1
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Kaur R, Nikkel DJ, Wetmore SD. Mechanism of Nucleic Acid Phosphodiester Bond Cleavage by Human Endonuclease V: MD and QM/MM Calculations Reveal a Versatile Metal Dependence. J Phys Chem B 2024; 128:9455-9469. [PMID: 39359137 DOI: 10.1021/acs.jpcb.4c05846] [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: 10/04/2024]
Abstract
Human endonuclease V (EndoV) catalytically removes deaminated nucleobases by cleaving the phosphodiester bond as part of RNA metabolism. Despite being implicated in several diseases (cancers, cardiovascular diseases, and neurological disorders) and potentially being a useful tool in biotechnology, details of the human EndoV catalytic pathway remain unclear due to limited experimental information beyond a crystal structure of the apoenzyme and select mutational data. Since a mechanistic understanding is critical for further deciphering the central roles and expanding applications of human EndoV in medicine and biotechnology, molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations were used to unveil the atomistic details of the catalytic pathway. Due to controversies surrounding the number of metals required for nuclease activity, enzyme-substrate models with different numbers of active site metals and various metal-substrate binding configurations were built based on structural data for other nucleases. Subsequent MD simulations revealed the structure and stability of the human EndoV-substrate complex for a range of active site metal binding architectures. Four unique pathways were then characterized using QM/MM that vary in metal number (one versus two) and modes of substrate coordination [direct versus indirect (water-mediated)], with several mechanisms being fully consistent with experimental structural, kinetic, and mutational data for related nucleases, including members of the EndoV family. Beyond uncovering key roles for several active site amino acids (D240 and K155), our calculations highlight that while one metal is essential for human EndoV activity, the enzyme can benefit from using two metals due to the presence of two suitable metal binding sites. By directly comparing one- versus two-metal-mediated P-O bond cleavage reactions within the confines of the same active site, our work brings a fresh perspective to the "number of metals" controversy.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge T1K 3M4, Alberta, Canada
| | - Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge T1K 3M4, Alberta, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge T1K 3M4, Alberta, Canada
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2
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Wang Y, Guo M, Xu X. Nanoproteases: Alternatives to Natural Protease for Biotechnological Applications. Chemistry 2024; 30:e202401178. [PMID: 38705854 DOI: 10.1002/chem.202401178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/07/2024]
Abstract
Some nanomaterials with intrinsic protease-like activity have the advantages of good stability, biosafety, low price, large-scale preparation and unique property of nanomaterials, which are promising alternatives for natural proteases in various applications. An especial term, "nanoprotease", has been coined to stress the intrinsic proteolytic property of these nanomaterials. As a new generation of artificial proteases, they have become a burgeoning field, attracting many researchers to design and synthesize high performance nanoproteases. In this review, we summarize recent progress on all types of nanoproteases with regard of their activity, mechanism and application and introduce a new and effective strategy for engineering high-performance nanoproteases. In addition, we discuss the challenges and opportunities of nanoprotease research in the future.
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Affiliation(s)
- Yaru Wang
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Mingxiu Guo
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Xiaolong Xu
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, 230026, P. R. China
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3
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Grabowska O, Zdrowowicz M, Milaș D, Żamojć K, Chmur K, Tesmar A, Kapica M, Chmurzyński L, Wyrzykowski D. Implications of albumin in cell culture media on the biological action of vanadates(V). Int J Biol Macromol 2023; 253:127875. [PMID: 37924912 DOI: 10.1016/j.ijbiomac.2023.127875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/06/2023]
Abstract
In this article, the implications of binding competition of vanadates(V) with dodecyl sulfates for bovine serum albumin on cytotoxicity of vanadium(V) species against prostate cancer cells have been investigated. The pH- and SDS-dependent vanadate(V)-BSA interactions were observed. At pH 5, there is only one site capable of binding ten vanadates(V) ions (logK(ITC)1 = 4.96 ± 0.06; ΔH(ITC)1 = -1.04 ± 0.03 kcal mol-1), whereas at pH 7 two distinctive binding sites on protein were found, saturated with two and seven V(V) ions, respectively (logK(ITC)1 = 6.11 ± 0.06; ΔH(ITC)1 = 0.78 ± 0.12 kcal mol-1; logK(ITC)2 = 4.80 ± 0.02; ΔH(ITC)2 = - 4.95 ± 0.14 kcal mol-1). SDS influences the stoichiometry and the stability of the resulting V(V)-BSA complexes. Finally, the cytotoxicity of vanadates(V) against prostate cancer cells (PC3 line) was examined in the presence and absence of SDS in the culture medium. In the case of a 24-h incubation with 100 μM vanadate(V), a ca. 20 % reduction in viability of PC3 cells was observed in the presence of SDS. However, in other considered cases (various concentrations and time of incubation) SDS does not affect the dose-dependent action of vanadates(V) on the investigated prostate cancer cells.
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Affiliation(s)
- Ola Grabowska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Magdalena Zdrowowicz
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Dan Milaș
- Faculty of Chemistry, Biology, Geography, West University Timișoara, Strada Johann Heinrich Pestalozzi 16, Timișoara, Romania
| | - Krzysztof Żamojć
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Katarzyna Chmur
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Aleksandra Tesmar
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Martyna Kapica
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Lech Chmurzyński
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Dariusz Wyrzykowski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
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Serafim LF, Jayasinghe-Arachchige VM, Wang L, Rathee P, Yang J, Moorkkannur N S, Prabhakar R. Distinct chemical factors in hydrolytic reactions catalyzed by metalloenzymes and metal complexes. Chem Commun (Camb) 2023. [PMID: 37366367 DOI: 10.1039/d3cc01380d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The selective hydrolysis of the extremely stable phosphoester, peptide and ester bonds of molecules by bio-inspired metal-based catalysts (metallohydrolases) is required in a wide range of biological, biotechnological and industrial applications. Despite the impressive advances made in the field, the ultimate goal of designing efficient enzyme mimics for these reactions is still elusive. Its realization will require a deeper understanding of the diverse chemical factors that influence the activities of both natural and synthetic catalysts. They include catalyst-substrate complexation, non-covalent interactions and the electronic nature of the metal ion, ligand environment and nucleophile. Based on our computational studies, their roles are discussed for several mono- and binuclear metallohydrolases and their synthetic analogues. Hydrolysis by natural metallohydrolases is found to be promoted by a ligand environment with low basicity, a metal bound water and a heterobinuclear metal center (in binuclear enzymes). Additionally, peptide and phosphoester hydrolysis is dominated by two competing effects, i.e. nucleophilicity and Lewis acid activation, respectively. In synthetic analogues, hydrolysis is facilitated by the inclusion of a second metal center, hydrophobic effects, a biological metal (Zn, Cu and Co) and a terminal hydroxyl nucleophile. Due to the absence of the protein environment, hydrolysis by these small molecules is exclusively influenced by nucleophile activation. The results gleaned from these studies will enhance the understanding of fundamental principles of multiple hydrolytic reactions. They will also advance the development of computational methods as a predictive tool to design more efficient catalysts for hydrolysis, Diels-Alder reaction, Michael addition, epoxide opening and aldol condensation.
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Affiliation(s)
- Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | | | - Lukun Wang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | - Parth Rathee
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | - Jiawen Yang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
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5
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Jayasinghe-Arachchige VM, Serafim LF, Hu Q, Ozen C, Moorkkannur SN, Schenk G, Prabhakar R. Elucidating the Roles of Distinct Chemical Factors in the Hydrolytic Activities of Hetero- and Homonuclear Synthetic Analogues of Binuclear Metalloenzymes. ACS Catal 2023. [DOI: 10.1021/acscatal.2c05758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Affiliation(s)
| | - Leonardo F. Serafim
- 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
| | - Cihan Ozen
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Sreerag N. Moorkkannur
- 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, Brisbane, Queensland 4072, Australia
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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6
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Aureliano M, Mitchell SG, Yin P. Editorial: Emerging polyoxometalates with biological, biomedical, and health applications. Front Chem 2022; 10:977317. [PMID: 36017169 PMCID: PMC9397140 DOI: 10.3389/fchem.2022.977317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Manuel Aureliano
- Faculdade de Ciências e Tecnologia, Campus de Gambelas, Universidade do Algarve, Faro, Portugal
- Centro de Ciências do Mar (CCMar), Universidade do Algarve, Faro, Portugal
- *Correspondence: Manuel Aureliano, ; Scott G. Mitchell, ; Panchao Yin,
| | - Scott G. Mitchell
- Instituto de Nanociencia y Materiales de Aragón (INMA), Consejo Superior de Investigaciones Científicas-Universidad de Zaragoza, Zaragoza, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Manuel Aureliano, ; Scott G. Mitchell, ; Panchao Yin,
| | - Panchao Yin
- South China University of Technology, Guangzhou, China
- *Correspondence: Manuel Aureliano, ; Scott G. Mitchell, ; Panchao Yin,
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7
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Gil A, Carbó JJ. Computational Modelling of the Interactions Between Polyoxometalates and Biological Systems. Front Chem 2022; 10:876630. [PMID: 35494630 PMCID: PMC9046717 DOI: 10.3389/fchem.2022.876630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/21/2022] [Indexed: 11/27/2022] Open
Abstract
Polyoxometalates (POMs) structures have raised considerable interest for the last years in their application to biological processes and medicine. Within this area, our mini-review shows that computational modelling is an emerging tool, which can play an important role in understanding the interaction of POMs with biological systems and the mechanisms responsible of their activity, otherwise difficult to achieve experimentally. During recent years, computational studies have mainly focused on the analysis of POM binding to proteins and other systems such as lipid bilayers and nucleic acids, and on the characterization of reaction mechanisms of POMs acting as artificial metalloproteases and phosphoesterases. From early docking studies locating binding sites, molecular dynamics (MD) simulations have allowed to characterize the nature of POM···protein interactions, and to evaluate the effect of the charge, size, and shape of the POM on protein affinity, including also, the atomistic description of chaotropic character of POM anions. Although these studies rely on the interaction with proteins and nucleic acid models, the results could be extrapolated to other biomolecules such as carbohydrates, triglycerides, steroids, terpenes, etc. Combining MD simulations with quantum mechanics/molecular mechanics (QM/MM) methods and DFT calculations on cluster models, computational studies are starting to shed light on the factors governing the activity and selectivity for the hydrolysis of peptide and phosphoester bonds catalysed by POMs.
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Affiliation(s)
- Adrià Gil
- ARAID Foundation, Zaragoza, Spain
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) CSIC, Universidad de Zaragoza, Zaragoza, Spain
- Faculdade de Ciências, BioISI—Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Lisboa, Portugal
- *Correspondence: Adrià Gil, ; Jorge J. Carbó,
| | - Jorge J. Carbó
- Department de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain
- *Correspondence: Adrià Gil, ; Jorge J. Carbó,
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Norjmaa G, Solé-Daura A, Besora M, Ricart JM, Carbó JJ. Peptide Hydrolysis by Metal (Oxa)cyclen Complexes: Revisiting the Mechanism and Assessing Ligand Effects. Inorg Chem 2021; 60:807-815. [PMID: 33411534 DOI: 10.1021/acs.inorgchem.0c02859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanism responsible for peptide bond hydrolysis by Co(III) and Cu(II) complexes with (oxa)cyclen ligands has been revisited by means of computational tools. We propose that the mechanism starts by substrate coordination and an outer-sphere attack on the amide C atom of a solvent water molecule assisted by the metal hydroxo moiety as a general base, which occurs through six-membered ring transition states. This new mechanism represents a more likely scenario than the previously proposed mechanisms that involved an inner-sphere nucleophilic attack through more strained four-membered rings transition states. The corresponding computed overall free-energy barrier of 25.2 kcal mol-1 for hydrolysis of the peptide bond in Phe-Ala by a cobalt(III) oxacyclen catalyst (1) is consistent with the experimental values obtained from rate constants. Also, we assessed the influence of the nature of the ligand throughout a systematic replacement of N by O atoms in the (oxa)cyclen ligand. Increasing the number of coordinating O atoms accelerates the reaction by increasing the Lewis acidity of the metal ion. On the other hand, the higher reactivity observed for the copper(II) oxacyclen catalyst with respect to the analogous Co(III) complex can be attributed to the larger Brönsted basicity of the copper(II) hydroxo ligand. Ultimately, the detailed understanding of the ligand and metal nature effects allowed us to identify the double role of the metal hydroxo complexes as Lewis acids and Brönsted bases and to rationalize the observed reactivity trends.
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Affiliation(s)
- Gantulga Norjmaa
- Department de Química Física i Inorgànica, Universitat Rovira i Virgili (URV), Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Albert Solé-Daura
- Department de Química Física i Inorgànica, Universitat Rovira i Virgili (URV), Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Maria Besora
- Department de Química Física i Inorgànica, Universitat Rovira i Virgili (URV), Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Josep M Ricart
- Department de Química Física i Inorgànica, Universitat Rovira i Virgili (URV), Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Jorge J Carbó
- Department de Química Física i Inorgànica, Universitat Rovira i Virgili (URV), Marcel·lí Domingo 1, 43007 Tarragona, Spain
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9
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Wakchaure PD, Ganguly B. Tuning the electronic effects in designing ligands for the inhibition of rotamase activity of FK506 binding protein. Theor Chem Acc 2021. [DOI: 10.1007/s00214-020-02717-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Solé-Daura A, Rodríguez-Fortea A, Poblet JM, Robinson D, Hirst JD, Carbó JJ. Origin of Selectivity in Protein Hydrolysis by Zr(IV)-Containing Metal Oxides as Artificial Proteases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02848] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Albert Solé-Daura
- Department de Quı́mica Fı́sica i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Antonio Rodríguez-Fortea
- Department de Quı́mica Fı́sica i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Josep M. Poblet
- Department de Quı́mica Fı́sica i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - David Robinson
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
- Department of Chemistry and Forensics, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Jorge J. Carbó
- Department de Quı́mica Fı́sica i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo 1, 43007 Tarragona, Spain
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11
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Conic D, Pierloot K, Parac-Vogt TN, Harvey JN. Mechanism of the highly effective peptide bond hydrolysis by MOF-808 catalyst under biologically relevant conditions. Phys Chem Chem Phys 2020; 22:25136-25145. [PMID: 33118561 DOI: 10.1039/d0cp04775a] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Efficient and selective hydrolysis of inert peptide bonds is of paramount importance. MOF-808, a metal-organic framework based on Zr6 nodes, can hydrolyze peptide bonds efficiently under biologically relevant conditions. However, the details of the catalyst structure and of the underlying catalytic reaction mechanism are challenging to establish. By means of DFT calculations we first investigate the speciation of the Zr6 nodes and identify the nature of ligands that bind to the Zr6O8H4-x core in aqueous conditions. The core is predicted to strongly prefer a Zr6O8H4 protonation state and to be predominantly decorated by bridging formate ligands, giving Zr6(μ3-O)4(μ3-OH)4(BTC)2(HCOO)6 and Zr6(μ3-O)4(μ3-OH)4(BTC)2(HCOO)5(OH)(H2O) as the most favorable structures at physiological pH. The GlyGly peptide can bind MOF in several different ways, with the preferred structure involving coordination through the terminal carboxylate analogously to the binding mode of formate ligand. The pre-reactive binding mode in which the amide carbonyl oxygen coordinates the metal core lies 7 kcal higher in free energy. The preferred reaction pathway is predicted to have two close-lying transition states, either of which could be the rate-determining step: nucleophilic attack on the amide carbon atom and C-N bond breaking, with calculated relative free energies of 31 and 32 kcal mol-1, respectively. Replacement of formate by water and hydroxide at the Zr6 node is predicted to be possible, but does not appear to play a role in the hydrolysis mechanism.
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Affiliation(s)
- Dragan Conic
- Division of Quantum Chemistry and Physical Chemistry, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium.
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12
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Solé-Daura A, Poblet JM, Carbó JJ. Structure-Activity Relationships for the Affinity of Chaotropic Polyoxometalate Anions towards Proteins. Chemistry 2020; 26:5799-5809. [PMID: 32104951 DOI: 10.1002/chem.201905533] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Indexed: 12/31/2022]
Abstract
The influence of the composition of chaotropic polyoxometalate (POM) anions on their affinity to biological systems was studied by means of atomistic molecular dynamics (MD) simulations. The variations in the affinity to hen egg-white lysozyme (HEWL) were analyzed along two series of POMs whereby the charge or the size and shape of the metal cluster are modified systematically. Our simulations revealed a quadratic relationship between the charge of the POM and its affinity to HEWL as a consequence of the parabolic growth of POM⋅⋅⋅water interaction with the charge. As the charge increases, POMs become less chaotropic (more kosmotropic) increasing the number and the strength of POM-water hydrogen bonds and structuring the solvation shell around the POM. This atomistic description explains the proportionally larger desolvation energies and less protein affinity for highly charged POMs, and consequently, the preference for moderate charge densities (q/M=0.33). Also, our simulations suggest that POM⋅⋅⋅protein interactions are size-specific. The cationic pockets of HEWL protein show a preference for Keggin-like structures, which display the optimal dimensions (≈1 nm). Finally, we developed a quantitative multidimensional model for protein affinity with predictive ability (r2 =0.97; q2 =0.88) using two molecular descriptors that account for the charge density (charge per metal atom ratio; q/M) and the size and shape (shape weighted-volume; VS ).
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Affiliation(s)
- Albert Solé-Daura
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel⋅lí Domingo 1, 43007, Tarragona, Spain
| | - Josep M Poblet
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel⋅lí Domingo 1, 43007, Tarragona, Spain
| | - Jorge J Carbó
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel⋅lí Domingo 1, 43007, Tarragona, Spain
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13
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Hu Q, Jayasinghe‐Arachchige VM, Sharma G, Serafim LF, Paul TJ, Prabhakar R. Mechanisms of peptide and phosphoester hydrolysis catalyzed by two promiscuous metalloenzymes (insulin degrading enzyme and glycerophosphodiesterase) and their synthetic analogues. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Qiaoyu Hu
- Department of Chemistry, University of Miami Coral Gables Florida
| | | | - Gaurav Sharma
- Department of Chemistry, University of Miami Coral Gables Florida
| | | | - Thomas J. Paul
- Department of Chemistry, University of Miami Coral Gables Florida
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami Coral Gables Florida
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14
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Hu Q, Jayasinghe-Arachchige VM, Zuchniarz J, Prabhakar R. Effects of the Metal Ion on the Mechanism of Phosphodiester Hydrolysis Catalyzed by Metal-Cyclen Complexes. Front Chem 2019; 7:195. [PMID: 31024887 PMCID: PMC6460053 DOI: 10.3389/fchem.2019.00195] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/14/2019] [Indexed: 12/01/2022] Open
Abstract
In this study, mechanisms of phosphodiester hydrolysis catalyzed by six di- and tetravalent metal-cyclen (M-C) complexes (Zn-C, Cu-C, Co-C, Ce-C, Zr-C and Ti-C) have been investigated using DFT calculations. The activities of these complexes were studied using three distinct mechanisms: (1) direct attack ( DA ), (2) catalyst-assisted ( CA ), and (3) water-assisted ( WA ). All divalent metal complexes (Zn-C, Cu-C and Co-C) coordinated to the BNPP substrate in a monodentate fashion and activated its scissile phosphoester bond. However, all tetravalent metal complexes (Ce-C, Zr-C, and Ti-C) interacted with BNPP in a bidentate manner and strengthened this bond. The DA mechanism was energetically the most feasible for all divalent M-C complexes, while the WA mechanism was favored by the tetravalent complexes, except Ce-C. The divalent complexes were found to be more reactive than their tetravalent counterparts. Zn-C catalyzed the hydrolysis with the lowest barrier among all M-C complexes, while Ti-C was the most reactive tetravalent complex. The activities of Ce-C and Zr-C, except Ti-C, were improved with an increase in the coordination number of the metal ion. The structural and mechanistic information provided in this study will be very helpful in the development of more efficient metal complexes for this critical reaction.
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Affiliation(s)
| | | | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL, United States
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