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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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Zhang M, Yang L, Ding W, Zhang H. The His23 and Lys79 pair determines the high catalytic efficiency of the inorganic pyrophosphatase of the haloacid dehalogenase superfamily. Biochim Biophys Acta Gen Subj 2022; 1866:130128. [PMID: 35278619 DOI: 10.1016/j.bbagen.2022.130128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 10/18/2022]
Abstract
Haloacid dehalogenase (HAD) superfamily members are mainly phosphomonoesterases, while BT2127 from Bacteroides thetaiotaomicron of the HAD superfamily is identified as an inorganic pyrophosphatase. In this study, to explore the roles of the Lys79 and His23 pair in the hydrolysis reaction of inorganic pyrophosphate (PPi) catalyzed by BT2127, a series of models were designed. Calculations were performed by using the density functional theory (DFT) method with the dispersion energy D3-B3LYP. The His23 and Lys79 pair plays a key role in the high catalytic efficiency of BT2127 with PPi. First, the His23 and Lys79 pair prompts Asp13 to easily provide a proton to the leaving group, which remarkably reduces the energy barrier of the phospho-transfer step; then, Lys79 provides a proton to the first leaving phosphate group via His23, produces a more electrically stabilized phosphate (H3PO4), makes this step exothermal, and further promotes the subsequent phospho-enzyme intermediate hydrolysis. The results suggest that the Lys79-His23 pair helps BT2127 reach high catalytic efficiency by strengthening the acid catalysis. Our study provides detailed chemical insights into the evolution of the inorganic pyrophosphatase function of BT2127 from the phosphomonoesterase of the HAD superfamily and the biomimetic enzyme design.
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Affiliation(s)
- Mingming Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, PR China
| | - Ling Yang
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, PR China.
| | - Wanjian Ding
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, PR China.
| | - Hao Zhang
- Biomedical Research Center, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, 730030, PR China.
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3
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Zlobin A, Diankin I, Pushkarev S, Golovin A. Probing the Suitability of Different Ca 2+ Parameters for Long Simulations of Diisopropyl Fluorophosphatase. Molecules 2021; 26:5839. [PMID: 34641383 PMCID: PMC8510429 DOI: 10.3390/molecules26195839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Organophosphate hydrolases are promising as potential biotherapeutic agents to treat poisoning with pesticides or nerve gases. However, these enzymes often need to be further engineered in order to become useful in practice. One example of such enhancement is the alteration of enantioselectivity of diisopropyl fluorophosphatase (DFPase). Molecular modeling techniques offer a unique opportunity to address this task rationally by providing a physical description of the substrate-binding process. However, DFPase is a metalloenzyme, and correct modeling of metal cations is a challenging task generally coming with a tradeoff between simulation speed and accuracy. Here, we probe several molecular mechanical parameter combinations for their ability to empower long simulations needed to achieve a quantitative description of substrate binding. We demonstrate that a combination of the Amber19sb force field with the recently developed 12-6 Ca2+ models allows us to both correctly model DFPase and obtain new insights into the DFP binding process.
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Affiliation(s)
- Alexander Zlobin
- Faculty of Bioengineering, Lomonosov Moscow State University, 119234 Moscow, Russia; (I.D.); (S.P.)
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Igor Diankin
- Faculty of Bioengineering, Lomonosov Moscow State University, 119234 Moscow, Russia; (I.D.); (S.P.)
- Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Sergey Pushkarev
- Faculty of Bioengineering, Lomonosov Moscow State University, 119234 Moscow, Russia; (I.D.); (S.P.)
| | - Andrey Golovin
- Faculty of Bioengineering, Lomonosov Moscow State University, 119234 Moscow, Russia; (I.D.); (S.P.)
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Sirius University of Science and Technology, 354340 Sochi, Russia
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Lyagin I, Efremenko E. Enzymes, Reacting with Organophosphorus Compounds as Detoxifiers: Diversity and Functions. Int J Mol Sci 2021; 22:1761. [PMID: 33578824 PMCID: PMC7916636 DOI: 10.3390/ijms22041761] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 01/05/2023] Open
Abstract
Organophosphorus compounds (OPCs) are able to interact with various biological targets in living organisms, including enzymes. The binding of OPCs to enzymes does not always lead to negative consequences for the body itself, since there are a lot of natural biocatalysts that can catalyze the chemical transformations of the OPCs via hydrolysis or oxidation/reduction and thereby provide their detoxification. Some of these enzymes, their structural differences and identity, mechanisms, and specificity of catalytic action are discussed in this work, including results of computational modeling. Phylogenetic analysis of these diverse enzymes was specially realized for this review to emphasize a great area for future development(s) and applications.
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Affiliation(s)
| | - Elena Efremenko
- Faculty of Chemistry, Lomonosov Moscow State University, Lenin Hills 1/3, 119991 Moscow, Russia;
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Abstract
The organophosphorus substances, including pesticides and nerve agents (NAs), represent highly toxic compounds. Standard decontamination procedures place a heavy burden on the environment. Given their continued utilization or existence, considerable efforts are being made to develop environmentally friendly methods of decontamination and medical countermeasures against their intoxication. Enzymes can offer both environmental and medical applications. One of the most promising enzymes cleaving organophosphorus compounds is the enzyme with enzyme commission number (EC): 3.1.8.2, called diisopropyl fluorophosphatase (DFPase) or organophosphorus acid anhydrolase from Loligo Vulgaris or Alteromonas sp. JD6.5, respectively. Structure, mechanisms of action and substrate profiles are described for both enzymes. Wild-type (WT) enzymes have a catalytic activity against organophosphorus compounds, including G-type nerve agents. Their stereochemical preference aims their activity towards less toxic enantiomers of the chiral phosphorus center found in most chemical warfare agents. Site-direct mutagenesis has systematically improved the active site of the enzyme. These efforts have resulted in the improvement of catalytic activity and have led to the identification of variants that are more effective at detoxifying both G-type and V-type nerve agents. Some of these variants have become part of commercially available decontamination mixtures.
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Mathe Z, Pantazis DA, Lee HB, Gnewkow R, Van Kuiken BE, Agapie T, DeBeer S. Calcium Valence-to-Core X-ray Emission Spectroscopy: A Sensitive Probe of Oxo Protonation in Structural Models of the Oxygen-Evolving Complex. Inorg Chem 2019; 58:16292-16301. [PMID: 31743026 PMCID: PMC6891804 DOI: 10.1021/acs.inorgchem.9b02866] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Indexed: 12/12/2022]
Abstract
Calcium is an abundant, nontoxic metal that finds many roles in synthetic and biological systems including the oxygen-evolving complex (OEC) of photosystem II. Characterization methods for calcium centers, however, are underdeveloped compared to those available for transition metals. Valence-to-core X-ray emission spectroscopy (VtC XES) selectively probes the electronic structure of an element's chemical environment, providing insight that complements the geometric information available from other techniques. Here, the utility of calcium VtC XES is established using an in-house dispersive spectrometer in combination with density functional theory. Spectral trends are rationalized within a molecular orbital framework, and Kβ2,5 transitions, derived from molecular orbitals with primarily ligand p character, are found to be a promising probe of the calcium coordination environment. In particular, it is shown that calcium VtC XES is sensitive to the electronic structure changes that accompany oxo protonation in Mn3CaO4-based molecular mimics of the OEC. Through correlation to calculations, the potential of calcium VtC XES to address unresolved questions regarding the mechanism of biological water oxidation is highlighted.
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Affiliation(s)
- Zachary Mathe
- Max Planck Institute
for Chemical Energy Conversion, Stiftstrasse 34−36, D-45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der
Ruhr, Germany
| | - Heui Beom Lee
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Richard Gnewkow
- Institute of Optics and Atomic Physics, Technical University of Berlin, Hardenbergstraße 36, D-10587 Berlin, Germany
| | - Benjamin E. Van Kuiken
- Max Planck Institute
for Chemical Energy Conversion, Stiftstrasse 34−36, D-45470 Mülheim an der Ruhr, Germany
| | - Theodor Agapie
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Serena DeBeer
- Max Planck Institute
for Chemical Energy Conversion, Stiftstrasse 34−36, D-45470 Mülheim an der Ruhr, Germany
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Theoretical Studies on Catalysis Mechanisms of Serum Paraoxonase 1 and Phosphotriesterase Diisopropyl Fluorophosphatase Suggest the Alteration of Substrate Preference from Paraoxonase to DFP. Molecules 2018; 23:molecules23071660. [PMID: 29986514 PMCID: PMC6100192 DOI: 10.3390/molecules23071660] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 12/18/2022] Open
Abstract
The calcium-dependent β-propeller proteins mammalian serum paraoxonase 1 (PON1) and phosphotriesterase diisopropyl fluorophosphatase (DFPase) catalyze the hydrolysis of organophosphorus compounds and enhance hydrolysis of various nerve agents. In the present work, the phosphotriesterase activity development between PON1 and DFPase was investigated by using the hybrid density functional theory method B3LYP. Based on the active-site difference between PON1 and DFPase, both the wild type and the mutant (a water molecule replacing Asn270 in PON1) models were designed. The results indicated that the substitution of a water molecule for Asn270 in PON1 had little effect on the enzyme activity in kinetics, while being more efficient in thermodynamics, which is essential for DFP hydrolysis. Structure comparisons of evolutionarily related enzymes show that the mutation of Asn270 leads to the catalytic Ca2+ ion indirectly connecting the buried structural Ca2+ ion via hydrogen bonds in DFPase. It can reduce the plasticity of enzymatic structure, and possibly change the substrate preference from paraoxon to DFP, which implies an evolutionary transition from mono- to dinuclear catalytic centers. Our studies shed light on the investigation of enzyme catalysis mechanism from an evolutionary perspective.
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Soares FV, de Castro AA, Pereira AF, Leal DHS, Mancini DT, Krejcar O, Ramalho TC, da Cunha EFF, Kuca K. Theoretical Studies Applied to the Evaluation of the DFPase Bioremediation Potential against Chemical Warfare Agents Intoxication. Int J Mol Sci 2018; 19:E1257. [PMID: 29690585 PMCID: PMC5979579 DOI: 10.3390/ijms19041257] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 04/16/2018] [Accepted: 04/19/2018] [Indexed: 11/30/2022] Open
Abstract
Organophosphorus compounds (OP) are part of a group of compounds that may be hazardous to health. They are called neurotoxic agents because of their action on the nervous system, inhibiting the acetylcholinesterase (AChE) enzyme and resulting in a cholinergic crisis. Their high toxicity and rapid action lead to irreversible damage to the nervous system, drawing attention to developing new treatment methods. The diisopropyl fluorophosphatase (DFPase) enzyme has been considered as a potent biocatalyst for the hydrolysis of toxic OP and has potential for bioremediation of this kind of intoxication. In order to investigate the degradation process of the nerve agents Tabun, Cyclosarin and Soman through the wild-type DFPase, and taking into account their stereochemistry, theoretical studies were carried out. The intermolecular interaction energy and other parameters obtained from the molecular docking calculations were used to construct a data matrix, which were posteriorly treated by statistical analyzes of chemometrics, using the PCA (Principal Components Analysis) multivariate analysis. The analyzed parameters seem to be quite important for the reaction mechanisms simulation (QM/MM). Our findings showed that the wild-type DFPase enzyme is stereoselective in hydrolysis, showing promising results for the catalytic degradation of the neurotoxic agents under study, with the degradation mechanism performed through two proposed pathways.
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Affiliation(s)
- Flávia V Soares
- Laboratory of Molecular Modeling, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, MG, Brazil.
| | - Alexandre A de Castro
- Laboratory of Molecular Modeling, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, MG, Brazil.
| | - Ander F Pereira
- Laboratory of Molecular Modeling, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, MG, Brazil.
| | - Daniel H S Leal
- Laboratory of Molecular Modeling, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, MG, Brazil.
- Department of Health Sciences, Federal University of Espírito Santo, 29932-540 São Mateus, ES, Brazil.
| | - Daiana T Mancini
- Laboratory of Molecular Modeling, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, MG, Brazil.
| | - Ondrej Krejcar
- Center for Basic and Applied Research, Faculty of Informatics and Management, University Hradec Kralove, 50003 Hradec Kralove, Czech Republic.
| | - Teodorico C Ramalho
- Laboratory of Molecular Modeling, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, MG, Brazil.
- Center for Basic and Applied Research, Faculty of Informatics and Management, University Hradec Kralove, 50003 Hradec Kralove, Czech Republic.
| | - Elaine F F da Cunha
- Laboratory of Molecular Modeling, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, MG, Brazil.
| | - Kamil Kuca
- Center for Basic and Applied Research, Faculty of Informatics and Management, University Hradec Kralove, 50003 Hradec Kralove, Czech Republic.
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9
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Purg M, Kamerlin SCL. Empirical Valence Bond Simulations of Organophosphate Hydrolysis: Theory and Practice. Methods Enzymol 2018; 607:3-51. [DOI: 10.1016/bs.mie.2018.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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10
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Purg M, Elias M, Kamerlin SCL. Similar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering. J Am Chem Soc 2017; 139:17533-17546. [PMID: 29113434 PMCID: PMC5724027 DOI: 10.1021/jacs.7b09384] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Indexed: 01/27/2023]
Abstract
Organophosphate hydrolases are proficient catalysts of the breakdown of neurotoxic organophosphates and have great potential as both biotherapeutics for treating acute organophosphate toxicity and as bioremediation agents. However, proficient organophosphatases such as serum paraoxonase 1 (PON1) and the organophosphate-hydrolyzing lactonase SsoPox are unable to hydrolyze bulkyorganophosphates with challenging leaving groups such as diisopropyl fluorophosphate (DFP) or venomous agent X, creating a major challenge for enzyme design. Curiously, despite their mutually exclusive substrate specificities, PON1 and diisopropyl fluorophosphatase (DFPase) have essentially identical active sites and tertiary structures. In the present work, we use empirical valence bond simulations to probe the catalytic mechanism of DFPase as well as temperature, pH, and mutational effects, demonstrating that DFPase and PON1 also likely utilize identical catalytic mechanisms to hydrolyze their respective substrates. However, detailed examination of both static structures and dynamical simulations demonstrates subtle but significant differences in the electrostatic properties and solvent penetration of the two active sites and, most critically, the role of residues that make no direct contact with either substrate in acting as "specificity switches" between the two enzymes. Specifically, we demonstrate that key residues that are structurally and functionally critical for the paraoxonase activity of PON1 prevent it from being able to hydrolyze DFP with its fluoride leaving group. These insights expand our understanding of the drivers of the evolution of divergent substrate specificity in enzymes with identical active sites and guide the future design of organophosphate hydrolases that hydrolyze compounds with challenging leaving groups.
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Affiliation(s)
- Miha Purg
- Science for Life
Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Mikael Elias
- Department of Biochemistry, Molecular Biology and Biophysics &
Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Shina Caroline Lynn Kamerlin
- Science for Life
Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
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