Strategy for the study of paramagnetic proteins with slow electronic relaxation rates by nmr spectroscopy: application to oxidized human [2Fe-2S] ferredoxin

NMR studies of paramagnetic proteins are hampered by the rapid relaxation of nuclei near the paramagnetic center, which prevents the application of conventional methods to investigations of the most interesting regions of such molecules. This problem is particularly acute in systems with slow electronic relaxation rates. We present a strategy that can be used with a protein with slow electronic relaxation to identify and assign resonances from nuclei near the paramagnetic center. Oxidized human [2Fe-2S] ferredoxin (adrenodoxin) was used to test the approach. The strategy involves six steps: (1) NMR signals from (1)H, (13)C, and (15)N nuclei unaffected or minimally affected by paramagnetic effects are assigned by standard multinuclear two- and three-dimensional (2D and 3D) spectroscopic methods with protein samples labeled uniformly with (13)C and (15)N. (2) The very broad, hyperfine-shifted signals from carbons in the residues that ligate the metal center are classified by amino acid and atom type by selective (13)C labeling and one-dimensional (1D) (13)C NMR spectroscopy. (3) Spin systems involving carbons near the paramagnetic center that are broadened but not hyperfine-shifted are elucidated by (13)C[(13)C] constant time correlation spectroscopy (CT-COSY). (4) Signals from amide nitrogens affected by the paramagnetic center are assigned to amino acid type by selective (15)N labeling and 1D (15)N NMR spectroscopy. (5) Sequence-specific assignments of these carbon and nitrogen signals are determined by 1D (13)C[(15)N] difference decoupling experiments. (6) Signals from (1)H nuclei in these spin systems are assigned by paramagnetic-optimized 2D and 3D (1)H[(13)C] experiments. For oxidized human ferredoxin, this strategy led to assignments (to amino acid and atom type) for 88% of the carbons in the [2Fe-2S] cluster-binding loops (residues 43-58 and 89-94). These included complete carbon spin-system assignments for eight of the 22 residues and partial assignments for each of the others. Sequence-specific assignments were determined for the backbone (15)N signals from nine of the 22 residues and ambiguous assignments for five of the others.     

Collocation Methods for Weakly Singular Second-kind Volterra Integral Equations with Non-smooth Solution

Collocation type methods are studied for the numerical solutionof the weakly singular Volterra integral equation of the secondkind: where the solution (t) is assumedto have the form f(t) = x(t)+r^?(t), x and being sufficientlysmooth. The solution is approximated near zero by a linear combinationof powers of t?, and away from zero by the usual polynomialrepresentation. Convergence is proved and many numerical experimentsare carried out with examples from the literature. A comparisonis made with a method of Brunner & Norsett (1981), originallydeveloped for (1) with a smooth solution. Special attentionis paid to the numerical approximation of the so-called momentintegrals which emerge in the collocation scheme.     

Solution and structural characterization of iron(II) complexes with ortho-halogenated phenolates: insights into potential substrate binding modes in hydroquinone dioxygenases

The new ligand cis,cis-1,3,5-tris-(E)-(tolylideneimino)cyclohexane (TACH-o-tolyl) forms a 1:1 complex with iron(II). Addition of substituted phenolates forms 1:1:1 ligand:iron:phenolate complexes, which have been characterized both in the solid state and in solution. There is complete binding of the phenolate to the complex only when there are ortho-halogens on the phenolate. The tertiary complexes with ortho-halo-substituted phenolates exhibit short Fe-halogen distances, and the complex containing a non-coordinating but similarly sized ortho-methyl phenolate has a significantly different conformation and coordination geometry. Therefore, it is likely that the metal-halogen interaction stabilizes the complexes. The iron(II)-halogen interaction in these complexes may explain the substrate specificity of PcpA and LinE, enzymes that preferentially bind phenols and hydroquinones containing halogen substituents in ortho positions.     

无机酸洗脱对胜利褐煤微晶结构及其自燃倾向性的影响

利用XRD、Raman、XPS和FT-IR表征技术,研究无机酸洗脱(HCl、H2SO4、HCl-HF)处理的胜利褐煤微晶结构的变化,采用自行设计的表面吸附仪-GC联用装置,对样品进行不同温度的低温脉冲氧化实验,考察了煤样在不同温度下氧吸附量的变化规律,通过低温脉冲氧吸附规律与TG/DTG和固定床燃烧实验关联,考察了煤样的自燃倾向。结果表明,无机酸洗脱对矿物质的脱除使得煤结构的有序度增加,石墨化程度提高,无机酸洗脱煤样与原煤相比吸氧量明显下降。随着吸附温度的升高,各煤样吸氧量明显增加,且随着脱除矿物质程度的增加,吸氧量呈减小的趋势,导致自燃倾向降低。     

Spectroscopy and reactivity of the type 1 copper site in Fet3p from Saccharomyces cerevisiae: correlation of structure with reactivity in the multicopper oxidases

Fet3p is a multicopper oxidase recently isolated from the yeast, Saccharomyces cerevisiae. Fet3p is functionally homologous to ceruloplasmin (Cp) in that both are ferroxidases. However, by sequence homology Fet3p is more similar to fungal laccase, and both contain a type 1 Cu site that lacks the axial methionine ligand present in the functional type 1 sites of Cp. To determine the contribution of the electronic structure of the type 1 Cu site of Fet3p to the ferroxidase mechanism, we have examined the absorption, circular dichroism, magnetic circular dichroism, electron paramagnetic resonance, and resonance Raman spectra of wild-type Fet3p and type 1 and type 2 Cu-depleted mutants. The spectroscopic features of the type 1 Cu site of Fet3p are nearly identical to those of fungal laccase, indicating a very similar three-coordinate geometry. We have also examined the reactivity of the type 1 Cu site by means of redox titrations and stopped-flow kinetics. From poised potential redox titrations, the E degrees of the type 1 Cu site is 427 mV, which is low for a three-coordinate type 1 Cu site. The kinetics of reduction of the type 1 Cu sites of four different multicopper oxidases with two different substrates were compared. The type 1 site of a plant laccase (Rhus vernicifera) is reduced moderately slowly by both Fe(II) and a bulky organic substrate, 1,4-hydroquinone (with 6 equiv of substrate, k(obs) = 0.029 and 0.013 s(-)(1), respectively). On the other hand, the type 1 site of a fungal laccase (Coprinus cinereus) is reduced very rapidly by both substrates (k(obs) > 23 s(-)(1)). In contrast, both Fet3p and Cp are rapidly reduced by Fe(II) (k(obs) > 23 s(-)(1)), but only very slowly by 1,4-hydroquinone (10- and 100-fold more slowly than plant laccase, respectively). Semiclassical theory is used to analyze the origin of these differences in reactivity in terms of type 1 Cu site accessibility to specific substrates.     

An approximate treatment of scattering based on the delta boundary operator

The development of a scheme to treat two-dimensional electromagneticscattering by electrically large, perfectly conducting bodiesis described. It incorporates the effects of surface curvatureand non-local phenomena and has the potential to provide thebasis for a general technique yielding more accurate predictionsthan the widely used physical optics method.     

Paramagnetic NMR spectroscopy and density functional calculations in the analysis of the geometric and electronic structures of iron-sulfur proteins

Paramagnetic NMR spectroscopy has been underutilized in the study of metalloproteins. One difficulty of the technique is that paramagnetic relaxation broadens signals from nuclei near paramagnetic centers. In systems with low electronic relaxation rates, this makes such signals difficult to observe or impossible to assign by traditional methods. We show how the challenges of detecting and assigning signals from nuclei near the metal center can be overcome through the combination of uniform and selective 2H, 13C, and 15N isotopic labeling with NMR experiments that utilize direct one-dimensional (2H, 13C, and 15N) and two-dimensional (13C-X) detection. We have developed methods for calculating NMR chemical shifts and relaxation rates by density functional theory (DFT) approaches. We use the correspondence between experimental NMR parameters and those calculated from structural models of iron-sulfur clusters derived from X-ray crystallography to validate the computational approach and to investigate how structural differences are manifested in these values. We have applied this strategy to three iron-sulfur proteins: Clostridium pasteurianum rubredoxin, Anabaena [2Fe-2S] ferredoxin, and human [2Fe-2S] ferredoxin. Provided that an accurate structural model of the iron-sulfur cluster and surrounding residues is available from diffraction data, our results show that DFT calculations can return NMR observables with excellent accuracy. This suggests that it might be possible to use calculations to refine structures or to generate structural models of active sites when crystal structures are unavailable. The approach has yielded insights into the electronic structures of these iron-sulfur proteins. In rubredoxin, the results show that substantial unpaired electron spin is delocalized across NH...S hydrogen bonds and that the reduction potential can be changed by 77 mV simply by altering the strength of one of these hydrogen bonds. In reduced [2Fe-2S] ferredoxins, hyperfine shift data have provided quantitative information on the degree of valence trapping. The approach described here for iron-sulfur proteins offers new avenues for detailed studies of these and other metalloprotein systems.     

(13)C[(13)C] 2D NMR: a novel strategy for the study of paramagnetic proteins with slow electronic relaxation rates

Oxidized human [2Fe-2S] ferredoxin has a notably slow electronic relaxation rate, which precludes the observation of signals from nuclei near the iron-sulfur cluster by conventional 2D or 3D methods that utilize proton detection. We have demonstrated the utility of (13)C[(13)C]CT-COSY in identifying connectivity information from fast relaxing carbon nuclei near the paramagnetic center, including those from residues that ligate the metal center.     

Correlation between hydrogen bond lengths and reduction potentials in Clostridium pasteurianum rubredoxin

15N NMR hyperfine-shift data were collected for wild-type and site-specific mutant (V44I, V44A, and V44G) Clostridium pasteurianum rubredoxins in the oxidized state. Whereas most of the (15)N NMR signals did not exhibit large systematic changes upon mutation of residue 44, the signal from the backbone nitrogen of residue 44 itself (arrows) shifted by approximately 400 ppm. These shifts were used to determine the lengths of the hydrogen bond between the backbone amide of residue 44 and the side-chain sulfur of cysteine-44, which is covalently ligated to the iron of the metal center. The results, which demonstrated that this hydrogen bond is shorter in mutants with higher reduction potential, point to the importance of hydrogen bonds in modulating the reduction potential of iron-sulfur proteins.