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Tzeli D, Raugei S, Xantheas SS. Quantitative Account of the Bonding Properties of a Rubredoxin Model Complex [Fe(SCH 3) 4] q, q = -2, -1, +2, +3. J Chem Theory Comput 2021; 17:6080-6091. [PMID: 34546757 DOI: 10.1021/acs.jctc.1c00485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron-sulfur clusters play important roles in biology as parts of electron-transfer chains and catalytic cofactors. Here, we report a detailed computational analysis of a structural model of the simplest natural iron-sulfur cluster of rubredoxin and its cationic counterparts. Specifically, we investigated adiabatic reduction energies, dissociation energies, and bonding properties of the low-lying electronic states of the complexes [Fe(SCH3)4]2-/1-/2+/3+ using multireference (CASSCF, MRCISD), and coupled cluster [CCSD(T)] methodologies. We show that the nature of the Fe-S chemical bond and the magnitude of the ionization potentials in the anionic and cationic [Fe(SCH3)4] complexes offer a physical rationale for the relative stabilization, structure, and speciation of these complexes. Anionic and cationic complexes present different types of chemical bonds: prevalently ionic in [Fe(SCH3)4]2-/1- complexes and covalent in [Fe(SCH3)4]2+/3+ complexes. The ionic bonds result in an energy gain for the transition [Fe(SCH3)4]2- → [Fe(SCH3)4]- (i.e., FeII → FeIII) of 1.5 eV, while the covalent bonds result in an energy loss for the transition [Fe(SCH3)4]2+ → [Fe(SCH3)4]3+ of 16.6 eV, almost half of the ionization potential of Fe2+. The ionic versus covalent bond character influences the Fe-S bond strength and length, that is, ionic Fe-S bonds are longer than covalent ones by about 0.2 Å (for FeII) and 0.04 Å (for FeII). Finally, the average Fe-S heterolytic bond strength is 6.7 eV (FeII) and 14.6 eV (FeIII) at the RCCSD(T) level of theory.
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Affiliation(s)
- Demeter Tzeli
- Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens 157 84, Greece.,Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 116 35, Greece
| | - Simone Raugei
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States
| | - Sotiris S Xantheas
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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Lin JC, Singh RRP, Cox DL. Theoretical study of DNA damage recognition via electron transfer from the [4Fe-4S] complex of MutY. Biophys J 2008; 95:3259-68. [PMID: 18599627 PMCID: PMC2547449 DOI: 10.1529/biophysj.108.132183] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Accepted: 06/11/2008] [Indexed: 11/18/2022] Open
Abstract
The mechanism of site-specific recognition of DNA by proteins has been a long-standing issue. The DNA glycosylase MutY, for instance, must find the rare 8-oxoguanine-adenine mismatches among the large number of basepairs in the DNA. This protein has a [4Fe-4S] cluster, which is highly conserved in species as diverse as Escherichia Coli and Homo sapiens. The mixed-valent nature of this cluster suggests that charge transfer may play a role in MutY's function. We have studied the energetics of the charge transfer in Bacillus stearothermophilus MutY-DNA complex using multiscale calculation including density functional theory and molecular dynamics. The [4Fe-4S] cluster in MutY is found to undergo 2+ to 3+ oxidation when coupling to DNA through hole transfer, especially when MutY is near an oxoguanine modified base (oxoG). Employing the Marcus theory for electron transfer, we find near optimal Frank-Condon factors for electron transfer from MutY to oxoguanine modified base. MutY has modest selectivity for oxoguanine over guanine due to the difference in oxidation potential. The tunneling matrix element is significantly reduced with the mutation R149W, whereas the mutation L154F reduces the tunneling matrix element as well as the Frank-Condon factor. Both L154F and R149W mutations are known to dramatically reduce or eliminate repair efficiency. We suggest a scenario where the charge transfer leads to a stabilization of the specific binding conformation, which is likely the recognition mode, thus enabling it to find the damaged site efficiently.
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Affiliation(s)
- Jong-Chin Lin
- Department of Physics, University of California, Davis, California 95616, USA
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Anderson JS, Hernández G, Lemaster DM. A billion-fold range in acidity for the solvent-exposed amides of Pyrococcus furiosus rubredoxin. Biochemistry 2008; 47:6178-88. [PMID: 18479148 DOI: 10.1021/bi800284y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The exchange rates of the static solvent-accessible amide hydrogens of Pyrococcus furiosus rubredoxin range from near the diffusion-limited rate to a billion-fold slower for the non-hydrogen-bonded Val 38 (eubacterial numbering). Hydrogen exchange directly monitors the kinetic acidity of the peptide nitrogen. Electrostatic solvation free energies were calculated by Poisson-Boltzmann methods for the individual peptide anions that form during the hydroxide-catalyzed exchange reaction to examine how well the predicted thermodynamic acidities match the experimentally determined kinetic acidities. With the exception of the Ile 12 amide, the differential exchange rate constant for each solvent-exposed amide proton that is not hydrogen bonded to a backbone carbonyl can be predicted within a factor of 6 (10 (0.78)) root-mean-square deviation (rmsd) using the CHARMM22 electrostatic parameter set and an internal dielectric value of 3. Under equivalent conditions, the PARSE parameter set yields a larger rmsd value of 1.28 pH units, while the AMBER parm99 parameter set resulted in a considerably poorer correlation. Either increasing the internal dielectric value to 4 or reducing it to a value of 2 significantly degrades the quality of the prediction. Assigning the excess charge of the peptide anion equally between the peptide nitrogen and the carbonyl oxygen also reduces the correlation to the experimental data. These continuum electrostatic calculations were further analyzed to characterize the specific structural elements that appear to be responsible for the wide range of peptide acidities observed for these solvent-exposed amides. The striking heterogeneity in the potential at sites along the protein-solvent interface should prove germane to the ongoing challenge of quantifying the contribution that electrostatic interactions make to the catalytic acceleration achieved by enzymes.
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Affiliation(s)
- Janet S Anderson
- Department of Chemistry, Union College, Schenectady, New York 12308, USA.
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LeMaster DM, Anderson JS, Hernández G. Spatial distribution of dielectric shielding in the interior of Pyrococcus furiosus rubredoxin as sampled in the subnanosecond timeframe by hydrogen exchange. Biophys Chem 2007; 129:43-8. [PMID: 17544203 PMCID: PMC2063458 DOI: 10.1016/j.bpc.2007.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Revised: 05/08/2007] [Accepted: 05/10/2007] [Indexed: 11/23/2022]
Abstract
Experimental pK values of ionizable sidechains provide the most direct test for models representing dielectric shielding within the interior of a protein. However, only the strongly shifted pK values are particularly useful for discriminating among models. NMR titration studies have usually found only one or two such shifted pK values in each protein, so that the fitting of the experimental data to a uniform internal dielectric (epsilon(int)) model is not well constrained. The observed variation among proteins for such epsilon(int) estimates may reflect nonuniformity of dielectric shielding within each protein interior or qualitative differences between individual proteins. The differential amide kinetic acidities for a series of metal-substituted rubredoxins are shown to be consistent with Poisson-Boltzmann predictions of dielectric shielding that is relatively uniform for all of the amides that are sensitive to the metal charge, a region which corresponds to roughly 1/3 of the internal volume. The effective epsilon(int) values near 6 that are found in this study are significantly lower than many such estimates derived from sidechain pK measurements. The differing timeframes in which dielectric relaxation can respond to the highly transient peptide anion as compared to the longer lived states of the charged sidechains offers an explanation for the lower apparent dielectric constant deduced from these measurements.
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Affiliation(s)
- David M. LeMaster
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, School of Public Health, University at Albany - SUNY, Empire State Plaza, Albany, New York, 12201 USA
| | - Janet S. Anderson
- Department of Chemistry, Union College, Schenectady, New York, 12308 USA
| | - Griselda Hernández
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, School of Public Health, University at Albany - SUNY, Empire State Plaza, Albany, New York, 12201 USA
- * Corresponding author Tel: (+1)518-474-4673, Fax: (+1)518-473-2900, E-mail:
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Sundararajan M, Hillier IH, Burton NA. Structure and Redox Properties of the Protein, Rubredoxin, and Its Ligand and Metal Mutants Studied by Electronic Structure Calculation. J Phys Chem A 2005; 110:785-90. [PMID: 16405354 DOI: 10.1021/jp054276a] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The changes in the structural and electronic properties accompanying metal ionization of the iron-containing protein, rubredoxin, and of some ligand and metal mutants, have been explored using density functional theory (DFT) calculations of the metal atom coordinated to the four immediate residues. Both isolated and embedded cluster studies have been carried out, the latter using the hybrid quantum mechanics/molecular mechanics (QM/MM) approach. The replacement of a cysteine by a serine residue has a considerable effect on both the electronic and geometric structure of the core, which can be qualitatively understood on the basis of the isolated cluster studies. The modulation of these properties caused by the protein environment is quite accurately described by the QM/MM calculations. The predicted core geometries are in good accord with both X-ray and EXAFS data, and the changes in the redox potentials are predicted, at least semiquantitatively, by considering only the core part of the protein.
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van den Bosch M, Swart M, Snijders JG, Berendsen HJC, Mark AE, Oostenbrink C, van Gunsteren WF, Canters GW. Calculation of the Redox Potential of the Protein Azurin and Some Mutants. Chembiochem 2005; 6:738-46. [PMID: 15747387 DOI: 10.1002/cbic.200400244] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Azurin from Pseudomonas aeruginosa is a small 128-residue, copper-containing protein. Its redox potential can be modified by mutating the protein. Free-energy calculations based on classical molecular-dynamics simulations of the protein and from mutants in aqueous solution at different pH values were used to compute relative redox potentials. The precision of the free-energy calculations with the lambda coupling-parameter approach is evaluated as function of the number and sequence of lambda values, the sampling time and initial conditions. It is found that the precision is critically dependent on the relaxation of hydrogen-bonding networks when changing the atomic-charge distribution due to a change of redox state or pH value. The errors in the free energies range from 1 to 10 k(B)T, depending on the type of process. Only qualitative estimates of the change in redox potential by protein mutation can be obtained.
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Affiliation(s)
- Marieke van den Bosch
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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Tan ML, Dolan EA, Ichiye T. Understanding Intramolecular Electron Transfer in Ferredoxin: A Molecular Dynamics Study. J Phys Chem B 2004. [DOI: 10.1021/jp046367y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ming-Liang Tan
- Department of Chemistry, Georgetown University, Washington, D.C. 20057-1227, and School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660
| | - Elizabeth A. Dolan
- Department of Chemistry, Georgetown University, Washington, D.C. 20057-1227, and School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, D.C. 20057-1227, and School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660
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Yang X, Wang XB, Wang LS, Niu S, Ichiye T. On the electronic structures of gaseous transition metal halide complexes, FeX4− and MX3− (M=Mn, Fe, Co, Ni, X=Cl, Br), using photoelectron spectroscopy and density functional calculations. J Chem Phys 2003. [DOI: 10.1063/1.1610431] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Niu S, Wang XB, Nichols JA, Wang LS, Ichiye T. Combined Quantum Chemistry and Photoelectron Spectroscopy Study of the Electronic Structure and Reduction Potentials of Rubredoxin Redox Site Analogues. J Phys Chem A 2003. [DOI: 10.1021/jp034316f] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shuqiang Niu
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, Department of Physics, Washington State University, 2710 University Drive, Richland, Washington 99352, and W. R. Wiley Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352
| | - Xue-Bin Wang
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, Department of Physics, Washington State University, 2710 University Drive, Richland, Washington 99352, and W. R. Wiley Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352
| | - Jeffrey A. Nichols
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, Department of Physics, Washington State University, 2710 University Drive, Richland, Washington 99352, and W. R. Wiley Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352
| | - Lai-Sheng Wang
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, Department of Physics, Washington State University, 2710 University Drive, Richland, Washington 99352, and W. R. Wiley Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352
| | - Toshiko Ichiye
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, Department of Physics, Washington State University, 2710 University Drive, Richland, Washington 99352, and W. R. Wiley Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352
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Marium I, Ali M. Determination of Protein in Pakistani Meal. JOURNAL OF MEDICAL SCIENCES 2001. [DOI: 10.3923/jms.2001.63.66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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