1
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Ruscic B, Bross DH. Accurate and reliable thermochemistry by data analysis of complex thermochemical networks using Active Thermochemical Tables: the case of glycine thermochemistry. Faraday Discuss 2024. [PMID: 39300834 DOI: 10.1039/d4fd00110a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Active Thermochemical Tables (ATcT) were successfully used to resolve the existing inconsistencies related to the thermochemistry of glycine, based on statistically analyzing and solving a thermochemical network that includes >3350 chemical species interconnected by nearly 35 000 thermochemically-relevant determinations from experiment and high-level theory. The current ATcT results for the 298.15 K enthalpies of formation are -394.70 ± 0.55 kJ mol-1 for gas phase glycine, -528.37 ± 0.20 kJ mol-1 for solid α-glycine, -528.05 ± 0.22 kJ mol-1 for β-glycine, -528.64 ± 0.23 kJ mol-1 for γ-glycine, -514.22 ± 0.20 kJ mol-1 for aqueous undissociated glycine, and -470.09 ± 0.20 kJ mol-1 for fully dissociated aqueous glycine at infinite dilution. In addition, a new set of thermophysical properties of gas phase glycine was obtained from a fully corrected nonrigid rotor anharmonic oscillator (NRRAO) partition function, which includes all conformers. Corresponding sets of thermophysical properties of α-, β-, and γ-glycine are also presented.
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Affiliation(s)
- Branko Ruscic
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois, USA.
| | - David H Bross
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois, USA.
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2
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Sabolović J. Bis(amino acidato)copper(II) compounds in blood plasma: a review of computed structural properties and amino acid affinities for Cu 2+ informing further pharmacological research. Arh Hig Rada Toksikol 2024; 75:159-171. [PMID: 39369326 DOI: 10.2478/aiht-2024-75-3871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 06/01/2024] [Indexed: 10/07/2024] Open
Abstract
Neutral bis(amino acidato)copper(II) [Cu(aa)2] coordination compounds are the physiological species of copper(II) amino acid compounds in blood plasma taking the form of bis(l-histidinato)copper(II) and mixed ternary copper(II)-l-histidine complexes, preferably with l-glutamine, l-threonine, l-asparagine, and l-cysteine. These amino acids have three functional groups that can bind metal ions: the common α-amino and carboxylate groups and a side-chain polar group. In Cu(aa)2, two coordinating groups per amino acid bind to copper(II) in-plane, while the third group can bind apically, which yields many possibilities for axial and planar bonds, that is, for bidentate and tridentate binding. So far, the experimental studies of physiological Cu(aa)2 compounds in solutions have not specified their complete geometries. This paper provides a brief review of my group's research on structural properties of physiological Cu(aa)2 calculated using the density functional theory (DFT) to locate low-energy conformers that can coexist in aqueous solutions. These DFT investigations have revealed high conformational flexibility of ternary Cu(aa)2 compounds for tridentate or bidentate chelation, which may explain copper(II) exchange reactions in the plasma and inform the development of small multifunctional copper(II)-binding drugs with several possible copper(II)-binding groups. Furthermore, our prediction of metal ion affinities for Cu2+ binding with amino-acid ligands in low-energy conformers with different coordination modes of five physiological Cu(aa)2 in aqueous solution supports the findings of their abundance in human plasma obtained with chemical speciation modelling.
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Affiliation(s)
- Jasmina Sabolović
- Institute for Medical Research and Occupational Health, Division of Occupational and Environmental Health, Zagreb, Croatia
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3
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Ramek M, Sabolović J. Structure prediction of physiological bis(amino acidato)copper(II) species in aqueous solution: The copper(II) compounds with l-glutamine and l-histidine. J Inorg Biochem 2024; 251:112430. [PMID: 38006660 DOI: 10.1016/j.jinorgbio.2023.112430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 11/27/2023]
Abstract
Neutral (l-histidinato)(l-glutaminato)copper(II) [Cu(His)(Gln)] has been established as the most abundant ternary copper(II) amino acid compound of the exchangeable copper(II) pool in blood plasma. The experimental studies of Cu(His)(Gln) and bis(glutaminato)copper(II) [Cu(Gln)2] in solutions did not specify their complete geometries. To determine the geometries, this paper investigates the conformers, energy landscapes, and a structure-magnetic parameters relation of Cu(Gln)2 and Cu(His)(Gln) by the density functional theory (DFT) calculations. We assume a glycine-like coordination of Gln (other coordination patterns are dismissed because of steric reasons), and three His in-plane copper(II) binding modes. The conformational analyses are performed in the gas phase and implicitly modeled aqueous solution. The reliability of the DFT relative electronic and Gibbs free energies of the Cu(His)(Gln) conformers is confirmed by benchmarking against the corresponding energies obtained by the domain-based local pair natural orbital coupled-cluster method with singles, doubles, and perturbative triples [DLPNO-CCSD(T)]. Several cis- and trans-Cu(His)(Gln) conformers with His in the histaminate-like and glycine-like modes have low Gibbs free energies, and the greatest estimated metal-binding affinities. The DFT-calculated magnetic parameters of the low-energy conformers reproduce best the experimental electron paramagnetic resonance parameters measured in aqueous solutions for trans- and cis-Cu(Gln)2 conformers having two oxygen atoms (either from Gln or water molecules) at the apical positions, and Cu(His)(Gln) conformers having His in the histaminate-like mode with an apically placed carboxylato oxygen atom. The predicted conformational flexibility of His‑copper(II)-amino acid compounds may be connected with their physiological abundance, and the role in copper(II) exchange reactions in blood plasma.
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Affiliation(s)
- Michael Ramek
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Jasmina Sabolović
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, HR-10000 Zagreb, Croatia.
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4
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Milach OA, Naidenov VE, Karankevich EG, Yurkova IL. Glycine and Histidine in Regulation of Free-Radical Dephosphorylation of Glycerol Phosphate in the Presence of Cu2+(Fe2+) Ions. RUSS J GEN CHEM+ 2022. [DOI: 10.1134/s107036322202013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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5
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Chetry N, Gomti Devi T, Karlo T. Synthesis and characterization of metal complex amino acid using spectroscopic methods and theoretical calculation. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131670] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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6
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Ganesan M, Paranthaman S. DISPERSION-CORRECTED DENSITY FUNCTIONAL THEORY STUDIES ON GLYCOLIC ACID-METAL COMPLEXES. J STRUCT CHEM+ 2021. [DOI: 10.1134/s0022476621080023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Ramek M, Pejić J, Sabolović J. Structure prediction of neutral physiological copper(II) compounds with l-cysteine and l-histidine. J Inorg Biochem 2021; 223:111536. [PMID: 34274876 DOI: 10.1016/j.jinorgbio.2021.111536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/19/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
Bis(aminoacidato)copper(II) [CuII(aa)2] coordination compounds are the physiological species of copper(II) amino acid compounds in blood plasma. Since there are no experimental data in the literature about the geometries that physiological CuII(aa)2 could form with l-cysteine (Cys), that is, for bis(l-cysteinato)copper(II) [Cu(Cys)2] and the ternary (l-histidinato)(l-cysteinato)copper(II) [Cu(His)(Cys)], this paper computationally examines the possible conformations that the two compounds could form with the Cys ligand having a protonated sulfur, as in the conventional zwitterion, which was determined to be prevailing in aqueous solution. These two amino acids can bind metals in a tridentate fashion and thus form many possible coordination patterns. Density functional calculations were performed for the conformational analyses in the gas phase and in implicitly modeled aqueous solution using a polarizable continuum model. Additionally, we examine which coordination mode, with thiol or thiolate group, is more stable. The Cys coordination via the amino N and carboxylato O atoms (a glycinato mode) is obtained as the most stable one in aqueous Cu(Cys)2, and also in Cu(His)(Cys) when the His glycinato or histaminato mode combines with the intact thiol group. Whereas the conformers with N and thiol S as the copper(II) donor atoms are predicted to be the least stable, those with the Cu-N and Cu-S(thiolate) bonding (and protonated carboxylato group) are the most stable. The differences are explained by different covalent and ionic contributions of Cu-S(thiol) vs. Cu-S(thiolate). The study can contribute to the insight into formation and reactivity of the copper(II) cysteinato complexes in solution.
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Affiliation(s)
- Michael Ramek
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Jelena Pejić
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, HR-10000 Zagreb, Croatia
| | - Jasmina Sabolović
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, HR-10000 Zagreb, Croatia.
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8
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Borah B, Devi TG. Characterization of Zn (l-Proline)2 complex using spectroscopic techniques and DFT analysis. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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9
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Comprehensive understanding of multiple binding of D-penicillamine with Cu2+-hexa aqua complex: a DFT approach. Struct Chem 2019. [DOI: 10.1007/s11224-019-01365-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Khalili B, Rimaz M. Interaction of l-proline with group IIB (Zn2+, Cd2+, Hg2+) metal cations in the gas and aqueous phases: a quantum computational study. CAN J CHEM 2016. [DOI: 10.1139/cjc-2015-0616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The gas and aqueous phase complexation geometries, electronic interactions, and metal ion affinities of Zn2+, Cd2+, and Hg2+ metal cations with the two most stable conformations of l-proline complexes were studied. The complexes were optimized by density functional theory (B3LYP) using the 6-311++G(d,p) orbital basis set and relativistic pseudopotentials for the metal cations. The interactions of the metal cations at different nucleophilic sites of l-proline were considered as were three modes of interactions including salt bridged, charge solvated 1, and charge solvated 2, which are indicative of binding in a bidentate manner through the carboxylate group, carbonyl and hydroxyl oxygen, and carbonyl oxygen and the nitrogen atom of l-proline. All of the coordination patterns were characterized by both charge transfer and ionic interactions between l-proline and the metal cation. The metal ion affinity (MIA) and interaction energy were also computed for all of the complexes at both the gas and aqueous phases. Results showed that the order of MIA at the gas and aqueous phases are different. MIA order at the gas phase was in the order of Zn2+ > Hg2+ > Cd2+ whereas at the aqueous phase, the order of Zn2+ > Cd2+ > Hg2+ was obtained for MIA. The infrared stretching vibrational modes of the N–H and O–H groups of free l-proline were compared with l-proline–M2+ in both CS1 and CS2 coordination patterns at the gas phase and results showed a considerable shift to lower frequency during complexation process.
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Affiliation(s)
- Behzad Khalili
- Department of Chemistry, Faculty of Sciences, University of Guilan, P.O. Box 41335-1914 Rasht, Iran
| | - Mehdi Rimaz
- Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran, Iran
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11
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Ash T, Debnath T, Banu T, Das AK. Exploration of Binding Interactions of Cu2+ with d-Penicillamine and its O- and Se- Analogues in Both Gas and Aqueous Phases: A Theoretical Approach. J Phys Chem B 2016; 120:3467-78. [DOI: 10.1021/acs.jpcb.5b11825] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tamalika Ash
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Tanay Debnath
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Tahamida Banu
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Abhijit K. Das
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
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12
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Umadevi P, Senthilkumar L. Metal-interacted histidine dimer: an ETS-NOCV and XANES study. RSC Adv 2016. [DOI: 10.1039/c6ra01264g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have analyzed the metal coordination in a histidine dimer, hydrated with a water molecule, based on the extended transition state scheme with the theory of natural orbitals for chemical valence (ETS-NOCV).
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Affiliation(s)
- P. Umadevi
- Department of Physics
- Bharathiar University
- Coimbatore
- India
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13
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Mandal S, Das G, Askari H. A combined experimental and quantum mechanical investigation on some selected metal complexes of l-serine with first row transition metal cations. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2014.10.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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14
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15
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Fedotova MV, Kruchinin SE. Ion-binding of glycine zwitterion with inorganic ions in biologically relevant aqueous electrolyte solutions. Biophys Chem 2014; 190-191:25-31. [DOI: 10.1016/j.bpc.2014.04.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/02/2014] [Accepted: 04/02/2014] [Indexed: 11/29/2022]
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16
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The effect of thiourea, l(−) cysteine and glycine additives on the mechanisms and kinetics of copper electrodeposition. J APPL ELECTROCHEM 2013. [DOI: 10.1007/s10800-013-0596-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Ansbacher T, Chourasia M, Shurki A. Copper-chaperones with dicoordinated Cu(I)-Unique protection mechanism. Proteins 2013; 81:1411-9. [DOI: 10.1002/prot.24291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/04/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Tamar Ansbacher
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Lise-Meitner Minerva Center for Computational Quantum Chemistry; The Hebrew University of Jerusalem; Jerusalem; 91120; Israel
| | - Mukesh Chourasia
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Lise-Meitner Minerva Center for Computational Quantum Chemistry; The Hebrew University of Jerusalem; Jerusalem; 91120; Israel
| | - Avital Shurki
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Lise-Meitner Minerva Center for Computational Quantum Chemistry; The Hebrew University of Jerusalem; Jerusalem; 91120; Israel
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18
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Latrous L, Tortajada J, Haldys V, Léon E, Correia C, Salpin JY. Gas-phase interactions of organotin compounds with glycine. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:795-806. [PMID: 23832935 DOI: 10.1002/jms.3223] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 03/08/2013] [Accepted: 04/22/2013] [Indexed: 06/02/2023]
Abstract
Gas-phase interactions of organotins with glycine have been studied by combining mass spectrometry experiments and quantum calculations. Positive-ion electrospray spectra show that the interaction of di- and tri-organotins with glycine results in the formation of [(R)2Sn(Gly)-H](+) and [(R)3Sn(Gly)](+) ions, respectively. Di-organotin complexes appear much more reactive than those involving tri-organotins. (MS/MS) spectra of the [(R)3Sn(Gly)](+) ions are indeed simple and only show elimination of intact glycine, generating the [(R)3Sn](+) carbocation. On the other hand, MS/MS spectra of [(R)2Sn(Gly)-H](+) complexes are characterized by numerous fragmentation processes. Six of them, associated with elimination of H2O, CO, H2O + CO and formation of [(R)2SnOH](+) (-57 u),[(R)2SnNH2](+) (-58 u) and [(R)2SnH](+) (-73 u), are systematically observed. Use of labeled glycines notably concludes that the hydrogen atoms eliminated in water and H2O + CO are labile hydrogens. A similar conclusion can be made for hydrogens of [(R2)SnOH](+) and [(R2)SnNH2](+) ions. Interestingly, formation [(R)2SnH](+) ions is characterized by a migration of one the α hydrogen of glycine onto the metallic center. Finally, several dissociation routes are observed and are characteristic of a given organic substituent. Calculations indicated that the interaction between organotins and glycine is mostly electrostatic. For [(R)2Sn(Gly)-H](+) complexes, a preferable bidentate interaction of the type η(2)-O,NH2 is observed, similar to that encountered for other metal ions. [(R)3Sn](+) ions strongly stabilize the zwitterionic form of glycine, which is practically degenerate with respect to neutral glycine. In addition, the interconversion between both forms is almost barrierless. Suitable mechanisms are proposed in order to account for the most relevant fragmentation processes.
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Affiliation(s)
- Latifa Latrous
- Laboratoire de Chimie-Analytique et Electrochimie, Département de Chimie, Faculté des Sciences de Tunis, Campus Universitaire, 2092, El Manar, Tunis, Tunisia.
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19
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Khodabandeh MH, Reisi H, Davari MD, Zare K, Zahedi M, Ohanessian G. Interaction Modes and Absolute Affinities of α-Amino Acids for Mn2+: A Comprehensive Picture. Chemphyschem 2013; 14:1733-45. [DOI: 10.1002/cphc.201200964] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 02/13/2013] [Indexed: 11/07/2022]
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20
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Jurinovich S, Degano I, Mennucci B. A Strategy for the Study of the Interactions between Metal–Dyes and Proteins with QM/MM Approaches: the Case of Iron–Gall Dye. J Phys Chem B 2012; 116:13344-52. [DOI: 10.1021/jp3083002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sandro Jurinovich
- Dipartimento di Chimica
e Chimica Industriale, Università di Pisa, Via Risorgimento 35, Pisa
56126, Italy
| | - Ilaria Degano
- Dipartimento di Chimica
e Chimica Industriale, Università di Pisa, Via Risorgimento 35, Pisa
56126, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica
e Chimica Industriale, Università di Pisa, Via Risorgimento 35, Pisa
56126, Italy
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21
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Bazsó G, Magyarfalvi G, Tarczay G. Tunneling Lifetime of the ttc/VIp Conformer of Glycine in Low-Temperature Matrices. J Phys Chem A 2012; 116:10539-47. [DOI: 10.1021/jp3076436] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gábor Bazsó
- Laboratory of Molecular
Spectroscopy, Institute of
Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
| | - Gábor Magyarfalvi
- Laboratory of Molecular
Spectroscopy, Institute of
Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
| | - György Tarczay
- Laboratory of Molecular
Spectroscopy, Institute of
Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
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22
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Bazsó G, Magyarfalvi G, Tarczay G. Near-infrared laser induced conformational change and UV laser photolysis of glycine in low-temperature matrices: Observation of a short-lived conformer. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.04.066] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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Yang G, Zhu R, Zhou L, Liu C. Interactions of Zn(II) with single and multiple amino acids. Insights from density functional and ab initio calculations. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1372-1383. [PMID: 23019170 DOI: 10.1002/jms.3075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Calculations were performed to study the interactions of metal ions (M) with (multiple) amino acids (AA) and fill the gap between single AA and proteins. A complete conformational search results in nine and eleven ZnGly isomers at B3P86 and MP2 levels, respectively, and four populated conformers of glycine are responsible for production of these isomers. For all M, the isomers via the OO and NO binding modes are the main constituents, and the OO mode is favored by stronger electrostatic interactions. Binding with more glycines causes larger structural distortions, improves relative stabilities of monodentate binding isomers and generates new binding modes (e.g. ZnB(III) via only the hydroxyl group). The scaling factor of Zn(Gly)(n) structures, the ratio of its binding affinity versus the sum of comprising ZnGly isomers, is linear with glycine number (n), and the linear relationship may not be altered by mutations of glycines and M. It thus allows to estimate M(AA)(n) binding affinities (n ≥ 2) from the comprising MAA structures and analyze their structures with kinetic methods. The DFT and MP2 results become comparable by increasing metal coordination, e.g. the ZnB(III) versus ZnA(I) (zwitterionic) relative energy differs by 41.9 kcal mol(-1) at B3P86 and MP2 levels and is close by addition of three water molecules (4.1 kcal mol(-1)). The presence of water solvent improves the relative stabilities of monodentate binding isomers and results in a broader conformational distribution.
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Affiliation(s)
- Gang Yang
- Institute of Theoretical Chemistry, Shandong University, Jinan, P R China.
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24
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Meng L, Hu A, Pang R, Lin Z. Extensive computational study on coordination of transition metal cations and water molecules to glutamic acid. J Phys Chem A 2012; 116:7177-88. [PMID: 22671921 DOI: 10.1021/jp303289p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the basis of the conformations of glutamic acid (Glu) and analysis of possible metal cation coordination and hydration modes, conformations of Glu metalated with transition metal cations (TMCs), Cu(+/2+), Zn(+/2+), and Fe(+/2+/3+) and hydrations of Glu-Cu(+/2+) and Glu-Zn(+/2+) complexes by up to three water molecules are determined by extensive computational searches. The BHandHLYP functional is chosen as the main computational method as its overall performance for treating the spin multiplicity of TMCs is similar to that of CCSD(T) and better than that of MP2 and B3LYP. All mono- and divalent TMCs prefer tridentate coordination to canonical Glu, while Fe(3+) favors a bidentate coordination to zwitterionic Glu. The ground state of Glu-Fe(+) is found to be a spin sextet. Metal ion affinities of Glu for the TMCs are determined, and an excellent agreement with the experiment for Cu(+) may be obtained if the entropic effect is properly accounted for. Effects of hydration on the stabilities of different Glu-Cu(+/2+)/Zn(+/2+) structures are discussed, and the hydration energies for up to three water molecules are obtained. For the global minimum to take the zwitterionic form, Glu-Zn(+) requires only monohydration, Glu-Zn(2+) needs to be trihydrated, while Glu-Cu(+/2) should be hydrated with four or more water molecules.
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Affiliation(s)
- Lingbiao Meng
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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25
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Shankar R, Kolandaivel P, Senthil kumar L. Coordination and binding properties of zwitterionic glutathione with transition metal cations. Inorganica Chim Acta 2012. [DOI: 10.1016/j.ica.2012.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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26
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1D-RISM study of glycine zwitterion hydration and ion-molecular complex formation in aqueous NaCl solutions. J Mol Liq 2012. [DOI: 10.1016/j.molliq.2012.03.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Ansbacher T, Shurki A. Predicting the coordination number within copper chaperones: Atox1 as case study. J Phys Chem B 2012; 116:4425-32. [PMID: 22480337 DOI: 10.1021/jp210678n] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The concentration of copper ions in biological systems is tightly regulated by metallochaperone proteins which are responsible for Cu(I) delivery to designated locations in the cell. These proteins contain a unique motif (MXCXXC) that binds Cu(I) very tightly and specifically but at the same time allows efficient metal transfer to target proteins that often contain a similar copper binding motif. It was found that binding to Cu(I) is achieved through the two cysteine residues in a low coordination number of 2-3 due to possible binding of a third external ligand. Understanding copper transport requires better understanding of copper coordination. Here we therefore focused on establishing a computational method that can predict the coordination number of copper in copper chaperones. The method is shown to be successful in predicting the coordination of Cu(I) within the human copper chaperone (Atox1). Based on the results, a possible rationale for this unique Cu(I) dicoordination in Atox1 is suggested.
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Affiliation(s)
- Tamar Ansbacher
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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ABIRAM A, KOLANDAIVEL P. INTERACTION OF THE TAUTOMERIC STATES OF HISTIDINE WITH Cu AND Zn METAL IONS – A THEORETICAL STUDY. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s021963360900499x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A density functional study on the interaction of Cu 2+ and Zn 2+ metal ions at the predominant positions of N τ– H and N π– H histidine tautomers has been performed. The fully optimized energy of the isolated histidine tautomers at B3LYP/6-311++G** level of theory depicts N τ– H tautomer to be much stable compared to that of the N π– H tautomer. The interaction of metal ions forms bidentate and tridentate complexes with N τ– H tautomer, while it is absent in the case of N π– H tautomer emphasizing the role of former in structural determination of liganated proteins. The Zn 2+ ion induces a barrier-free proton transfer when interacted at the carbonyl position of N τ– H histidine tautomer necessitating the tautomer to be in the zwitterionic form for complexation. The thermodynamical analysis predicts a blue shift in the NH and CO stretching vibrational frequencies and suggests N τ– H tautomer to be best suitable for Cu 2+ and Zn 2+ ion interactions. The topological and charge transfer studies in concert with frontier molecular orbital (FMO) analysis confirm the covalent interaction, validating the findings based on the geometrical data.
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Affiliation(s)
- A. ABIRAM
- Department of Physics, Bharathiar University, Coimbatore-641 046, India
| | - P. KOLANDAIVEL
- Department of Physics, Bharathiar University, Coimbatore-641 046, India
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TAVASOLI ELHAM, FATTAHI ALIREZA. DFT STUDY OF BOND ENERGIES AND ATTACHMENT SITES OF SAMPLE DIVALENT CATIONS (Mg2+, Ca2+, Zn2+) TO HISTIDINE IN THE GAS PHASE. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633609004642] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In view of better understanding interactions of amino acids and peptides with metallic cations in the isolated state, the model system histidine– M 2+ ( M 2+ = Mg 2+, Ca 2+, Zn 2+) has been studied theoretically. The computations have been performed with the help of the density functional theory (DFT) and the B3LYP functional. The extended basis set was the standard 6-311++G**. All the molecular complexes obtained by the interaction between several energetically low-lying tautomers/conformers/zwitterions of histidine and the cations on different binding sites were considered. Our study shows that complexes of histidine with Mg 2+, Ca 2+, Zn 2+ are rather similar. In the isolated state, the most stable form corresponds to a tridentate complex in which the cation interacts with oxygen and two nitrogen atoms: one from the terminal NH 2 and one from the imidazole ring. All computations indicate that the metal ion affinity (MIA) decreases on going from Zn 2+ to Mg 2+ and Ca 2+, for the considered amino acid. This indicates that histidine prefers to bind to the transition metal cation rather than alkali earth metals. The influence of theses cations on the acidity of histidine were also considered. As expected, upon metal complexation, proton dissociation of histidine becomes much more favorable, that is, its acidity becomes much less endothermic.
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Affiliation(s)
- ELHAM TAVASOLI
- Department of Chemistry, Sharif University of Technology, P. O. Box 11365-9516, Tehran, Iran
| | - ALIREZA FATTAHI
- Department of Chemistry, Sharif University of Technology, P. O. Box 11365-9516, Tehran, Iran
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30
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Quantum chemical studies on the role of water microsolvation in interactions between group 12 metal species (Hg2+, Cd2+, and Zn2+) and neutral and deprotonated cysteines. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0975-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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Effect of regular hydration on gas phase structural stability of [zwitterionic alanine+M+] (M+=Li+, Na+, K+) complexes: A quantum chemical study. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2010.11.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Irshaidat T. Effect of the metal ion and the medium on the electronic structure of anthranilic acid: a modelling study on the Li and the BeH derivatives. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2010.544304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Tareq Irshaidat
- a Department of Chemistry , Al-Hussein Bin Talal University , Maan, Jordan
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33
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Corral I, Yáñez M. [MLn]2+ doubly charged systems: modeling, bonding, life times and unimolecular reactivity. Phys Chem Chem Phys 2011; 13:14848-64. [DOI: 10.1039/c1cp20622b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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34
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Shankar R, Kolandaivel P, Senthilkumar L. Interaction studies of cysteine with Li+, Na+, K+, Be2+, Mg2+, and Ca2+ metal cation complexes. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1786] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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35
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Ansbacher T, Srivastava HK, Martin JML, Shurki A. Can DFT methods correctly and efficiently predict the coordination number of copper(I) complexes? A case study. J Comput Chem 2010; 31:75-83. [PMID: 19412907 DOI: 10.1002/jcc.21277] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The coordination number of various experimentally known Cu(I) compounds is studied using density functional theory. Various basis sets are tested, aiming to establish a reliable level for prediction of the coordination number of these and other Cu(I) complexes. It is found that most levels exhibit correct trends, namely, the bulkier ligands demonstrate larger preference for coordination of two ligands. Proper absolute values are obtained when dispersion corrections are also included in the calculations. It is concluded that the fairly small modified 6-31+G* basis set due to Pulay represents a good compromise between accuracy and efficiency, followed by Balabanov and Peterson's all-electron aug-cc-pVDZ basis set. The overall energy is decomposed into various components whose relative contribution to the overall tendency of forming a complex with a particular coordination is examined. It is shown that two opposing contributions play a major role: the interaction energy of the ligand being added and the deformation energy of the copper's coordination sphere prior to the ligand addition. The former being a stabilizing contribution, leads to higher coordination numbers while the later, a destabilizing contribution, is shown to favor lower coordination numbers.
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Affiliation(s)
- Tamar Ansbacher
- Department of Medicinal Chemistry and Natural Products, School of Pharmacy, The Lise-Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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37
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Yang G, Xing C, Liu CB, Fu YJ, Zhou LJ, Zu YG. First-principle conformational analysis of glycine residues in the alphabeta-tubulin dimer. Interdiscip Sci 2009; 1:196-203. [PMID: 20640838 DOI: 10.1007/s12539-009-0021-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Revised: 11/27/2008] [Accepted: 02/12/2009] [Indexed: 05/29/2023]
Abstract
Amino acids, especially glycine, have been extensively studied whereas their conformational behaviors in proteins are rather limited. In this work, all the polypeptides containing glycine residues are truncated from the alphabeta-tubulin dimer and refined with the partial optimization technique, where the backbone atoms of the previous and posterior residues to the glycine residues are fixed at the experimental Cartesian positions whereas the others fully relaxed. The combination of the polypeptide models and partial optimization technique is validated by twolayer ONIOM calculations, being effective to retain the local structures of proteins and meanwhile optimizing the concerned glycine residues towards energy minima. Owing to the lack of side chains, various types of hydrogen bonding interactions are detected in the glycine residues. The conformational analyses of proteins are mainly based on the dihedrals. Theta(1)( angleH(5)C(2)C(3)O(4)), Theta(2)( angleH(6)C(2)C(3)O(4)) and Theta(3)( angleN(1)C(2)C(3)O(4)) are the three key dihedrals to determine the glycine conformations, which were found to change synchronously and correlate with each other by four linear equations. It thus provided the first evidence of the correlation of intra-dihedrals for the amino acid residues in proteins. In addition, the three dihedrals of the gas-phase glycine conformations were also found to suit well with these linear equations, elucidating the rationality of using amino acids as the computational models of proteins.
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Affiliation(s)
- Gang Yang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China.
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38
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Su P, Li H. Energy decomposition analysis of covalent bonds and intermolecular interactions. J Chem Phys 2009; 131:014102. [DOI: 10.1063/1.3159673] [Citation(s) in RCA: 749] [Impact Index Per Article: 49.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Lee GY. Interaction of Proline with Cu+and Cu2+Ions in the Gas PhaseGab Yong Lee*Department of Life Chemistry, Catholic University of Daegu, Gyeongsan 712‐702, Korea(Received March 3, 2009)INTRODUCTIONCopper ions are the most important transitionmetals involved in several biological processes ofliving systems, including oxidation, dioxygentransport, and charge transfer.1 The study of interactionsbetween the metal ion and amino acids hasattracted considerable attention from experimental2-6and theoretical6-11 viewpoints. Thermochemicalinformation on interactions between the metal ion and biological. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2009. [DOI: 10.5012/jkcs.2009.53.3.257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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40
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O’Brien JT, Prell JS, Steill JD, Oomens J, Williams ER. Changes in Binding Motif of Protonated Heterodimers Containing Valine and Amines Investigated Using IRMPD Spectroscopy between 800 and 3700 cm−1 and Theory. J Am Chem Soc 2009; 131:3905-12. [DOI: 10.1021/ja809928h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jeremy T. O’Brien
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jeffrey D. Steill
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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41
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Cheng W, Jiang H, Zhang D, Zhang C. A DFT study of the reactions of the Cu+ ion with methylamine and dimethylamine. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.10.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Constantino E, Tortajada J, Sodupe M, Rodríguez-Santiago L. Coordination Properties of Lysine Interacting with Co(I) and Co(II). A Theoretical and Mass Spectrometry Study. J Phys Chem A 2008; 112:12385-92. [DOI: 10.1021/jp805764y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E. Constantino
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain, and Laboratoire Analyse et Modélisation pour l’Analyse et l’Environnement, CNRS UMR 8587, Université d’Evry-Val-d’Essonne, Boulevard François Mitterrand, 91025 Evry Cedex, France
| | - J. Tortajada
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain, and Laboratoire Analyse et Modélisation pour l’Analyse et l’Environnement, CNRS UMR 8587, Université d’Evry-Val-d’Essonne, Boulevard François Mitterrand, 91025 Evry Cedex, France
| | - M. Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain, and Laboratoire Analyse et Modélisation pour l’Analyse et l’Environnement, CNRS UMR 8587, Université d’Evry-Val-d’Essonne, Boulevard François Mitterrand, 91025 Evry Cedex, France
| | - L. Rodríguez-Santiago
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain, and Laboratoire Analyse et Modélisation pour l’Analyse et l’Environnement, CNRS UMR 8587, Université d’Evry-Val-d’Essonne, Boulevard François Mitterrand, 91025 Evry Cedex, France
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HU ZF, LUO L, HU YH. Theoretical and Experimental Study of Complex Ions from Reactions of Al+(Cu+) with Amine Molecules. CHINESE J CHEM 2008. [DOI: 10.1002/cjoc.200890210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Bush MF, Oomens J, Saykally RJ, Williams ER. Effects of Alkaline Earth Metal Ion Complexation on Amino Acid Zwitterion Stability: Results from Infrared Action Spectroscopy. J Am Chem Soc 2008; 130:6463-71. [DOI: 10.1021/ja711343q] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew F. Bush
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Richard J. Saykally
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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45
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Kwon HJ, Lee GY. A DFT Study on Magnesium Ion Affinity of Glycine. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2008. [DOI: 10.5012/jkcs.2008.52.2.207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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46
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Jover J, Bosque R, Sales J. A comparison of the binding affinity of the common amino acids with different metal cations. Dalton Trans 2008:6441-53. [DOI: 10.1039/b805860a] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Ke Y, Zhao J, Verkerk UH, Hopkinson AC, Siu KWM. Histidine, Lysine, and Arginine Radical Cations: Isomer Control via the Choice of Auxiliary Ligand (L) in the Dissociation of [CuII(L)(amino acid)]•2+ Complexes. J Phys Chem B 2007; 111:14318-28. [DOI: 10.1021/jp0746648] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuyong Ke
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - Junfang Zhao
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - Udo H. Verkerk
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - Alan C. Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - K. W. Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
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Xiang F, Cukier RI, Bu Y. Ca2+ selectivity of the sarcoplasmic reticulum Ca2+-ATPase at the enzyme-water interface and in the Ca2+ entrance channel. J Phys Chem B 2007; 111:12282-93. [PMID: 17914795 DOI: 10.1021/jp073883q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sarcoplasmic reticulum (SR) Ca(2+)-ATPase, a P-type transmembrane protein, can transport Ca(2+) from the cytoplasmic to the luminal side over other cations specifically. The proposed Ca(2+) entrance channel, composed of the main-chain carbonyl oxygen and side-chain carboxyl oxygen atoms of the amino acids, opens on the enzyme surface, just above the biphospholipid layer membrane-water interface, where Trp residues are frequently found. In this work, the physicochemical nature of Ca(2+) selectivity over Mg(2+) on the surface of the SR Ca(2+)-ATPase has been investigated using the density functional theory (DFT) method. The selection process can be regarded as the first step of the specificity of the enzyme to transport Ca(2+). Subsequently, the specificity of the entrance channel to conduct Ca(2+) over other cations has also been explored. As revealed by thermodynamic analyses, either the aromatic or the aliphatic amino acid residues distributed on the surface of Ca(2+)-ATPase have a bigger affinity to Mg(2+) than to Ca(2+), resulting in a concentration decrease of free Mg(2+) in the local region. Thus, Ca(2+) can transport into the Ca(2+)-entrance channel more easily. Whereafter, for a small quantity of Mg(2+) entering this channel accompanying the Ca(2+) current, the strong electrostatic interactions between Mg(2+) and the ligands will limit the activity of this metal ion, which facilitates the weakly bonded Ca(2+) passing through the channel at a relatively high rate, as suggested by the "sticky-pore" hypothesis. Furthermore, the corresponding theoretical investigations have demonstrated that the increase of the ligand electronegativity can enhance their discrimination between these two cations effectively.
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Affiliation(s)
- Feng Xiang
- Key Laboratory for Colloid and Interface Chemistry of Ministry of Education, The Modeling & Simulation Chemistry Division, Shandong University, Jinan 250100, P. R. China
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Fleming GJ, McGill PR, Idriss H. Gas phase interaction of L
-proline with Be2+
, Mg2+
and Ca2+
ions: a computational study. J PHYS ORG CHEM 2007. [DOI: 10.1002/poc.1249] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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E. Rezabal,*, Marino T, Mercero JM, Russo N, Ugalde JM. Assessment of Approximate Density Functional Methods for the Study of the Interactions of Al(III) with Aromatic Amino Acids. J Chem Theory Comput 2007; 3:1830-6. [DOI: 10.1021/ct700027n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E. Rezabal,*
- Kimika Fakultatea, Euskal Herriko Unibertsitatea and Donostia International Physics Center (DIPC), P. K. 1072, 20080 Donostia, Euskadi, Spain, and Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite - Centro d'Eccellenza MIUR, Universitá della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - T. Marino
- Kimika Fakultatea, Euskal Herriko Unibertsitatea and Donostia International Physics Center (DIPC), P. K. 1072, 20080 Donostia, Euskadi, Spain, and Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite - Centro d'Eccellenza MIUR, Universitá della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - J. M. Mercero
- Kimika Fakultatea, Euskal Herriko Unibertsitatea and Donostia International Physics Center (DIPC), P. K. 1072, 20080 Donostia, Euskadi, Spain, and Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite - Centro d'Eccellenza MIUR, Universitá della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - N. Russo
- Kimika Fakultatea, Euskal Herriko Unibertsitatea and Donostia International Physics Center (DIPC), P. K. 1072, 20080 Donostia, Euskadi, Spain, and Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite - Centro d'Eccellenza MIUR, Universitá della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - J. M. Ugalde
- Kimika Fakultatea, Euskal Herriko Unibertsitatea and Donostia International Physics Center (DIPC), P. K. 1072, 20080 Donostia, Euskadi, Spain, and Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite - Centro d'Eccellenza MIUR, Universitá della Calabria, I-87030 Arcavacata di Rende (CS), Italy
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