0065, United States
| | - Ghader Bashiri
- Laboratory of Structural Biology and Maurice Wilkins Center for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Edward N Baker
- Laboratory of Structural Biology and Maurice Wilkins Center for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Kayunta Johnson-Winters
- Department of Chemistry and Biochemistry, University of Texas at Arlington, TX 76019-0065, United States.
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17
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Andriukonis E, Gorokhova E. Kinetic 15N-isotope effects on algal growth. Sci Rep 2017; 7:44181. [PMID: 28281640 PMCID: PMC5345060 DOI: 10.1038/srep44181] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/06/2017] [Indexed: 12/25/2022] Open
Abstract
Stable isotope labeling is a standard technique for tracing material transfer in molecular, ecological and biogeochemical studies. The main assumption in this approach is that the enrichment with a heavy isotope has no effect on the organism metabolism and growth, which is not consistent with current theoretical and empirical knowledge on kinetic isotope effects. Here, we demonstrate profound changes in growth dynamics of the green alga Raphidocelis subcapitata grown in 15N-enriched media. With increasing 15N concentration (0.37 to 50 at%), the lag phase increased, whereas maximal growth rate and total yield decreased; moreover, there was a negative relationship between the growth and the lag phase across the treatments. The latter suggests that a trade-off between growth rate and the ability to adapt to the high 15N environment may exist. Remarkably, the lag-phase response at 3.5 at% 15N was the shortest and deviated from the overall trend, thus providing partial support to the recently proposed Isotopic Resonance hypothesis, which predicts that certain isotopic composition is particularly favorable for living organisms. These findings confirm the occurrence of KIE in isotopically enriched algae and underline the importance of considering these effects when using stable isotope labeling in field and experimental studies.
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Affiliation(s)
- Eivydas Andriukonis
- Faculty of Chemistry and Geosciences, Department of Physical Chemistry, Vilnius University, Vilnius, Lithuania
- Laboratory of Bio-Nanotechnology, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Elena Gorokhova
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
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18
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Reyes AC, Amyes TL, Richard JP. Structure-Reactivity Effects on Intrinsic Primary Kinetic Isotope Effects for Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase. J Am Chem Soc 2016; 138:14526-14529. [PMID: 27769116 PMCID: PMC5105681 DOI: 10.1021/jacs.6b07028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Primary deuterium
kinetic isotope effects (1°DKIE) on (kcat/KGA, M–1 s–1) for dianion (X2–) activated
hydride transfer from NADL to glycolaldehyde (GA) catalyzed by glycerol-3-phosphate
dehydrogenase were determined over a 2100-fold range of enzyme reactivity:
(X2–, 1°DKIE); FPO32–, 2.8 ± 0.1; HPO32–, 2.5 ±
0.1; SO42–, 2.8 ± 0.2; HOPO32–, 2.5 ± 0.1; S2O32–, 2.9 ± 0.1; unactivated; 2.4 ± 0.2.
Similar 1°DKIEs were determined for kcat. The observed 1°DKIEs are essentially independent of changes
in enzyme reactivity with changing dianion activator. The results
are consistent with (i) fast and reversible ligand binding; (ii) the
conclusion that the observed 1°DKIEs are equal to the intrinsic
1°DKIE on hydride transfer from NADL to GA; (iii) similar intrinsic
1°DKIEs on GPDH-catalyzed reduction of the substrate pieces and
the whole physiological substrate dihydroxyacetone phosphate. The
ground-state binding interactions for different X2– are similar, but there are large differences in the transition state
interactions for different X2–. The changes in transition
state binding interactions are expressed as changes in kcat and are proposed to represent changes in stabilization
of the active closed form of GPDH. The 1°DKIEs are much smaller
than observed for enzyme-catalyzed hydrogen transfer that occurs mainly
by quantum-mechanical tunneling.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
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19
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Vogt C, Dorer C, Musat F, Richnow HH. Multi-element isotope fractionation concepts to characterize the biodegradation of hydrocarbons — from enzymes to the environment. Curr Opin Biotechnol 2016; 41:90-98. [DOI: 10.1016/j.copbio.2016.04.027] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/22/2016] [Accepted: 04/29/2016] [Indexed: 10/21/2022]
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20
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Cook ME, Bütz DE, Yang M, Sand JM. Host-targeted approaches to managing animal health: old problems and new tools. Domest Anim Endocrinol 2016; 56 Suppl:S11-22. [PMID: 27345308 DOI: 10.1016/j.domaniend.2016.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 04/19/2016] [Accepted: 04/19/2016] [Indexed: 01/03/2023]
Abstract
Our fellow medical and regulatory scientists question the animal producer's dependence on antibiotics and antimicrobial chemicals in the production of animal products. Retail distributors and consumers are putting even more pressure on the animal industry to find new ways to produce meat without antibiotics and chemicals. In addition, federal funding agencies are increasingly pressuring researchers to conduct science that has application. In the review that follows, we outline our approach to finding novel ways to improve animal performance and health. We use a strict set of guidelines in our applied research as follows: (1) Does the work have value to society? (2) Does our team have the skills to innovate in the field? (3) Is the product we produce commercially cost-effective? (4) Are there any reasons why the general consumer will reject the technology? (5) Is it safe for the animal, consumer, and the environment? Within this framework, we describe 4 areas of research that have produced useful products, areas that we hope other scientists will likewise explore and innovate such as (1) methods to detect infection in herds and flocks, (2) methods to control systemic and mucosal inflammation, (3) improvements to intestinal barrier function, and (4) methods to strategically potentiate immune defense. We recognize that others are working in these areas, using different strategies, but believe our examples will illustrate the vast opportunity for research and innovation in a world without antibiotics. Animal scientists have been given a new challenge that may help shape the future of both animal and human medicine.
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Affiliation(s)
- M E Cook
- Animal Sciences Department, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - D E Bütz
- Animal Sciences Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - M Yang
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - J M Sand
- Animal Sciences Department, University of Wisconsin-Madison, Madison, WI 53706, USA
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21
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Quantification of fumarate and investigation of endogenous and exogenous fumarate stability in rat plasma by LC-MS/MS. Bioanalysis 2016; 8:661-75. [PMID: 26978279 DOI: 10.4155/bio-2015-0026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Fumaric acid is a commonly used excipient in pharmaceutical products. It is not known if its presence may lead to fluctuation of endogenous fumarate levels. An LC-MS/MS method was developed and validated to quantify fumarate in support of a toxicokinetics study. RESULTS Stability evaluation showed that endogenous fumarate was stable for 6 h at room temperature, while exogenously added fumaric acid was converted to malate within 1 h due to the presence of fumarase. Citric acid, a fumarase inhibitor, prevented the conversion of added fumaric acid in rat plasma. CONCLUSION The method was validated in citric acid stabilized rat plasma using a surrogate matrix approach. A discrepancy in stability was observed between endogenous fumarate and exogenously added fumaric acid.
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22
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Pinpointing dynamic coupling in enzymes for efficient drug design. Future Sci OA 2016; 2:FSO95. [PMID: 28031945 PMCID: PMC5137909 DOI: 10.4155/fsoa.2015.0017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 12/21/2015] [Indexed: 11/17/2022] Open
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23
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Glycosynthesis in a waterworld: new insight into the molecular basis of transglycosylation in retaining glycoside hydrolases. Biochem J 2015; 467:17-35. [PMID: 25793417 DOI: 10.1042/bj20141412] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Carbohydrates are ubiquitous in Nature and play vital roles in many biological systems. Therefore the synthesis of carbohydrate-based compounds is of considerable interest for both research and commercial purposes. However, carbohydrates are challenging, due to the large number of sugar subunits and the multiple ways in which these can be linked together. Therefore, to tackle the challenge of glycosynthesis, chemists are increasingly turning their attention towards enzymes, which are exquisitely adapted to the intricacy of these biomolecules. In Nature, glycosidic linkages are mainly synthesized by Leloir glycosyltransferases, but can result from the action of non-Leloir transglycosylases or phosphorylases. Advantageously for chemists, non-Leloir transglycosylases are glycoside hydrolases, enzymes that are readily available and exhibit a wide range of substrate specificities. Nevertheless, non-Leloir transglycosylases are unusual glycoside hydrolases in as much that they efficiently catalyse the formation of glycosidic bonds, whereas most glycoside hydrolases favour the mechanistically related hydrolysis reaction. Unfortunately, because non-Leloir transglycosylases are almost indistinguishable from their hydrolytic counterparts, it is unclear how these enzymes overcome the ubiquity of water, thus avoiding the hydrolytic reaction. Without this knowledge, it is impossible to rationally design non-Leloir transglycosylases using the vast diversity of glycoside hydrolases as protein templates. In this critical review, a careful analysis of literature data describing non-Leloir transglycosylases and their relationship to glycoside hydrolase counterparts is used to clarify the state of the art knowledge and to establish a new rational basis for the engineering of glycoside hydrolases.
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24
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Crowell JK, Li W, Pierce BS. Oxidative uncoupling in cysteine dioxygenase is gated by a proton-sensitive intermediate. Biochemistry 2014; 53:7541-8. [PMID: 25387045 DOI: 10.1021/bi501241d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cysteine dioxygenase (CDO) is a non-heme mononuclear iron enzyme that catalyzes the O2-dependent oxidation of l-cysteine (Cys) to produce cysteine sulfinic acid (CSA). This enzyme catalyzes the first committed step in Cys catabolism; thus, it is central to mammalian sulfur metabolism and redox homeostasis. Ironically, despite nearly 45 years of continued research on CDO, essentially no information has been reported with respect to its kinetic mechanism. In this work, the timing of chemical steps in the CDO kinetic mechanism is investigated by pH/pD-dependent steady-state kinetics and solvent isotope effects on kcat, kcat/KM, and (O2/CSA) coupling. Normal solvent kinetic isotope effects of 1.45 ± 0.05 and 2.0 ± 0.1 are observed in kcat-pL and kcat/KM-pL profiles, respectively. Proton inventory experiments within the pL-independent region (pL 8.5) suggest multiple solvent-exchangeable protons in flight for both kcat and kcat/KM data. The influence of solvent viscosity was also investigated to probe non-chemical steps and to verify that the apparent isotope effects were not attributable to increased solvent viscosity of D2O reactions relative to H2O. Although solvent viscosity did have a modest influence on kcat and kcat/KM, the response is not sufficient to account for the observed solvent isotope effects. This suggests that product release is only partially rate-limiting for CDO catalysis. Most crucially, proton inventory of (O2/CSA) coupling indicates that a proton-sensitive transition state directly follows O2 activation. Thus, protonation of a transient species preceding Cys oxidation is gated by protons in flight. This behavior provides valuable insight into the kinetically masked transients generated during catalysis.
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Affiliation(s)
- Joshua K Crowell
- Department of Chemistry and Biochemistry, College of Sciences, The University of Texas at Arlington , Arlington, Texas 76019, United States
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25
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Luk LP, Loveridge EJ, Allemann RK. Different dynamical effects in mesophilic and hyperthermophilic dihydrofolate reductases. J Am Chem Soc 2014; 136:6862-5. [PMID: 24779446 PMCID: PMC4046772 DOI: 10.1021/ja502673h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Indexed: 01/18/2023]
Abstract
The role of protein dynamics in the reaction catalyzed by dihydrofolate reductase from the hyperthermophile Thermotoga maritima (TmDHFR) has been examined by enzyme isotope substitution ((15)N, (13)C, (2)H). In contrast to all other enzyme reactions investigated previously, including DHFR from Escherichia coli (EcDHFR), for which isotopic substitution led to decreased reactivity, the rate constant for the hydride transfer step is not affected by isotopic substitution of TmDHFR. TmDHFR therefore appears to lack the coupling of protein motions to the reaction coordinate that have been identified for EcDHFR catalysis. Clearly, dynamical coupling is not a universal phenomenon that affects the efficiency of enzyme catalysis.
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Affiliation(s)
- Louis
Y. P. Luk
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - E. Joel Loveridge
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Rudolf K. Allemann
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
- Cardiff
Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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26
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Feng X, Tang YJ. Evaluation of isotope discrimination in 13C-based metabolic flux analysis. Anal Biochem 2011; 417:295-7. [DOI: 10.1016/j.ab.2011.06.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 06/17/2011] [Indexed: 12/18/2022]
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27
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Lee CC, Hu Y, Ribbe MW. Tracing the Hydrogen Source of Hydrocarbons Formed by Vanadium Nitrogenase. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100869] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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Lee CC, Hu Y, Ribbe MW. Tracing the hydrogen source of hydrocarbons formed by vanadium nitrogenase. Angew Chem Int Ed Engl 2011; 50:5545-7. [PMID: 21538750 DOI: 10.1002/anie.201100869] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Indexed: 11/05/2022]
Affiliation(s)
- Chi Chung Lee
- Molecular Biology & Biochemistry, University of California, Irvine, 2236/2448 McGaugh Hall, Irvine, CA 92697-3900, USA
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29
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Zhu C, Warncke K. Kinetic isolation and characterization of the radical rearrangement step in coenzyme B12-dependent ethanolamine ammonia-lyase. J Am Chem Soc 2010; 132:9610-5. [PMID: 20578695 DOI: 10.1021/ja907769g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The transient decay reaction kinetics of the 1,1,2,2-(2)H(4)-aminoethanol generated Co(II)-substrate radical pair catalytic intermediate in ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium have been measured by using time-resolved, full-spectrum X-band continuous-wave electron paramagnetic resonance (EPR) spectroscopy in frozen aqueous solution over the temperature range of 190-207 K. The decay reaction involves sequential passage through the rearrangement step [substrate radical --> product radical] and the step [product radical --> diamagnetic product] that involves hydrogen atom transfer (HT) from carbon C5' of the adenosine moiety of the cofactor to the product radical C2 center. As found for the (1)H-substrate radical [Zhu, C.; Warncke, K. Biophys. J. 2008, 95, 5890], the decay kinetics for the (2)H-substrate radical over 190-207 K represent two noninteracting populations (fast decay population: normalized amplitude = 0.44 +/- 0.07; observed rate constant, k(obs,f) = 5.3 x 10(-5)-1.1 x 10(-3) s(-1); slow decay population: k(obs,s) = 6.1 x 10(-6)-2.9 x 10(-4) s(-1)). The (1)H/(2)H isotope effects (IE) for the fast and slow decay reactions are 1.4 +/- 0.2 and 0.79 +/- 0.11, respectively. The IE on the fast phase is uniform over the temperature interval, and the value is consistent with an alpha-secondary hydrogen kinetic IE, which arises from changes in the force constants of the C-H bonds in the substrate radical structure, upon passing from the substrate radical state to the rearrangement transition state. Therefore, we propose that k(obs,f) represents the rate constant for the radical rearrangement and that this step is the rate-determining step in substrate radical decay. The Arrhenius activation energy for the (1)H-substrate radical rearrangement (13.5 +/- 0.4 kcal/mol) is consistent with values from quantum chemical calculations performed on simple models. The results show that the core, radical rearrangement reaction is culled from the catalytic cycle in the low-temperature system, thus establishing the system for detailed transient kinetic and spectroscopic analysis of protein structural and dynamic contributions to EAL catalysis.
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Affiliation(s)
- Chen Zhu
- Department of Physics, Emory University, Atlanta, Georgia 30322, USA
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30
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Gelabert R, Moreno M, Lluch JM. A Theoretical Assessment of Factors Causing Different Molecular Volumes in Isotopologues. J Phys Chem A 2009; 113:14161-9. [DOI: 10.1021/jp906766c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Ricard Gelabert
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Miquel Moreno
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - José M. Lluch
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
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31
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Hay S, Scrutton NS. H-transfers in Photosystem II: what can we learn from recent lessons in the enzyme community? PHOTOSYNTHESIS RESEARCH 2008; 98:169-177. [PMID: 18766465 DOI: 10.1007/s11120-008-9326-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Accepted: 06/28/2008] [Indexed: 05/26/2023]
Abstract
Over the last 10 years, studies of enzyme systems have demonstrated that, in many cases, H-transfers occur by a quantum mechanical tunneling mechanism analogous to long-range electron transfer. H-transfer reactions can be described by an extension of Marcus theory and, by substituting hydrogen with deuterium (or even tritium), it is possible to explore this theory in new ways by employing kinetic isotope effects. Because hydrogen has a relatively short deBroglie wavelength, H-transfers are controlled by the width of the reaction barrier. By coupling protein dynamics to the reaction coordinate, enzymes have the potential ability to facilitate more efficient H-tunneling by modulating barrier properties. In this review, we describe recent advances in both experimental and theoretical studies of enzymatic H-transfer, in particular the role of protein dynamics or promoting motions. We then discuss possible consequences with regard to tyrosine oxidation/reduction kinetics in Photosystem II.
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Affiliation(s)
- Sam Hay
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, Manchester, UK.
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Kresge N, Simoni RD, Hill RL. Determining Enzyme Mechanisms by Kinetic Analysis: the Work of W. Wallace Cleland. J Biol Chem 2006. [DOI: 10.1016/s0021-9258(19)35036-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Rahier A, Darnet S, Bouvier F, Camara B, Bard M. Molecular and enzymatic characterizations of novel bifunctional 3beta-hydroxysteroid dehydrogenases/C-4 decarboxylases from Arabidopsis thaliana. J Biol Chem 2006; 281:27264-77. [PMID: 16835224 DOI: 10.1074/jbc.m604431200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have isolated two cDNAs from Arabidopsis thaliana encoding bifunctional 3beta-hydroxysteroid dehydrogenase/C-4 decarboxylases (3betaHSD/D) involved in sterol synthesis, termed At3betaHSD/D1 and At3betaHSD/D2. Transformation of the yeast ergosterol auxotroph erg26 mutant, which lacks 3betaHSD/D activity, with the At3betaHSD/D1 isoform or with At3betaHSD/D2 isoform containing a C-terminal At3betaHSD/D1 endoplasmic reticulum-retrieval sequence restored growth and ergosterol synthesis in erg26. An in vitro enzymatic assay revealed high 3betaHSD/D activity for both isoenzymes in the corresponding microsomal extracts. The two At3betaHSD/D isoenzymes showed similar substrate specificities that required free 3beta-hydroxyl and C-4-carboxyl groups but were quite tolerant in terms of variations of the sterol nucleus and side chain structures. Data obtained with 4alpha-carboxy-cholest-7-en-3beta-ol and its 3alpha-deuterated analog revealed that 3alpha-hydrogen-carbon bond cleavage is not the rate-limiting step of the reaction. In planta reduction on the expression of the 3betaHSD/D gene as a consequence of VIGS-mediated gene silencing in Nicotiana benthamiana led to a substantial accumulation of 3beta-hydroxy-4beta,14-dimethyl-5alpha-ergosta-9beta,19-cyclo-24(24(1))-en-4alpha-carboxylic acid, consistent with a decrease in 3betaHSD/D activity. These two novel oxidative decarboxylases constitute the first molecularly and functionally characterized HSDs from a short chain dehydrogenase/reductase family in plants.
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Affiliation(s)
- Alain Rahier
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, 28 Rue Goethe, 67083 Strasbourg Cedex, France.
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Abstract
Instrumentation and methods exist for highly precise analyses of the stable-isotopic composition of organic compounds separated by GC. The general approach combines a conventional GC, a chemical reaction interface, and a specialized isotope-ratio mass spectrometer (IRMS). Most existing GC hardware and methods are amenable to isotope-ratio detection. The interface continuously and quantitatively converts all organic matter, including column bleed, to a common molecular form for isotopic measurement. C and N are analyzed as CO2 and N2, respectively, derived from combustion of analytes. H and O are analyzed as H2 and CO produced by pyrolysis/reduction. IRMS instruments are optimized to provide intense, highly stable ion beams, with extremely high precision realized via a system of differential measurements in which ion currents for all major isotopologs are simultaneously monitored. Calibration to an internationally recognized scale is achieved through comparison of closely spaced sample and standard peaks. Such systems are capable of measuring 13C/12C ratios with a precision approaching 0.1 per thousand (for values reported in the standard delta notation), four orders of magnitude better than that typically achieved by conventional "organic" mass spectrometers. Detection limits to achieve this level of precision are typically < 1 nmol C (roughly 10 ng of a typical hydrocarbon) injected on-column. Achievable precision and detection limits are correspondingly higher for N, O, and H, in that order.
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Affiliation(s)
- Alex L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA.
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Pu J, Gao J, Truhlar DG. Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions. Chem Rev 2006; 106:3140-69. [PMID: 16895322 PMCID: PMC4478620 DOI: 10.1021/cr050308e] [Citation(s) in RCA: 288] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jingzhi Pu
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Jiali Gao
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
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Svedruzić D, Jónsson S, Toyota CG, Reinhardt LA, Ricagno S, Lindqvist Y, Richards NGJ. The enzymes of oxalate metabolism: unexpected structures and mechanisms. Arch Biochem Biophys 2005; 433:176-92. [PMID: 15581576 DOI: 10.1016/j.abb.2004.08.032] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2004] [Revised: 08/31/2004] [Indexed: 10/26/2022]
Abstract
Oxalate degrading enzymes have a number of potential applications, including medical diagnosis and treatments for hyperoxaluria and other oxalate-related diseases, the production of transgenic plants for human consumption, and bioremediation of the environment. This review seeks to provide a brief overview of current knowledge regarding the major classes of enzymes and related proteins that are employed in plants, fungi, and bacteria to convert oxalate into CO(2) and/or formate. Not only do these enzymes employ intriguing chemical strategies for cleaving the chemically unreactive C-C bond in oxalate, but they also offer the prospect of providing new insights into the molecular processes that underpin the evolution of biological catalysts.
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Affiliation(s)
- Drazenka Svedruzić
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
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Whittaker JW. The radical chemistry of galactose oxidase. Arch Biochem Biophys 2005; 433:227-39. [PMID: 15581579 DOI: 10.1016/j.abb.2004.08.034] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Revised: 08/31/2004] [Indexed: 11/15/2022]
Abstract
Galactose oxidase is a free radical metalloenzyme containing a novel metalloradical complex, comprised of a protein radical coordinated to a copper ion in the active site. The unusually stable protein radical is formed from the redox-active side chain of a cross-linked tyrosine residue (Tyr-Cys). Biochemical studies on galactose oxidase have revealed a new class of oxidation mechanisms based on this free radical coupled-copper catalytic motif, defining an emerging family of enzymes, the radical-copper oxidases. Isotope kinetics and substrate reaction profiling have provided insight into the elementary steps of substrate oxidation in these enzymes, complementing structural studies on their active site. Galactose oxidase is remarkable in the extent to which free radicals are involved in all aspects of the enzyme function: serving as a key feature of the active site structure, defining the characteristic reactivity of the complex, and directing the biogenesis of the Tyr-Cys cofactor during protein maturation.
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Affiliation(s)
- James W Whittaker
- Department of Environmental and Biomolecular Systems, OGI School of Science and Engineering, Oregon Health and Science University, 20000 N.W. Walker Road, Beaverton, OR 97006, USA.
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Abstract
Accelerator mass spectrometry (AMS) traces isotopically labeled biochemicals and provides significant new directions for understanding molecular kinetics and dynamics in biological systems. AMS traces low-abundance radioisotopes for high specificity but detects them with MS for high sensitivity. AMS reduces radiation exposure doses to levels safe for use in human volunteers of all ages. Total radiation exposures are equivalent to those obtained in very short airplane flights, a commonly accepted radiation risk. Waste products seldom reach the Nuclear Regulatory Commission (NRC) definition of radioactive waste material for (14)C and (3)H. Attomoles of labeled compounds are quantified in milligram-sized samples, such as 20 microl of blood. AMS is available from several facilities that offer services and new spectrometers that are affordable. Detailed examples of designing AMS studies are provided, and the methods of analyzing AMS data are outlined.
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Affiliation(s)
- John S Vogel
- Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, California, USA
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Minasian SG, Whittaker MM, Whittaker JW. Stereoselective Hydrogen Abstraction by Galactose Oxidase. Biochemistry 2004; 43:13683-93. [PMID: 15504031 DOI: 10.1021/bi048554s] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The fungal enzyme galactose oxidase is a radical copper oxidase that catalyzes the oxidation of a broad range of primary alcohols to aldehydes. Previous mechanistic studies have revealed a large substrate deuterium kinetic isotope effect on galactose oxidase turnover whose magnitude varies systematically over a series of substituted benzyl alcohols, reflecting a change in the character of the transition state for substrate oxidation. In this work, these detailed mechanistic studies have been extended using a series of stereospecifically monodeuterated substrates, including 1-O-methyl-alpha-D-galactose as well as unsubstituted benzyl alcohol and 3- and 4-methoxy and 4-nitrobenzyl derivatives. Synthesis of all of these substrates was based on oxidation of the alpha,alpha'-dideuterated alcohol to the corresponding (2)H-labeled aldehyde, followed by asymmetric hydroboration using alpha-pinene/9-BBN reagents to form the stereoisomeric alcohols. Products from enzymatic oxidation of each of these substrates were characterized by mass spectrometry to quantitatively evaluate the substrate dependence of the stereoselectivity of the catalytic reaction. For all of these substrates, the selectivity for pro-S hydrogen abstraction was at least 95%. This selectivity appears to be a direct consequence of constraints imposed by the enzyme on the orientation of substrates bearing a branched beta-carbon. Steady state analysis of kinetic isotope effects on V/K has resolved individual contributions from primary and alpha-secondary kinetic isotope effects in the reaction, providing a test for the involvement of an electron transfer redox equilibrium in the oxidation process. Multiple isotope effect measurements utilizing simultaneous labeling of the substrate and solvent have contributed to refinement of the relation between proton transfer and hydrogen atom transfer steps in substrate oxidation.
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Affiliation(s)
- Stefan G Minasian
- Department of Environmental and Biomolecular Systems, OGI School of Science and Engineering, Oregon Health and Sciences University, 20000 Northwest Walker Road, Beaverton, Oregon 97006, USA
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