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Chakravorty DK, Li P, Tran TT, Bayse CA, Merz KM. Metal Ion Capture Mechanism of a Copper Metallochaperone. Biochemistry 2016; 55:501-9. [DOI: 10.1021/acs.biochem.5b01217] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dhruva K. Chakravorty
- Institute
for Cyber Enabled Research, Michigan State University, 567 Wilson
Road, East Lansing, Michigan 48824, United States
- Department
of Chemistry, University of New Orleans, 2000 Lakeshore Drive, New Orleans, Louisiana 70148, United States
- Department
of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, United States
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Pengfei Li
- Department
of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, United States
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Trang T. Tran
- Department
of Chemistry, University of New Orleans, 2000 Lakeshore Drive, New Orleans, Louisiana 70148, United States
| | - Craig A. Bayse
- Department of Chemistry & Biochemistry, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Kenneth M. Merz
- Institute
for Cyber Enabled Research, Michigan State University, 567 Wilson
Road, East Lansing, Michigan 48824, United States
- Department
of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, United States
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
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Hoff BH, Sundby E. Preparation of pharmaceutical important fluorinated 1-arylethanols using isolated enzymes. Bioorg Chem 2013; 51:31-47. [DOI: 10.1016/j.bioorg.2013.09.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/06/2013] [Accepted: 09/12/2013] [Indexed: 10/26/2022]
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Olsson E, Martinez A, Teigen K, Jensen VR. Formation of the iron-oxo hydroxylating species in the catalytic cycle of aromatic amino acid hydroxylases. Chemistry 2011; 17:3746-58. [PMID: 21351297 DOI: 10.1002/chem.201002910] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Indexed: 12/20/2022]
Abstract
The first part of the catalytic cycle of the pterin-dependent, dioxygen-using nonheme-iron aromatic amino acid hydroxylases, leading to the Fe(IV)=O hydroxylating intermediate, has been investigated by means of density functional theory. The starting structure in the present investigation is the water-free Fe-O(2) complex cluster model that represents the catalytically competent form of the enzymes. A model for this structure was obtained in a previous study of water-ligand dissociation from the hexacoordinate model complex of the X-ray crystal structure of the catalytic domain of phenylalanine hydroxylase in complex with the cofactor (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH(4)) (PAH-Fe(II)-BH(4)). The O-O bond rupture and two-electron oxidation of the cofactor are found to take place via a Fe-O-O-BH(4) bridge structure that is formed in consecutive radical reactions involving a superoxide ion, O(2)(-). The overall effective free-energy barrier to formation of the Fe(IV)=O species is calculated to be 13.9 kcal mol(-1), less than 2 kcal mol(-1) lower than that derived from experiment. The rate-limiting step is associated with a one-electron transfer from the cofactor to dioxygen, whereas the spin inversion needed to arrive at the quintet state in which the O-O bond cleavage is finalized, essentially proceeds without activation.
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Affiliation(s)
- Elaine Olsson
- Department of Chemistry, University of Bergen, Allégaten 41, 5007 Bergen, Norway
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Yang CM, Zhang J. Insights into intramolecular Trp and His side-chain orientation and stereospecific π interactions surrounding metal centers: an investigation using protein metal-site mimicry in solution. Chemistry 2011; 16:10854-65. [PMID: 20669189 DOI: 10.1002/chem.200903149] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Metal-binding scaffolds incorporating a Trp/His-paired epitope are instrumental in giving novel insights into the physicochemical basis of functional and mechanistic versatility conferred by the Trp-His interplay at a metal site. Herein, by coupling biometal site mimicry and (1)H and (13)C NMR spectroscopy experiments, modular constructs EDTA-(L-Trp, L-His) (EWH; EDTA=ethylenediamino tetraacetic acid) and DTPA-(L-Trp, L-His) (DWH; DTPA=diethylenetriamino pentaacetic acid) were employed to dissect the static and transient physicochemical properties of hydrophobic/hydrophilic aromatic interactive modes surrounding biometal centers. The binding feature and identities of the stoichiometric metal-bound complexes in solution were investigated by using (1)H and (13)C NMR spectroscopy, which facilitated a cross-validation of the carboxylate, amide oxygen, and tertiary amino groups as the primary ligands and indole as the secondary ligand, with the imidazole (Im) N3 nitrogen being weakly bound to metals such as Ca(2+) owing to a multivalency effect. Surrounding the metal centers, the stereospecific orientation of aromatic rings in the diastereoisomerism is interpreted with the Ca(2+)-EWH complex. With respect to perturbed Trp side-chain rotamer heterogeneity, drastically restricted Trp side-chain flexibility and thus a dynamically constrained rotamer interconversion due to π interactions is evident from the site-selective (13)C NMR spectroscopic signal broadening of the Trp indolyl C3 atom. Furthermore, effects of Trp side-chain fluctuation on indole/Im orientation were the subject of a 2D NMR spectroscopy study by using the Ca(2+)-bound state; a C-H2(indolyl)/C-H5(Im(+)) connectivity observed in the NOESY spectra captured direct evidence that the N-H1 of the Ca(2+)-Im(+) unit interacted with the pyrrole ring of the indole unit in Ca(2+)-bound EWH but not in DWH, which is assignable to a moderately static, anomalous, T-shaped, interplanar π(+)-π stacking alignment. Nevertheless, a comparative (13)C NMR spectroscopy study of the two homologous scaffolds revealed that the overall response of the indole unit arises predominantly from global attractions between the indole ring and the entire positively charged first coordination sphere. The study thus demonstrates the coordination-sphere/geometry dependence of the Trp/His side-chain interplay, and established that π interactions allow (13)C NMR spectroscopy to offer a new window for investigating Trp rotamer heterogeneity near metal-binding centers.
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Affiliation(s)
- Chi Ming Yang
- Neurochemistry & Biophysical Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
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Ming Yang C. Biometal binding-site mimicry with modular, hetero-bifunctionally modified architecture encompassing a Trp/His motif: Insights into spatiotemporal noncovalent interactions from a comparative spectroscopic study. Dalton Trans 2011; 40:3008-27. [DOI: 10.1039/c0dt00237b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Theory of Hydride-Proton Transfer (HPT) Carbonyl Reduction by [OsIII(tpy)(Cl)(NH═CHCH3)(NSAr)]. J Am Chem Soc 2010; 132:16318-20. [DOI: 10.1021/ja106403e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Mutation of outer-shell residues modulates metal ion co-ordination strength in a metalloenzyme. Biochem J 2010; 429:313-21. [DOI: 10.1042/bj20100233] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The metal ion co-ordination sites of many metalloproteins have been characterized by a variety of spectroscopic techniques and small-molecule model systems, revealing many important insights into the structural determinants of metal ion co-ordination. However, our understanding of this fundamentally and practically important phenomenon remains frustratingly simplistic; in many proteins it is essentially impossible to predict metal ion specificity and the effects of remote ‘outer-shell’ residues on metal ion co-ordination strength are also poorly defined. This is exemplified by our inability to explain why metalloenzymes with identical metal ion co-ordination spheres, such as the closely related orthologues of bacterial PTE (phosphotriesterase) from Agrobacterium radiobacter and Pseudomonas diminuta, display different metal ion specificity and co-ordination strength. In the present study, we present a series of PTE variants that all possess identical metal ion co-ordination spheres, yet display large differences in their metal ion co-ordination strength. Using measurement of the rates of metal ion dissociation from the active site alongside analysis of structural data obtained through X-ray crystallography, we show that ‘outer-shell’ residues provide essential support for the metal ion ligands, in effect buttressing them in their optimal orientation. Remote mutations appear to modulate metal ion interactions by increasing or decreasing the stabilizing effects of these networks. The present study therefore provides a description of how the greater protein fold can be modified to ‘tune’ the strength of metal ion co-ordination and metal ion specificity, as well as reinforcing the concept of proteins as ensembles of conformational states with unique structures and biochemical properties.
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Petersen L, Ardèvol A, Rovira C, Reilly PJ. Molecular Mechanism of the Glycosylation Step Catalyzed by Golgi α-Mannosidase II: A QM/MM Metadynamics Investigation. J Am Chem Soc 2010; 132:8291-300. [DOI: 10.1021/ja909249u] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luis Petersen
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Albert Ardèvol
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Carme Rovira
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Peter J. Reilly
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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Sorkin A, Truhlar DG, Amin EA. Energies, Geometries, and Charge Distributions of Zn Molecules, Clusters, and Biocenters from Coupled Cluster, Density Functional, and Neglect of Diatomic Differential Overlap Models. J Chem Theory Comput 2009; 5:1254-65. [PMID: 26609716 DOI: 10.1021/ct900038m] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present benchmark databases of Zn-ligand bond distances, bond angles, dipole moments, and bond dissociation energies for Zn-containing small molecules and Zn coordination compounds with H, CH3, C2H5, NH3, O, OH, H2O, F, Cl, S, and SCH3 ligands. The test set also includes clusters with Zn-Zn bonds. In addition, we calculated dipole moments and binding energies for Zn centers in coordination environments taken from zinc metalloenzyme X-ray structures, representing both structural and catalytic zinc centers. The benchmark values are based on relativistic-core coupled cluster calculations. These benchmark calculations are used to test the predictions of four density functionals, namely B3LYP and the more recently developed M05-2X, M06, and M06-2X levels of theory, and six semiempirical methods, including neglect of diatomic differential overlap (NDDO) calculations incorporating the new PM3 parameter set for Zn called ZnB, developed by Brothers and co-workers, and the recent PM6 parametrization of Stewart. We found that the best DFT method to reproduce dipole moments and dissociation energies of our Zn compound database is M05-2X, which is consistent with a previous study employing a much smaller and less diverse database and a much larger set of density functionals. Here we show that M05-2X geometries and single-point coupled cluster calculations with M05-2X geometries can also be used as benchmarks for larger compounds, where coupled cluster optimization is impractical, and in particular we use this strategy to extend the geometry, binding energy, and dipole moment databases to additional molecules, and we extend the tests involving crystal-site coordination compounds to two additional proteins. We find that the most predictive NDDO methods for our training set are PM3 and MNDO/d. Notably, we also find large errors in B3LYP for the coordination compounds based on experimental X-ray geometries.
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Affiliation(s)
- Anastassia Sorkin
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959, and Department of, Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota, 55455-0431
| | - Donald G Truhlar
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959, and Department of, Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota, 55455-0431
| | - Elizabeth A Amin
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959, and Department of, Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota, 55455-0431
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Frison G, Ohanessian G. Metal-histidine-glutamate as a regulator of enzymatic cycles: a case study of carbonic anhydrase. Phys Chem Chem Phys 2009; 11:374-83. [DOI: 10.1039/b812916a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Hong R, Magistrato A, Carloni P. Anthrax Lethal Factor Investigated by Molecular Simulations. J Chem Theory Comput 2008; 4:1745-56. [DOI: 10.1021/ct8001877] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Rolando Hong
- International School for Advanced Studies (SISSA/ISAS), CNR-INFM-Democritos National Simulation Center, and Italian Institute of Technology (IIT), Trieste, Italy
| | - Alessandra Magistrato
- International School for Advanced Studies (SISSA/ISAS), CNR-INFM-Democritos National Simulation Center, and Italian Institute of Technology (IIT), Trieste, Italy
| | - Paolo Carloni
- International School for Advanced Studies (SISSA/ISAS), CNR-INFM-Democritos National Simulation Center, and Italian Institute of Technology (IIT), Trieste, Italy
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Simona F, Magistrato A, Vera DMA, Garau G, Vila AJ, Carloni P. Protonation state and substrate binding to B2 metallo-beta-lactamase CphA from Aeromonas hydrofila. Proteins 2007; 69:595-605. [PMID: 17623844 DOI: 10.1002/prot.21476] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The zinc enzymes metallo beta-lactamases counteract the beneficial action of beta-lactam antibiotics against bacterial infections, by hydrolyzing their beta-lactam rings. To understand structure/function relationships on a representative member of this class, the B2 M beta L CphA, we have investigated the H-bond pattern at the Zn enzymatic active site and substrate binding mode by molecular simulation methods. Extensive QM calculations at the DFT-BLYP level on eleven models of the protein active site, along with MD simulations of the protein in aqueous solution, allow us to propose two plausible protonation states for the unbound enzyme, which are probably in equilibrium. Docking procedures along with MD simulations and QM calculations suggest that in the complex between the enzyme and its substrate (biapenem), the latter is stable in only one of the two protonation states, in addition it exhibits two different binding modes, of which only one agrees with previous proposals. In both cases, the substrate is polarized as in aqueous solution. We conclude that addressing mechanistic issues on this class of enzymes requires a careful procedure to assign protonation states and substrate docking modes.
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Affiliation(s)
- F Simona
- SISSA, Via Beirut 2-4, 34014 Grignano, Trieste, Italy
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De Vivo M, Cavalli A, Carloni P, Recanatini M. Computational Study of the Phosphoryl Transfer Catalyzed by a Cyclin-Dependent Kinase. Chemistry 2007; 13:8437-44. [PMID: 17636466 DOI: 10.1002/chem.200700044] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A cyclin-dependent kinase, Cdk2, catalyzes the transfer of the gamma-phosphate from ATP to a threonine or serine residue of its polypeptide substrates. Here, we investigate aspects of the reaction mechanism of Cdk2 by gas-phase density functional calculations, classical molecular dynamics, and Car-Parrinello QM/MM simulations. We focus on the role of the conserved Asp127 and on the nature of the phosphoryl transfer reaction mechanism catalyzed by Cdk2. Our findings suggest that Asp127 is active in its deprotonated form by assisting the formation of the near-attack orientation of the substrate serine or threonine. Therefore, the residue does not act as a general base during the catalysis. The mechanism for the phosphoryl transfer is a single SN2-like concerted step, which shows a phosphorane-like transition state geometry. Although the resulting reaction mechanism is in agreement with a previous density functional study of the same catalytic reaction mechanism (Cavalli et al., Chem. Comm. 2003, 1308-1309), the reaction barrier is considerably lower when QM/MM calculations are performed, as in this study ( approximately 42 kcal mol(-1) QM vs. approximately 24 kcal mol(-1) QM/MM); this indicates that important roles for the catalysis are played by the protein environment and solvent waters. Because of the high amino acid sequence conservation among the whole family of cyclin-dependent kinases (CDKs), these results could be general for the CDK family.
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Affiliation(s)
- Marco De Vivo
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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Testa B, Krämer SD. The biochemistry of drug metabolism--an introduction: Part 2. Redox reactions and their enzymes. Chem Biodivers 2007; 4:257-405. [PMID: 17372942 DOI: 10.1002/cbdv.200790032] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review continues a general presentation of the metabolism of drugs and other xenobiotics started in a recent issue of Chemistry & Biodiversity. This Part 2 presents the numerous oxidoreductases involved, their nomenclature, relevant biochemical properties, catalytic mechanisms, and the very diverse reactions they catalyze. Many medicinally, environmentally, and toxicologically relevant examples are presented and discussed. Cytochromes P450 occupy a majority of the pages of Part 2, but a large number of relevant oxidoreductases are also considered, e.g., flavin-containing monooxygenases, amine oxidases, molybdenum hydroxylases, peroxidases, and the innumerable dehydrogenases/reductases.
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Affiliation(s)
- Bernard Testa
- Department of Pharmacy, University Hospital Centre (CHUV), Rue du Bugnon, CH-1011 Lausanne.
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Yang CM, Li X, Wei W, Li Y, Duan Z, Zheng J, Huang T. Dissecting the General Physicochemical Properties of Noncovalent Interactions Involving Tyrosine Side Chain as a Second-Shell Ligand in Biomolecular Metal-Binding Site Mimetics: An Experimental Study Combining Fluorescence,13C NMR Spectroscopy and ESI Mass Spectrometry. Chemistry 2007; 13:3120-30. [PMID: 17201001 DOI: 10.1002/chem.200600661] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Detailed physicochemical features inherent in the dynamic cation-pi interactions of aromatic amino acid side chains in the secondary coordination spheres around metal ions were extracted and mapped by intrinsic tyrosine fluorescence titration experiments with two homologous, artificially engineered metal-binding scaffolds which mimic metal-binding sites in metalloproteins. A newly formulated method for the treatment of fluorescence titration data allows straightforward assessment of both the magnitudes and properties of metal-chelation-assisted cation-aromatic interactions (K2) underlying a proposed two-step metallosupramolecular association process. The unprecedented linear platform-motif correlations between the two contrasting scaffolds in their changes in tyrosine fluorescence on binding of 3d metal cations help to elucidate the properties of general cation-arene recognition corresponding to the metal-responsive characteristics of the second-shell Tyr residue surrounding the metal-binding sites in the supramolecular context, and thereby define a new noncovalent design principle for metal-ion recognition in aqueous solution. As supported by NMR spectroscopic and ESI-MS analyses and molecular mechanics force field calculations, the systematic study exemplifies the concept of using steady-state tyrosine fluorescence as a powerful tool for comprehensive descriptions of cation-pi interactions in the extended environment of a metal-binding site. We established that the physicochemical properties pertaining to indirect metal-arene interactions are highly dependent on the electronic properties of the metal ions. This work suggests that second-shell cation-pi interactions may play more diverse roles, including modulation of structure, reactivity, and function of metal-binding sites, than the previously well-established direct cation-pi interactions involving hard cations (e.g., alkali metal ions). Moreover, such a study will continue to complement theoretical predications and/or the early experimental investigations in organic solvents.
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Affiliation(s)
- Chi Ming Yang
- Neurochemistry and Physical Organic Chemistry, Nankai University, Tianjin 300071, China.
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Ribeiro JB, de Sousa LMA, Soares MDV, Ramos MDCKV, de Aquino Neto FR, Fraga CAM, Leite SGF, Cordeiro Y, Antunes OA. Microbial reduction of α-acetyl-γ-butyrolactone. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.tetasy.2006.03.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Oldfield E. Quantum chemical studies of protein structure. Philos Trans R Soc Lond B Biol Sci 2005; 360:1347-61. [PMID: 16147526 PMCID: PMC1569496 DOI: 10.1098/rstb.2003.1421] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2003] [Accepted: 09/24/2003] [Indexed: 11/12/2022] Open
Abstract
Quantum chemical methods now permit the prediction of many spectroscopic observables in proteins and related model systems, in addition to electrostatic properties, which are found to be in excellent accord with those determined from experiment. I discuss the developments over the past decade in these areas, including predictions of nuclear magnetic resonance chemical shifts, chemical shielding tensors, scalar couplings and hyperfine (contact) shifts, the isomer shifts and quadrupole splittings in Mössbauer spectroscopy, molecular energies and conformations, as well as a range of electrostatic properties, such as charge densities, the curvatures, Laplacians and Hessians of the charge density, electrostatic potentials, electric field gradients and electrostatic field effects. The availability of structure/spectroscopic correlations from quantum chemistry provides a basis for using numerous spectroscopic observables in determining aspects of protein structure, in determining electrostatic properties which are not readily accessible from experiment, as well as giving additional confidence in the use of these techniques to investigate questions about chemical bonding and chemical reactions.
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Affiliation(s)
- Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, 61801, USA.
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Linder DP, Rodgers KR. A Theoretical Study of Imidazole- and Thiol-Based Zinc Binding Groups Relevant to Inhibition of Metzincins. J Phys Chem B 2004. [DOI: 10.1021/jp037474f] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Douglas P. Linder
- Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105
| | - Kenton R. Rodgers
- Department of Chemistry, Biochemistry, and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105
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Affiliation(s)
- Francesco Musiani
- Department of Agro-Environmental Science and Technology, University of Bologna, Viale Giuseppe Fanin 40, I-40127 Bologna, Italy, and International School for Advanced Studies (SISSA/ISAS) and INFM DEMOCRITOS Simulation Center, Via Beirut 2-4, I-34014 Trieste, Italy
| | - Paolo Carloni
- Department of Agro-Environmental Science and Technology, University of Bologna, Viale Giuseppe Fanin 40, I-40127 Bologna, Italy, and International School for Advanced Studies (SISSA/ISAS) and INFM DEMOCRITOS Simulation Center, Via Beirut 2-4, I-34014 Trieste, Italy
| | - Stefano Ciurli
- Department of Agro-Environmental Science and Technology, University of Bologna, Viale Giuseppe Fanin 40, I-40127 Bologna, Italy, and International School for Advanced Studies (SISSA/ISAS) and INFM DEMOCRITOS Simulation Center, Via Beirut 2-4, I-34014 Trieste, Italy
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Lin YL, Lim C. Factors Governing the Protonation State of Zn-Bound Histidine in Proteins: A DFT/CDM Study. J Am Chem Soc 2004; 126:2602-12. [PMID: 14982470 DOI: 10.1021/ja038827r] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have performed systematic theoretical studies to elucidate the factors governing the His protonation/deprotonation state in Zn-binding sites, especially those containing the ubiquitous Zn-His-Asp/Glu triad. Specifically, we have addressed the following three questions: (1) How does the transfer of the Zn-bound His imidazole proton to the second-shell Asp/Glu carboxylate oxygen depend on the composition of the other first-shell ligands and the solvent accessibility of the metal-binding site? (2) Can any second-shell ligand with a proton acceptor group such as the backbone carbonyl oxygen also act as a proton acceptor? (3) What is the effect of the Asp/Glu in the Zn-His-Asp/Glu triad on the Zn-bound water protonation state? To address these questions, we used a combination of quantum mechanical and continuum dielectric methods to compute the free energies for deprotonating a Zn-bound imidazole/water in various Zn complexes. The calculations show that whether the Zn-bound His is protonated or deprotonated depends on (1) the solvent accessibility of the metal-binding site, and (2) the Lewis acid ability of Zn, which is indirectly determined by both the first- and the second-shell Zn ligands. The calculations also show that the effect of the Zn-His-Asp/Glu interaction on the nucleophilicity of the Zn-bound water depends on the solvent accessibility of the catalytic Zn site. Furthermore, they show that the Asp/Glu side chain in the Zn-His-Asp/Glu triad can increase the negative charge of its partner, His, and create an anionic hole that may stabilize a cation in buried cavities, provided that the Zn complex is cationic/neutral. The findings of this work are in accord with available experimental data.
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Affiliation(s)
- Yen-lin Lin
- Institute of Biomedical Science, Academic Sinica, Taipei 11529, Taiwan ROC
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