Analytical characterization of IgG Fc subclass variants through high-resolution separation combined with multiple LC-MS identification.

With the rapid growth of recombinant monoclonal antibodies and intravenous immunoglobulin (IVIg) medicines, the understanding of human immunoglobulin G (IgG) subclasses becomes more necessary. It is essential to develop effective techniques and methodologies which have the capability for deep characterization. We have created an approach by applying LC and liquid chromatography-mass spectrometry (LC-MS) methods to thoroughly characterize Fc/2 sequence variants for human IgG subclasses in complex samples. Identification and relative quantitation of sequence variants have been provided. Unique glycan information of each IgG subclass can also be obtained by this method. The approach was based on high-resolution HPLC separation followed by intact LC-MS. Peptide mapping was performed following sample fractionation to identify sequence variants. IVIg, a purified IgG mixture from pooled human plasma of thousands of blood donors, was selected as an example for method development. The amino acid sequence variants in IgG Fc/2 constant region were fully investigated for all subclasses by these methods. A total of 19 sequence variants were identified, and their relative abundances were quantitated, which included six variants in IgG1, eight in IgG2, three in IgG3, and two in IgG4. Unique glycan data was also provided for each Fc subclass, which is particularly important for IgG3; glycans from this subclass have only previously been reported together with IgG2 or IgG4. The method described in this paper has been proved to be an effective approach for deep characterization of IgG Fc/2 for complex samples. The findings of IVIg from these studies are also valuable for better understanding of human IgGs.

The active form of the Saccharomyces cerevisiae ribonucleotide reductase small subunit is a heterodimer in vitro and in vivo.

The class I ribonucleotide reductases (RNRs) are composed of two homodimeric subunits: R1 and R2. R2 houses a diferric-tyrosyl radical (Y*) cofactor. Saccharomyces cerevisiae has two R2s: Y2 (beta2) and Y4 (beta'2). Y4 is an unusual R2 because three residues required for iron binding have been mutated. While the heterodimer (betabeta') is thought to be the active form, several rnr4delta strains are viable. To resolve this paradox, N-terminally epitope-tagged beta and beta' were expressed in E. coli or integrated into the yeast genome. In vitro exchange studies reveal that when apo-(His6)-beta2 ((His)beta2) is mixed with beta'2, apo-(His)betabeta' forms quantitatively within 2 min. In contrast, holo-betabeta' fails to exchange with apo-(His)beta2 to form holo-(His)betabeta and beta'2. Isolation of genomically encoded tagged beta or beta' from yeast extracts gave a 1:1 complex of beta and beta', suggesting that betabeta' is the active form. The catalytic activity, protein concentrations, and Y* content of the rnr4delta and wild type (wt) strains were compared to clarify the role of beta' in vivo. The Y* content of rnr4delta is 15-fold less than that of wt, consistent with the observed low activity of rnr4delta extracts (<0.01 nmol min(-1) mg(-1)) versus wt (0.06 +/- 0.01 nmol min(-1) mg(-1)). (FLAG)beta2 isolated from the rnr4delta strain has a specific activity of 2 nmol min(-1) mg(-1), similar to that of reconstituted apo-(His)beta2 (10 nmol min(-1) mg(-1)), but significantly less than holo-(His)betabeta' (approximately 2000 nmol min(-1) mg(-1)). These studies together demonstrate that beta' plays a crucial role in cluster assembly in vitro and in vivo and that the active form of the yeast R2 is betabeta'.

EPR distance measurements support a model for long-range radical initiation in E. coli ribonucleotide reductase.

The class I E. coli ribonucleotide reductase, composed of homodimers of R1 and R2, catalyzes the conversion of nucleoside diphosphates to deoxynucleoside diphosphates. The reduction process involves the tyrosyl radical on R2 that generates a transient thiyl radical on R1 over a proposed distance of 35 A. A mechanism-based inhibitor, 2'-azido-2'-deoxyuridine-5'-diphosphate, that reduces the tyrosyl radical on R2 and forms a nitrogen-centered radical on R1 has provided a method to measure the diagonal distance between the two subunits. PELDOR and DQC paramagnetic resonance methods give rise to a distance of 48 A, similar to that calculated from a docking model of the R1 and R2 structures.

Structure of the nitrogen-centered radical formed during inactivation of E. coli ribonucleotide reductase by 2'-azido-2'-deoxyuridine-5'-diphosphate: trapping of the 3'-ketonucleotide.

Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides providing the monomeric precursors required for DNA replication and repair. The class I RNRs are composed of two homodimeric subunits: R1 and R2. R1 has the active site where nucleotide reduction occurs, and R2 contains the diiron tyrosyl radical (Y*) cofactor essential for radical initiation on R1. Mechanism-based inhibitors, such as 2'-azido-2'-deoxyuridine-5'-diphosphate (N(3)UDP), have provided much insight into the reduction mechanism. N(3)UDP is a stoichiometric inactivator that, upon interaction with RNR, results in loss of the Y* in R2 and formation of a nitrogen-centered radical (N*) covalently attached to C225 (R-S-N*-X) in the active site of R1. N(2) is lost prior to N* formation, and after its formation, stoichiometric amounts of 2-methylene-3-furanone, pyrophosphate, and uracil are also generated. On the basis of the hyperfine interactions associated with N*, it was proposed that N* is also covalently attached to the nucleotide through either the oxygen of the 3'-OH (R-S-N*-O-R') or the 3'-C (R-S-N*-C-OH). To distinguish between the proposed structures, the inactivation was carried out with 3'-[(17)O]-N(3)UDP and N* was examined by 9 and 140 GHz EPR spectroscopy. Broadening of the N* signal was detected and the spectrum simulated to obtain the [(17)O] hyperfine tensor. DFT calculations were employed to determine which structures are in best agreement with the simulated hyperfine tensor and our previous ESEEM data. The results are most consistent with the R-S-N*-C-OH structure and provide evidence for the trapping of a 3'-ketonucleotide in the reduction process.

Resonant inelastic X-ray scattering (RIXS) spectroscopy at the Mn K absorption pre-edge-a direct probe of the 3d orbitals.

A study of the Mn K absorption pre-edges in oxides using resonant inelastic X-ray scattering (RIXS) spectroscopy is presented. The energy transfer dimension enhances the separation of the pre-edge (predominantly 1s to 3d transitions) from the main K-edge and a detailed analysis is thus possible. The RIXS spectra are sensitive to the Mn spin state. The technique thus yields detailed information on the electronic structure that is not accessible in conventional K-edge absorption spectroscopy. The line splittings can be understood within a ligand field multiplet model, showing the importance of (2p,3d) two-electron interactions that give rise to the spin-sensitivity.

Orientation of calcium in the Mn4Ca cluster of the oxygen-evolving complex determined using polarized strontium EXAFS of photosystem II membranes.

The oxygen-evolving complex of photosystem II (PS II) in green plants and algae contains a cluster of four Mn atoms in the active site, which catalyzes the photoinduced oxidation of water to dioxygen. Along with Mn, calcium and chloride ions are necessary cofactors for proper functioning of the complex. The current study using polarized Sr EXAFS on oriented Sr-reactivated samples shows that Fourier peak II, which fits best to Mn at 3.5 A rather than lighter atoms (C, N, O, or Cl), is dichroic, with a larger magnitude at 10 degrees (angle between the PS II membrane normal and the X-ray electric field vector) and a smaller magnitude at 80 degrees . Analysis of the dichroism of the Sr EXAFS yields a lower and upper limit of 0 degrees and 23 degrees for the average angle between the Sr-Mn vectors and the membrane normal and an isotropic coordination number (number of Mn neighbors to Sr) of 1 or 2 for these layered PS II samples. The results confirm the contention that Ca (Sr) is proximal to the Mn cluster and lead to refined working models of the heteronuclear Mn(4)Ca cluster of the oxygen-evolving complex in PS II.

The electronic structure of Mn in oxides, coordination complexes, and the oxygen-evolving complex of photosystem II studied by resonant inelastic X-ray scattering.

Resonant inelastic X-ray scattering (RIXS) was used to collect Mn K pre-edge spectra and to study the electronic structure in oxides, molecular coordination complexes, as well as the S1 and S2 states of the oxygen-evolving complex (OEC) of photosystem II (PS II). The RIXS data yield two-dimensional plots that can be interpreted along the incident (absorption) energy or the energy transfer axis. The second energy dimension separates the pre-edge (predominantly 1s to 3d transitions) from the main K-edge, and a detailed analysis is thus possible. The 1s2p RIXS final-state electron configuration along the energy transfer axis is identical to conventional L-edge absorption spectroscopy, and the RIXS spectra are therefore sensitive to the Mn spin state. This new technique thus yields information on the electronic structure that is not accessible in conventional K-edge absorption spectroscopy. The line splittings can be understood within a ligand field multiplet model, i.e., (3d,3d) and (2p,3d) two-electron interactions are crucial to describe the spectral shapes in all systems. We propose to explain the shift of the K pre-edge absorption energy upon Mn oxidation in terms of the effective number of 3d electrons (fractional 3d orbital population). The spectral changes in the Mn 1s2p(3/2) RIXS spectra between the PS II S1 and S2 states are small compared to that of the oxides and two of the coordination complexes (Mn(III)(acac)3 and Mn(IV)(sal)2(bipy)). We conclude that the electron in the step from S1 to S2 is transferred from a strongly delocalized orbital.

Chloride ligation in inorganic manganese model compounds relevant to photosystem II studied using X-ray absorption spectroscopy.

Chloride ions are essential for proper function of the photosynthetic oxygen-evolving complex (OEC) of Photosystem II (PS II). Although proposed to be directly ligated to the Mn cluster of the OEC, the specific structural and mechanistic roles of chloride remain unresolved. This study utilizes X-ray absorption spectroscopy (XAS) to characterize the Mn-Cl interaction in inorganic compounds that contain structural motifs similar to those proposed for the OEC. Three sets of model compounds are examined; they possess core structures Mn(IV)(3)O(4)X (X=Cl, F, or OH) that contain a di-micro-oxo and two mono-micro-oxo bridges or Mn(IV)(2)O(2)X (X=Cl, F, OH, OAc) that contain a di-micro-oxo bridge. Each set of compounds is examined for changes in the XAS spectra that are attributable to the replacement of a terminal OH or F ligand, or bridging OAc ligand, by a terminal Cl ligand. The X-ray absorption near edge structure (XANES) shows changes in the spectra on replacement of OH, OAc, or F by Cl ligands that are indicative of the overall charge of the metal atom and are consistent with the electronegativity of the ligand atom. Fourier transforms (FTs) of the extended X-ray absorption fine structure (EXAFS) spectra reveal a feature that is present only in compounds where chloride is directly ligated to Mn. These FT features were simulated using various calculated Mn-X interactions (X=O, N, Cl, F), and the best fits were found when a Mn-Cl interaction at a 2.2-2.3 A bond distance was included. There are very few high-valent Mn halide complexes that have been synthesized, and it is important to make such a comparative study of the XANES and EXAFS spectra because they have the potential for providing information about the possible presence or absence of halide ligation to the Mn cluster in PS II.

Mn oxidation states in tri- and tetra-nuclear Mn compounds structurally relevant to photosystem II: Mn K-edge X-ray absorption and Kß X-ray emission spectroscopy studies.

X-Ray spectroscopy is used to examine the effect of the manganese oxidation state for a series of Mn model compounds. Sensitive to Mn oxidation and structural symmetry, X-ray absorption and emission spectroscopy (XAS and XES) provide complementary insights. However, few benchmark examples of complexes with similar structures but in different oxidation states are available to evaluate data from unknown structures like the oxygen evolving complex (OEC) of Photosystem II (PSII). This study examines two types of compounds prepared in a variety of Mn oxidation states and which possess chemical structures with Mn-Mn interactions (~2.7 Å and ~3.3 Å) that have been observed in the OEC. Model complexes with core compositions Mn3O and Mn4O2 contain combinations of Mn in either a reduced (II) or oxidized (III) state. Within each set of compounds, complexes with higher Mn oxidation states have absorption K-edge energy values that are higher (1.6-2.2 eV) than those of their more reduced counterparts. This trend is accordingly reversed in the Kß emission spectroscopy where the first moment energy values are lower (0.09-0.12 eV) for compounds with higher Mn oxidation states. We will discuss in detail, how these trends can be quantitatively used to characterize the effects of the Mn oxidation state as well as the surrounding ligand environment on the observed X-ray spectra. The results are discussed with respect to previously obtained data on different S-states of the OEC.

Calcium EXAFS establishes the Mn-Ca cluster in the oxygen-evolving complex of photosystem II.

The proximity of Ca to the Mn cluster of the photosynthetic water-oxidation complex is demonstrated by X-ray absorption spectroscopy. We have collected EXAFS data at the Ca K-edge using active PS II membrane samples that contain approximately 2 Ca per 4 Mn. These samples are much less perturbed than previously investigated Sr-substituted samples, which were prepared after Ca depletion. The new Ca EXAFS clearly shows backscattering from Mn at 3.4 A, a distance that agrees with that surmised from previously recorded Mn EXAFS. This result is also consistent with earlier related experiments at the Sr K-edge, using samples that contained functional Sr, that show Mn is approximately 3.5 A distant from Sr. The totality of the evidence clearly advances the notion that the catalytic center of oxygen evolution is a Mn-Ca heteronuclear cluster.

The Mn cluster in the S(0) state of the oxygen-evolving complex of photosystem II studied by EXAFS spectroscopy: are there three Di-mu-oxo-bridged Mn(2) moieties in the tetranuclear Mn complex?

A key component required for an understanding of the mechanism of the evolution of molecular oxygen by the photosynthetic oxygen-evolving complex (OEC) in photosystem II (PS II) is the knowledge of the structures of the Mn cluster in the OEC in each of its intermediate redox states, or S-states. In this paper, we report the first detailed structural characterization using Mn extended X-ray absorption fine structure (EXAFS) spectroscopy of the Mn cluster of the OEC in the S(0) state, which exists immediately after the release of molecular oxygen. On the basis of the EXAFS spectroscopic results, the most likely interpretation is that one of the di-mu-oxo-bridged Mn-Mn moieties in the OEC has increased in distance from 2.7 A in the dark-stable S(1) state to 2.85 A in the S(0) state. Furthermore, curve fitting of the distance heterogeneity present in the EXAFS data from the S(0) state leads to the intriguing possibility that three di-mu-oxo-bridged Mn-Mn moieties may exist in the OEC instead of the two di-mu-oxo-bridged Mn-Mn moieties that are widely used in proposed structural models for the OEC. This possibility is developed using novel structural models for the Mn cluster in the OEC which are consistent with the structural information available from EXAFS and the recent X-ray crystallographic structure of PS II at 3.8 A resolution.

Strontium EXAFS Reveals the Proximity of Calcium to the Manganese Cluster of Oxygen-Evolving Photosystem II.

The oxygen-evolving complex of Photosystem II (PS II) in green plants and algae contains a cluster of four manganese atoms in the active site, which catalyzes the photoinduced oxidation of water to dioxygen. Along with Mn, calcium and chloride ions are necessary cofactors for proper functioning of the complex. A key unresolved question is whether Ca is close to the Mn cluster, within about 3.5 Å. To further test and verify this finding, we substituted strontium for Ca and probed from the Sr point-of-view for any nearby Mn. Sr has been shown to replace Ca and still maintain enzyme activity (about 40% of normal rate). The extended X-ray absorption fine structure (EXAFS) of Sr-PS II probes the local environment around the Sr cofactor to detect any nearby Mn. We focused on the functional Sr by removing nonessential, loosely bound Sr in the protein environment. For comparison, an inactive sample was prepared by treating the intact PS II with hydroxylamine to disrupt the Mn cluster and to produce nonfunctional enzyme. Sr EXAFS results indicate major differences in the phase and amplitude between the functional (intact) and nonfunctional (NH2OH-treated) samples. In intact samples, the Fourier transform of the Sr EXAFS shows a peak that is missing in inactive samples. This Fourier peak II is best simulated by two Mn neighbors at a distance of 3.5 Å. Thus, with X-ray absorption studies on Sr-reconstituted PS II, we confirm the proximity of Ca (Sr) cofactor to the Mn cluster and show that the active site is a Mn-Ca heteronuclear cluster.