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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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Recent Advancements in Developments of Novel Fluorescent Probes: In Cellulo Recognitions of Alkaline Phosphatases. Symmetry (Basel) 2022. [DOI: 10.3390/sym14081634] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Alkaline phosphatase (ALP) is one of the vital phospho-ester bond cleaving biocatalysts that has inevitable significance in cellular systems, viz., early-stage osteoblast differentiation, cell integrity in tissues, bone mineralization, cancer biomarker, liver dysfunction, cellular osmotic pressure, protein folding and many more. Variation from optimal levels of ALP in intra and extracellular fluids can cause severe diseases, including death. Due to these reasons, ALP is considered as a vital biomarker for various preclinical and medical diagnosis. Fluorescence image-based diagnosis is the most widely used method, owing to its simplicity, robustness, non-invasive properties and excellent spatio-temporal resolution (up to the nM/pM level), as compared to conventional analytical techniques, such as the electroanalytical method, nuclear magnetic resonance (NMR) and high-performance liquid chromatography (HPLC). Most of the reviews reported for ALP’s recognition in the literature scarcely explain the structurally related, photophysical and biophysical parameters; and the sub-cellular localizations. Considering these facts, in order to enhance the opto-analytical parameters of fluorescence-based diagnostic materials at the cellular level, herein we have systematically documented recent developments in the opto-analytical capabilities of quencher-free probes for ALP, used in in vitro (biological buffers) to in cellulo conditions, along with in vivo models.
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3
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Serafim LF, Jayasinghe-Arachchige VM, Wang L, Prabhakar R. Promiscuous Catalytic Activity of a Binuclear Metallohydrolase: Peptide and Phosphoester Hydrolyses. J Chem Inf Model 2022; 62:2466-2480. [PMID: 35451306 DOI: 10.1021/acs.jcim.2c00214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, chemical promiscuity of a binuclear metallohydrolase Streptomyces griseus aminopeptidase (SgAP) has been investigated using DFT calculations. SgAP catalyzes two diverse reactions, peptide and phosphoester hydrolyses, using its binuclear (Zn-Zn) core. On the basis of the experimental information, mechanisms of these reactions have been investigated utilizing leucine p-nitro aniline (Leu-pNA) and bis(4-nitrophenyl) phosphate (BNPP) as the substrates. The computed barriers of 16.5 and 16.8 kcal/mol for the most plausible mechanisms proposed by the DFT calculations are in good agreement with the measured values of 13.9 and 18.3 kcal/mol for the Leu-pNA and BNPP hydrolyses, respectively. The former was found to occur through the transfer of two protons, while the latter with only one proton transfer. They are in line with the experimental observations. The cleavage of the peptide bond was the rate-determining process for the Leu-pNA hydrolysis. However, the creation of the nucleophile and its attack on the electrophile phosphorus atom was the rate-determining step for the BNPP hydrolysis. These calculations showed that the chemical nature of the substrate and its binding mode influence the nucleophilicity of the metal bound hydroxyl nucleophile. Additionally, the nucleophilicity was found to be critical for the Leu-pNA hydrolysis, whereas double Lewis acid activation was needed for the BNPP hydrolysis. That could be one of the reasons why peptide hydrolysis can be catalyzed by both mononuclear and binuclear metal cofactors containing hydrolases, while phosphoester hydrolysis is almost exclusively by binuclear metallohydrolases. These results will be helpful in the development of versatile catalysts for chemically distinct hydrolytic reactions.
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Affiliation(s)
- Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Lukun Wang
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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4
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Wei WM, Xu YL, Zheng RH, Zhao T, Fang W, Qin YD. Theoretical Study on the Mechanism of the Acylate Reaction of β-Lactamase. ACS OMEGA 2021; 6:12598-12604. [PMID: 34056410 PMCID: PMC8154126 DOI: 10.1021/acsomega.1c00592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 05/25/2023]
Abstract
Using density functional theory and a cluster approach, we study the reaction potential surface and compute Gibbs free energies for the acylate reaction of β-lactamase with penicillin G, where the solvent effect is important and taken into consideration. Two reaction paths are investigated: one is a multi-step process with a rate-limit energy barrier of 19.1 kcal/mol, which is relatively small, and the reaction can easily occur; the other is a one-step process with a barrier of 45.0 kcal/mol, which is large and thus makes the reaction hard to occur. The reason why the two paths have different barriers is explained.
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Affiliation(s)
- Wen-Mei Wei
- School
of Basic Medical Sciences, Anhui Medical
University, Hefei, Anhui 230032, P.
R. China
| | - Yan-Li Xu
- School
of Basic Medical Sciences, Anhui Medical
University, Hefei, Anhui 230032, P.
R. China
| | - Ren-Hui Zheng
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, Institute of
Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, P. R. China
| | - Tingting Zhao
- School
of Basic Medical Sciences, Anhui Medical
University, Hefei, Anhui 230032, P.
R. China
| | - Weijun Fang
- School
of Basic Medical Sciences, Anhui Medical
University, Hefei, Anhui 230032, P.
R. China
| | - Yi-De Qin
- School
of Basic Medical Sciences, Anhui Medical
University, Hefei, Anhui 230032, P.
R. China
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5
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Suardíaz R, Lythell E, Hinchliffe P, van der Kamp M, Spencer J, Fey N, Mulholland AJ. Catalytic mechanism of the colistin resistance protein MCR-1. Org Biomol Chem 2021; 19:3813-3819. [PMID: 33606866 PMCID: PMC8097703 DOI: 10.1039/d0ob02566f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/11/2021] [Indexed: 12/19/2022]
Abstract
The mcr-1 gene encodes a membrane-bound Zn2+-metalloenzyme, MCR-1, which catalyses phosphoethanolamine transfer onto bacterial lipid A, making bacteria resistant to colistin, a last-resort antibiotic. Mechanistic understanding of this process remains incomplete. Here, we investigate possible catalytic pathways using DFT and ab initio calculations on cluster models and identify a complete two-step reaction mechanism. The first step, formation of a covalent phosphointermediate via transfer of phosphoethanolamine from a membrane phospholipid donor to the acceptor Thr285, is rate-limiting and proceeds with a single Zn2+ ion. The second step, transfer of the phosphoethanolamine group to lipid A, requires an additional Zn2+. The calculations suggest the involvement of the Zn2+ orbitals directly in the reaction is limited, with the second Zn2+ acting to bind incoming lipid A and direct phosphoethanolamine addition. The new level of mechanistic detail obtained here, which distinguishes these enzymes from other phosphotransferases, will aid in the development of inhibitors specific to MCR-1 and related bacterial phosphoethanolamine transferases.
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Affiliation(s)
- Reynier Suardíaz
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK. and School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK and Departamento de Química Física, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain
| | - Emily Lythell
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK. and School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Marc van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK. and School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Natalie Fey
- 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.
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7
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Sharma G, Jayasinghe-Arachchige VM, Hu Q, Schenk G, Prabhakar R. Effect of Chemically Distinct Substrates on the Mechanism and Reactivity of a Highly Promiscuous Metallohydrolase. ACS Catal 2020. [DOI: 10.1021/acscatal.9b04847] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Gaurav Sharma
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Qiaoyu Hu
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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8
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Lythell E, Suardíaz R, Hinchliffe P, Hanpaibool C, Visitsatthawong S, Oliveira ASF, Lang EJM, Surawatanawong P, Lee VS, Rungrotmongkol T, Fey N, Spencer J, Mulholland AJ. Resistance to the “last resort” antibiotic colistin: a single-zinc mechanism for phosphointermediate formation in MCR enzymes. Chem Commun (Camb) 2020; 56:6874-6877. [DOI: 10.1039/d0cc02520h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Simulations show the mono-zinc form of MCR to be stable and competent for covalent phospho(ethanolamine) intermediate formation.
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9
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Yu MJ, Wu J, Chen SL. Mechanism and Inhibitor Exploration with Binuclear Mg Ketol-Acid Reductoisomerase: Targeting the Biosynthetic Pathway of Branched-Chain Amino Acids. Chembiochem 2019; 21:381-391. [PMID: 31309701 DOI: 10.1002/cbic.201900363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Indexed: 01/01/2023]
Abstract
Binuclear Mg ketol-acid reductoisomerase (KARI), which converts (S)-2-acetolactate into (R)-2,3-dihydroxyisovalerate, is responsible for the second step of the biosynthesis of branched-chain amino acids in plants and microorganisms and thus serves as a key inhibition target potentially without effects on mammals. Here, through the use of density functional calculations and a chemical model, the KARI-catalyzed reaction has been demonstrated to include the initial deprotonation of the substrate C2 hydroxy group, bridged by the two Mg ions, alkyl migration from the C2-alkoxide carbon atom to the C3-carbonyl carbon atom, and hydride transfer from a nicotinamide adenine dinucleotide phosphate [NAD(P)H] cofactor to C2. A dead-end mechanism with a hydride transferred to the C3 carbonyl group has been ruled out. The nucleophilicity (migratory aptitude) of the migrating carbon atom and the provision of additional negative charge to the di-Mg coordination sphere have significant effects on the steps of alkyl migration and hydride transfer, respectively. Other important mechanistic characteristics are also revealed. Inspired by the mechanism, an inhibitor (2-carboxylate-lactic acid) was designed and predicted by barrier analysis to be effective in inactivating KARI, hence probably enriching the antifungal and antibacterial library. Two types of slow substrate analogues (2-trihalomethyl acetolactic acids and 2-glutaryl lactic acid) were also found.
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Affiliation(s)
- Ming-Jia Yu
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Jue Wu
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
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10
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Fatima T, Rani S, Fischer S, Efferth T, Kiani FA. The hydrolysis of 6-phosphogluconolactone in the second step of pentose phosphate pathway occurs via a two-water mechanism. Biophys Chem 2018; 240:98-106. [PMID: 30014892 DOI: 10.1016/j.bpc.2018.06.002] [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: 05/06/2018] [Revised: 06/08/2018] [Accepted: 06/09/2018] [Indexed: 11/28/2022]
Abstract
Hydrolysis reaction marks the basis of life yet the mechanism of this crucial biochemical reaction is not completely understood. We recently reported the mechanisms of hydrolysis of nucleoside triphosphate and phosphate monoester. These two reactions hydrolyze P-O-P and P-O-C linkages, respectively. Here, we present the mechanism of hydrolysis of δ-6-phosphogluconolactone, which is an important precursor in the second step of the pentose phosphate pathway. Its hydrolysis requires the cleavage of C-O-C linkage and its mechanism is hitherto unknown. We report three mechanisms of hydrolysis of δ-6-phosphogluconolactone based on density functional computations. In the energetically most favorable mechanism, two water molecules participate in the hydrolysis reaction and the mechanism is sequential, i.e., activation of the attacking water molecule (OH bond breaking) precedes that of the cleavage of the CO bond of the C-O-C linkage. The rate-limiting energy barrier of this mechanism is comparable to the reported experimental free energy barrier. This mechanism has similarities with the mechanism of triphosphate hydrolysis and that of hydrolytic cleavage of DNA in EcoRV enzyme. This two-water sequential hydrolysis mechanism could be the unified mechanism required for the hydrolysis of other hydrolysable species in living cells.
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Affiliation(s)
- Tabeer Fatima
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Sector H-12, 44000 Islamabad, Pakistan; Department of Biotechnology, University of Sialkot, 51310 Sialkot, Pakistan
| | - Sadaf Rani
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Sector H-12, 44000 Islamabad, Pakistan
| | - Stefan Fischer
- Interdisciplinary Center for Scientific Computing, The University of Heidelberg, D-69120 Heidelberg, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Farooq Ahmad Kiani
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Sector H-12, 44000 Islamabad, Pakistan; Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, 02118 Boston, MA, United States.
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11
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Zhang H, Yang L, Ding W, Ma Y. Theoretical Studies on the Catalytic Cycle of Histidine Acid Phosphatases Revealing an Acid Proof Mechanism. J Phys Chem B 2018; 122:7530-7538. [DOI: 10.1021/acs.jpcb.8b04808] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hao Zhang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, P. R. China
| | - Ling Yang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Wanjian Ding
- College of Chemistry, Beijing Normal University, Beijing 100086, P. R. China
| | - Yingying Ma
- Institute of Mining Technology, Inner Mongolia University of Technology. Hohhot 010051, P. R. China
- Inner Mongolia Key Laboratory of Theoretical and Computational Chemistry Simulation. Hohhot 010051, P. R. China
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12
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How does binuclear zinc amidohydrolase FwdA work in the initial step of methanogenesis: From formate to formyl-methanofuran. J Inorg Biochem 2018; 185:71-79. [PMID: 29778928 DOI: 10.1016/j.jinorgbio.2018.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/05/2018] [Accepted: 05/08/2018] [Indexed: 11/22/2022]
Abstract
The initial step of methanogenesis is the fixation of CO2 to formyl-methanofuran (formyl-MFR) catalyzed by formyl-MFR dehydrogenase, which can be divided into two half reactions. Herein, the second half reaction catalyzed by FwdA (formyl-methanofuran dehydrogenase subunit A), i.e., from formate to formyl-methanofuran, has been investigated using density functional theory and a chemical model based on the X-ray crystal structure. The calculations indicate that, compared with other well-known di-zinc hydrolases, the FwdA reaction employs a reverse mechanism, including the nucleophilic attack of MFR amine on formate carbon leading to a tetrahedral gem-diolate intermediate, two steps of proton transfer from amine to formate moieties assisted by the Asp385, and the CO bond dissociation to form the formyl-MFR product. The second step of proton transfer from the amine moiety to the Asp385 is rate-limiting with an overall barrier of 21.2 kcal/mol. The two zinc ions play an important role in stabilizing the transition states and intermediates, in particular the negative charge at the formate moiety originated from the nucleophilic attack of the MFR amine. The work here appends a crucial piece in the methanogenic mechanistics and advances the understanding of the global carbon cycle.
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13
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Blackman AG, Gahan LR. Metal-coordinated Hydroxide as a Nucleophile: a Brief History. Z Anorg Allg Chem 2018. [DOI: 10.1002/zaac.201800045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Allan G. Blackman
- Centre for Biomedical and Chemical Sciences; School of Science; Auckland University of Technology; Private Bag 92006 Auckland New Zealand
| | - Lawrence R. Gahan
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane Queensland Australia
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14
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Campesato L, Marforio TD, Giacinto P, Calvaresi M, Bottoni A. A Full QM Computational Study of the Catalytic Mechanism of α-1,4-Glucan Lyases. Chemphyschem 2018; 19:1514-1521. [DOI: 10.1002/cphc.201701332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Lara Campesato
- Dipartimento di Chimica “Giacomo Ciamician”; Alma Mater Studiorum - Università di Bologna; via Francesco Selmi 2 40126 Bologna Italy
| | - Tainah Dorina Marforio
- Dipartimento di Chimica “Giacomo Ciamician”; Alma Mater Studiorum - Università di Bologna; via Francesco Selmi 2 40126 Bologna Italy
| | - Pietro Giacinto
- Dipartimento di Chimica “Giacomo Ciamician”; Alma Mater Studiorum - Università di Bologna; via Francesco Selmi 2 40126 Bologna Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica “Giacomo Ciamician”; Alma Mater Studiorum - Università di Bologna; via Francesco Selmi 2 40126 Bologna Italy
| | - Andrea Bottoni
- Dipartimento di Chimica “Giacomo Ciamician”; Alma Mater Studiorum - Università di Bologna; via Francesco Selmi 2 40126 Bologna Italy
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15
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Andresen E, Peiter E, Küpper H. Trace metal metabolism in plants. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:909-954. [PMID: 29447378 DOI: 10.1093/jxb/erx465] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 12/04/2017] [Indexed: 05/18/2023]
Abstract
Many trace metals are essential micronutrients, but also potent toxins. Due to natural and anthropogenic causes, vastly different trace metal concentrations occur in various habitats, ranging from deficient to toxic levels. Therefore, one focus of plant research is on the response to trace metals in terms of uptake, transport, sequestration, speciation, physiological use, deficiency, toxicity, and detoxification. In this review, we cover most of these aspects for the essential micronutrients copper, iron, manganese, molybdenum, nickel, and zinc to provide a broader overview than found in other recent reviews, to cross-link aspects of knowledge in this very active research field that are often seen in a separated way. For example, individual processes of metal usage, deficiency, or toxicity often were not mechanistically interconnected. Therefore, this review also aims to stimulate the communication of researchers following different approaches, such as gene expression analysis, biochemistry, or biophysics of metalloproteins. Furthermore, we highlight recent insights, emphasizing data obtained under physiologically and environmentally relevant conditions.
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Affiliation(s)
- Elisa Andresen
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Plant Biophysics and Biochemistry, Branišovská, Ceské Budejovice, Czech Republic
| | - Edgar Peiter
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Plant Nutrition Laboratory, Betty-Heimann-Strasse, Halle (Saale), Germany
| | - Hendrik Küpper
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Plant Biophysics and Biochemistry, Branišovská, České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, Department of Experimental Plant Biology, Branišovská, České Budějovice, Czech Republic
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16
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Zhang H, Yang L, Ding W, Ma Y. The pH-dependent activation mechanism of Ser102 in Escherichia coli alkaline phosphatase: a theoretical study. J Biol Inorg Chem 2017; 23:277-284. [DOI: 10.1007/s00775-017-1529-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 12/17/2017] [Indexed: 12/22/2022]
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17
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Abstract
The quantum chemical cluster approach is a powerful method for investigating enzymatic reactions. Over the past two decades, a large number of highly diverse systems have been studied and a great wealth of mechanistic insight has been developed using this technique. This Perspective reviews the current status of the methodology. The latest technical developments are highlighted, and challenges are discussed. Some recent applications are presented to illustrate the capabilities and progress of this approach, and likely future directions are outlined.
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Affiliation(s)
- Fahmi Himo
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University , SE-106 91 Stockholm, Sweden
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18
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Sanjeev R, Ravi R, Jagannadham V, Skelton AA. Experimental and Quantum Mechanical Study of Nucleophilic Substitution Reactions of meta- and para-Substituted Benzyl Bromides with Benzylamine in Methanol: Synergy Between Experiment and Theory. Aust J Chem 2017. [DOI: 10.1071/ch16061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This work involves the experimental and theoretical study of the nucleophilic substitution of meta- and para-substituted benzyl bromides with benzylamine. Conductometric rate experiments confirm the applicability of the Hammett linear free-energy relationship to this system. To gain a deep understanding of the physical chemistry at play, a quantum mechanical study of the reaction is also conducted. The quantum mechanical calculations not only reproduce the experimental free energy of activation, but also provide greater insights at the molecular and atomic level. Isolation of the calculated transition state structure and application of the Hammett equation to its electronic, structural, and energetic properties are studied.
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Roston D, Cui Q. Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects. J Am Chem Soc 2016; 138:11946-57. [PMID: 27541005 PMCID: PMC5705178 DOI: 10.1021/jacs.6b07347] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes are powerful catalysts, and a thorough understanding of the sources of their catalytic power will facilitate many medical and industrial applications. Here we have studied the catalytic mechanism of alkaline phosphatase (AP), which is one of the most catalytically proficient enzymes known. We have used quantum mechanics calculations and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to model a variety of isotope effects relevant to the reaction of AP. We have calculated equilibrium isotope effects (EIEs), binding isotope effects (BIEs), and kinetic isotope effects (KIEs) for a range of phosphate mono- and diester substrates. The results agree well with experimental values, but the model for the reaction's transition state (TS) differs from the original interpretation of those experiments. Our model indicates that isotope effects on binding make important contributions to measured KIEs on V/K, which complicated interpretation of the measured values. Our results provide a detailed interpretation of the measured isotope effects and make predictions that can test the proposed model. The model indicates that the substrate is deformed in the ground state (GS) of the reaction and partially resembles the TS. The highly preorganized active site preferentially binds conformations that resemble the TS and not the GS, which induces the substrate to adapt to the enzyme, rather than the other way around-as with classic "induced fit" models. The preferential stabilization of the TS over the GS is what lowers the barrier to the chemical step.
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Affiliation(s)
- Daniel Roston
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin , Madison, Wisconsin 53706, United States
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Roston D, Demapan D, Cui Q. Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site. J Am Chem Soc 2016; 138:7386-94. [PMID: 27186960 DOI: 10.1021/jacs.6b03156] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A reaction's transition state (TS) structure plays a critical role in determining reactivity and has important implications for the design of catalysts, drugs, and other applications. Here, we explore TS structure in the enzyme alkaline phosphatase using hybrid Quantum Mechanics/Molecular Mechanics simulations. We find that minor perturbations to the substrate have major effects on TS structure and the way the enzyme stabilizes the TS. Substrates with good leaving groups (LGs) have little cleavage of the phosphorus-LG bond at the TS, while substrates with poor LGs have substantial cleavage of that bond. The results predict nonlinear free energy relationships for a single rate-determining step, and substantial differences in kinetic isotope effects for different substrates; both trends were observed in previous experimental studies, although the original interpretations differed from the present model. Moreover, due to different degrees of phosphorus-LG bond cleavage at the TS for different substrates, the LG is stabilized by different interactions at the TS: while a poor LG is directly stabilized by an active site zinc ion, a good LG is mainly stabilized by active site water molecules. Our results demonstrate the considerable plasticity of TS structure and stabilization in enzymes. Furthermore, perturbations to reactivity that probe TS structure experimentally (i.e., substituent effects) may substantially perturb the TS they aim to probe, and thus classical experimental approaches such as free energy relations should be interpreted with care.
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Affiliation(s)
- Daniel Roston
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Darren Demapan
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin , Madison, Wisconsin 53706, United States
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Ji JN, Chen SL. μ3-Oxo stabilized by three metal cations is a sufficient nucleophile for enzymatic hydrolysis of phosphate monoesters. Dalton Trans 2016; 45:2517-22. [PMID: 26699843 DOI: 10.1039/c5dt03899e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diverse species have previously been proposed to be effective nucleophiles in the enzymatic hydrolysis of phosphate esters. A novel penta-metal cluster (two Fe(3+) and three Ca(2+)) was recently discovered in the active site of PhoX alkaline phosphatase, with the revelation of the architecture of μ3-oxo bridging one Ca(2+) and two antiferromagnetically coupled Fe(3+). In this work, using density functional theory calculations, the μ3-oxo stabilized by three cations has been demonstrated to be a new type of effective nucleophile. The calculations give strong support to the "ping-pong" mechanism involving the nucleophilic attack of the μ3-oxo on the substrate phosphor and the subsequent hydrolysis of the covalent phospho-enzyme intermediate. A base mechanism with the μ3-oxo acting as a general base to activate an additional water molecule has further been demonstrated to be inaccessible. The results advance the understanding of the enzymatic hydrolysis of phosphate esters and may give important inspiration for the exploration of multinuclear biomimetic catalysts.
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Affiliation(s)
- Jian-Nan Ji
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry, Beijing Institute of Technology, Beijing 100081, China.
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22
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Qi SC, Hayashi JI, Zhang L. Recent application of calculations of metal complexes based on density functional theory. RSC Adv 2016. [DOI: 10.1039/c6ra16168e] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Recent application of density functional theory (DFT) for metal complexes is reviewed to show the achievements of DFT and the challenges for it, as well as the methods for selecting proper functionals.
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Affiliation(s)
- Shi-Chao Qi
- Institute for Materials Chemistry and Engineering
- Kyushu University
- Kasuga
- Japan
| | - Jun-ichiro Hayashi
- Institute for Materials Chemistry and Engineering
- Kyushu University
- Kasuga
- Japan
| | - Lu Zhang
- Institute for Materials Chemistry and Engineering
- Kyushu University
- Kasuga
- Japan
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23
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Liao RZ, Siegbahn PEM. Phosphate Hydrolysis by the Fe2–Ca3-Dependent Alkaline Phosphatase PhoX: Mechanistic Insights from DFT calculations. Inorg Chem 2015; 54:11941-7. [DOI: 10.1021/acs.inorgchem.5b02268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rong-Zhen Liao
- Key Laboratory of Material Chemistry for
Energy Conversion and Storage, Ministry of Education, School of Chemistry
and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Per E. M. Siegbahn
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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24
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Guo N, Zhong JY, Chen SL, Liu JQ, Min Q, Shi RX. Experimental and theoretical studies of hydrolysis of nerve agent sarin by binuclear zinc biomimetic catalysts. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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DeYonker NJ, Webster CE. A Theoretical Study of Phosphoryl Transfers of Tyrosyl-DNA Phosphodiesterase I (Tdp1) and the Possibility of a "Dead-End" Phosphohistidine Intermediate. Biochemistry 2015; 54:4236-47. [PMID: 26121557 DOI: 10.1021/acs.biochem.5b00396] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tyrosyl-DNA phosphodiesterase I (Tdp1) is a DNA repair enzyme conserved across eukaryotes that catalyzes the hydrolysis of the phosphodiester bond between the tyrosine residue of topoisomerase I and the 3'-phosphate of DNA. Atomic level details of the mechanism of Tdp1 are proposed and analyzed using a fully quantum mechanical, geometrically constrained model. The structural basis for the computational model is the vanadate-inhibited crystal structure of human Tdp1 (hTdp1, Protein Data Bank entry 1RFF ). Density functional theory computations are used to acquire thermodynamic and kinetic data along the catalytic pathway, including the phosphoryl transfer and subsequent hydrolysis. Located transition states and intermediates along the reaction coordinate suggest an associative phosphoryl transfer mechanism with five-coordinate phosphorane intermediates. Similar to both theoretical and experimental results for phospholipase D, the proposed mechanism for hTdp1 also includes the thermodynamically favorable possibility of a four-coordinate phosphohistidine "dead-end" product.
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Affiliation(s)
- Nathan J DeYonker
- ‡Department of Chemistry, The University of Memphis, 213 Smith Chemistry Building, Memphis, Tennessee 38152, United States
| | - Charles Edwin Webster
- †Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States.,‡Department of Chemistry, The University of Memphis, 213 Smith Chemistry Building, Memphis, Tennessee 38152, United States
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26
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Borosky GL. Catalytic Activity of Human Placental Alkaline Phosphatase (PLAP): Insights from a Computational Study. J Phys Chem B 2014; 118:14302-13. [DOI: 10.1021/jp511221c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Gabriela L. Borosky
- INFIQC, CONICET and Departamento
de Matemática y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba 5000, Argentina
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