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Bowling PE, Dasgupta S, Herbert JM. Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites. J Chem Inf Model 2024; 64:3912-3922. [PMID: 38648614 DOI: 10.1021/acs.jcim.4c00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
In constructing finite models of enzyme active sites for quantum-chemical calculations, atoms at the periphery of the model must be constrained to prevent unphysical rearrangements during geometry relaxation. A simple fixed-atom or "coordinate-lock" approach is commonly employed but leads to undesirable artifacts in the form of small imaginary frequencies. These preclude evaluation of finite-temperature free-energy corrections, limiting thermochemical calculations to enthalpies only. Full-dimensional vibrational frequency calculations are possible by replacing the fixed-atom constraints with harmonic confining potentials. Here, we compare that approach to an alternative strategy in which fixed-atom contributions to the Hessian are simply omitted. While the latter strategy does eliminate imaginary frequencies, it tends to underestimate both the zero-point energy and the vibrational entropy while introducing artificial rigidity. Harmonic confining potentials eliminate imaginary frequencies and provide a flexible means to construct active-site models that can be used in unconstrained geometry relaxations, affording better convergence of reaction energies and barrier heights with respect to the model size, as compared to models with fixed-atom constraints.
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Affiliation(s)
- Paige E Bowling
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, California 92093, United States
| | - John M Herbert
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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2
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Sowińska A, Rostkowski M, Krzemińska A, Englman T, Gelman F, Dybala-Defratyka A. Insights into generalization of the rate-limiting steps of the dehalogenation by LinB and DhaA: A computational approach. Arch Biochem Biophys 2023:109675. [PMID: 37343813 DOI: 10.1016/j.abb.2023.109675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/23/2023]
Abstract
LinB and DhaA are well-known haloalkane dehalogenases (HLDs) capable of converting a plethora of halogenated alkanes, also those considered persistent pollutants. The dehalogenation reaction that these two enzymes catalyze has been studied to determine its rate-limiting step (rls) for the last two decades now. As a result, it has been determined that HLDs can show different rate-limiting steps for individual substrates, and at this point we do not have a basis for any generalization in this matter. Therefore, in this work we aimed at gaining insights into the enzymatic dehalogenation of selected dibromo- and bromochloro-ethanes and propanes by LinB and DhaA using computational approach to determine whether defined structural similarities of the substrates result in a unified mechanism and the same rls. By predicting halogen binding isotope effects (BIEs) as well as computing interaction energy for each HLD-ligand complex the nature of the protein-ligand interactions has been characterized. Furthermore, C and Br kinetic isotope effects (KIEs) as well as the minimum free energy paths (MFEPs) were computed to investigate the chemical reaction for the selected systems. Accuracy of the approach and robustness of the computational predictions were validated by measuring KIEs on the selected reactions. Overall results strongly indicate that any generalization with respect to the enzymatic process involving various ligands in the case of DhaA is impossible, even if the considered ligands are structurally very similar as those analyzed in the present study. Moreover, even small structural differences such as changing of one of the (non-leaving) halogen substituents may lead to significant changes in the enzymatic process and result in a different rls in the case of LinB. It has also been demonstrated that KIEs themselves cannot be used as rls indicators in the reactions catalyzed by the studied HLDs.
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Affiliation(s)
- Agata Sowińska
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Michał Rostkowski
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Agnieszka Krzemińska
- Institute of Physics, Lodz University of Technology, Wolczanska 217/221, 93-005, Lodz, Poland
| | - Tzofia Englman
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Faina Gelman
- Geological Survey of Israel, Yeshayahu Leibowitz 32, Jerusalem, 9692100, Israel
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland.
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Unprecedently large 37Cl/ 35Cl equilibrium isotopic fractionation on nano-confinement of chloride anion. Sci Rep 2022; 12:1768. [PMID: 35110604 PMCID: PMC8811032 DOI: 10.1038/s41598-022-05629-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/14/2022] [Indexed: 11/09/2022] Open
Abstract
Confinement can result in unusual properties leading to new, exciting discoveries in the nano-realm. One such consequence of confinement at the nanoscale is extremally large isotopic fractionation, especially at sub-van der Waals distances. Herein, on the example of chlorine isotope effects, we show that at conditions of nanoencapsulation these effects may reach values by far larger than observed for the bulk environment, which in the case of nanotubes can lead to practical applications (e.g., in isotopic enrichment) and needs to be considered in analytical procedures that employ nanomaterials.
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Paneth A, Paneth P. Isotopic Consequences of Host-Guest Interactions; Noncovalent Chlorine Isotope Effects. J Phys Chem B 2021; 125:1874-1880. [PMID: 33570409 PMCID: PMC8023698 DOI: 10.1021/acs.jpcb.0c10691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/24/2021] [Indexed: 12/03/2022]
Abstract
Although weak intermolecular interactions are the essence of most processes of key importance in medicine, industry, environment, and life cycles, their characterization is still not sufficient. Enzymatic dehalogenations that involve chloride anion interaction within a host-guest framework is one of the many examples. Recently published experimental results on host-guest systems provided us with models suitable to assess isotopic consequences of these noncovalent interactions. Herein, we report the influence of environmental and structural variations on chlorine isotope effects. We show that these effects, although small, may obscure mechanistic interpretations, as well as analytical protocols of dehalogenation processes.
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Affiliation(s)
- Agata Paneth
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland
| | - Piotr Paneth
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
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Kannath S, Adamczyk P, Wu L, Richnow HH, Dybala-Defratyka A. Can Alkaline Hydrolysis of γ-HCH Serve as a Model Reaction to Study Its Aerobic Enzymatic Dehydrochlorination by LinA? Int J Mol Sci 2019; 20:ijms20235955. [PMID: 31779285 PMCID: PMC6929183 DOI: 10.3390/ijms20235955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/22/2019] [Accepted: 11/24/2019] [Indexed: 12/26/2022] Open
Abstract
Hexachlorocyclohexane (HCH) isomers constitute a group of persistent organic pollutants. Their mass production and treatment have led to a global environmental problem that continues to this day. The characterization of modes of degradation of HCH by isotope fractionation is a current challenge. Multi isotope fractionation analysis provides a concept to characterize the nature of enzymatic and chemical transformation reactions. The understanding of the kinetic isotope effects (KIE) on bond cleavage reaction contributes to analyses of the mechanism of chemical and enzymatic reactions. Herein, carbon, chlorine, and hydrogen kinetic isotope effects are measured and predicted for the dehydrochlorination reaction of γ-HCH promoted by the hydroxyl ion in aqueous solution. Quantum mechanical (QM) microsolvation with an implicit solvation model and path integral formalism in combination with free-energy perturbation and umbrella sampling (PI-FEP/UM) and quantum mechanical/molecular mechanical QM/MM potentials for including solvent effects as well as calculating isotope effects are used and analyzed with respect to their performance in reproducing measured values. Reaction characterization is discussed based on the magnitudes of obtained isotope effects. The comparative analysis between the chemical dehydrochlorination of γ-HCH in aqueous media and catalyzed reaction by dehydrochlorinase, LinA is presented and discussed. Based on the values of isotope effects, these two processes seem to occur via the same net mechanism.
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Affiliation(s)
- Suraj Kannath
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 112, 90-924 Lodz, Poland; (S.K.); (P.A.)
| | - Paweł Adamczyk
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 112, 90-924 Lodz, Poland; (S.K.); (P.A.)
| | - Langping Wu
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany; (L.W.); (H.H.R.)
- Departments of Civil & Mineral Engineering, University of Toronto, 35 St. George St., Toronto, ON M5S 1A4, Canada
| | - Hans H. Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany; (L.W.); (H.H.R.)
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 112, 90-924 Lodz, Poland; (S.K.); (P.A.)
- Correspondence: ; Tel.: +48-42-631-3198
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Schilling IE, Hess R, Bolotin J, Lal R, Hofstetter TB, Kohler HPE. Kinetic Isotope Effects of the Enzymatic Transformation of γ-Hexachlorocyclohexane by the Lindane Dehydrochlorinase Variants LinA1 and LinA2. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:2353-2363. [PMID: 30674184 DOI: 10.1021/acs.est.8b04234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Compound-specific isotope analysis (CSIA) can provide insights into the natural attenuation processes of hexachlorocyclohexanes (HCHs), an important class of persistent organic pollutants. However, the interpretation of HCH stable isotope fractionation is conceptually challenging. HCHs exist as different conformers that can be converted into each other, and the enzymes responsible for their transformation discriminate among those HCH conformers. Here, we investigated the enzyme specificity of apparent 13C- and 2H-kinetic isotope effects (AKIEs) associated with the dehydrochlorination of γ-HCH (lindane) by two variants of the lindane dehydrochlorinases LinA1 and LinA2. While LinA1 and LinA2 attack γ-HCH at different trans-1,2-diaxial H-C-C-Cl moieties, the observed C and H isotope fractionation was large, typical for bimolecular eliminations, and was not affected by conformational mobility. 13C-AKIEs for transformation by LinA1 and LinA2 were the same (1.024 ± 0.001 and 1.025 ± 0.001, respectively), whereas 2H-AKIEs showed minor differences (2.4 ± 0.1 and 2.6 ± 0.1). Variations of isotope effects between LinA1 and LinA2 are small and in the range reported for different degrees of C-H bond cleavage in transition states of dehydrochlorination reactions. The large C and H isotope fractionation reported here for experiments with pure enzymes contrasts with previous observations from whole cell experiments and suggests that specific uptake processes by HCH-degrading microorganisms might modulate the observable HCH isotope fractionation at contaminated sites.
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Affiliation(s)
- Iris E Schilling
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf , Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , CH-8092 Zürich , Switzerland
| | - Ramon Hess
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , CH-8092 Zürich , Switzerland
| | - Jakov Bolotin
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf , Switzerland
| | - Rup Lal
- Department of Zoology , University of Delhi , Delhi 110007 , India
| | - Thomas B Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf , Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , CH-8092 Zürich , Switzerland
| | - Hans-Peter E Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , CH-8600 Dübendorf , Switzerland
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Manna RN, Grzybkowska A, Gelman F, Dybala-Defratyka A. Carbon-bromine bond cleavage - A perspective from bromine and carbon kinetic isotope effects on model debromination reactions. CHEMOSPHERE 2018; 193:17-23. [PMID: 29126061 DOI: 10.1016/j.chemosphere.2017.10.153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 10/13/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
In this work, we explore the effect of solvent on 13C and 81Br kinetic isotope effects (KIEs) during elimination of bromine substituent from brominated organic compounds promoted by hydroxyl anion. In the present study, we investigate HBr elimination from 2-bromoethylbenzene in three different polar media (water, ethanol, and acetonitrile) as well as bromide ion elimination from 1,2-dibromoethane upon nucleophilic substitution by the hydroxyl ion in aqueous solution using carbon and bromine isotope analysis as mechanistic tools. We reconsider the hypothesis that the magnitude of leaving group halide KIE should visibly depend on the solvent and bond-breaking in a protic solvent should be accompanied by hydrogen bonding which would result in less zero-point energy loss than in an aprotic solvent. Modeling the elimination reaction using the available popular theoretical methods along with different approaches for including environment effects we demonstrate in the presented study no interpretable effect of the solvent on the transition state structure and hence on the theoretically predicted KIEs. The comparison of the magnitudes of carbon and bromine kinetic isotope effects for two different mechanistic pathways (elimination vs substitution) is also discussed.
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Affiliation(s)
- Rabindra Nath Manna
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; Indian Association for the Cultivation of Science, Physical Chemistry, 2A and 2B Raja S C Mullick Road, Kolkata, West Bengal, 700032, India
| | - Anna Grzybkowska
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Faina Gelman
- Geological Survey of Israel, Malkhei Israel St. 30, 95501 Jerusalem, Israel
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
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