메뉴 건너뛰기




Volumn 129, Issue 32, 2007, Pages 9927-9940

How can a single second sphere amino acid substitution cause reduction midpoint potential changes of hundreds of millivolts?

Author keywords

[No Author keywords available]

Indexed keywords

CATALYST ACTIVITY; HYDROGEN PEROXIDE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; ORGANIC SOLVENTS; PROTEINS; PROTONATION;

EID: 34547884637     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja069224t     Document Type: Article
Times cited : (44)

References (98)
  • 7
    • 0000579916 scopus 로고    scopus 로고
    • Fe-superoxide dismutase
    • Wieghardt, K, Huber, R, Poulos, T. L, Messerschmidt, A, Eds, Wiley and Sons: Chichester
    • Miller, A.-F. Fe-superoxide dismutase. In Handbook of Metalloproteins; Wieghardt, K., Huber, R., Poulos, T. L., Messerschmidt, A., Eds.; Wiley and Sons: Chichester, 2001; Vol. 1, pp 668-682.
    • (2001) Handbook of Metalloproteins , vol.1 , pp. 668-682
    • Miller, A.-F.1
  • 16
    • 85069419176 scopus 로고    scopus 로고
    • FeSOD residues are named according to the numbering of E. coli FeSOD, and MnSOD residues, according to the numbering of E. coli MnSOD.
    • FeSOD residues are named according to the numbering of E. coli FeSOD, and MnSOD residues, according to the numbering of E. coli MnSOD.
  • 44
    • 0039892284 scopus 로고
    • Becke, A. D. J. Chem. Phys. 1986, 84 (8), 4524-4539.
    • (1986) J. Chem. Phys , vol.84 , Issue.8 , pp. 4524-4539
    • Becke, A.D.1
  • 45
    • 5944261746 scopus 로고
    • Perdew, J. P. Phys. Rev. B 1986, 33 (12), 8822-8824.
    • (1986) Phys. Rev. B , vol.33 , Issue.12 , pp. 8822-8824
    • Perdew, J.P.1
  • 47
    • 85069425958 scopus 로고    scopus 로고
    • Otwinowski, Z.; Minor, W. DENZO and SCALEPACK. In Crystallography of Biological Macromolecules; Rossmann, G., Arnold, E., Eds.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 2001; F, pp 226-235.
    • Otwinowski, Z.; Minor, W. DENZO and SCALEPACK. In Crystallography of Biological Macromolecules; Rossmann, G., Arnold, E., Eds.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 2001; Vol. F, pp 226-235.
  • 51
    • 85069419816 scopus 로고    scopus 로고
    • LaMar, G. N. Spin Delocalization and Electronic Structure. In NMR of Paramagnetic Molecules; LaMar, G. N., Horrocks, W. D., Jr., Holm, R. H., Eds.; Academic Press: New York, 1973; pp 86-127.
    • LaMar, G. N. Spin Delocalization and Electronic Structure. In NMR of Paramagnetic Molecules; LaMar, G. N., Horrocks, W. D., Jr., Holm, R. H., Eds.; Academic Press: New York, 1973; pp 86-127.
  • 54
    • 85069421402 scopus 로고    scopus 로고
    • 2+SOD as weak NMR resonances slightly offset from the main ones. These could reflect a small tendency of the His69 ring to adopt an alternate conformation in which the imidazole ring is flipped, or tautomerization.
    • 2+SOD as weak NMR resonances slightly offset from the main ones. These could reflect a small tendency of the His69 ring to adopt an alternate conformation in which the imidazole ring is flipped, or tautomerization.
  • 55
    • 85069426017 scopus 로고    scopus 로고
    • 2+SOD NMR line widths are greater than those observed for the other two variants, possibly as a reflection of slower electron spin relaxation.
    • 2+SOD NMR line widths are greater than those observed for the other two variants, possibly as a reflection of slower electron spin relaxation.
  • 56
    • 85069424005 scopus 로고    scopus 로고
    • 2+SOD). Resonance assignments for the mutant proteins are required before specific proposals can be made; however differences of comparable magnitude were observed upon ionization of Tyr34, indicating that they may be explained by changes in H-bonding and/or side chain packing.
    • 2+SOD). Resonance assignments for the mutant proteins are required before specific proposals can be made; however differences of comparable magnitude were observed upon ionization of Tyr34, indicating that they may be explained by changes in H-bonding and/or side chain packing.
  • 57
    • 85069423129 scopus 로고    scopus 로고
    • We can distinguish S, 5/2 when each d orbital contains one unpaired electron and the ligand field is not strong, from S, 3/2 or 1/2 when there are more or stronger-field ligands
    • We can distinguish S = 5/2 when each d orbital contains one unpaired electron and the ligand field is not strong, from S = 3/2 or 1/2 when there are more or stronger-field ligands.
  • 60
    • 85069424077 scopus 로고    scopus 로고
    • Coordination of Glu69 as a sixth ligand is excluded by our crystal structures. Yikilmaz, et al. Biochemistry 2006, 45, 1151-1161.
    • Coordination of Glu69 as a sixth ligand is excluded by our crystal structures. Yikilmaz, et al. Biochemistry 2006, 45, 1151-1161.
  • 65
    • 85069425874 scopus 로고    scopus 로고
    • Detailed MCD, analyses of these mutants' Fe sites will be published separately
    • Detailed MCD, EPR, and computational analyses of these mutants' Fe sites will be published separately.
    • EPR, and computational
  • 66
    • 85069423343 scopus 로고    scopus 로고
    • Based on our experience with other mutants, it seems less likely that deprotonation of Tyr34 is occurring but not affecting any of the paramagnetically dispersed resonances.
    • Based on our experience with other mutants, it seems less likely that deprotonation of Tyr34 is occurring but not affecting any of the paramagnetically dispersed resonances.
  • 67
    • 85069421052 scopus 로고    scopus 로고
    • The rmsd between backbone heavy atoms of the 1.6 Å structure and the 1.1 Å structure is 0.4 Å.
    • The rmsd between backbone heavy atoms of the 1.6 Å structure and the 1.1 Å structure is 0.4 Å.
  • 68
    • 85069424931 scopus 로고    scopus 로고
    • Although we were not able to resolve discrete density for labile protons in the active site, aliphatic (nonexchangable) H atoms were visible on side chains in numerous areas of the structure
    • Although we were not able to resolve discrete density for labile protons in the active site, aliphatic (nonexchangable) H atoms were visible on side chains in numerous areas of the structure.
  • 69
    • 85069426653 scopus 로고    scopus 로고
    • Averaged over four sites per crystallographic unit cell
    • Averaged over four sites per crystallographic unit cell.
  • 70
    • 85069420429 scopus 로고    scopus 로고
    • 4 structures were identified of which 2 were suspect.
    • 4 structures were identified of which 2 were suspect.
  • 72
    • 85069422856 scopus 로고    scopus 로고
    • Carboxylates or carboxylic acids in which one O is H-bonded to water were identified in the Cambridge Structural Database. For 166 carboxylates receiving an H-bond from water, the average C-O distance for the H-bonded O was 1.24 Å (0.0L2) and the average C-O distance for the non-H-bonded O was 1.26 Å (0.012, These two distances are not significantly different, although there was a slight tendency for the O engaged in an H-bond to have a longer bond to C. In contrast, in 13 structures of neutral carboxylic acids donating an H-bond to water, the protonated O had an average C-O bond length that was 1.31 Å (0.015, more than 3 standard deviations longer than the double bonded C-O average distance of 1.22 Å 0.015, indicating localization of the double bond
    • Carboxylates or carboxylic acids in which one O is H-bonded to water were identified in the Cambridge Structural Database. For 166 carboxylates receiving an H-bond from water, the average C-O distance for the H-bonded O was 1.24 Å (0.0L2) and the average C-O distance for the non-H-bonded O was 1.26 Å (0.012). These two distances are not significantly different, although there was a slight tendency for the O engaged in an H-bond to have a longer bond to C. In contrast, in 13 structures of neutral carboxylic acids donating an H-bond to water, the protonated O had an average C-O bond length that was 1.31 Å (0.015), more than 3 standard deviations longer than the double bonded C-O average distance of 1.22 Å (0.015), indicating localization of the double bond.
  • 73
    • 85069419633 scopus 로고    scopus 로고
    • Glu 159 was chosen as a control on the basis of its excellent electron density and low B values.
    • Glu 159 was chosen as a control on the basis of its excellent electron density and low B values.
  • 75
    • 85069423876 scopus 로고    scopus 로고
    • In both models, Tyr34, Glu69, and coordinated solvent were neutral. In one, Tyr34's hydroxyl H was directed toward Glu69 to donate an H-bond; in the other, Tyr34's hydroxyl H was directed away from Glu69 and Tyr34 accepted an H-bond from Glu69.
    • In both models, Tyr34, Glu69, and coordinated solvent were neutral. In one, Tyr34's hydroxyl H was directed toward Glu69 to donate an H-bond; in the other, Tyr34's hydroxyl H was directed away from Glu69 and Tyr34 accepted an H-bond from Glu69.
  • 76
    • 85069421035 scopus 로고    scopus 로고
    • While the residue mutated derives from the second sphere, one interpretation of our results is that altered H-bonding resulting from the mutation in effect changes the nature of a first sphere residue, from more OH--like to more H2O-like
    • 2O-like.
  • 77
    • 85069419311 scopus 로고    scopus 로고
    • It is reasonable that the nearby net-positively charged Fe center would disfavor protonation of His69
    • It is reasonable that the nearby net-positively charged Fe center would disfavor protonation of His69.
  • 79
    • 85069425660 scopus 로고    scopus 로고
    • m increases by 60 mV per unit decrease in pH.
    • m increases by 60 mV per unit decrease in pH.
  • 80
    • 85069423446 scopus 로고    scopus 로고
    • Q69E-Fe3+SOD's high affinity for a sixth ligand could represent effective long-range ionization of hydrated Glu69, via the equilibrium: Glu, H2O ↔ GluH, OH
    • -).
  • 83
    • 85069423332 scopus 로고    scopus 로고
    • 2+SOD we estimate a pK near 11. Both are consistent with experimental data on WT-FeSOD.
    • 2+SOD we estimate a pK near 11. Both are consistent with experimental data on WT-FeSOD.
  • 86
    • 85069425992 scopus 로고    scopus 로고
    • This is consistent with the fact that Glu's intrinsic pK falls between those of water coordinated to Fe3+ and water coordinated to Fe2
    • 2+.
  • 87
    • 85069424527 scopus 로고    scopus 로고
    • We do not place strong emphasis on energies calculated for restrained models because they were not fully optimized. However an optimized model of the Q69E-FeSOD active site yielded an Em 400 mV higher than that of WT-FeSOD when both oxidized states were assumed to be pentacoordinate, for ease of comparison. Thus, simplifed active sites are able to reproduce a large fraction of the observed elevation of Q69E-FeSOD's Em relative to WT-FeSOD, lending credibility to the computational results, in general
    • m relative to WT-FeSOD, lending credibility to the computational results, in general.
  • 88
    • 85069423155 scopus 로고    scopus 로고
    • However the free energy of dissociation of water must be taken into account when relating the energies of the two formulations
    • However the free energy of dissociation of water must be taken into account when relating the energies of the two formulations.
  • 89
    • 85069423811 scopus 로고    scopus 로고
    • Q69H-FeSOD was found to retain a WT-like active site structure [Yikilmaz, et al. Biochemistry 2006, 45, 1151-1161
    • Q69H-FeSOD was found to retain a WT-like active site structure [Yikilmaz, et al. Biochemistry 2006, 45, 1151-1161].
  • 94
    • 85069426906 scopus 로고    scopus 로고
    • m of Q69E-FeSOD.
    • m of Q69E-FeSOD.
  • 95
    • 85069424244 scopus 로고    scopus 로고
    • ox = 4.3, yielding 680 mV. More details are provided in the Supporting Information.
    • ox = 4.3, yielding 680 mV. More details are provided in the Supporting Information.
  • 97
    • 85069426187 scopus 로고    scopus 로고
    • m is proportional to the energy of the oxidized state minus that of the reduced state, of the active site.
    • m is proportional to the energy of the oxidized state minus that of the reduced state, of the active site.
  • 98
    • 85069421238 scopus 로고    scopus 로고
    • m by approximately 140 mV.
    • m by approximately 140 mV.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.