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Szaleniec M, Oleksy G, Sekuła A, Aleksić I, Pietras R, Sarewicz M, Krämer K, Pierik AJ, Heider J. Modeling the Initiation Phase of the Catalytic Cycle in the Glycyl-Radical Enzyme Benzylsuccinate Synthase. J Phys Chem B 2024; 128:5823-5839. [PMID: 38848492 PMCID: PMC11194802 DOI: 10.1021/acs.jpcb.4c01237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/09/2024]
Abstract
The reaction of benzylsuccinate synthase, the radical-based addition of toluene to a fumarate cosubstrate, is initiated by hydrogen transfer from a conserved cysteine to the nearby glycyl radical in the active center of the enzyme. In this study, we analyze this step by comprehensive computer modeling, predicting (i) the influence of bound substrates or products, (ii) the energy profiles of forward- and backward hydrogen-transfer reactions, (iii) their kinetic constants and potential mechanisms, (iv) enantiospecificity differences, and (v) kinetic isotope effects. Moreover, we support several of the computational predictions experimentally, providing evidence for the predicted H/D-exchange reactions into the product and at the glycyl radical site. Our data indicate that the hydrogen transfer reactions between the active site glycyl and cysteine are principally reversible, but their rates differ strongly depending on their stereochemical orientation, transfer of protium or deuterium, and the presence or absence of substrates or products in the active site. This is particularly evident for the isotope exchange of the remaining protium atom of the glycyl radical to deuterium, which appears dependent on substrate or product binding, explaining why the exchange is observed in some, but not all, glycyl-radical enzymes.
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Affiliation(s)
- Maciej Szaleniec
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy
of Sciences, Kraków 31-201, Poland
| | - Gabriela Oleksy
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy
of Sciences, Kraków 31-201, Poland
- Department
of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg 35043, Germany
| | - Anna Sekuła
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy
of Sciences, Kraków 31-201, Poland
| | - Ivana Aleksić
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy
of Sciences, Kraków 31-201, Poland
| | - Rafał Pietras
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków 31-007, Poland
| | - Marcin Sarewicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków 31-007, Poland
| | - Kai Krämer
- Department
of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg 35043, Germany
| | - Antonio J. Pierik
- Biochemistry,
Faculty of ChemistryRPTU Kaiserslautern-Landau, Kaiserslautern D-67663, Germany
| | - Johann Heider
- Department
of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg 35043, Germany
- Synmikro-Center
for Synthetic Microbiology, Philipps University
Marburg, Marburg 35043, Germany
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Suess CJ, Martins FL, Croft AK, Jäger CM. Radical Stabilization Energies for Enzyme Engineering: Tackling the Substrate Scope of the Radical Enzyme QueE. J Chem Inf Model 2019; 59:5111-5125. [PMID: 31730347 DOI: 10.1021/acs.jcim.9b00017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Experimental assessment of catalytic reaction mechanisms and profiles of radical enzymes can be severely challenging due to the reactive nature of the intermediates and sensitivity of cofactors such as iron-sulfur clusters. Here, we present an enzyme-directed computational methodology for the assessment of thermodynamic reaction profiles and screening for radical stabilization energies (RSEs) for the assessment of catalytic turnovers in radical enzymes. We have applied this new screening method to the radical S-adenosylmethione enzyme 7-carboxy-7-deazaguanine synthase (QueE), following a detailed molecular dynamics (MD) analysis that clarifies the role of both specific enzyme residues and bound Mg2+, Ca2+, or Na+. The MD simulations provided the basis for a statistical approach to sample different conformational outcomes. RSE calculation at the M06-2X/6-31+G* level of theory provided the most computationally cost-effective assessment of enzyme-based energies, facilitated by an initial triage using semiempirical methods. The impact of intermolecular interactions on RSE was clearly established, and application to the assessment of potential alternative substrates (focusing on radical clock type rearrangements) proposes a selection of carbon-substituted analogues that would react to afford cyclopropylcarbinyl radical intermediates as candidates for catalytic turnover by QueE.
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Affiliation(s)
- Christian J Suess
- Department of Chemical and Environmental Engineering , The University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Floriane L Martins
- Department of Chemical and Environmental Engineering , The University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Anna K Croft
- Department of Chemical and Environmental Engineering , The University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering , The University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
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Gupta PK, Esser A, Forbert H, Marx D. Toward theoretical terahertz spectroscopy of glassy aqueous solutions: partially frozen solute-solvent couplings of glycine in water. Phys Chem Chem Phys 2019; 21:4975-4987. [PMID: 30758388 DOI: 10.1039/c8cp07489e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular-level understanding of THz spectra of aqueous solutions under ambient conditions has been greatly advanced in recent years. Here, we go beyond previous analyses by performing ab initio molecular dynamics simulations of glycine in water with artificially frozen solute or solvent molecules, respectively, while computing the total THz response as well as its decomposition into mode-specific resonances based on the "supermolecular solvation complex" technique. Clamping the water molecules and keeping glycine moving breaks the coupling of glycine to the structural dynamics of the solvent, however, the polarization and dielectric solvation effects in the static solvation cage are still at work since the full electronic structure of the quenched solvent is taken into account. The complementary approach of fixing glycine reveals both the dynamical and electronic response of the solvation cage at the level of its THz response. Moreover, to quantitatively account for the electronic contribution solely due to solvent embedding, the solute species is "vertically desolvated", thus preserving the fully coupled solute-solvent motion in terms of the solute's structural dynamics in solution, while its electronic structure is no longer subject to solute-solvent polarization and charge transfer effects. When referenced to the free simulation of Gly(aq), this three-fold approach allows us to decompose the THz spectral contributions due to the correlated solute-solvent dynamics into entirely structural and purely electronic effects. Beyond providing hitherto unknown insights, the observed systematic changes of THz spectra in terms of peak shifts and lineshape modulations due to conformational freezing and frozen solvation cages might be useful to investigate the solvation of molecules in highly viscous H-bonding solvents such as ionic liquids and even in cryogenic ices as relevant to polar stratospheric and dark interstellar clouds.
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Affiliation(s)
- Prashant Kumar Gupta
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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An ab iniio study on the micro-solvation of amino acids: On the number of water molecules necessary to stabilize the zwitter ion. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2018.12.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Affiliation(s)
- Belinda L. Slakman
- Department of Chemical Engineering Northeastern University Boston Massachusetts
| | - Richard H. West
- Department of Chemical Engineering Northeastern University Boston Massachusetts
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Chan B, Rintelman J, Wood GPF, Radom L, Gordon MS. Solvation of the Glycyl Radical. J Phys Chem A 2018; 122:7212-7217. [PMID: 30160481 DOI: 10.1021/acs.jpca.8b06833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The effect of adding explicit water molecules to the neutral (N) and zwitterionic (Z) forms of the glycyl radical has been examined. The results show that a minimum of three water molecules is required to stabilize the Z radical as a local minimum, with an energy gap of 123 kJ mol-1 between the N and Z forms at this point, in favor of the N form. Increasing the number of water molecules to ∼20 leads to a converged Z-N energy difference of ∼50 kJ mol-1 still in favor of the N form, even though the radical is not considered fully solvated from a structural point of view. Thus, energetic convergence is determined mainly by solvation of the polar functional groups, and a complete coverage of the entire molecule is not necessary. Because aqueous closed-shell glycine exists as a zwitterion while aqueous glycyl radical prefers the neutral form, the conversion between the two necessitates a change along the hydrogen-abstraction reaction pathway. In this regard, the transition structure for α-hydrogen abstraction by the ·OH radical has greater resemblance to glycine than to the glycyl radical. Overall, the barrier for hydrogen abstraction from Z glycine is larger than that from the N isomer, and this might act to provide some protection against radical damage to the free amino acid in the (aqueous) biological environment.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering , Nagasaki University , Bunkyo 1-14 , Nagasaki 852-8521 , Japan.,School of Chemistry , University of Sydney , Sydney , NSW 2006 , Australia
| | - Jamie Rintelman
- Department of Chemistry , Iowa State University , Ames , Iowa 50011 , United States
| | - Geoffrey P F Wood
- School of Chemistry , University of Sydney , Sydney , NSW 2006 , Australia
| | - Leo Radom
- School of Chemistry , University of Sydney , Sydney , NSW 2006 , Australia
| | - Mark S Gordon
- Department of Chemistry , Iowa State University , Ames , Iowa 50011 , United States
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Janbazi M, T. Azar Y, Ziaie F. EPR parameters of L-α-alanine radicals in aqueous solution: a first-principles study. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1456684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mehdi Janbazi
- Radiation Application Research School, Nuclear Science and Technology Research Institute, Tehran, Iran
| | - Yavar T. Azar
- Physics and Accelerator Research School, Nuclear Science and Technology Research Institute, Tehran, Iran
| | - Farhood Ziaie
- Radiation Application Research School, Nuclear Science and Technology Research Institute, Tehran, Iran
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Jäger CM, Croft AK. Radical Reaction Control in the AdoMet Radical Enzyme CDG Synthase (QueE): Consolidate, Destabilize, Accelerate. Chemistry 2017; 23:953-962. [PMID: 27859789 PMCID: PMC5347944 DOI: 10.1002/chem.201604719] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Indexed: 12/29/2022]
Abstract
Controlling radical intermediates and thus catalysing and directing complex radical reactions is a central feature of S-adensosylmethionine (SAM)-dependent radical enzymes. We report ab initio and DFT calculations highlighting the specific influence of ion complexation, including Mg2+ , identified as a key catalytic component on radical stability and reaction control in 7-carboxy-7-deazaguanine synthase (QueE). Radical stabilisation energies (RSEs) of key intermediates and radical clock-like model systems of the enzyme-catalysed rearrangement of 6-carboxytetrahydropterin (CPH4), reveals a directing role of Mg2+ in destabilising both the substrate-derived radical and corresponding side reactions, with the effect that the experimentally-observed rearrangement becomes dominant over possible alternatives. Importantly, this is achieved with minimal disruption of the thermodynamics of the substrate itself, affording a novel mechanism for an enzyme to both maintain binding potential and accelerate the rearrangement step. Other mono and divalent ions were probed with only dicationic species achieving the necessary radical conformation to facilitate the reaction.
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Affiliation(s)
- Christof M. Jäger
- The University of NottinghamDepartment of Chemical and Environmental EngineeringUniversity ParkNottinghamNG7 2RDUnited Kingdom
| | - Anna K. Croft
- The University of NottinghamDepartment of Chemical and Environmental EngineeringUniversity ParkNottinghamNG7 2RDUnited Kingdom
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Pathak AK. Stabilizing the zwitter-ionic form of amino acids in the gas phase: An ab initio study on the minimum number of solvents and ions. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.07.058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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10
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Lin RJ, Jang S, Kim H, Wu CC, Li FY. Site specificity on OH α-H abstraction reaction for a zwitterionic β-hairpin peptide in aqueous solution: a theoretical investigation. J Phys Chem B 2013; 117:771-83. [PMID: 23252826 DOI: 10.1021/jp308879r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein backbone oxidation was investigated by studying the α-H abstraction reaction in a ß-hairpin peptide, called Chignolin (PDB ID 1UAO), with density functional theory calculation at B3LYP/6-31G(d,p) without any constraint. In order to stabilize the zwitterionic form of Chignolin with the salt bridges, the effects of aqueous solution were implemented by using microsolvation combined with a conductor-like polarizable continuum model (CPCM). Comparison between three glycine residues located at three different sites in Chignolin was used to examine the possible site specificity of this backbone oxidation. To construct the reaction profile of these α-H abstraction reactions, the pre- and postreactive complexes along with their associated transition states were located and verified with the intrinsic reaction coordinate (IRC) method. The bond dissociation energy and reaction rates of these OH α-H abstraction reactions were calculated with transition state theory. The differences in this abstraction reaction between the neutral and zwitterionic forms of Chignolin were also compared. A molecular dynamics simulation was implemented to study the explicit solvation effect on the abstracted Chignolin structure. The range of the simulation time scale covers from femtoseconds to microseconds, i.e., from onset of the abstraction to the abstracted products reaching thermal equilibrium. Our results show that there are three kinds of site-specificity in this abstraction reaction. The reactivity and stability of the abstraction products and their abstraction modes are all dependent on the location where OH attacks. Furthermore, the free energy landscapes of these abstraction products are distinctively different. This may imply that the pathological disorders or diseases caused by this type of radicals are also dependent on the abstraction location.
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Affiliation(s)
- Ren-Jie Lin
- Department of Chemistry, National Chung Hsing University, Taichung, Taiwan 402, Republic of China
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11
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Recent Progress in Density Functional Methodology for Biomolecular Modeling. STRUCTURE AND BONDING 2013. [DOI: 10.1007/978-3-642-32750-6_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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12
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Hao Q, Song T, Ng DCM, Quan Q, Siu CK, Chu IK. Arginine-Facilitated Isomerization: Radical-Induced Dissociation of Aliphatic Radical Cationic Glycylarginyl(iso)leucine Tripeptides. J Phys Chem B 2012; 116:7627-34. [DOI: 10.1021/jp301882p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Qiang Hao
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
- Department
of Biology and Chemistry, City University of Hong Kong, Hong Kong, China
| | - Tao Song
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Dominic C. M. Ng
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Quan Quan
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Chi-Kit Siu
- Department
of Biology and Chemistry, City University of Hong Kong, Hong Kong, China
| | - Ivan K. Chu
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
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13
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Lin RJ, Jang S, Wu CC, Liu YL, Li FY. Site specificity of OH α-H abstraction reaction for a β-hairpin peptide: An ab initio study. J Comput Chem 2011; 32:3409-22. [DOI: 10.1002/jcc.21920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 07/01/2011] [Accepted: 07/25/2011] [Indexed: 12/13/2022]
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14
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Grigoropoulos A, Szilagyi RK. In silico evaluation of proposed biosynthetic pathways for the unique dithiolate ligand of the H-cluster of [FeFe]-hydrogenase. J Comput Chem 2011; 32:3194-206. [DOI: 10.1002/jcc.21901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 07/02/2011] [Accepted: 07/03/2011] [Indexed: 12/30/2022]
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15
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Kim CK, Park BH, Lee HW, Kim CK. Comprehensive Studies on the Free Energies of Solvation and Conformers of Glycine: A Theoretical Study. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.6.1985] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Song T, Ng DCM, Quan Q, Siu CK, Chu IK. Arginine-Facilitated α- and π-Radical Migrations in Glycylarginyltryptophan Radical Cations. Chem Asian J 2011; 6:888-98. [DOI: 10.1002/asia.201000677] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2010] [Indexed: 12/16/2022]
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Sun J, Bousquet D, Forbert H, Marx D. Glycine in aqueous solution: solvation shells, interfacial water, and vibrational spectroscopy from ab initio molecular dynamics. J Chem Phys 2010; 133:114508. [DOI: 10.1063/1.3481576] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Grigoropoulos A, Szilagyi RK. Evaluation of biosynthetic pathways for the unique dithiolate ligand of the FeFe hydrogenase H-cluster. J Biol Inorg Chem 2010; 15:1177-82. [DOI: 10.1007/s00775-010-0698-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 08/18/2010] [Indexed: 10/19/2022]
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Ng DCM, Song T, Siu SO, Siu CK, Laskin J, Chu IK. Formation, Isomerization, and Dissociation of α-Carbon-Centered and π-Centered Glycylglycyltryptophan Radical Cations. J Phys Chem B 2010; 114:2270-80. [DOI: 10.1021/jp908599a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dominic C. M. Ng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China, Pacific Northwest National Laboratory, Fundamental Sciences Division, Richland, Washington, and Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Tao Song
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China, Pacific Northwest National Laboratory, Fundamental Sciences Division, Richland, Washington, and Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - S. O. Siu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China, Pacific Northwest National Laboratory, Fundamental Sciences Division, Richland, Washington, and Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - C. K. Siu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China, Pacific Northwest National Laboratory, Fundamental Sciences Division, Richland, Washington, and Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Julia Laskin
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China, Pacific Northwest National Laboratory, Fundamental Sciences Division, Richland, Washington, and Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Ivan K. Chu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China, Pacific Northwest National Laboratory, Fundamental Sciences Division, Richland, Washington, and Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
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