1
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Sementilli A, Rengifo RF, Li W, Stewart AM, Stewart KL, Twahir U, Kim Y, Yue J, Mehta AK, Shearer J, Warncke K, Lynn DG. Engineering Synthetic Electron Transfer Chains from Metallopeptide Membranes. Inorg Chem 2024; 63:2899-2908. [PMID: 38127051 PMCID: PMC10865380 DOI: 10.1021/acs.inorgchem.3c02861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
The energetic and geometric features enabling redox chemistry across the copper cupredoxin fold contain key components of electron transfer chains (ETC), which have been extended here by templating the cross-β bilayer assembly of a synthetic nonapeptide, HHQALVFFA-NH2 (K16A), with copper ions. Similar to ETC cupredoxin plastocyanin, these assemblies contain copper sites with blue-shifted (λmax 573 nm) electronic transitions and strongly oxidizing reduction potentials. Electron spin echo envelope modulation and X-ray absorption spectroscopies define square planar Cu(II) sites containing a single His ligand. Restrained molecular dynamics of the cross-β peptide bilayer architecture support metal ion coordination stabilizing the leaflet interface and indicate that the relatively high reduction potential is not simply the result of distorted coordination geometry (entasis). Cyclic voltammetry (CV) supports a charge-hopping mechanism across multiple copper centers placed 10-12 Å apart within the assembled peptide leaflet interface. This metal-templated scaffold accordingly captures the electron shuttle and cupredoxin functionality in a peptide membrane-localized electron transport chain.
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Affiliation(s)
- Anthony Sementilli
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Rolando F. Rengifo
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Wei Li
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Andrew M. Stewart
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Katie L. Stewart
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Umar Twahir
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Youngsun Kim
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Jipeng Yue
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Anil K. Mehta
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Jason Shearer
- Department
of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | - Kurt Warncke
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - David G. Lynn
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
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2
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Sunda AP, Sharma AK. Molecular Insights into Cu/Zn Metal Response to the Amyloid β-Peptide (1-42). ACS PHYSICAL CHEMISTRY AU 2024; 4:57-66. [PMID: 38283784 PMCID: PMC10811771 DOI: 10.1021/acsphyschemau.3c00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 01/30/2024]
Abstract
Aβ1-40 peptide and Aβ1-42 peptide are the building units of beta-amyloid plaques present in Alzheimer's disease (AD)-affected brain. The binding affinity of various divalent metal ions such as Cu and Zn present in AD-affected brain with different amino acids available in Aβ-peptide became the focus to explore their role in soluble neurotoxic oligomer formation. Cu2+ metal ions are known to enhance the neurotoxicity of the Aβ1-42 peptide by catalyzing the formation of soluble neurotoxic oligomers. The competitive preference of both Cu2+ and Zn2+ simultaneously to interact with the Aβ-peptide is unknown. The divalent Cu and Zn ions were inserted in explicit aqueous Aβ1-42 peptide configurations to get insights into the binding competence of these metal ions with peptides using classical molecular dynamics (MD) simulations. The metal-ion interactions reveal that competitive binding preferences of various peptide sites become metal-ion-specific and differ significantly. For Cu2+, interactions are found to be more significant with respect to those of Asp-7, His-6, Glu-11, and His-14. Asp-1, Glu-3, Asp-7, His-6, Glu-11, and His-13 amino acid residues show higher affinity toward Zn2+ ions. MD simulations show notable variation in the solvent-accessible surface area in the hydrophobic region of the peptide. Infinitesimal mobility was obtained for Zn2+ compared to Cu2+ in an aqueous solution and Cu2+ diffusivity deviated significantly at different time scales, proving its labile features in aqueous Aβ1-42 peptides.
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Affiliation(s)
- Anurag Prakash Sunda
- Department
of Chemistry, J. C. Bose University of Science
and Technology, YMCA, Faridabad 121006, India
| | - Anuj Kumar Sharma
- Department
of Chemistry, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Ajmer 305817, India
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3
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Gielnik M, Szymańska A, Dong X, Jarvet J, Svedružić ŽM, Gräslund A, Kozak M, Wärmländer SKTS. Prion Protein Octarepeat Domain Forms Transient β-Sheet Structures upon Residue-Specific Binding to Cu(II) and Zn(II) Ions. Biochemistry 2023. [PMID: 37163663 DOI: 10.1021/acs.biochem.3c00129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Misfolding of the cellular prion protein (PrPC) is associated with the development of fatal neurodegenerative diseases called transmissible spongiform encephalopathies (TSEs). Metal ions appear to play a crucial role in PrPC misfolding. PrPC is a combined Cu(II) and Zn(II) metal-binding protein, where the main metal-binding site is located in the octarepeat (OR) region. Thus, the biological function of PrPC may involve the transport of divalent metal ions across membranes or buffering concentrations of divalent metal ions in the synaptic cleft. Recent studies have shown that an excess of Cu(II) ions can result in PrPC instability, oligomerization, and/or neuroinflammation. Here, we have used biophysical methods to characterize Cu(II) and Zn(II) binding to the isolated OR region of PrPC. Circular dichroism (CD) spectroscopy data suggest that the OR domain binds up to four Cu(II) ions or two Zn(II) ions. Binding of the first metal ion results in a structural transition from the polyproline II helix to the β-turn structure, while the binding of additional metal ions induces the formation of β-sheet structures. Fluorescence spectroscopy data indicate that the OR region can bind both Cu(II) and Zn(II) ions at neutral pH, but under acidic conditions, it binds only Cu(II) ions. Molecular dynamics simulations suggest that binding of either metal ion to the OR region results in the formation of β-hairpin structures. As the formation of β-sheet structures can be a first step toward amyloid formation, we propose that high concentrations of either Cu(II) or Zn(II) ions may have a pro-amyloid effect in TSE diseases.
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Affiliation(s)
- Maciej Gielnik
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, PL 61-614 Poznań, Poland
| | - Aneta Szymańska
- Department of Biomedical Chemistry, Faculty of Chemistry, Gdańsk University, PL 80-308 Gdańsk, Poland
| | - Xiaolin Dong
- Chemistry Section, Stockholm University, 10691 Stockholm, Sweden
| | - Jüri Jarvet
- Chemistry Section, Stockholm University, 10691 Stockholm, Sweden
- The National Institute of Chemical Physics and Biophysics, 12618 Tallinn, Estonia
| | - Željko M Svedružić
- Department of Biotechnology, University of Rijeka, HR 51000 Rijeka, Croatia
| | - Astrid Gräslund
- Chemistry Section, Stockholm University, 10691 Stockholm, Sweden
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, PL 61-614 Poznań, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, PL 30-392 Kraków, Poland
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4
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Martins LS, Gonçalves RWA, Moraes JJS, Alves CN, Silva JRA. Computational Analysis of Triazole-Based Kojic Acid Analogs as Tyrosinase Inhibitors by Molecular Dynamics and Free Energy Calculations. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238141. [PMID: 36500237 PMCID: PMC9735930 DOI: 10.3390/molecules27238141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022]
Abstract
Molecular docking, molecular dynamics (MD) simulations and the linear interaction energy (LIE) method were used here to predict binding modes and free energy for a set of 1,2,3-triazole-based KA analogs as potent inhibitors of Tyrosinase (TYR), a key metalloenzyme of the melanogenesis process. Initially, molecular docking calculations satisfactorily predicted the binding mode of evaluated KA analogs, where the KA part overlays the crystal conformation of the KA inhibitor into the catalytic site of TYR. The MD simulations were followed by the LIE method, which reproduced the experimental binding free energies for KA analogs with an r2 equal to 0.97, suggesting the robustness of our theoretical model. Moreover, the van der Waals contributions performed by some residues such as Phe197, Pro201, Arg209, Met215 and Val218 are responsible for the binding recognition of 1,2,3-triazole-based KA analogs in TYR catalytic site. Finally, our calculations provide suitable validation of the combination of molecular docking, MD, and LIE approaches as a powerful tool in the structure-based drug design of new and potent TYR inhibitors.
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Affiliation(s)
- Lucas Sousa Martins
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - Reinaldo W. A. Gonçalves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - Joana J. S. Moraes
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, Brazil
- Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, Brazil
- Correspondence: (C.N.A.); (J.R.A.S.)
| | - José Rogério A. Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, Brazil
- Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém 66075-110, Brazil
- Correspondence: (C.N.A.); (J.R.A.S.)
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5
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Da-yang TE, Fifen JJ, Conradie J, Conradie MM. Structures, temperature effect, binding and clustering energies of Cu2+(MeOH)n=1-8 clusters and extrapolations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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6
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Da Silva WDB, Dias RP, Da Silva JCS. Refining details of the structural and electronic properties of the Cu B site in pMMO enzyme through sequential molecular dynamics/CPKS-EPR calculations. Phys Chem Chem Phys 2022; 24:16611-16621. [PMID: 35730560 DOI: 10.1039/d2cp01217k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work investigated the structural and electronic properties of the copper mononuclear site of the PmoB part of the pMMO enzyme at the molecular level. We propose that the CuB catalytic site in the soluble portion of pMMO at room temperature and under physiological conditions is a mononuclear copper complex in a distorted octahedral arrangement with the residues His33, His137, and His139 on the equatorial base and two water molecules on the axial axis. Our view was based on the molecular dynamics results and DFT calculations of the electronic paramagnetic resonance parameters and comparisons with experimental EPR data. This new proposed model for the CuB site brings additional support concerning the recent experimental evidence, which pointed out that a saturated coordination sphere of the copper ion in the CuB center is an essential factor that makes it less efficient than the CuC site in the methane oxidation. Therefore, according to the CuB site model proposed here, an additional step involving a displacement of at least one water molecule of the copper coordination sphere by the O2 molecule prior to its activation must be necessary. This scenario is less likely to occur in the CuC center once this one is buried in the alpha-helices, which are part of the pMMO structure bound to the membrane wall, and consequently located in a less solvent-exposed region. In addition, we also present a simple and efficient sequential S-MD/CPKS protocol to compute EPR parameters that can, in principle, be expanded for the study of other copper-containing proteins.
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Affiliation(s)
- William Daniel B Da Silva
- LQCBio: Laboratório de Química Computacional e Modelagem de Biomoléculas, Instituto de Química e Biotecnologia, IQB, Universidade Federal de Alagoas, Campus A. C. Simões, 57072-900, Maceió, AL, Brazil.
| | - Roberta P Dias
- GIMMM: Grupo Interdisciplinar de Modelagem Molecular e Simulação de Materiais, Núcleo Interdisciplinar de Ciências Exatas e da Natureza - NICEN, Campus do Agreste, Universidade Federal de Pernambuco, 55002-970, Caruaru, PE, Brazil
| | - Júlio C S Da Silva
- LQCBio: Laboratório de Química Computacional e Modelagem de Biomoléculas, Instituto de Química e Biotecnologia, IQB, Universidade Federal de Alagoas, Campus A. C. Simões, 57072-900, Maceió, AL, Brazil.
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7
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Rahnamoun A, O'Hearn KA, Kaymak MC, Li Z, Merz KM, Aktulga HM. A Polarizable Cationic Dummy Metal Ion Model. J Phys Chem Lett 2022; 13:5334-5340. [PMID: 35675715 DOI: 10.1021/acs.jpclett.2c01279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A novel locally polarizable multisite model based on the original cation dummy atom (CDA) model is described for molecular dynamics simulations of ions in condensed phases. Polarization effects are introduced by the electronegativity equalization model (EEM) method where charges on the metal ion and its dummy atoms can fluctuate to respond to the environment. This model includes explicit polarization and ion-induced interactions and can be coupled with nonpolarizable or polarizable water models, making it more transferable to simpler force fields. This approach allows us to enhance the original fixed charge CDA model where the charge distribution cannot adapt to the local solvent structure. To illustrate the new CDApol model, we examined properties of the Zn2+, Al3+, and Zr4+ ions in aqueous solution. The polarizable model and Lennard-Jones parameters were refined for octahedrally coordinated Zn2+, Al3+, and Zr4+ CDAs to reproduce thermodynamic and geometrical properties. Using this locally polarizable model, we were able to obtain the experimental hydration free energy, ion-oxygen distance, and coordination number coupled with the standard 12-6 Lennard-Jones model. This model can be used in myriad additional applications where local polarization and charge transfer is important.
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Affiliation(s)
- Ali Rahnamoun
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
- Department of Computer Science and Engineering, Michigan State University, 428 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Kurt A O'Hearn
- Department of Computer Science and Engineering, Michigan State University, 428 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Mehmet Cagri Kaymak
- Department of Computer Science and Engineering, Michigan State University, 428 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Zhen Li
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Hasan Metin Aktulga
- Department of Computer Science and Engineering, Michigan State University, 428 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
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8
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Sun Z, Lin L, He J, Ding D, Wang T, Li J, Li M, Liu Y, Li Y, Yuan M, Huang B, Li H, Sun G. Regulating the Spin State of Fe III Enhances the Magnetic Effect of the Molecular Catalysis Mechanism. J Am Chem Soc 2022; 144:8204-8213. [PMID: 35471968 DOI: 10.1021/jacs.2c01153] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Aqueous-phase oxygen evolution reaction (OER) is the bottleneck of water splitting. The formation of the O-O bond involves the generation of paramagnetic oxygen molecules from the diamagnetic hydroxides. The spin configurations might play an important role in aqueous-phase molecular electrocatalysis. However, spintronic electrocatalysis is almost an uncultivated land for the exploration of the oxygen molecular catalysis process. Herein, we present a novel magnetic FeIII site spin-splitting strategy, wherein the electronic structure and spin states of the FeIII sites are effectively induced and optimized by the Jahn-Teller effect of Cu2+. The theoretical calculations and operando attenuated total reflectance-infrared Fourier transform infrared (ATR FT-IR) reveal the facilitation for the O-O bond formation, which accelerates the production of O2 from OH- and improves the OER activity. The Cu1-Ni6Fe2-LDH catalyst exhibits a low overpotential of 210 mV at 10 mA cm-2 and a low Tafel slope (33.7 mV dec-1), better than those of the initial Cu0-Ni6Fe2-LDHs (278 mV, 101.6 mV dec-1). With the Cu2+ regulation, we have realized the transformation of NiFe-LDHs from ferrimagnets to ferromagnets and showcase that the OER performance of Cu-NiFe-LDHs significantly increases compared with that of NiFe-LDHs under the effect of a magnetic field for the first time. The magnetic-field-assisted Cu1-Ni6Fe2-LDHs provide an ultralow overpotential of 180 mV at 10 mA cm-2, which is currently one of the best OER performances. The combination of the magnetic field and spin configuration provides new principles for the development of high-performance catalysts and understandings of the catalytic mechanism from the spintronic level.
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Affiliation(s)
- Zemin Sun
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China.,Beijing Key Laboratory of Energy Conversion and Storage Materials Institution, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Liu Lin
- Beijing Key Laboratory of Energy Conversion and Storage Materials Institution, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jinlu He
- School of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot 010021, China
| | - Dajie Ding
- Beijing Key Laboratory of Energy Conversion and Storage Materials Institution, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Tongyue Wang
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
| | - Jie Li
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
| | - Mingxuan Li
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
| | - Yicheng Liu
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
| | - Yayin Li
- Beijing Key Laboratory of Energy Conversion and Storage Materials Institution, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Mengwei Yuan
- Beijing Key Laboratory of Energy Conversion and Storage Materials Institution, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Binbin Huang
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
| | - Huifeng Li
- Beijing Key Laboratory of Energy Conversion and Storage Materials Institution, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Genban Sun
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China.,Beijing Key Laboratory of Energy Conversion and Storage Materials Institution, College of Chemistry, Beijing Normal University, Beijing 100875, China
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9
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Copper(II) import and reduction are dependent on His-Met clusters in the extracellular amino terminus of human copper transporter-1. J Biol Chem 2022; 298:101631. [PMID: 35090891 PMCID: PMC8867124 DOI: 10.1016/j.jbc.2022.101631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 11/22/2022] Open
Abstract
Copper(I) is an essential metal for all life forms. Though Cu(II) is the most abundant and stable state, its reduction to Cu(I) via an unclear mechanism is prerequisite for its bioutilization. In eukaryotes, the copper transporter-1 (CTR1) is the primary high-affinity copper importer, although its mechanism and role in Cu(II) reduction remain uncharacterized. Here we show that extracellular amino-terminus of human CTR1 contains two methionine-histidine clusters and neighboring aspartates that distinctly bind Cu(I) and Cu(II) preceding its import. We determined that hCTR1 localizes at the basolateral membrane of polarized MDCK-II cells and that its endocytosis to Common-Recycling-Endosomes is regulated by reduction of Cu(II) to Cu(I) and subsequent Cu(I) coordination by the methionine cluster. We demonstrate the transient binding of both Cu(II) and Cu(I) during the reduction process is facilitated by aspartates that also act as another crucial determinant of hCTR1 endocytosis. Mutating the first Methionine cluster (7Met-Gly-Met9) and Asp13 abrogated copper uptake and endocytosis upon copper treatment. This phenotype could be reverted by treating the cells with reduced and nonreoxidizable Cu(I). We show that histidine clusters, on other hand, bind Cu(II) and are crucial for hCTR1 functioning at limiting copper. Finally, we show that two N-terminal His-Met-Asp clusters exhibit functional complementarity, as the second cluster is sufficient to preserve copper-induced CTR1 endocytosis upon complete deletion of the first cluster. We propose a novel and detailed mechanism by which the two His-Met-Asp residues of hCTR1 amino-terminus not only bind copper, but also maintain its reduced state, crucial for intracellular uptake.
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10
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Zhang Y, Jiang Y, Qiu Y, Zhang H. Rational Design of Nonbonded Point Charge Models for Highly Charged Metal Cations with Lennard-Jones 12-6 Potential. J Chem Inf Model 2021; 61:4613-4629. [PMID: 34467756 DOI: 10.1021/acs.jcim.1c00723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we developed nonbonded point charge models using a simple Lennard-Jones (LJ) 12-6 potential for highly charged metal cations (18 trivalent and 6 tetravalent ions) for use with 11 water models of TIP3P, OPC3, SPC/E, SPC/Eb, TIP3P-FB, a99SB-disp, TIP4P-Ew, OPC, TIP4P/2005, TIP4P-D, and TIP4P-FB. The designed models simultaneously reproduce the hydration free energy (HFE) and ion-oxygen distance (IOD) in the first hydration shell with an error within 1 kcal/mol and 0.01 Å on average, respectively, and yield reasonable coordination numbers for most cations. Such performance is equivalent to the previously reported point charge models using a more complex 12-6-4 LJ-type potential, while the LJ R parameters of our models are much close to Shannon's revised effective ion radii than that of the 12-6-4 models. Our designed models overestimate the diffusion constants of several trivalent ions by 5-68%. The performance in predicting osmotic coefficients of trivalent chlorides in aqueous solution depends on the salt type. A calibration of cation-anion interacting LJ parameters reproduces the experimental osmotic coefficients of an AlCl3 solution at 0.2-3.0 mol/L. The effectiveness of our new models is further demonstrated by simulating a metalloprotein system with four force field/water combinations. This work facilitates accurate modeling of metal-containing systems by a variety of force fields and water models in aqueous solution.
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Affiliation(s)
- Yongguang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yejie Qiu
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
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11
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Li C, Chen W, Lin X, Zhang S, Wang Y, He X, Ren Y. Molecular dynamics study on the stability of foot-and-mouth disease virus particle in salt solution. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1951262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Chen Li
- State Key Laboratory of Multiphase Complex System, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, People’s Republic of China
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Wei Chen
- State Key Laboratory of Multiphase Complex System, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, People’s Republic of China
- Dalian National Laboratory for Clean Energy, Dalian, People’s Republic of China
| | - Xuan Lin
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Songping Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yufei Wang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Xianfeng He
- State Key Laboratory of Multiphase Complex System, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, People’s Republic of China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Ying Ren
- State Key Laboratory of Multiphase Complex System, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, People’s Republic of China
- Innovation Academy of Green Manufacture, Chinese Academy of Sciences, Beijing, People’s Republic of China
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12
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Peng J, Zhang Y, Jiang Y, Zhang H. Developing and Assessing Nonbonded Dummy Models of Magnesium Ion with Different Hydration Free Energy References. J Chem Inf Model 2021; 61:2981-2997. [PMID: 34080414 DOI: 10.1021/acs.jcim.1c00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A large diversity in the targeted hydration free energies (HFEs) during model parameterization of metal ions was reported in the literature with a difference by dozens of kcal/mol. Here, we developed a series of nonbonded dummy models of the Mg2+ ion targeting different HFE references in TIP3P water, followed by assessments of the designed models in the simulations of MgCl2 solution and biological systems. Together with the comparison of existing models, we conclude that the difference in the targeted HFEs has a limited influence on the model performance, while the usability of these models differs from case to case. The feasibility of reproducing more properties of Mg2+ such as diffusion constants and water exchange rates using a nonbonded dummy model is demonstrated. Underestimated activity derivative and osmotic coefficient of MgCl2 solutions in high concentration reveal a necessity for further optimization of ion-pair interactions. The developed dummy models are applicable to metal coordination with Asp, Glu, and His residues in metalloenzymes, and the performance in predicting monodentate or bidentate binding modes of Asp/Glu residues depends on the complexity of metal centers and the choice of protein force fields. When both the binding modes coexist, the nonbonded dummy models outperform point charge models, probably in need of considering polarization of metal-binding residues by, for instance, charge calibration in classical force fields. This work is valuable for the use and further development of magnesium ion models for simulations of metal-containing systems with good accuracy.
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Affiliation(s)
- Jiarong Peng
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yongguang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
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13
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Cardoso R, Valente R, Souza da Costa CH, da S. Gonçalves Vianez JL, Santana da Costa K, de Molfetta FA, Nahum Alves C. Analysis of Kojic Acid Derivatives as Competitive Inhibitors of Tyrosinase: A Molecular Modeling Approach. Molecules 2021; 26:2875. [PMID: 34066283 PMCID: PMC8152073 DOI: 10.3390/molecules26102875] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 12/15/2022] Open
Abstract
Tyrosinases belong to the functional copper-containing proteins family, and their structure contains two copper atoms, in the active site, which are coordinated by three histidine residues. The biosynthesis of melanin in melanocytes has two stages depending on the actions of the natural substrates L-DOPA and L-tyrosine. The dysregulation of tyrosinase is involved in skin cancer initiation. In the present study, using molecular modeling tools, we analyzed the inhibition activity of tyrosinase activity using kojic acid (KA) derivatives designed from aromatic aldehydes and malononitrile. All derivatives showed conformational affinity to the enzyme active site, and a favorable distance to chelate the copper ion, which is essential for enzyme function. Molecular dynamics simulations revealed that the derivatives formed promising complexes, presenting stable conformations with deviations between 0.2 and 0.35 Å. In addition, the investigated KA derivatives showed favorable binding free energies. The most stable KA derivatives showed the following binding free energies: -17.65 kcal mol-1 (D6), -18.07 kcal mol-1 (D2), -18.13 (D5) kcal mol-1, and -10.31 kcal mol-1 (D4). Our results suggest that these derivatives could be potent competitive inhibitors of the natural substrates of L-DOPA (-12.84 kcal mol-1) and L-tyrosine (-9.04 kcal mol-1) in melanogenesis.
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Affiliation(s)
- Richelly Cardoso
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará–UFPA, Guamá, Belém-PA 66075-10, Brazil; (R.C.); (F.A.d.M.)
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará–UFPA, Guamá, Belém-PA 66075-10, Brazil;
| | - Renan Valente
- Laboratório de Sistemas Moleculares Complexos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará–UFPA, Guamá, Belém-PA 66075-10, Brazil;
| | - Clauber Henrique Souza da Costa
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará–UFPA, Guamá, Belém-PA 66075-10, Brazil;
| | | | - Kauê Santana da Costa
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará–UFPA, Guamá, Belém-PA 66075-10, Brazil;
- Universidade Federal do Oeste do Pará, Instituto de Biodiversidade, Santarém-PA 68035-110, Brazil
| | - Fábio Alberto de Molfetta
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará–UFPA, Guamá, Belém-PA 66075-10, Brazil; (R.C.); (F.A.d.M.)
| | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará–UFPA, Guamá, Belém-PA 66075-10, Brazil;
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14
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Mariadasse R, Rajmichael R, Dwivedy A, Amala M, Ahmad M, Mutharasappan N, Biswal BK, Jeyakanthan J. Characterization of putative transcriptional regulator (PH0140) and its distal homologue. Cell Signal 2021; 84:110031. [PMID: 33932498 DOI: 10.1016/j.cellsig.2021.110031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/13/2021] [Accepted: 04/26/2021] [Indexed: 11/28/2022]
Abstract
In this study, a phylogenetic tree was constructed using 1854 sequences of various Lrp/AnsC (FFRPs) and ArsR proteins from pathogenic and non-pathogenic organisms. Despite having sequence similarities, FFRPs and ArsR proteins functioning differently as a transcriptional regulator and de-repressor in the presence of exogenous amino acids and metal ions, respectively. To understand these functional differences, the structures of various FFRPs and ArsR proteins (134 sequences) were modeled. Several ArsR proteins exhibited high similarity to the FFRPs while in few proteins, unusual structural folds were observed. However, the Helix-turn-Helix (HTH) domains are common among them and the ligand-binding domains are structurally dissimilar suggest the differences in their binding preferences. Despite low sequence conservation, most of these proteins revealed negatively charged surfaces in the active site pockets. Representative structures (PH0140 and TtArsR protein) from FFRPs and ArsR protein families were considered and evaluated for their functional differences using molecular modeling studies. Our earlier study has explained the binding preference of exogenous Tryptophan and the related transcriptional regulatory mechanism of PH0140 protein. In this study, a Cu2+ ion-induced de-repression mechanism of the TtArsR-DNA complex was characterized through docking and molecular dynamics. Further, the proteins were purified and their efficiency for sensing Tryptophan and Cu2+ ions were analyzed using cyclic voltammetry. Overall, the study explores the structural evolution and functional difference of FFRPs and ArsR proteins that present the possibilities of PH0140 and TtArsR as potential bio-sensory molecules.
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Affiliation(s)
- Richard Mariadasse
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 004, India
| | - Raji Rajmichael
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 004, India
| | | | - Mathimaran Amala
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 004, India
| | | | - Nachiappan Mutharasappan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 004, India
| | | | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 004, India.
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15
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Malloum A, Fifen JJ, Conradie J. Determination of the absolute solvation free energy and enthalpy of the proton in solutions. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114919] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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16
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A Rare Natural Benzo[ k, l]xanthene as a Turn-Off Fluorescent Sensor for Cu 2+ Ion. Int J Mol Sci 2020; 21:ijms21186933. [PMID: 32967305 PMCID: PMC7555586 DOI: 10.3390/ijms21186933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/28/2022] Open
Abstract
Rapid and efficient analyses of copper ions are crucial to providing key information for Cu2+ in living cells because of their biological importance. In this study, we reported one new turn-off fluorescent sensor for Cu2+ with a benzo[k,l]xanthene core, which served as an efficient cation sensor for copper ion over a wide range of other cations (Na+, K+, Ag+, Hg2+, Cd2+, Co2+, Ni2+, Zn2+, Mg2+, and Fe3+) owing to the catechol group in the aromatic core. The sensor showed selectivity for Cu2+ over other ions; the logKβ for Cu2+ binding to compound 1 had a value of 13.265. In the presence of Cu2+, sensor 1 provided significant fluorescence decrement; Co2+, and Ni2+ caused a fluorescence decrement when employed at a higher concentration than Cu2+, while Na+, K+, Hg2+, Cd2+, Zn2+, and Mg2+ metal ions produced only minor changes in fluorescence intensity. Fluorescence experiments demonstrate that compound 1 may have an application as a fluorescent probe for detecting Cu2+ with a limit of detection of 0.574 µM.
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17
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Evaluating the Performance of a Non-Bonded Cu 2+ Model Including Jahn-Teller Effect into the Binding of Tyrosinase Inhibitors. Int J Mol Sci 2020; 21:ijms21134783. [PMID: 32640730 PMCID: PMC7369908 DOI: 10.3390/ijms21134783] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 02/08/2023] Open
Abstract
Tyrosinase (TYR) is a metalloenzyme classified as a type-3 copper protein, which is involved in the synthesis of melanin through a catalytic process beginning with the conversion of the amino acid l-Tyrosine (l-Tyr) to l-3,4-dihydroxyphenylalanine (l-DOPA). It plays an important role in the mechanism of melanogenesis in various organisms including mammals, plants, and fungi. Herein, we used a combination of computational molecular modeling techniques including molecular dynamic (MD) simulations and the linear interaction energy (LIE) model to evaluate the binding free energy of a set of analogs of kojic acid (KA) in complex with TYR. For the MD simulations, we used a dummy model including the description of the Jahn–Teller effect for Cu2+ ions in the active site of this enzyme. Our results show that the LIE model predicts the TYR binding affinities of the inhibitor in close agreement to experimental results. Overall, we demonstrate that the classical model provides a suitable description of the main interactions between analogs of KA and Cu2+ ions in the active site of TYR.
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18
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Li Z, Song LF, Li P, Merz KM. Systematic Parametrization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. J Chem Theory Comput 2020; 16:4429-4442. [PMID: 32510956 DOI: 10.1021/acs.jctc.0c00194] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Divalent metal ions play important roles in biological and materials systems. Molecular dynamics simulation is an efficient tool to investigate these systems at the microscopic level. Recently, four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB) have been developed and better represent the physical properties of water than previous models. Metal ion parameters are dependent on the water model employed, making it necessary to develop metal ion parameters for select new water models. In the present work, we performed parameter scanning for the 12-6 Lennard-Jones nonbonded model of divalent metal ions in conjunction with the four new water models as well as four previous water models (TIP3P, SPC/E, TIP4P, and TIP4P-Ew). We found that these new three-point and four-point water models provide comparable or significantly improved performance for the simulation of divalent metal ions when compared to previous water models in the same category. Among all eight water models, the OPC3 water model yields the best performance for the simulation of divalent metal ions in the aqueous phase when using the 12-6 model. On the basis of the scanning results, we independently parametrized the 12-6 model for 24 divalent metal ions with each of the four new water models. As noted previously, the 12-6 model still fails to simultaneously reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values even with these new water models. To solve this problem, we parametrized the 12-6-4 model for the 16 divalent metal ions for which we have both experimental HFE and IOD values for each of the four new water models. The final parameters are able to reproduce both the experimental HFE and IOD values accurately. To validate the transferability of our parameters, we carried out benchmark calculations to predict the energies and geometries of ion-water clusters as well as the ion diffusivity coefficient of Mg2+. By comparison to quantum chemical calculations and experimental data, these results show that our parameters are well designed and have excellent transferability. The metal ion parameters for the 12-6 and 12-6-4 models reported herein can be employed in simulations of various biological and materials systems when using the OPC3, OPC, TIP3P-FB, or TIP4P-FB water model.
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Affiliation(s)
- Zhen Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Lin Frank Song
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Pengfei Li
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States.,Department of Biochemistry and Molecular Biology, Michigan State University,East Lansing, Michigan 48824, United States
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19
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Pelaez-Aguilar A, Valdés-García G, French-Pacheco L, Pastor N, Amero C, Rivillas-Acevedo L. Site-Specific Interactions with Copper Promote Amyloid Fibril Formation for λ6aJL2-R24G. ACS OMEGA 2020; 5:7085-7095. [PMID: 32280849 PMCID: PMC7143407 DOI: 10.1021/acsomega.9b03220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/03/2020] [Indexed: 06/11/2023]
Abstract
Light-chain amyloidosis (AL) is one of the most common systemic amyloidoses, and it is characterized by the deposition of immunoglobulin light chain (LC) variable domains as insoluble amyloid fibers in vital organs and tissues. The recombinant protein 6aJL2-R24G contains λ6a and JL2 germline genes and also contains the Arg24 by Gly substitution. This mutation is present in 25% of all amyloid-associated λ6 LC cases, reduces protein stability, and increases the propensity to form amyloid fibers. In this study, it was found that the interaction of 6aJL2-R24G with Cu(II) decreases the thermal stability of the protein and accelerates the amyloid fibril formation, as observed by fluorescence spectroscopy. Isothermal calorimetry titration showed that Cu(II) binds to the protein with micromolar affinity. His99 may be one of the main Cu(II) interaction sites, as observed by nuclear magnetic resonance spectroscopy. The binding of Cu(II) to His99 induces larger fluctuations of the CDR1 and loop C″, as shown by molecular dynamics simulations. Thus, Cu(II) binding may be inducing the loss of interactions between CDR3 and CDR1, making the protein less stable and more prone to form amyloid fibers. This study provides insights into the mechanism of metal-induced aggregation of the 6aJL2-R24G protein and sheds light on the bio-inorganic understanding of AL disease.
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Affiliation(s)
- Angel
E. Pelaez-Aguilar
- Centro
de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
| | - Gilberto Valdés-García
- Department
of Molecular Medicine and Bioprocesses, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Leidys French-Pacheco
- Centro
de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
| | - Nina Pastor
- Centro
de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
- Department
of Molecular Medicine and Bioprocesses, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Carlos Amero
- Centro
de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
| | - Lina Rivillas-Acevedo
- Centro
de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
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20
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Huy Pham DQ, Krupa P, Nguyen HL, La Penna G, Li MS. Computational Model to Unravel the Function of Amyloid-β Peptides in Contact with a Phospholipid Membrane. J Phys Chem B 2020; 124:3300-3314. [DOI: 10.1021/acs.jpcb.0c00771] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Dinh Quoc Huy Pham
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Pawel Krupa
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Hoang Linh Nguyen
- Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward, Thu
Duc District, 00133 Ho Chi Minh City, Vietnam
| | - Giovanni La Penna
- National Research Council of Italy (CNR), Institute for Chemistry of Organometallic Compounds (ICCOM), 50019 Florence, Italy
- National Institute for Nuclear Physics (INFN), Section of Roma-Tor Vergata, 00186 Roma, Italy
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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21
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MacDermott-Opeskin H, McDevitt CA, O'Mara ML. Comparing Nonbonded Metal Ion Models in the Divalent Cation Binding Protein PsaA. J Chem Theory Comput 2020; 16:1913-1923. [PMID: 32059108 DOI: 10.1021/acs.jctc.9b01180] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Divalent metal cations are essential for many biological processes; however, accurately modeling divalent metal ions has proved a significant challenge for molecular dynamics force fields. Here we show that the choice of ion model influences the observed dynamics in PsaA, a metal binding protein from Streptococcus pneumoniae. We conduct extensive unbiased simulations and free energy calculations of PsaA bound to its cognate ligand Mn2+ and inhibitory ligand Zn2+ using three nonbonded ion models: a 12-6 model, a 12-6-4 model, and a multisite model. The observed coordination geometries and metal binding dynamics are sensitive to the choice of ion model, with the most dramatic differences observed in free energy calculations of ion release. We show that the conformational ensemble of Mn-bound PsaA is more similar to the crystallographic metal bound open state. This work extends the current model of PsaA metal binding and provides a framework for the rationalization of experimentally determined metal binding behavior. Our findings support the use of the 12-6-4 ion model for further simulations of divalent cation binding proteins.
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Affiliation(s)
- Hugo MacDermott-Opeskin
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Christopher A McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Megan L O'Mara
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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22
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Da-yang TE, Fifen JJ, Malloum A, Lahmar S, Nsangou M, Conradie J. Structures of the solvated copper(ii) ion in ammonia at various temperatures. NEW J CHEM 2020. [DOI: 10.1039/c9nj05169d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated theoretically the structures and relative stabilities of the solvated copper(ii) ion in ammonia, Cu2+(NH3)n, n = 1–10.
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Affiliation(s)
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Alhadji Malloum
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
- Department of Physics
| | - Souad Lahmar
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Tunis
- Tunisia
| | - Mama Nsangou
- University of Maroua
- Maroua
- Cameroon
- Department of Physics
- Faculty of Science
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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23
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Gupta M, Svendsen HF. Understanding Carbamate Formation Reaction Thermochemistry of Amino Acids as Solvents for Postcombustion CO 2 Capture. J Phys Chem B 2019; 123:8433-8447. [PMID: 31513397 DOI: 10.1021/acs.jpcb.9b06447] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The carbamate stability constant for a data set of 10 amino acids, having potential for being postcombustion CO2 capture (PCC) solvents, has been calculated using various implicit and explicit solvation shell models. This work also includes an extensive study of gas-phase free energy and enthalpy for the amino acid carbamate formation reaction with the Hartree Fock method, density functional methods [B3LYP/6-311++G(d,p)], and composite methods (G3MP2B3, G3MP2, CBS-QB3, and G4MP2). Ideal PCC solvent properties require finding a profitable tradeoff between various thermodynamic and system optimization parameters. Benchmark gaseous-phase and solution-phase thermodynamic properties given in this work can help in making informed decisions when choosing promising PCC solvents. The temperature dependency of the carbamate stability constant of amino acids is predicted using PCM and SM8T implicit solvation models. PCC is a temperature swing absorption-desorption process, and the high-temperature sensitivity of the ln KcAmCOO- value is of vital importance in attaining cost-efficient processes.
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Affiliation(s)
- Mayuri Gupta
- Department of Chemical Engineering , Norwegian University of Science and Technology , 7491 Trondheim , Norway
| | - Hallvard F Svendsen
- Department of Chemical Engineering , Norwegian University of Science and Technology , 7491 Trondheim , Norway
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24
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Coskuner O, Uversky VN. Intrinsically disordered proteins in various hypotheses on the pathogenesis of Alzheimer's and Parkinson's diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 166:145-223. [PMID: 31521231 DOI: 10.1016/bs.pmbts.2019.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Amyloid-β (Aβ) and α-synuclein (αS) are two intrinsically disordered proteins (IDPs) at the centers of the pathogenesis of Alzheimer's and Parkinson's diseases, respectively. Different hypotheses have been proposed for explanation of the molecular mechanisms of the pathogenesis of these two diseases, with these two IDPs being involved in many of these hypotheses. Currently, we do not know, which of these hypothesis is more accurate. Experiments face challenges due to the rapid conformational changes, fast aggregation processes, solvent and paramagnetic effects in studying these two IDPs in detail. Furthermore, pathological modifications impact their structures and energetics. Theoretical studies using computational chemistry and computational biology have been utilized to understand the structures and energetics of Aβ and αS. In this chapter, we introduce Aβ and αS in light of various hypotheses, and discuss different experimental and theoretical techniques that are used to study these two proteins along with their weaknesses and strengths. We suggest that a promising solution for studying Aβ and αS at the center of varying hypotheses could be provided by developing new techniques that link quantum mechanics, statistical mechanics, thermodynamics, bioinformatics to machine learning. Such new developments could also lead to development in experimental techniques.
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Affiliation(s)
- Orkid Coskuner
- Turkish-German University, Molecular Biotechnology, Istanbul, Turkey.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States; Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Moscow, Russia.
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25
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Nash A, Rhodes J. Simulations of CYP51A from Aspergillus fumigatus in a model bilayer provide insights into triazole drug resistance. Med Mycol 2019; 56:361-373. [PMID: 28992260 PMCID: PMC5895076 DOI: 10.1093/mmy/myx056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 07/14/2017] [Indexed: 11/26/2022] Open
Abstract
Azole antifungal drugs target CYP51A in Aspergillus fumigatus by binding with the active site of the protein, blocking ergosterol biosynthesis. Resistance to azole antifungal drugs is now common, with a leucine to histidine amino acid substitution at position 98 the most frequent, predominantly conferring resistance to itraconazole, although cross-resistance has been reported in conjunction with other mutations. In this study, we create a homology model of CYP51A using a recently published crystal structure of the paralog protein CYP51B. The derived structures, wild type, and L98H mutant are positioned within a lipid membrane bilayer and subjected to molecular dynamics simulations in order improve the accuracy of both models. The structural analysis from our simulations suggests a decrease in active site surface from the formation of hydrogen bonds between the histidine substitution and neighboring polar side chains, potentially preventing the binding of azole drugs. This study yields a biologically relevant structure and set of dynamics of the A. fumigatus Lanosterol 14 alpha-demethylase enzyme and provides further insight into azole antifungal drug resistance.
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Affiliation(s)
- Anthony Nash
- Department of Chemistry, University College London, London, United Kingdom
| | - Johanna Rhodes
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
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26
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Lunghi A, Sanvito S. A unified picture of the covalent bond within quantum-accurate force fields: From organic molecules to metallic complexes' reactivity. SCIENCE ADVANCES 2019; 5:eaaw2210. [PMID: 31172029 PMCID: PMC6544456 DOI: 10.1126/sciadv.aaw2210] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/17/2019] [Indexed: 06/01/2023]
Abstract
Computational studies of chemical processes taking place over extended size and time scales are inaccessible by electronic structure theories and can be tackled only by atomistic models such as force fields. These have evolved over the years to describe the most diverse systems. However, as we improve the performance of a force field for a particular physical/chemical situation, we are also moving away from a unified description. Here, we demonstrate that a unified picture of the covalent bond is achievable within the framework of machine learning-based force fields. Ridge regression, together with a representation of the atomic environment in terms of bispectrum components, can be used to map a general potential energy surface for molecular systems at chemical accuracy. This protocol sets the ground for the generation of an accurate and universal class of potentials for both organic and organometallic compounds with no specific assumptions on the chemistry involved.
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27
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Strodel B, Coskuner-Weber O. Transition Metal Ion Interactions with Disordered Amyloid-β Peptides in the Pathogenesis of Alzheimer's Disease: Insights from Computational Chemistry Studies. J Chem Inf Model 2019; 59:1782-1805. [PMID: 30933519 DOI: 10.1021/acs.jcim.8b00983] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Monomers and oligomers of the amyloid-β peptide aggregate to form the fibrils found in the brains of Alzheimer's disease patients. These monomers and oligomers are largely disordered and can interact with transition metal ions, affecting the mechanism and kinetics of amyloid-β aggregation. Due to the disordered nature of amyloid-β, its rapid aggregation, as well as solvent and paramagnetic effects, experimental studies face challenges in the characterization of transition metal ions bound to amyloid-β monomers and oligomers. The details of the coordination chemistry between transition metals and amyloid-β obtained from experiments remain debated. Furthermore, the impact of transition metal ion binding on the monomeric or oligomeric amyloid-β structures and dynamics are still poorly understood. Computational chemistry studies can serve as an important complement to experimental studies and can provide additional knowledge on the binding between amyloid-β and transition metal ions. Many research groups conducted first-principles calculations, ab initio molecular dynamics simulations, quantum mechanics/classical mechanics simulations, and classical molecular dynamics simulations for studying the interplay between transition metal ions and amyloid-β monomers and oligomers. This review summarizes the current understanding of transition metal interactions with amyloid-β obtained from computational chemistry studies. We also emphasize the current view of the coordination chemistry between transition metal ions and amyloid-β. This information represents an important foundation for future metal ion chelator and drug design studies aiming to combat Alzheimer's disease.
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Affiliation(s)
- Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich GmbH , Jülich 52425 , Germany.,Institute of Theoretical and Computational Chemistry , Heinrich Heine University Düsseldorf , Universitätstrasse 1 , Düsseldorf 40225 , Germany
| | - Orkid Coskuner-Weber
- Molecular Biotechnology , Turkish-German University , Sahinkaya Caddesi, No. 86, Beykoz , Istanbul 34820 , Turkey
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28
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Tomin M, Tomić S. Oxidase or peptidase? A computational insight into a putative aflatoxin oxidase from Armillariella tabescens. Proteins 2019; 87:390-400. [PMID: 30681192 DOI: 10.1002/prot.25661] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 01/04/2019] [Accepted: 01/22/2019] [Indexed: 01/05/2023]
Abstract
Aflatoxin oxidase (AFO), an enzyme isolated from Armillariella tabescens, has been reported to degrade aflatoxin B1 (AFB1). However, recent studies reported sequence and structure similarities with the dipeptidyl peptidase III (DPP III) family of enzymes and confirmed peptidase activity toward DPP III substrates. In light of these investigations, an extensive computational study was performed in order to improve understanding of the AFO functions. Steered MD simulations revealed long-range domain motions described as protein opening, characteristic for DPPs III and necessary for substrate binding. Newly identified open and partially open forms of the enzyme closely resemble those of the human DPP III orthologue. Docking of a synthetic DPP III substrate Arg2 -2-naphthylamide revealed a binding mode similar to the one found in crystal structures of human DPP III complexes with peptides with the S1 and S2 subsites' amino acid residues conserved. On the other hand, no energetically favorable AFB1 binding mode was detected, suggesting that aflatoxins are not good substrates of AFO. High plasticity of the zinc ion coordination sphere within the active site, consistent with that of up to date studied DPPs III, was observed as well. A detailed electrostatic analysis of the active site revealed a predominance of negatively charged regions, unsuitable for the binding of the neutral AFB1. The present study is in line with the most recent experimental study on this enzyme, both suggesting that AFO is a typical member of the DPP III family.
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Affiliation(s)
- Marko Tomin
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sanja Tomić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
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29
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Carvalho HF, Branco RJF, Leite FAS, Matzapetakis M, Roque ACA, Iranzo O. Hydrolytic zinc metallopeptides using a computational multi-state design approach. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01364d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combination of multi-state design and long-timescale conformational dynamics as a powerful strategy to obtain metalloenzymes.
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Affiliation(s)
- Henrique F. Carvalho
- UCIBIO
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
| | - Ricardo J. F. Branco
- UCIBIO
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
| | - Fábio A. S. Leite
- UCIBIO
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
| | - Manolis Matzapetakis
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- 2780-157 Oeiras
- Portugal
| | - A. Cecília A. Roque
- UCIBIO
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
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30
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Zuo Z, Liu J. Assessing the Performance of the Nonbonded Mg 2+ Models in a Two-Metal-Dependent Ribonuclease. J Chem Inf Model 2018; 59:399-408. [PMID: 30521334 DOI: 10.1021/acs.jcim.8b00627] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Magnesium ions (Mg2+), abundant in living cells, are essential for biomolecular structure, dynamics, and function. The biological importance of Mg2+ has motivated continuous development and improvement of various Mg2+ models for molecular dynamics (MD) simulations during the last decades. There are four types of nonbonded Mg2+ models: the point charge models based on a 12-6 or 12-6-4 type Lennard-Jones (LJ) potential, and the multisite models based on a 12-6 or 12-6-4 LJ potential. Here, we systematically assessed the performance of these four types of nonbonded Mg2+ models (21 models in total) in terms of maintaining a challenging intermediate state configuration captured in the structure of a prototypical two-metal-ion RNase H complex with an RNA/DNA hybrid. Our data demonstrate that the 12-6-4 multisite models, which account for charge-induced dipole interactions, perform the best in reproducing all the unique coordination modes in this intermediate state and maintaining the correct carboxylate denticity. Our benchmark work provides a useful guideline for MD simulations and structural refinement of Mg2+-containing biomolecular systems.
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Affiliation(s)
- Zhicheng Zuo
- Department of Pharmaceutical Sciences , University of North Texas System College of Pharmacy, University of North Texas Health Science Center , Fort Worth , Texas 76107 , United States
| | - Jin Liu
- Department of Pharmaceutical Sciences , University of North Texas System College of Pharmacy, University of North Texas Health Science Center , Fort Worth , Texas 76107 , United States
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31
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Prasetyo N, Hünenberger PH, Hofer TS. Single-Ion Thermodynamics from First Principles: Calculation of the Absolute Hydration Free Energy and Single-Electrode Potential of Aqueous Li + Using ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:6443-6459. [PMID: 30284829 DOI: 10.1021/acs.jctc.8b00729] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A recently proposed thermodynamic integration (TI) approach formulated in the framework of quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulations is applied to study the structure, dynamics, and absolute intrinsic hydration free energy Δs GM+,wat◦ of the Li+ ion at a correlated ab initio level of theory. Based on the results, standard values (298.15 K, ideal gas at 1 bar, ideal solute at 1 molal) for the absolute intrinsic hydration free energy [Formula: see text] of the proton, the surface electric potential jump χwat◦ upon entering bulk water, and the absolute single-electrode potential [Formula: see text] of the reference hydrogen electrode are calculated to be -1099.9 ± 4.2 kJ·mol-1, 0.13 ± 0.08 V, and 4.28 ± 0.04 V, respectively, in excellent agreement with the standard values recommended by Hünenberger and Reif on the basis of an extensive evaluation of the available experimental data (-1100 ± 5 kJ·mol-1, 0.13 ± 0.10 V, and 4.28 ± 0.13 V). The simulation results for Li+ are also compared to those for Na+ and K+ from a previous study in terms of relative hydration free energies ΔΔs GM+,wat◦ and relative electrode potentials [Formula: see text]. The calculated values are found to agree extremely well with the experimental differences in standard conventional hydration free energies ΔΔs GM+,wat• and redox potentials [Formula: see text]. The level of agreement between simulation and experiment, which is quantitative within error bars, underlines the substantial accuracy improvement achieved by applying a highly demanding QM/MM approach at the resolution-of-identity second-order Møller-Plesset perturbation (RIMP2) level over calculations relying on purely molecular mechanical or density functional theory (DFT) descriptions. A detailed analysis of the structural and dynamical properties of the Li+ hydrate indicates that a correct description of the solvation structure and dynamics is achieved as well at this level of theory. Consideration of the QM/MM potential-energy components also shows that the partitioning into QM and MM zones does not induce any significant energetic artifact for the system considered.
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Affiliation(s)
- Niko Prasetyo
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria.,Austria-Indonesia Centre (AIC) for Computational Chemistry , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia.,Department of Chemistry, Faculty of Mathematics and Natural Sciences , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie , ETH Zürich, ETH-Hönggerberg , HCI Building , CH-8093 Zürich , Switzerland
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria
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32
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Coskuner-Weber O. Revisiting Cu(II) Bound Amyloid-β40 and Amyloid-β42 Peptides: Varying Coordination Chemistries. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2018. [DOI: 10.18596/jotcsa.424144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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33
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Maurer D, Enugala TR, Hamnevik E, Bauer P, Lüking M, Petrović D, Hillier H, Kamerlin SCL, Dobritzsch D, Widersten M. Stereo- and Regioselectivity in Catalyzed Transformation of a 1,2-Disubstituted Vicinal Diol and the Corresponding Diketone by Wild Type and Laboratory Evolved Alcohol Dehydrogenases. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01762] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Dirk Maurer
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Thilak Reddy Enugala
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Emil Hamnevik
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Paul Bauer
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
- Biophysics, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden
| | - Malin Lüking
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Dušan Petrović
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Heidi Hillier
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Shina C. L. Kamerlin
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Doreen Dobritzsch
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Mikael Widersten
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
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34
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Hofer TS, Hünenberger PH. Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration. J Chem Phys 2018; 148:222814. [DOI: 10.1063/1.5000799] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Centre for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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35
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Maršavelski A, Petrović D, Bauer P, Vianello R, Kamerlin SCL. Empirical Valence Bond Simulations Suggest a Direct Hydride Transfer Mechanism for Human Diamine Oxidase. ACS OMEGA 2018; 3:3665-3674. [PMID: 30023875 PMCID: PMC6044848 DOI: 10.1021/acsomega.8b00346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
Diamine oxidase (DAO) is an enzyme involved in the regulation of cell proliferation and the immune response. This enzyme performs oxidative deamination in the catabolism of biogenic amines, including, among others, histamine, putrescine, spermidine, and spermine. The mechanistic details underlying the reductive half-reaction of the DAO-catalyzed oxidative deamination which leads to the reduced enzyme cofactor and the aldehyde product are, however, still under debate. The catalytic mechanism was proposed to involve a prototropic shift from the substrate-Schiff base to the product-Schiff base, which includes the rate-limiting cleavage of the Cα-H bond by the conserved catalytic aspartate. Our detailed mechanistic study, performed using a combined quantum chemical cluster approach with empirical valence bond simulations, suggests that the rate-limiting cleavage of the Cα-H bond involves direct hydride transfer to the topaquinone cofactor-a mechanism that does not involve the formation of a Schiff base. Additional investigation of the D373E and D373N variants supported the hypothesis that the conserved catalytic aspartate is indeed essential for the reaction; however, it does not appear to serve as the catalytic base, as previously suggested. Rather, the electrostatic contributions of the most significant residues (including D373), together with the proximity of the Cu2+ cation to the reaction site, lower the activation barrier to drive the chemical reaction.
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Affiliation(s)
- Aleksandra Maršavelski
- Computational
Organic Chemistry and Biochemistry Group, Division of Organic Chemistry
and Biochemistry, Ruđer Bošković
Institute, Bijenička
cesta 54, 10000 Zagreb, Croatia
- Department
of Chemistry, Faculty of Science, University
of Zagreb, Horvatovac
102a, 10000 Zagreb, Croatia
- Department
of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Dušan Petrović
- Department
of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Paul Bauer
- Department
of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
- Department
of Biophysics, SciLifeLab, KTH Royal Institute
of Technology, S-10691 Stockholm, Sweden
| | - Robert Vianello
- Computational
Organic Chemistry and Biochemistry Group, Division of Organic Chemistry
and Biochemistry, Ruđer Bošković
Institute, Bijenička
cesta 54, 10000 Zagreb, Croatia
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36
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Petrović D, Szeler K, Kamerlin SCL. Challenges and advances in the computational modeling of biological phosphate hydrolysis. Chem Commun (Camb) 2018; 54:3077-3089. [PMID: 29412205 DOI: 10.1039/c7cc09504j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphate ester hydrolysis is fundamental to many life processes, and has been the topic of substantial experimental and computational research effort. However, even the simplest of phosphate esters can be hydrolyzed through multiple possible pathways that can be difficult to distinguish between, either experimentally, or computationally. Therefore, the mechanisms of both the enzymatic and non-enzymatic reactions have been historically controversial. In the present contribution, we highlight a number of technical issues involved in reliably modeling these computationally challenging reactions, as well as proposing potential solutions. We also showcase examples of our own work in this area, discussing both the non-enzymatic reaction in aqueous solution, as well as insights obtained from the computational modeling of organophosphate hydrolysis and catalytic promiscuity amongst enzymes that catalyze phosphoryl transfer.
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Affiliation(s)
- Dušan Petrović
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
| | - Klaudia Szeler
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
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37
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Martín EI, Sánchez-Coronilla A, Navas J, Gómez-Villarejo R, Gallardo JJ, Alcántara R, Fernández-Lorenzo C. Unraveling the role of the base fluid arrangement in metal-nanofluids used to enhance heat transfer in concentrating solar power plants. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2017.12.153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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Barrozo A, Liao Q, Esguerra M, Marloie G, Florián J, Williams NH, Kamerlin SCL. Computer simulations of the catalytic mechanism of wild-type and mutant β-phosphoglucomutase. Org Biomol Chem 2018; 16:2060-2073. [DOI: 10.1039/c8ob00312b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
β-Phosphoglucomutase (β-PGM) has served as an important model system for understanding biological phosphoryl transfer.
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Affiliation(s)
- Alexandre Barrozo
- Science for Life Laboratory
- Department of Cell and Molecular Biology
- Uppsala University
- S-75124 Uppsala
- Sweden
| | - Qinghua Liao
- Science for Life Laboratory
- Department of Cell and Molecular Biology
- Uppsala University
- S-75124 Uppsala
- Sweden
| | - Mauricio Esguerra
- Science for Life Laboratory
- Department of Cell and Molecular Biology
- Uppsala University
- S-75124 Uppsala
- Sweden
| | - Gaël Marloie
- Science for Life Laboratory
- Department of Cell and Molecular Biology
- Uppsala University
- S-75124 Uppsala
- Sweden
| | - Jan Florián
- Department of Chemistry and Biochemistry
- Loyola University Chicago
- Chicago
- USA
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39
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Liao Q, Pabis A, Strodel B, Kamerlin SCL. Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions. J Phys Chem Lett 2017; 8:5408-5414. [PMID: 29022713 PMCID: PMC5672556 DOI: 10.1021/acs.jpclett.7b02358] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/12/2017] [Indexed: 05/28/2023]
Abstract
Modeling metalloproteins often requires classical molecular dynamics (MD) simulations in order to capture their relevant motions, which in turn necessitates reliable descriptions of the metal centers involved. One of the most successful approaches to date is provided by the "cationic dummy model", where the positive charge of the metal ion is transferred toward dummy particles that are bonded to the central metal ion in a predefined coordination geometry. While this approach allows for ligand exchange, and captures the correct electrostatics as demonstrated for different divalent metal ions, current dummy models neglect ion-induced dipole interactions. In the present work, we resolve this weakness by taking advantage of the recently introduced 12-6-4 type Lennard-Jones potential to include ion-induced dipole interactions. We revise our previous dummy model for Mg2+ and demonstrate that the resulting model can simultaneously reproduce the experimental solvation free energy and metal-ligand distances without the need for artificial restraints or bonds. As ion-induced dipole interactions become particularly important for highly charged metal ions, we develop dummy models for the biologically relevant ions Al3+, Fe3+, and Cr3+. Finally, the effectiveness of our new models is demonstrated in MD simulations of several diverse (and highly challenging to simulate) metalloproteins.
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Affiliation(s)
- Qinghua Liao
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, Uppsala 75124, Sweden
| | - Anna Pabis
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, Uppsala 75124, Sweden
| | - Birgit Strodel
- Institute
of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute
of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Shina Caroline Lynn Kamerlin
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, Uppsala 75124, Sweden
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40
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Zhang H, Jiang Y, Yan H, Cui Z, Yin C. Comparative Assessment of Computational Methods for Free Energy Calculations of Ionic Hydration. J Chem Inf Model 2017; 57:2763-2775. [DOI: 10.1021/acs.jcim.7b00485] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haiyang Zhang
- Department
of Biological Science and Engineering, School of Chemistry and Biological
Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yang Jiang
- Beijing
Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Box 53, 100029 Beijing, China
| | - Hai Yan
- Department
of Biological Science and Engineering, School of Chemistry and Biological
Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Ziheng Cui
- Beijing
Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Box 53, 100029 Beijing, China
| | - Chunhua Yin
- Department
of Biological Science and Engineering, School of Chemistry and Biological
Engineering, University of Science and Technology Beijing, 100083 Beijing, China
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41
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Zhang H, Jiang Y, Yan H, Yin C, Tan T, van der Spoel D. Free-Energy Calculations of Ionic Hydration Consistent with the Experimental Hydration Free Energy of the Proton. J Phys Chem Lett 2017; 8:2705-2712. [PMID: 28561580 DOI: 10.1021/acs.jpclett.7b01125] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Computational free-energy correction strategies and the choice of experimental proton hydration free energy, ΔGs*(H+), are analyzed to investigate the apparent controversy in experimental thermodynamics of ionic hydration. Without corrections, the hydration free-energy (ΔGhyd) calculations match experiments with ΔGs*(H+) = -1064 kJ/mol as reference. Using the Galvani surface potential the resulting (real) ΔGhyd are consistent with ΔGs*(H+) = -1098 kJ/mol. When applying, in an ad hoc manner, the discrete solvent correction, ΔGhyd matching the "consensus" ΔGs*(H+) of -1112 kJ/mol are obtained. This analysis rationalizes reports on ΔGhyd calculations for ions using different experimental references. For neutral amino acid side chains ΔGhyd are independent of the water model, whereas there are large differences in ΔGhyd due to the water model for charged species, suggesting that long-range ordering of water around ions yields an important contribution to the ΔGhyd. These differences are reduced significantly when applying consistent corrections, but to obtain the most accurate results it is recommended to use the water model belonging to the force field.
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Affiliation(s)
- Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing , 100083 Beijing, China
| | - Yang Jiang
- Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Box 53, 100029 Beijing, China
| | - Hai Yan
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing , 100083 Beijing, China
| | - Chunhua Yin
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing , 100083 Beijing, China
| | - Tianwei Tan
- Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Box 53, 100029 Beijing, China
| | - David van der Spoel
- Uppsala Center for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
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42
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Masetti M, Musiani F, Bernetti M, Falchi F, Cavalli A, Ciurli S, Recanatini M. Development of a multisite model for Ni(II) ion in solution from thermodynamic and kinetic data. J Comput Chem 2017; 38:1834-1843. [PMID: 28558120 DOI: 10.1002/jcc.24827] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/12/2017] [Accepted: 04/14/2017] [Indexed: 12/14/2022]
Abstract
Force-field parameters are developed for a multisite model of Ni(II) ions to be used in molecular dynamics simulations combined to enhanced sampling methods. The performances of two charge-partitioning schemes are validated by taking into account structural, thermodynamic, and kinetic observables. One of the two models, featuring partial charges on the dummy atoms only, matches both Ni(II) free energy of solvation and water exchange rates. Such model is particularly suited to study complexation events at a fully dynamic description. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Matteo Masetti
- Laboratory of Computational Medicinal Chemistry, Department of Pharmacy and Biotechnology, Alma Mater Studiorum - Università di Bologna, Via Belmeloro 6, Bologna, I-40126, Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, Alma Mater Studiorum - Università di Bologna, Viale G. Fanin 40, Bologna, I-40127, Italy
| | - Mattia Bernetti
- Laboratory of Computational Medicinal Chemistry, Department of Pharmacy and Biotechnology, Alma Mater Studiorum - Università di Bologna, Via Belmeloro 6, Bologna, I-40126, Italy
- Compunet, Istituto Italiano di Tecnologia, Via Morego 30, Genova, I-16163, Italy
| | - Federico Falchi
- Compunet, Istituto Italiano di Tecnologia, Via Morego 30, Genova, I-16163, Italy
| | - Andrea Cavalli
- Laboratory of Computational Medicinal Chemistry, Department of Pharmacy and Biotechnology, Alma Mater Studiorum - Università di Bologna, Via Belmeloro 6, Bologna, I-40126, Italy
- Compunet, Istituto Italiano di Tecnologia, Via Morego 30, Genova, I-16163, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, Alma Mater Studiorum - Università di Bologna, Viale G. Fanin 40, Bologna, I-40127, Italy
| | - Maurizio Recanatini
- Laboratory of Computational Medicinal Chemistry, Department of Pharmacy and Biotechnology, Alma Mater Studiorum - Università di Bologna, Via Belmeloro 6, Bologna, I-40126, Italy
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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44
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Ye H, Su Z, Tang F, Wang M, Chen G, Wang J, Xu S. Excitation Dependent Phosphorous Property and New Model of the Structured Green Luminescence in ZnO. Sci Rep 2017; 7:41460. [PMID: 28150699 PMCID: PMC5288693 DOI: 10.1038/srep41460] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/13/2016] [Indexed: 11/24/2022] Open
Abstract
The copper induced green luminescence (GL) with two sets of fine structures in ZnO crystal has been found for several decades (i.e., R. Dingle, Phys. Rev. Lett. 23, 579 (1969)), but the physical origin of the doublet still remains as an open question up to now. In this paper, we provide new insight into the mechanism of the structured GL band in terms of new experimental findings and theoretical calculations. It is found, for the first time, that the GL signal exhibits persistent afterglow for tens of minutes after the switch-off of below-band-gap excitation light but it cannot occur under above-band-gap excitation. Such a phosphorous property may be interpreted as de-trapping and feeding of electrons from a shallow trapping level via the conduction band to the Cu-related luminescence centers where the Cu3+ ion is proposed to work as the final state of the GL emission. From first-principles calculation, such a Cu3+ ion in wurtzite ZnO prefers a high spin 3d8 state with two non-degenerated half-filled orbitals due to the Jahn-Teller effect, probably leading to the double structures in photoluminescence spectrum. Therefore, this model gives a comprehensively new understanding on the mechanism of the structured GL band in ZnO.
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Affiliation(s)
- Honggang Ye
- Department of Physics, Shenzhen Institute of Research and Innovation, The University of Hong Kong, Pokfulam Road, Hong Kong, China.,Department of Applied Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zhicheng Su
- Department of Physics, Shenzhen Institute of Research and Innovation, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Fei Tang
- Department of Physics, Shenzhen Institute of Research and Innovation, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Mingzheng Wang
- Department of Physics, Shenzhen Institute of Research and Innovation, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Guangde Chen
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jian Wang
- Department of Physics, Shenzhen Institute of Research and Innovation, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Shijie Xu
- Department of Physics, Shenzhen Institute of Research and Innovation, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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45
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Liao Q, Owen MC, Olubiyi OO, Barz B, Strodel B. Conformational Transitions of the Amyloid-β Peptide Upon Copper(II) Binding and pH Changes. Isr J Chem 2017. [DOI: 10.1002/ijch.201600108] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Qinghua Liao
- Institute of Complex Systems: Structural Biochemistry (ICS-6); Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Michael C. Owen
- Institute of Complex Systems: Structural Biochemistry (ICS-6); Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Olujide O. Olubiyi
- Department of Pharmacology and Therapeutics; College of Medicine and Health Sciences; Afe Babalola University; Nigeria
| | - Bogdan Barz
- Institute of Complex Systems: Structural Biochemistry (ICS-6); Forschungszentrum Jülich GmbH; 52425 Jülich Germany
- Institute of Theoretical and Computational Chemistry; Heinrich Heine University Düsseldorf; 40225 Düsseldorf Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6); Forschungszentrum Jülich GmbH; 52425 Jülich Germany
- Institute of Theoretical and Computational Chemistry; Heinrich Heine University Düsseldorf; 40225 Düsseldorf Germany
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46
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Wallin C, Kulkarni YS, Abelein A, Jarvet J, Liao Q, Strodel B, Olsson L, Luo J, Abrahams JP, Sholts SB, Roos PM, Kamerlin SCL, Gräslund A, Wärmländer SKTS. Characterization of Mn(II) ion binding to the amyloid-β peptide in Alzheimer's disease. J Trace Elem Med Biol 2016; 38:183-193. [PMID: 27085215 DOI: 10.1016/j.jtemb.2016.03.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 03/17/2016] [Indexed: 12/28/2022]
Abstract
Growing evidence links neurodegenerative diseases to metal exposure. Aberrant metal ion concentrations have been noted in Alzheimer's disease (AD) brains, yet the role of metals in AD pathogenesis remains unresolved. A major factor in AD pathogenesis is considered to be aggregation of and amyloid formation by amyloid-β (Aβ) peptides. Previous studies have shown that Aβ displays specific binding to Cu(II) and Zn(II) ions, and such binding has been shown to modulate Aβ aggregation. Here, we use nuclear magnetic resonance (NMR) spectroscopy to show that Mn(II) ions also bind to the N-terminal part of the Aβ(1-40) peptide, with a weak binding affinity in the milli- to micromolar range. Circular dichroism (CD) spectroscopy, solid state atomic force microscopy (AFM), fluorescence spectroscopy, and molecular modeling suggest that the weak binding of Mn(II) to Aβ may not have a large effect on the peptide's aggregation into amyloid fibrils. However, identification of an additional metal ion displaying Aβ binding reveals more complex AD metal chemistry than has been previously considered in the literature.
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Affiliation(s)
- Cecilia Wallin
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Yashraj S Kulkarni
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, 751 24 Uppsala, Sweden
| | - Axel Abelein
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden; Department of Neurobiology, Care Sciences and Society (NVS), H1, Division of Neurogeriatrics, Karolinska Institutet, Novum Pl 5 14157 Huddinge, Stockholm, Sweden
| | - Jüri Jarvet
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden; The National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Qinghua Liao
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, Jülich, 52425, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, Jülich, 52425, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Lisa Olsson
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Jinghui Luo
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden; Chemical Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Jan Pieter Abrahams
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland; Laboratory of Biomolecular Research, Paul Scherrer Institute, Department of Biology and Chemistry, OFLC/102CH-5232 Villigen PSI, Switzerland
| | - Sabrina B Sholts
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden; Department of Anthropology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC 20013, USA
| | - Per M Roos
- Institute of Environmental Medicine, Karolinska Institutet, Nobels väg 13, 171 77 Stockholm, Sweden; Department of Clinical Physiology, Capio St.Göran Hospital, St.Göransplan 1, 112 19 Stockholm, Sweden
| | - Shina C L Kamerlin
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, 751 24 Uppsala, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Sebastian K T S Wärmländer
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden.
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47
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Purg M, Pabis A, Baier F, Tokuriki N, Jackson C, Kamerlin SCL. Probing the mechanisms for the selectivity and promiscuity of methyl parathion hydrolase. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2016.0150. [PMID: 27698033 PMCID: PMC5052733 DOI: 10.1098/rsta.2016.0150] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/01/2016] [Indexed: 05/27/2023]
Abstract
Diverse organophosphate hydrolases have convergently evolved the ability to hydrolyse man-made organophosphates. Thus, these enzymes are attractive model systems for studying the factors shaping enzyme functional evolution. Methyl parathion hydrolase (MPH) is an enzyme from the metallo-β-lactamase superfamily, which hydrolyses a wide range of organophosphate, aryl ester and lactone substrates. In addition, MPH demonstrates metal-ion-dependent selectivity patterns. The origins of this remain unclear, but are linked to open questions about the more general role of metal ions in functional evolution and divergence within enzyme superfamilies. Here, we present detailed mechanistic studies of the paraoxonase and arylesterase activities of MPH complexed with five different transition metal ions, and demonstrate that the hydrolysis reactions proceed via similar pathways and transition states. However, while it is possible to discern a clear structural origin for the selectivity between different substrates, the selectivity between different metal ions appears to lie instead in the distinct electrostatic properties of the metal ions themselves, which causes subtle changes in transition state geometries and metal-metal distances at the transition state rather than significant structural changes in the active site. While subtle, these differences can be significant for shaping the metal-ion-dependent activity patterns observed for this enzyme.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.
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Affiliation(s)
- Miha Purg
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala 75124, Sweden
| | - Anna Pabis
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala 75124, Sweden
| | - Florian Baier
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, Canada V6T 1Z4
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, Canada V6T 1Z4
| | - Colin Jackson
- Research School of Chemistry, Building 138, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala 75124, Sweden
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48
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Pietra F. On Dioxygen Permeation of MaL Laccase from the Thermophilic Fungus Melanocarpus albomyces: An all-Atom Molecular Dynamics Investigation. Chem Biodivers 2016; 13:1493-1501. [DOI: 10.1002/cbdv.201600062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/09/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Francesco Pietra
- Accademia Lucchese di Scienze, Lettere e Arti, Classe di Scienze; Palazzo Pretorio IT-55100 Lucca
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49
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Tiiman A, Luo J, Wallin C, Olsson L, Lindgren J, Jarvet J, Per R, Sholts SB, Rahimipour S, Abrahams JP, Karlström AE, Gräslund A, Wärmländer SK. Specific Binding of Cu(II) Ions to Amyloid-Beta Peptides Bound to Aggregation-Inhibiting Molecules or SDS Micelles Creates Complexes that Generate Radical Oxygen Species. J Alzheimers Dis 2016; 54:971-982. [DOI: 10.3233/jad-160427] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ann Tiiman
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Sweden
| | - Jinghui Luo
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Sweden
- Chemical Research Laboratory, University of Oxford, UK
| | - Cecilia Wallin
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Sweden
| | - Lisa Olsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Sweden
| | | | - Jϋri Jarvet
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Sweden
- The National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Roos Per
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Physiology, Capio St.Göran Hospital, Stockholm, Sweden
| | - Sabrina B. Sholts
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Sweden
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Shai Rahimipour
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, Israel
| | - Jan Pieter Abrahams
- Biozentrum, University of Basel, Switzerland & Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | | | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Sweden
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50
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Jiang Y, Zhang H, Tan T. Rational Design of Methodology-Independent Metal Parameters Using a Nonbonded Dummy Model. J Chem Theory Comput 2016; 12:3250-60. [DOI: 10.1021/acs.jctc.6b00223] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yang Jiang
- Beijing
Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Haiyang Zhang
- Department
of Biological Science and Engineering, School of Chemistry and Biological
Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Tianwei Tan
- Beijing
Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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