1
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Li TT, Chen X, Huo D, Arifuzzaman M, Qiao S, Jin WB, Shi H, Li XV, Iliev ID, Artis D, Guo CJ. Microbiota metabolism of intestinal amino acids impacts host nutrient homeostasis and physiology. Cell Host Microbe 2024; 32:661-675.e10. [PMID: 38657606 DOI: 10.1016/j.chom.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 01/23/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
The intestine and liver are thought to metabolize dietary nutrients and regulate host nutrient homeostasis. Here, we find that the gut microbiota also reshapes the host amino acid (aa) landscape via efficiently metabolizing intestinal aa. To identify the responsible microbes/genes, we developed a metabolomics-based assay to screen 104 commensals and identified candidates that efficiently utilize aa. Using genetics, we identified multiple responsible metabolic genes in phylogenetically diverse microbes. By colonizing germ-free mice with the wild-type strain and their isogenic mutant deficient in individual aa-metabolizing genes, we found that these genes regulate the availability of gut and circulatory aa. Notably, microbiota genes for branched-chain amino acids (BCAAs) and tryptophan metabolism indirectly affect host glucose homeostasis via peripheral serotonin. Collectively, at single-gene level, this work characterizes a microbiota-encoded metabolic activity that affects host nutrient homeostasis and provides a roadmap to interrogate microbiota-dependent activity to improve human health.
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Affiliation(s)
- Ting-Ting Li
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Xi Chen
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Da Huo
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Mohammad Arifuzzaman
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Shanshan Qiao
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Wen-Bing Jin
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Huiqing Shi
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Xin V Li
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Iliyan D Iliev
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - David Artis
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Chun-Jun Guo
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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2
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Wick CR, Smith DM. Modeling the Reactions Catalyzed by Coenzyme B 12 Dependent Enzymes: Accuracy and Cost-Quality Balance. J Phys Chem A 2018; 122:1747-1755. [PMID: 29389127 DOI: 10.1021/acs.jpca.7b11798] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The reactions catalyzed by coenzyme B12 dependent enzymes are formally initiated by the homolytic cleavage of a carbon-cobalt bond and a subsequent or concerted H-atom-transfer reaction. A reasonable model chemistry for describing those reactions should, therefore, account for an accurate description of both reactions. The inherent limitation due to the necessary system size renders the coenzyme B12 system a suitable candidate for DFT or hybrid QM/MM methods; however, the accurate description of both homolytic Co-C cleavage and H-atom-transfer reactions within this framework is challenging and can lead to controversial results with varying accuracy. We present an assessment study of 16 common density functionals applied to prototypical model systems for both reactions. H-abstraction reactions were modeled on the basis of four reference reactions designed to resemble a broad range of coenzyme B12 reactions. The Co-C cleavage reaction is treated by an ONIOM(QM/MM) setup that is in excellent agreement with solution-phase experimental data and is as accurate as full DFT calculations on the complete model system. We find that the meta-GGAs TPSS-D3 and M06L-D3 and the meta-hybrid M06-D3 give the best overall performance with MUEs for both types of reactions below 10 kJ mol-1. Our recommended model chemistry allows for a fast and accurate description of coenzyme B12 chemistry that is readily applicable to study the reactions in an enzymatic framework.
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Affiliation(s)
- Christian R Wick
- Division of Physical Chemistry, Group for Computational Life Sciences, Ruđer Bošković Institute , Bijenička cesta 54, 10000 Zagreb, Croatia
| | - David M Smith
- Division of Physical Chemistry, Group for Computational Life Sciences, Ruđer Bošković Institute , Bijenička cesta 54, 10000 Zagreb, Croatia.,Center for Computational Chemistry, FAU Erlangen-Nürnberg , Nägelsbachstrasse 25, 91052 Erlangen, Germany
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3
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Clark LD, Dikiy I, Chapman K, Rödström KE, Aramini J, LeVine MV, Khelashvili G, Rasmussen SG, Gardner KH, Rosenbaum DM. Ligand modulation of sidechain dynamics in a wild-type human GPCR. eLife 2017; 6:28505. [PMID: 28984574 PMCID: PMC5650471 DOI: 10.7554/elife.28505] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/20/2017] [Indexed: 11/13/2022] Open
Abstract
GPCRs regulate all aspects of human physiology, and biophysical studies have deepened our understanding of GPCR conformational regulation by different ligands. Yet there is no experimental evidence for how sidechain dynamics control allosteric transitions between GPCR conformations. To address this deficit, we generated samples of a wild-type GPCR (A2AR) that are deuterated apart from 1H/13C NMR probes at isoleucine δ1 methyl groups, which facilitated 1H/13C methyl TROSY NMR measurements with opposing ligands. Our data indicate that low [Na+] is required to allow large agonist-induced structural changes in A2AR, and that patterns of sidechain dynamics substantially differ between agonist (NECA) and inverse agonist (ZM241385) bound receptors, with the inverse agonist suppressing fast ps-ns timescale motions at the G protein binding site. Our approach to GPCR NMR creates a framework for exploring how different regions of a receptor respond to different ligands or signaling proteins through modulation of fast ps-ns sidechain dynamics.
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Affiliation(s)
- Lindsay D Clark
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, United States.,Molecular Biophysics Graduate Program, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Igor Dikiy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, United States
| | - Karen Chapman
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Karin Ej Rödström
- Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - James Aramini
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, United States
| | - Michael V LeVine
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States.,Institute for Computational Bioscience, Weill Cornell Medical College, New York, United States
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States.,Institute for Computational Bioscience, Weill Cornell Medical College, New York, United States
| | - Søren Gf Rasmussen
- Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, United States.,Department of Chemistry and Biochemistry, City College of New York, New York, United States.,Biochemistry, Chemistry and Biology PhD Programs, Graduate Center, City University of New York, New York, United States
| | - Daniel M Rosenbaum
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, United States.,Molecular Biophysics Graduate Program, The University of Texas Southwestern Medical Center, Dallas, United States
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4
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He Y, Guo Z, Jin P, Jiao C, Tian H, Zhu W. Optimizing the Chemical Recognition Process of a Fluorescent Chemosensor for α-Ketoglutarate. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b00263] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ye He
- Key Laboratory for Advanced
Materials and Institute of Fine Chemicals, Shanghai Key Laboratory
of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Zhiqian Guo
- Key Laboratory for Advanced
Materials and Institute of Fine Chemicals, Shanghai Key Laboratory
of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Pengwei Jin
- Key Laboratory for Advanced
Materials and Institute of Fine Chemicals, Shanghai Key Laboratory
of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Changhong Jiao
- Key Laboratory for Advanced
Materials and Institute of Fine Chemicals, Shanghai Key Laboratory
of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - He Tian
- Key Laboratory for Advanced
Materials and Institute of Fine Chemicals, Shanghai Key Laboratory
of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Weihong Zhu
- Key Laboratory for Advanced
Materials and Institute of Fine Chemicals, Shanghai Key Laboratory
of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
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5
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Román-Meléndez GD, von Glehn P, Harvey JN, Mulholland AJ, Marsh ENG. Role of active site residues in promoting cobalt-carbon bond homolysis in adenosylcobalamin-dependent mutases revealed through experiment and computation. Biochemistry 2014; 53:169-77. [PMID: 24341954 PMCID: PMC3928028 DOI: 10.1021/bi4012644] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Adenosylcobalamin (AdoCbl) serves as a source of reactive free radicals that are generated by homolytic scission of the coenzyme's cobalt-carbon bond. AdoCbl-dependent enzymes accelerate AdoCbl homolysis by ∼10(12)-fold, but the mechanism by which this is accomplished remains unclear. We have combined experimental and computational approaches to gain molecular-level insight into this process for glutamate mutase. Two residues, glutamate 330 and lysine 326, form hydrogen bonds with the adenosyl group of the coenzyme. A series of mutations that impair the enzyme's ability to catalyze coenzyme homolysis and tritium exchange with the substrate by 2-4 orders of magnitude were introduced at these positions. These mutations, together with the wild-type enzyme, were also characterized in silico by molecular dynamics simulations of the enzyme-AdoCbl-substrate complex with AdoCbl modeled in the associated (Co-C bond formed) or dissociated [adenosyl radical with cob(II)alamin] state. The simulations reveal that the number of hydrogen bonds between the adenosyl group and the protein side chains increases in the homolytically dissociated state, with respect to the associated state, for both the wild-type and mutant enzymes. The mutations also cause a progressive increase in the mean distance between the 5'-carbon of the adenosyl radical and the abstractable hydrogen of the substrate. Interestingly, the distance between the 5'-carbon and substrate hydrogen, determined computationally, was found to inversely correlate with the log k for tritium exchange (r = 0.93) determined experimentally. Taken together, these results point to a dual role for these residues: they both stabilize the homolytic state through electrostatic interactions between the protein and the dissociated coenzyme and correctly position the adenosyl radical to facilitate the abstraction of hydrogen from the substrate.
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Affiliation(s)
| | - Patrick von Glehn
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - Jeremy N. Harvey
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - E. Neil G. Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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6
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Rommel JB, Liu Y, Werner HJ, Kästner J. Role of tunneling in the enzyme glutamate mutase. J Phys Chem B 2012; 116:13682-9. [PMID: 23127187 DOI: 10.1021/jp308526t] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The role of quantum mechanical atom tunneling during the conversion of glutamate to methylaspartate catalyzed by glutamate mutase is investigated by quantum mechanical/molecular mechanical (QM/MM) simulations based on coupled cluster and density functional calculations. The use of instanton theory allows us to calculate the tunneling contributions of up to 78 atoms in the active site. We calculate kinetic isotope effects (KIEs) and compare them to experimental data. The simulations lead to deuterium KIEs of 10 for the hydrogen abstraction from glutamate substrate and 16 for the hydrogen abstraction from methylaspartate substrate, which are consistent with the experimental results. The hydrogen abstraction from methylaspartate has higher primary deuterium and tritium (46.1) KIEs than the abstraction from glutamate. The tunneling effect increases the reaction rate by a factor of 12.3 for the hydrogen abstraction from methylaspartate at 0. Tunneling is supported by the environment by preparing the enzyme through classical motions. Consideraton of the tunneling contributions of more and more atoms around the active center shows that the motions at the ribose ring play a central role during the tunneling enhancement of the hydrogen transfers. Our simulations give new insight into the catalytic process in glutamate mutase and the way enzymes use tunneling effects for a successful catalysis.
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Affiliation(s)
- Judith B Rommel
- Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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7
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Adenosylcobalamin enzymes: theory and experiment begin to converge. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1154-64. [PMID: 22516318 DOI: 10.1016/j.bbapap.2012.03.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 02/04/2012] [Accepted: 03/27/2012] [Indexed: 11/21/2022]
Abstract
Adenosylcobalamin (coenzyme B(12)) serves as the cofactor for a group of enzymes that catalyze unusual rearrangement or elimination reactions. The role of the cofactor as the initiator of reactive free radicals needed for these reactions is well established. Less clear is how these enzymes activate the coenzyme towards homolysis and control the radicals once generated. The availability of high resolution X-ray structures combined with detailed kinetic and spectroscopic analyses have allowed several adenosylcobalamin enzymes to be computationally modeled in some detail. Computer simulations have generally obtained good agreement with experimental data and provided valuable insight into the mechanisms of these unusual reactions. Importantly, atomistic modeling of the enzymes has allowed the role of specific interactions between protein, substrate and coenzyme to be explored, leading to mechanistic predictions that can now be tested experimentally. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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8
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Rommel JB, Kästner J. The fragmentation-recombination mechanism of the enzyme glutamate mutase studied by QM/MM simulations. J Am Chem Soc 2011; 133:10195-203. [PMID: 21612278 DOI: 10.1021/ja202312d] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The radical mechanism of the conversion of glutamate to methylaspartate catalyzed by glutamate mutase is studied with quantum mechanical/molecular mechanical (QM/MM) simulations based on density functional theory (DFT/MM). The hydrogen transfer between the substrate and the cofactor is found to be rate limiting with a barrier of 101.1 kJ mol(-1). A careful comparison to the uncatalyzed reaction in water is performed. The protein influences the reaction predominantly electrostatically and to a lesser degree sterically. Our calculations shed light on the atomistic details of the reaction mechanism. The well-known arginine claw and Glu 171 ( Clostridium cochlearium notation) are found to have the strongest influence on the reaction. However, a catalytic role of Glu 214, Lys 322, Gln 147, Glu 330, Lys 326, and Met 294 is found as well. The arginine claw keeps the intermediates in place and is probably responsible for the enantioselectivity. Glu 171 temporarily accepts a proton from the glutamyl radical intermediate and donates it back at the end of the reaction. We relate our results to experimental data when available. Our simulations lead to further understanding of how glutamate mutase catalyzes the carbon skeleton rearrangement of glutamate.
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Affiliation(s)
- Judith B Rommel
- Computational Biochemistry Group, Institute of Theoretical Chemistry, University of Stuttgart, Stuttgart, Germany
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9
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Warren JJ, Tronic TA, Mayer JM. Thermochemistry of proton-coupled electron transfer reagents and its implications. Chem Rev 2010; 110:6961-7001. [PMID: 20925411 PMCID: PMC3006073 DOI: 10.1021/cr100085k] [Citation(s) in RCA: 1182] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jeffrey J. Warren
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700
| | - Tristan A. Tronic
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700
| | - James M. Mayer
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700
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10
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Sandala GM, Smith DM, Radom L. Modeling the reactions catalyzed by coenzyme B12-dependent enzymes. Acc Chem Res 2010; 43:642-51. [PMID: 20136160 DOI: 10.1021/ar900260c] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes accelerate chemical reactions with an exceptional selectivity that makes life itself possible. Understanding the factors responsible for this efficient catalysis is of utmost importance in our quest to harness the tremendous power of enzymes. Computational chemistry has emerged as an important adjunct to experimental chemistry and biochemistry in this regard, because it provides detailed insights into the relationship between structure and function in a systematic and straightforward manner. In this Account, we highlight our recent high-level theoretical investigations toward this end in studying the radical-based reactions catalyzed by enzymes dependent on coenzyme B(12) (or adenosylcobalamin, AdoCbl). In addition to their fundamental position in biology, the AdoCbl-dependent enzymes represent a valuable framework within which to understand Nature's method of efficiently handling high-energy species to execute very specific reactions. The AdoCbl-mediated reactions are characterized by the interchange of a hydrogen atom and a functional group on adjacent carbon atoms. Our calculations are consistent with the conclusion that the main role of AdoCbl is to provide a source of radicals, thus moving the 1,2-rearrangements onto the radical potential energy surface. Our studies also show that the radical rearrangement step is facilitated by partial proton transfer involving the substrate. Specifically, we observe that the energy requirements for radical rearrangement are reduced dramatically with appropriate partial protonation or partial deprotonation or sometimes (synergistically) both. Such interactions are particularly relevant to enzyme catalysis, because it is likely that the local amino acid environment in the active site of an enzyme can function in this capacity through hydrogen bonding. Finally, our calculations indicate that the intervention of a very stable radical along the reaction pathway may inactivate the enzyme, demonstrating that sustained catalysis depends on a delicate energy balance. Radical-based enzyme reactions are often difficult to probe experimentally, so theoretical investigations have a particularly valuable role to play in their study. Our research demonstrates that a small-model approach can provide important and revealing insights into the mechanism of action of AdoCbl-dependent enzymes.
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Affiliation(s)
- Gregory M. Sandala
- School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
- Centre for Computational Solutions in the Life Sciences, Ruđer Bošković Institute, 10002 Zagreb, Croatia
| | - David M. Smith
- Centre for Computational Solutions in the Life Sciences, Ruđer Bošković Institute, 10002 Zagreb, Croatia
| | - Leo Radom
- School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
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Marsh ENG, Patterson DP, Li L. Adenosyl radical: reagent and catalyst in enzyme reactions. Chembiochem 2010; 11:604-21. [PMID: 20191656 PMCID: PMC3011887 DOI: 10.1002/cbic.200900777] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Indexed: 12/17/2022]
Abstract
Adenosine is undoubtedly an ancient biological molecule that is a component of many enzyme cofactors: ATP, FADH, NAD(P)H, and coenzyme A, to name but a few, and, of course, of RNA. Here we present an overview of the role of adenosine in its most reactive form: as an organic radical formed either by homolytic cleavage of adenosylcobalamin (coenzyme B(12), AdoCbl) or by single-electron reduction of S-adenosylmethionine (AdoMet) complexed to an iron-sulfur cluster. Although many of the enzymes we discuss are newly discovered, adenosine's role as a radical cofactor most likely arose very early in evolution, before the advent of photosynthesis and the production of molecular oxygen, which rapidly inactivates many radical enzymes. AdoCbl-dependent enzymes appear to be confined to a rather narrow repertoire of rearrangement reactions involving 1,2-hydrogen atom migrations; nevertheless, mechanistic insights gained from studying these enzymes have proved extremely valuable in understanding how enzymes generate and control highly reactive free radical intermediates. In contrast, there has been a recent explosion in the number of radical-AdoMet enzymes discovered that catalyze a remarkably wide range of chemically challenging reactions; here there is much still to learn about their mechanisms. Although all the radical-AdoMet enzymes so far characterized come from anaerobically growing microbes and are very oxygen sensitive, there is tantalizing evidence that some of these enzymes might be active in aerobic organisms including humans.
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Affiliation(s)
- E. Neil G. Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Dustin P. Patterson
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University – Purdue University Indianapolis, Indianapolis, IN 46202, USA
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12
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Li X, Chung LW, Paneth P, Morokuma K. DFT and ONIOM(DFT:MM) studies on Co-C bond cleavage and hydrogen transfer in B12-dependent methylmalonyl-CoA mutase. Stepwise or concerted mechanism? J Am Chem Soc 2009; 131:5115-25. [PMID: 19309090 DOI: 10.1021/ja807677z] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The considerable protein effect on the homolytic Co-C bond cleavage to form the 5'-deoxyadenosyl (Ado) radical and cob(II)alamin and the subsequent hydrogen transfer from the methylmalonyl-CoA substrate to the Ado radical in the methylmalonyl-CoA mutase (MMCM) have been extensively studied by DFT and ONIOM(DFT/MM) methods. Several quantum models have been used to systematically study the protein effect. The calculations have shown that the Co-C bond dissociation energy is very much reduced in the protein, compared to that in the gas phase. The large protein effect can be decomposed into the cage effect, the effect of coenzyme geometrical distortion, and the protein MM effect. The largest contributor is the MM effect, which mainly consists of the interaction of the QM part of the coenzyme with the MM part of the coenzyme and the surrounding residues. In particular, Glu370 plays an important role in the Co-C bond cleavage process. These effects tremendously enhance the stability of the Co-C bond cleavage state in the protein. The initial Co-C bond cleavage and the subsequent hydrogen transfer were found to occur in a stepwise manner in the protein, although the concerted pathway for the Co-C bond cleavage coupled with the hydrogen transfer is more favored in the gas phase. The assumed concerted transition state in the protein has more deformation of the coenzyme and the substrate and has less interaction with the protein than the stepwise route. Key factors and residues in promoting the enzymatic reaction rate have been discussed in detail.
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Affiliation(s)
- Xin Li
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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13
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Sandala GM, Smith DM, Radom L. The carbon-skeleton rearrangement in tropane alkaloid biosynthesis. J Am Chem Soc 2008; 130:10684-90. [PMID: 18627156 DOI: 10.1021/ja801869a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High-level quantum chemistry calculations have been performed to examine the carbon-skeleton rearrangement of the tropane alkaloid littorine to hyoscyamine. Two pathways involving radical and carbocation intermediates have been investigated in this regard, namely, stepwise (or fragmentation-recombination) and concerted. The fragmentation products are calculated to be of high energy for both the radical- and carbocation-based mechanisms (136.3 and 170.9 kJ mol(-1), respectively). Similarly, the rearrangement barrier for the radical-based concerted pathway is calculated to be quite high (135.6 kJ mol(-1)). In contrast, the carbocation-based concerted pathway is found to be associated with a relatively low barrier (47.4 kJ mol(-1)). The ionization energy of the substrate-derived radical 3a is calculated to be 7.01 eV, suggesting that its oxidation to generate the substrate-derived carbocation 3b ought to be facile. In an attempt to investigate how an enzyme might modulate the rearrangement barriers, the separate and combined influences of partially protonating the migrating group and partially deprotonating the spectator OH group of the substrate were investigated. Such interactions can lead to significant reductions in the rearrangement barrier for both the radical- and carbocation-based concerted pathways, although the carbocation pathway continues to have significantly lower energy requirements. Also, the relatively high (gas-phase) acidity of the OH group of the product-related carbocation 4b indicates that the direct formation of hyoscyamine aldehyde (6) is a highly exothermic process. Although we would not wish to rule out alternative possibilities, our calculations suggest that a concerted rearrangement mechanism involving carbocations constitutes a viable low-energy pathway for the carbon-skeleton rearrangement in tropane alkaloid biosynthesis.
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Affiliation(s)
- Gregory M Sandala
- School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia.
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14
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MENG XM, ZOU LF, XIE M, FU Y. Strength of C–H Bonds at Nitrogenα-Position:Implication for Metabolic Stability of Nitrogen-containing Drug Molecules. CHINESE J CHEM 2008. [DOI: 10.1002/cjoc.200890147] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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15
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Abstract
Methane has long been known to be used as a carbon and energy source by some aerobic alpha- and delta-proteobacteria. In these organisms the metabolism of methane starts with its oxidation with O(2) to methanol, a reaction catalyzed by a monooxygenase and therefore restricted to the aerobic world. Methane has recently been shown to also fuel the growth of anaerobic microorganisms. The oxidation of methane with sulfate and with nitrate have been reported, but the mechanisms of anaerobic methane oxidation still remains elusive. Sulfate-dependent methane oxidation is catalyzed by methanotrophic archaea, which are related to the Methanosarcinales and which grow in close association with sulfate-reducing delta-proteobacteria. There is evidence that anaerobic methane oxidation with sulfate proceeds at least in part via reversed methanogenesis involving the nickel enzyme methyl-coenzyme M reductase for methane activation, which under standard conditions is an endergonic reaction, and thus inherently slow. Methane oxidation coupled to denitrification is mediated by bacteria belonging to a novel phylum and does not involve methyl-coenzyme M reductase. The first step in methane oxidation is most likely the exergonic formation of 2-methylsuccinate from fumarate and methane catalyzed by a glycine-radical enzyme.
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Affiliation(s)
- Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany.
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Sharma PK, Chu ZT, Olsson MHM, Warshel A. A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes. Proc Natl Acad Sci U S A 2007; 104:9661-6. [PMID: 17517615 PMCID: PMC1887576 DOI: 10.1073/pnas.0702238104] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Indexed: 11/18/2022] Open
Abstract
The catalytic power of enzymes containing coenzyme B(12) cofactor has been, in some respects, the "last bastion" for the strain hypothesis. The present work explores the origin of this effect by using simulation methods that overcome the sampling difficulties of previous energy minimization studies. It is found that the major part of the catalytic effect is due to the electrostatic interaction between the ribose and the protein, and that the strain contribution is very small. Remarkably, enzymes can use electrostatic effects even in a radical process, when the charge distribution of the reacting fragments does not change significantly during the reaction. Electrostatic catalysis can, in such cases, be obtained by attaching a polar group to the leaving fragment and designing an active site that interacts more strongly with this group in the product state than in the reactant state. The finding that evolution had to use this trick provides further evidence to the observation that it is extremely hard to catalyze enzymatic reactions by nonelectrostatic factors. The trick used by B(12) enzymes may, in fact, be a very powerful new strategy in enzyme design.
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Affiliation(s)
- Pankaz K. Sharma
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062
| | - Zhen T. Chu
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062
| | - Mats H. M. Olsson
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062
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