Medium-range order in alkali metaphosphate glasses and melts investigated by reverse Monte Carlo simulations and diffraction analysis.

Reverse Monte Carlo simulations have been performed on the alkali metaphosphate glasses Na0.5Li0.5PO3 and LiPO3 concerning structural experimental data obtained by neutron and x-ray diffraction at 300 K for both systems and versus temperature up to the melting point for the mixed composition. It appears that the contrast effect due to the negative scattering length of Li is not the only reason for the difference in the intensity of the prepeak observed in both systems. The main structural difference lies in the intermediate-range order, while the short-range order is quite similar in both systems. Moreover, it is shown that the intensity increase of the prepeak in the Na0.5Li0.5PO3 structure factor is due to the partial structure factors of the PO4 tetrahedron, sustaining the hypothesis of an ordering between several PO4 tetrahedra and voids with temperature

The Five-To-Six-Coordination Transition of Ferric Human Serum Heme-Albumin Is Allosterically-Modulated by Ibuprofen and Warfarin: A Combined XAS and MD Study

Human serum albumin (HSA) is involved physiologically in heme scavenging; in turn, heme-albumin (HSA-heme-Fe) displays globin-like properties. Here, the allosteric effect of ibuprofen and warfarin on the local atomic structure around the ferric heme-Fe (heme-Fe(III)) atom of HSA-heme-Fe (HSA-heme-Fe(III)) has been probed by Fe-K edge X-ray absorption spectroscopy (XAS). The quantitative analysis of the Fe-K edge extended X-ray absorption fine structure (EXAFS) signals and modeling of the near edge (XANES) spectral features demonstrated that warfarin and ibuprofen binding modify the local structure of the heme-Fe(III). Combined XAS data analysis and targeted molecular dynamics (MD) simulations provided atomic resolution insights of protein structural rearrangements required to accommodate the heme-Fe(III) upon ibuprofen and warfarin binding. In the absence of drugs, the heme-Fe(III) atom is penta-coordinated having distorted 4 + 1 configuration made by the nitrogen atoms of the porphyrin ring and the oxygen phenoxy atom of the Tyr161 residue. MD simulations show that ibuprofen and warfarin association to the secondary fatty acid (FA) binding site 2 (FA2) induces a reorientation of domain I of HSA-heme-Fe(III), this leads to the redirection of the His146 residue providing an additional bond to the heme-Fe(III) atom, providing the 5 + 1 configuration. The comparison of Fe-K edge XANES spectra calculated using MD structures with those obtained experimentally confirms the reliability of the proposed structural model. As a whole, combining XAS and MD simulations it has been possible to provide a reliable model of the heme-Fe(III) atom coordination state and to understand the complex allosteric transition occurring in HSA-heme-Fe(III) upon ibuprofen and warfarin binding

The Five-To-Six-Coordination Transition of Ferric Human Serum Heme-Albumin Is Allosterically-Modulated by Ibuprofen and Warfarin: A Combined XAS and MD Study

Human serum albumin (HSA) is involved physiologically in heme scavenging; in turn, heme-albumin (HSA-heme-Fe) displays globin-like properties. Here, the allosteric effect of ibuprofen and warfarin on the local atomic structure around the ferric heme-Fe (heme-Fe(III)) atom of HSA-heme-Fe (HSA-heme-Fe(III)) has been probed by Fe-K edge X-ray absorption spectroscopy (XAS). The quantitative analysis of the Fe-K edge extended X-ray absorption fine structure (EXAFS) signals and modeling of the near edge (XANES) spectral features demonstrated that warfarin and ibuprofen binding modify the local structure of the heme-Fe(III). Combined XAS data analysis and targeted molecular dynamics (MD) simulations provided atomic resolution insights of protein structural rearrangements required to accommodate the heme-Fe(III) upon ibuprofen and warfarin binding. In the absence of drugs, the heme-Fe(III) atom is penta-coordinated having distorted 4 + 1 configuration made by the nitrogen atoms of the porphyrin ring and the oxygen phenoxy atom of the Tyr161 residue. MD simulations show that ibuprofen and warfarin association to the secondary fatty acid (FA) binding site 2 (FA2) induces a reorientation of domain I of HSA-heme-Fe(III), this leads to the redirection of the His146 residue providing an additional bond to the heme-Fe(III) atom, providing the 5 + 1 configuration. The comparison of Fe-K edge XANES spectra calculated using MD structures with those obtained experimentally confirms the reliability of the proposed structural model. As a whole, combining XAS and MD simulations it has been possible to provide a reliable model of the heme-Fe(III) atom coordination state and to understand the complex allosteric transition occurring in HSA-heme-Fe(III) upon ibuprofen and warfarin binding

Local atomic structure of HSA-heme-Fe(III), ibuprofen-HSA-heme-Fe(III), and warfarin-HSA-heme-Fe(III) around the heme-Fe(III) atom as obtained by EXAFS data analysis, compared with the average coordination distances of models (PDB and SMD).

<p>The standard uncertainty on the parameters refined for the EXAFS data analysis are reported in parenthesis (last digit variation). The and R² parameters (EXAFS analysis) are reported (see text). The last right columns contain the number of neighbors and average distance of the structure used for XANES models. The C₄ coordination shell is included in the XANES simulations.</p>a<p>Coordination numbers were fixed to the crystallographic values. Noticeably, refining N_I and N_II in HSA-heme-Fe(III) data, they changed less than 10% well within the estimated uncertainty. Therefore, we can safely assume correct the five-coordination of the heme-Fe(III) atom in the HSA-heme-Fe(III)-complex in solution fixing N_I = 4 and N_II = 1.</p

Conformational transition of HSA-heme-Fe(III) upon ligand binding to the FA2 site.

<p>Panel A. Three-dimensional representation of the starting crystal structure (cyan, PDB entry 1O9X <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104231#pone.0104231-Zunszain1" target="_blank">[22]</a>) of HSA-heme-Fe(III). Heme-Fe(III) and the His146 and Tyr161 residues are highlighted in blue. The Glu131-Arg145 α-helix is represented in magenta. Panel B. Three-dimensional representation of the final model (orange) of HSA-heme-Fe(III) obtained via SMDS. Heme-Fe(III) and the His146 and Tyr161 residues are highlighted in red. The Glu131-Arg145 α-helix is represented in green. Panel C. Superposition of the starting crystal structure and of the final model of HSA-heme-Fe(III). The picture has been drawn using the UCSF Chimera package <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104231#pone.0104231-Pettersen1" target="_blank">[67]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104231#pone.0104231-Meng1" target="_blank">[68]</a>.</p

XANES data: comparison of Fe-K edge XANES measured on HSA-heme-Fe(III), ibuprofen-HSA-heme-Fe(III), and warfarin-HSA-heme-Fe(III).

<p>The effect of drugs is mainly evident at the main XANES peak (arrow) while the edge position is largely unchanged, signaling the same Fe electronic state in HSA and drug added samples. All XAS data were collected at low temperature (around 20 K) and pH 7.0 (1.0×10⁻¹ M phosphate buffer).</p

Semi-quantitative analysis of Fe(III) pre-edge peaks and comparison with reference compounds.

<p>In the inset, the experimental Fe(III) pre-edge peak (red symbols) of HSA-heme-Fe(III) and warfarin-HSA-heme-Fe(III) are modelled combining an arctangent function (gray line), simulating the onset of the continuous electron states, and Gaussian peaks (blue lines), representing the transitions to localized electronic states. The grey ellipses enclose the values of Fe(III) pre-edge peak integrated areas versus their centroid positions, measured on tetra-, penta-, and hexa- coordinated Fe(III) reference compounds (labelled <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104231#pone.0104231-Curry1" target="_blank">[4]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104231#pone.0104231-Curry2" target="_blank">[5]</a>, and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104231#pone.0104231-Bhattacharya1" target="_blank">[6]</a>, respectively; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104231#pone.0104231-Giuli1" target="_blank">[56]</a>). The pre-edge peak parameters of HSA-heme-Fe(III) (red circle) fall in the region of penta-coordinated Fe(III), while ibuprofen-HSA-heme-Fe(III) and warfarin-HSA-heme-Fe(III) pre-edge peaks parameters (blue circles) are in the region corresponding to hexa-coordinated Fe(III) compounds. The pre-edge fitting of drug-bound HSA-heme-Fe(III) samples requires an additional peak (labelled B) in the region about 2 eV above the main one (labelled A). Analogous components have been reported in ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104231#pone.0104231-Westre1" target="_blank">[54]</a>. The size of red and blue symbols takes into account for best fit incertitude.</p

EXAFS data fitting.

<p>Experimental data (points) and best fit (full lines) for all the analyzed samples are shown. The partial contributions (shells) used for the refinement of each spectrum are shown (vertically shifted for clarity); the structural parameters are reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104231#pone-0104231-t001" target="_blank">Table 1</a>. The residuals (experimental data minus best fit) are shown, at the bottom for each sample.</p

HSA structure.

<p>(Top) The heme (red) fits the FA1 site in subdomain IB. Sudlow's site I (in subdomain IIA, corresponding to FA7) is occupied by warfarin (magenta). Sudlow's site II (in subdomain IIIA, corresponding to FA3–FA4) and FA6 (in subdomain IIB) are occupied by ibuprofen (blue). Atomic coordinates were taken from PDB entries 1O9X <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104231#pone.0104231-Zunszain1" target="_blank">[22]</a>, 2BXD <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104231#pone.0104231-Ghuman1" target="_blank">[10]</a>, and 2BXG <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104231#pone.0104231-Ghuman1" target="_blank">[10]</a>, picture drawn using the UCSF Chimera package <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104231#pone.0104231-Pettersen1" target="_blank">[67]</a>. (Bottom) The local heme-Fe(III) structure is highlighted, the atoms belonging to the heme-Fe(III) coordination shells are labeled.</p

The Five-To-Six-Coordination Transition of Ferric Human Serum Heme-Albumin Is Allosterically-Modulated by Ibuprofen and Warfarin: A Combined XAS and MD Study

Human serum albumin (HSA) is involved physiologically in heme scavenging; in turn, heme-albumin (HSA-heme-Fe) displays globin-like properties. Here, the allosteric effect of ibuprofen and warfarin on the local atomic structure around the ferric heme-Fe (heme-Fe(III)) atom of HSA-heme-Fe (HSA-heme-Fe(III)) has been probed by Fe-K edge X-ray absorption spectroscopy (XAS). The quantitative analysis of the Fe-K edge extended X-ray absorption fine structure (EXAFS) signals and modeling of the near edge (XANES) spectral features demonstrated that warfarin and ibuprofen binding modify the local structure of the heme-Fe(III). Combined XAS data analysis and targeted molecular dynamics (MD) simulations provided atomic resolution insights of protein structural rearrangements required to accommodate the heme-Fe(III) upon ibuprofen and warfarin binding. In the absence of drugs, the heme-Fe(III) atom is penta-coordinated having distorted 4 + 1 configuration made by the nitrogen atoms of the porphyrin ring and the oxygen phenoxy atom of the Tyr161 residue. MD simulations show that ibuprofen and warfarin association to the secondary fatty acid (FA) binding site 2 (FA2) induces a reorientation of domain I of HSA-heme-Fe(III), this leads to the redirection of the His146 residue providing an additional bond to the heme-Fe(III) atom, providing the 5 + 1 configuration. The comparison of Fe-K edge XANES spectra calculated using MD structures with those obtained experimentally confirms the reliability of the proposed structural model. As a whole, combining XAS and MD simulations it has been possible to provide a reliable model of the heme-Fe(III) atom coordination state and to understand the complex allosteric transition occurring in HSA-heme-Fe(III) upon ibuprofen and warfarin binding