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Volumn 126, Issue 12, 2004, Pages 3777-3788

Electronic and Spectroscopic Studies of the Non-Heme Reduced Binuclear Iron Sites of Two Ribonucleotide Reductase Variants: Comparison to Reduced Methane Monooxygenase and Contributions to O2 Reactivity

Author keywords

[No Author keywords available]

Indexed keywords

HAMILTONIANS; IRON; PROBABILITY DENSITY FUNCTION; PROTEINS; SUBSTITUTION REACTIONS;

EID: 1642395353     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0374731     Document Type: Article
Times cited : (40)

References (81)
  • 13
    • 1642417132 scopus 로고    scopus 로고
    • note
    • R2 is the subunit of RNR that contains the binuclear iron active site. MMOH is the hydroxylase component of MMO.
  • 16
    • 1642311682 scopus 로고    scopus 로고
    • note
    • peroxo.
  • 23
    • 1642357162 scopus 로고    scopus 로고
    • note
    • Both His118 and His241 are monodentate on all structures described and remain so for the rest of this paper.
  • 26
    • 1642404144 scopus 로고    scopus 로고
    • note
    • 2) indicates that both irons are bridged by the same oxygen on the carboxylate which binds in a bidentate fashion to one Fe.
  • 42
    • 0032540695 scopus 로고    scopus 로고
    • BP86 was selected as the functional in this investigation as there is a good correlation between the electronic structure of biferric peroxo complexes and that predicted by BP86 calcuations (Brunold, T. C.; et al. J. Am. Chem. Soc. 1998, 120, 5674-5690).
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 5674-5690
    • Brunold, T.C.1
  • 43
    • 1642412264 scopus 로고    scopus 로고
    • manuscript in preparation
    • Skulan, A. J., manuscript in preparation.
    • Skulan, A.J.1
  • 44
    • 1642296981 scopus 로고    scopus 로고
    • note
    • Geometry convergence criteria were as follows: change in total energy, ΔE < 5e-5 hartrees, maximum local energy gradient, δE/δS < 4.5e-4 hartrees/Å, δE/δS(RMS) < 3e-4 hartrees/Å, ΔS < 1.8e-3 Å, ΔS(RMS) < 1.2e-5 Å. Frequency calculations to verify that true minima had been attained were not possible as Jaguar 4.1 and subsequent Jaguar 5.0 have not implemented parallelized analytical frequency determination, Such calculations will be performed once this functionality has been added.
  • 45
    • 1642405781 scopus 로고    scopus 로고
    • note
    • The residue truncation was performed as follows: the α-carbon was replaced by a hydrogen atom with concomitant shortening of the α-C-β-C bond to 1.08 Å, with the β-C retaining its original position. This hydrogen was then frozen in all geometry optimizations.
  • 46
    • 1642417133 scopus 로고    scopus 로고
    • note
    • -. The positions of the heavy atoms (C, N, O) were frozen along with the positions of hydrogens replacing carbon atoms. Q43 and Q87 were modeled differently (as formamide and ammonia, respectively) as the R-group nitrogen of Q43 was located 2.8 Å from a carboxylate oxygen on D237 suggesting hydrogen bonding between these two residues which may have been of importance to the geometry of the active site. W/F48 residue, the second substitution from wt, was not included in the model as it does not coordinate to either iron or iron-coordinated residues.
  • 47
    • 1642355559 scopus 로고    scopus 로고
    • note
    • 2-) by the D84E substitution and the introduction of a water molecule which is hydrogen-bonded to E84 in the variant.
  • 49
    • 1642290495 scopus 로고    scopus 로고
    • note
    • CD was taken on a solution at 5 °C while MCD data were taken on a glass at 1.6 K.
  • 51
    • 1642329539 scopus 로고    scopus 로고
    • note
    • Because the CD/MCD of the R2-W48F/D84E are almost the same as the single variant, they are not included for clarity.
  • 53
    • 1642298639 scopus 로고    scopus 로고
    • note
    • -1 for the single variant and are included in Supporting Information S2.
  • 58
    • 1642410646 scopus 로고    scopus 로고
    • note
    • -1 band in Figure 2b.
  • 59
    • 1642347416 scopus 로고    scopus 로고
    • note
    • -1, equally good fits could be obtained using an axial (z-polarized) or rhombic (y-polarized) model.
  • 62
    • 1642323193 scopus 로고    scopus 로고
    • note
    • These starting geometries included (4C, 4C), (4C, 5C), and (5C, 5C) with E84 and E204 mono- or bidentate and E115 and E238 in μ-1,3 or μ-1,1 bridging geometries.
  • 76
    • 1642326364 scopus 로고    scopus 로고
    • note
    • The interaction is complicated by the nonzero torsion angle between the two iron atoms and the carboxylate (ψ = 32°), which leads to mixing of the carboxylate in-plane and out-of-plane O(2p) and causes the relationship between the carboxylate orbitals to be less clear in figures 12c and 12d (in contrast with figures 12a and 12b in which the perpendicular orientation of the bridging E238 O(2p) orbitals is well illustrated).
  • 78
    • 1642407428 scopus 로고    scopus 로고
    • note
    • It should be noted that the steric interaction between Y122 and E84 is not required in the geometry optimizations to reproduce the bidentate coordination of E84 to Fe1 (Figure 10). The model used for the R2-W48F/D84E active site replaces the Y122 residue with a water molecule where C is modeled by a hydrogen (with its coordinates frozen during the optimizations) and O as the water oxygen (also frozen during optimization). Thus, there is no phenyl ring present to interact with the aliphatic chain of E84, although the effects of this interaction, the addition of TIP93 and the displacement of Y122 relative to wt, are included.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.