A quantitative XANES analysis of the calcium high-affinity binding site of the purple membrane

HwMR is a novel magnesium-associated protein

Microbial rhodopsins (MRho) are vital proteins in Haloarchaea for solar light sensing in extreme living environments. Among them, Haloquadratum walsbyi (Hw) is a species known to survive high MgCl₂ concentrations, with a total of three MRhos identified, including a high-acid-tolerance light-driven proton outward pump, HwBR, a chloride-insensitive chloride pump, HwHR, and a functionally unknown HwMR. Here, we showed that HwMR is the sole magnesium-sensitive MRho among all tested MRho proteins from Haloarchaea. We identified at least D84 as one of the key residues mediating such magnesium ion association in HwMR. Sequence analysis and molecular modeling suggested HwMR to have an extra H8 helix in the cytosolic region like those in signal-transduction-type MRho of deltarhodopsin-3 (dR-3) and Anabaena sensory rhodopsin (ASR). Further, HwMR showed a distinctly prolonged M-state formation under a high concentration of Mg²⁺. On the other hand, an H8 helix truncated mutant preserved photocycle kinetics like the wild type, but it led to missing M-state structure. Our findings clearly suggested not only that HwMR is a novel Mg²⁺-associated protein but that the association with both Mg²⁺ and the H8 domain stabilizes M-state formation in HwMR. We conclude that Mg²⁺ association and H8 are crucial in stabilizing HwMR M state, which is a well-known photoreceptor signaling state.

Surface Sorption Site and Complexation Structure of Ca2+ at the Goethite-Water Interface: A Molecular Dynamics Simulation and Quantitative XANES Analysis

The molecular-level surface complexation structure of Ca²⁺ at the goethite/water interface remains unclear. We investigated the sorption of Ca²⁺ on the surfaces of goethite using classical molecular dynamics (MD) simulations and Ca K-edge X-ray absorption near edge structure (XANES) spectroscopy. The XANES results showed that Ca²⁺ was sequestered by goethite dominantly via sorption at pH ≤ 9, whereas the Ca(OH)₂ surface precipitate formed at pH 10 for an initial Ca²⁺ concentration of 2 mM. The MD simulations showed that Ca²⁺ dominantly absorbed on the (100) and (110) surfaces of goethite via bidentate binuclear complexation by forming ≡(Fe-OH)₂Ca²⁺·5H₂O species, whereas little Ca²⁺ adsorbed on the (021) surface. The theoretical Ca K-edge XANES spectrum calculations gave a mean Ca-O interatomic distance of 2.34 Å (2.23-2.55 Å) and a Ca-Fe interatomic distance of 3.80 Å (3.79-3.81 Å) at goethite/water interface. Our results may shed some light on the geochemical cycling of calcium and other related cations and anions.

Contemporary Use of Anomalous Diffraction in Biomolecular Structure Analysis

The normal elastic X-ray scattering that depends only on electron density can be modulated by an "anomalous" component due to resonance between X-rays and electronic orbitals. Anomalous scattering thereby precisely identifies atomic species, since orbitals distinguish atomic elements, which enables the multi- and single-wavelength anomalous diffraction (MAD and SAD) methods. SAD now predominates in de novo structure determination of biological macromolecules, and we focus here on the prevailing SAD method. We describe the anomalous phasing theory and the periodic table of phasing elements that are available for SAD experiments, differentiating between those readily accessible for at-resonance experiments and those that can be effective away from an edge. We describe procedures for present-day SAD phasing experiments and we discuss optimization of anomalous signals for challenging applications. We also describe methods for using anomalous signals as molecular markers for tracing and element identification. Emerging developments and perspectives are discussed in brief.

The status of strontium in biological apatites: an XANES/EXAFS investigation

Osteoporosis represents a major public health problem through its association with fragility fractures. The public health burden of osteoporotic fractures will rise in future generations, due in part to an increase in life expectancy. Strontium-based drugs have been shown to increase bone mass in postmenopausal osteoporosis patients and to reduce fracture risk but the molecular mechanisms of the action of these Sr-based drugs are not totally elucidated. The local environment of Sr(2+) cations in biological apatites present in pathological and physiological calcifications in patients without such Sr-based drugs has been assessed. In this investigation, X-ray absorption spectra have been collected for 17 pathological and physiological calcifications. These experimental data have been combined with a set of numerical simulations using the ab initio FEFF9 X-ray spectroscopy program which takes into account possible distortion and Ca/Sr substitution in the environment of the Sr(2+) cations. For selected samples, Fourier transforms of the EXAFS modulations have been performed. The complete set of experimental data collected on 17 samples indicates that there is no relationship between the nature of the calcification (physiological and pathological) and the adsorption mode of Sr(2+) cations (simple adsorption or insertion). Such structural considerations have medical implications. Pathological and physiological calcifications correspond to two very different preparation procedures but are associated with the same localization of Sr(2+) versus apatite crystals. Based on this study, it seems that for supplementation of Sr at low concentration, Sr(2+) cations will be localized into the apatite network.

Combination of extended X-ray absorption fine structure spectroscopy with lipidic cubic phases for the study of cation binding in bacteriorhodopsin

We have performed a quantitative X-ray absorption fine structure analysis of bacteriorhodopsin in purple membrane patches and in lipidic cubic phases regenerated with Mn(2+). Lipidic cubic phases and purple membrane results have been compared, demonstrating that the lipidic cubic phase process does not introduce relevant distortions in the local geometry of the cation binding sites. For both samples, we have observed similarities for Mn(2+) coordination in terms of type, number, and average distances of surrounding atoms, indicating a first coordination shell composed by 6 O atoms, and 3/4 C atoms located in the second coordination shell.

Calcium binding to the purple membrane: A molecular dynamics study

The purple membrane (PM) is a specialized membrane patch found in halophilic archaea, containing the photoreceptor bacteriorhodopsin (bR). It is long known that calcium ions bind to the PM, but their position and role remain elusive to date. Molecular dynamics simulations in conjunction with a highly detailed model of the PM have been used to investigate the stability of calcium ions placed at three proposed cation binding sites within bR, one near the Schiff base, one in the region of the proton release group, and one near Glu9. The simulations suggest that, of the sites investigated, the binding of calcium ions was most likely at the proton release group. Binding in the region of the Schiff base, while possible, was associated with significant changes in local geometry. Calcium ions placed near Glu9 in the interior of bR (simultaneously to a Ca(2+) near the Schiff base and another one near the Glu194-Glu204 site) were not stable. The results obtained are discussed in relation to recent experimental observations and theoretical considerations.

X-ray absorption and molecular dynamics study of cation binding sites in the purple membrane

The present work describes the results of a study aimed at identifying candidate cation binding sites on the extracellular region of bacteriorhodopsin, including a site near the retinal pocket. The approach used is a combined effort involving computational chemistry methods (computation of cation affinity maps and molecular dynamics) together with the Extended X-Ray Absorption Fine Structure (EXAFS) technique to obtain relevant information about the local structure of the protein in the neighborhood of Mn(2+) ions in different affinity binding sites. The results permit the identification of a high-affinity binding site where the ion is coordinated simultaneously to Asp212(-) and Asp85(-). Comparison of EXAFS data of the wild type protein with the quadruple mutant E9Q/E74Q/E194Q/E204Q at pH 7.0 and 10.0 demonstrate that extracellular glutamic acid residues are involved in cation binding.

MXAN Analysis of the XANES Energy Region of a Mononuclear Copper Complex: Applications to Bioinorganic Systems

The near edge XAS spectra of the mononuclear copper complex [Cu(TMPA)(OH(2))](ClO(4))(2) (1) have been simulated using the multiple scattering edge simulation package MXAN (or Minuit XANes). These simulations, which employ the muffin-tin (MT) approximation, have been compared to simulations generated using the finite-difference method (FDM) to evaluate the effect of MT corrections. The sensitivity of the MXAN method was tested using structural models that included several different variations on the bond angles and bond distances for the first-shell atoms of 1. The sensitivity to small structural changes was also evaluated by comparing MXAN simulations of 1 and of structurally modified [Cu(TMPA)(L)](n)(+) complexes [where L = -O-(F(8)TPP)Fe(III), -F, -OPO(2)(O-p-nitrophenyl)Zn(II)(TMPA), and -NCMe] to the experimental data. The accuracy of the bond distances obtained from the MXAN simulations was then examined by comparison to the metrics of the crystal structures. The results show that MXAN can successfully extract geometric information from the edge structure of an XAS spectrum. The systematic application of MXAN to 1 indicates that this approach is sensitive to small structural changes in the molecule that are manifested in the XAS edge spectrum. These results represent the first step toward the application of this methodology to bioinorganic and biological systems.