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Cebranopadol (CBP) is a novel analgesic acting as agonist at the nociceptin (NOP) and μ-opioid (MOP) receptors, exhibiting high potency and efficacy as an antinociceptive and antihypersensitive drug. The binding conformation and the dynamical interactions of CBP with the NOP receptor have been investigated by molecular docking, molecular dynamics (MD) in the microsecond time scale, and hybrid quantum mechanics/molecular mechanics (QM/MM). CBP binds to the NOP receptor as a bidentate ligand of the aspartate D1303,32 by means of both its fluoroindole and dimethyl nitrogens. Starting from the known crystal structure of the inactive state of the receptor, in complex with the antagonist compound-24 (NOP-C24) the comparative analysis of 1 μs MD trajectories of the NOP-C24 complex itself and the NOP_free and NOP-CBP complexes provides new insights on the already known microswitches related to receptor activation, in the frame of the extended ternary complex model. The agonist acts by destabilizing the inactive c...

In this contribution we analyzed the Vanadium speciation and structural local environment in two V-bearing Na-phosphate glasses by means of V K-edge X-ray Absorption Spectroscopy. The two glasses have starting molar proportions Na2O:V2O5:P2O5 equal to 45:10:45 (NaPV10) and 10:80:10 (NaPV80). Accurate analysis of the pre-edge peak of the two glasses allowed to determine the presence of [4]V5+ and [5]V5+ in NaPV80 and of [5]V4+ and [6]V4+ in NaPV10. EXAFS derived V–O distances for the two glasses are in agreement with literature data for the above mentioned V species. The determined V local geometries and the EXAFS derived bond distances have been used to build four structural models for [4]V5+, [5]V5+, [5]V4+ and [6]V4+ in the studied glasses; these models have been in turn used to calculate theoretical XANES spectra by means of the MXAN code. The partial contributions of each V species have been summed in order to fit the experimental XANES spectra of the two glasses. Iterative fitting of the structural parameters of each structural model resulted in a good agreement between experimental and theoretical XANES data. The analysis strategy used in the present work allowed to gain information of V speciation and on the structural local environment of the [4]V5+, [5]V5+, [5]V4+ and [6]V4+ species present in the analyzed glasses. Combined use of different spectral regions and data analysis routines allowed to successfully simulate XANES spectra and to gain an in depth knowledge of V local environment even in a complex system like amorphous glass containing different V species.

Graphical abstract, Short Linear Motifs (SLiMs) are functional protein microdomains that typically mediate interactions between a short linear region in one protein and a globular domain in another. Surface Plasmon Resonance assays have been performed to determine the binding affinity between PDZ domain of wild type human PALS1 protein and tetradecapeptides representing the SLiMs sequences of SARS-CoV-1 and SARS-CoV-2 E proteins (E-SLiMs). SARS-CoV-2 E-SLiM binds to the human target protein with a higher affinity compared to SARS-CoV-1, showing a difference significantly greater than previously reported using the F318W mutant of PALS1 protein and shorter target peptides. Moreover, molecular dynamics simulations have provided clear evidence of the structural determinants driving this binding process. Specifically, the Arginine 69 residue in the SARS-CoV-2 E-SLiM is the key residue able to both enhance the specific polar interaction with negatively charged pockets of the PALS1 PDZ domain and reduce significantly the mobility of the viral peptide. These experimental and computational data are reinforced by the comparison of the interaction between the PALS1 PDZ domain with the natural ligand CRB1, as well as the corresponding E-SLiMs of other coronavirus members such as MERS and OCF43. Our results provide a model at the molecular level of the strategies used to mimic the endogenous SLiM peptide in the binding of the tight junctions of the host cell, explaining one of the possible reasons of the severity of the infection and pulmonary inflammation by SARS-CoV-2.

The nociceptin/orphanin FQ (N/OFQ)/N/OFQ receptor (NOP) system controls different biological functions including pain and cough reflex. Mixed NOP/opioid receptor agonists elicit similar effects to strong opioids but with reduced side effects. In this work, 31 peptides with the general sequence [Tyr/Dmt1,Xaa5]N/OFQ(1-13)-NH2 were synthesized and pharmacologically characterized for their action at human recombinant NOP/opioid receptors. The best results in terms of NOP versus mu opioid receptor potency were obtained by substituting both Tyr1 and Thr5 at the N-terminal portion of N/OFQ(1-13)-NH2 with the noncanonical amino acid Dmt. [Dmt1,5]N/OFQ(1-13)-NH2 has been identified as the most potent dual NOP/mu receptor peptide agonist so far described. Experimental data have been complemented by in silico studies to shed light on the molecular mechanisms by which the peptide binds the active form of the mu receptor. Finally, the compound exerted antitussive effects in an in vivo model of cough.

The Envelope (E) protein of SARS-CoV-2 is the most enigmatic protein among the four structural ones. Most of its current knowledge is based on the direct comparison to the SARS E protein, initially mistakenly undervalued and subsequently proved to be a key factor in the ER-Golgi localization and in tight junction disruption. We compared the genomic sequences of E protein of SARS-CoV-2, SARS-CoV and the closely related genomes of bats and pangolins obtained from the GISAID and GenBank databases. When compared to the known SARS E protein, we observed a significant difference in amino acid sequence in the C-terminal end of SARS-CoV-2 E protein. Subsequently, in silico modelling analyses of E proteins conformation and docking provide evidences of a strengthened binding of SARS-CoV-2 E protein with the tight junction-associated PALS1 protein. Based on our computational evidences and on data related to SARS-CoV, we believe that SARS-CoV-2 E protein interferes more stably with PALS1 leading to an enhanced epithelial barrier disruption, amplifying the inflammatory processes, and promoting tissue remodelling. These findings raise a warning on the underestimated role of the E protein in the pathogenic mechanism and open the route to detailed experimental investigations.

Background: The Envelope (E) protein of SARS-CoV-2 is the most enigmatic protein among the four structural ones on the viral genome. Most of the current knowledge on the E protein is based on the direct comparison to the SARS E protein, initially mistakenly undervalued and subsequently proved to be a key factor in the ER-Golgi localization and in tight junction disruption. Methods: We compared the genomic sequences of E protein of SARS-CoV-2, SARS-CoV and the closely related genomes of bats and pangolins obtained from the GISAID and GenBank databases. Multiple sequence alignments were done with the Geneious software using the MAFFT algorithm. In silico modelling analyses of E proteins conformation and docking with PALS1 were performed with the Schrodinger Suite.Results: When compared to the known SARS E protein, we observed a different amino acidic sequence in the C-terminal of SARS-CoV-2 E protein which might have a key role in the current COVID-19 pathogenesis. In silico docking results provide evidence of a strengthened binding of SARS-CoV-2 E protein with the tight junction-associated PALS1 protein.Conclusions: We suggest that SARS-CoV-2 E protein may interfere with the tight junction stability and formation leading to an enhanced epithelial barrier disruption, amplifying the inflammatory processes, and promoting tissue remodelling. These findings raise a warning on the underestimated role of the E protein in the pathogenic mechanism and could open the route to detailed experimental investigations.

X-ray absorption spectroscopy (XAS) is a powerful method for obtaining electronic and structural information around a well-defined absorbing atom site of different types of matter, from biological systems to condensed materials in almost all possible thermodynamics conditions. The low energy part of the XAS spectrum, from the rising edge up to few hundreds eV, the so called XANES (X-ray absorption near-edge structure) region, is extremely rich of electronic and structural information, like, for example, the oxidation state, overall symmetry, interatomic distances and angles . In this paper we present in details the MXAN method and a new reengineered release of the code proposed in the literature some years ago which allows a complete fit of the XANES energy region in term of well-defined set of structural parameters. This approach is based on the comparison between experimental data and many theoretical calculations performed by varying selected structural parameters starting from a putative structure, i.e. from a well-defined initial geometrical configuration around the absorber. The X-ray photo-absorption cross sections are derived using full multiple-scattering theory, i.e. the scattering path operator is calculated exactly without any series expansion. In this way the analysis can start from the edge without any limitations in the energy range and polarization conditions. Here we present in detail the theoretical background behind the code and new capabilities implemented from theory in this last version of the program as the analysis of XANES data coming from time-dependent spectra. The code is provided with modern technology for rapid deployment of binaries based on Docker runtime so that, without source compiling, its execution reduces to just a command line striking for a full parallel (shared memory) run even using complex construct like memory filesystem in a transparent way to the end-user. Program summary Program Title: MXAN CPC Library link to program files: https://doi.org/10.17632/4k9363vcvh.1 Licensing provisions: GPLv3 Programming language: FORTRAN90 External routines/libraries: MKL or OpenBLAS library Nature of problem: In MXAN (Minuit XANES) program we implemented a fitting procedure based on a full Multiple Scattering (MS) theory [1] able to extract local structural information around the absorbing atom from experimental XANES data. The MXAN method has been successfully used for studying many known and unknown molecular systems, yielding structural geometries and metrics comparable to X-ray diffraction and/or EXAFS results [2] , [3] , [4] . The release of this new code paves the route to new possibilities available now in the latest version of the program, as the analysis of XANES data coming from time-dependent and structural disordered systems. Solution method: MXAN program is based on the comparison between experimental data and iterative theoretical calculations performed by varying selected structural parameters starting from a well-defined initial geometrical configuration around the absorber. The calculation of XANES spectra is performed within the so-called full MS approach, i.e. the inverse of the scattering path operator is computed exactly, avoiding any “a-priori” selection of the relevant MS paths [5] , [6] . The fit procedure is performed in the energy space without the use of any Fourier transform algorithm; polarized spectra can be easily analyzed because the calculation is performed using the full MS approach [1] . The optimization in the space of the parameters is achieved using the CERN-library MINUIT [7] routines minimizing the square residual. Additional comments including restrictions and unusual features: Depending on the molecular system under study and on the operating runtime conditions the program may or may not fit into available host RAM memory. The present release of the code is limited to a single SMP machine by running in parallel using OpenMP and/or the multi-threaded version of MKL or OpenBLAS.

Nociceptin (NCC, also known as FQ (N/OFQ)) is the 17-amino acid neuropeptide, endogenous ligand for the G-protein-coupled receptor (NOP, also known as ORL-1). In this study, starting from the recently reported x-ray structure at pH 7 of NOP in complex with an antagonist, new insights, to our knowledge, on the binding geometry of NCC to NOP have been provided in silico. After a rigid docking of NCC in an α -helix conformation, molecular dynamics (MD) and metadynamics (METAD), a method for the analysis of free-energy surfaces (FES), were performed on the protein-peptide complex. Free-energy profiles were obtained as a function of the α -helix content of different segments of the 17-mer ligand, and a structural ensemble of conformations of NCC, corresponding to the minimum of the FES, was extracted, thus representing the NCC bound to the inactive form of NOP. The structural features were compared with many known experimental data. The pose of the "message" domain (residues 1–4) of NCC differs from that of the known NOP antagonists, as being slightly slipped deeper inside the protein core. A residual α -helix content in the central part of the peptide (residues 4–9) is maintained, whereas the C-terminal segment (residues 13–17) is unstructured and highly flexible. An important stabilization due to interactions with residues D130 and D110 of the receptor has been found, in agreement with the large decrease in agonist potency reported for the D130A and D110A mutants. The importance of the extracellular domain 2 (ECL2) in the selectivity toward the endogenous ligand has been confirmed. A pivotal role for the conserved residue N133 is suggested and further supported by a study of the N133A in silico mutant. Accordingly, N133 can work as a molecular microswitch driving the change between the inactive and active NOP conformations, in the framework of an extended H-bond and water network rearrangement in the deep binding site.

Antagonists of the nociceptin receptor (NOP) are raising interest for their possible clinical use as antidepressant drugs. Recently, the structure of NOP in complex with some piperidine-based antagonists has been revealed by X-ray crystallography. In this study, a multi-flexible docking (MF-docking) procedure, i.e. docking to multiple receptor conformations extracted by preliminary molecular dynamics trajectories, together with hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have been carried out to provide the binding mode of two novel NOP antagonists, one of them selective (BTRX-246040, formerly named LY-2940094) and one non selective (AT-076), i.e. able to inactivate NOP as well as the classical µ- k- and δ-opioid receptors (MOP KOP and DOP). According to our results, the pivotal role of residue D1303,32 (upper indexes are Ballesteros–Weinstein notations) is analogous to that enlighten by the already known X-ray structures of opioid receptors: binding of the molecules are predicted to require a slight readjustment of the hydrophobic pocket (residues Y1313,33, M1343,36, I2195,43, Q2806,52 and V2836,55) in the orthosteric site of NOP, accommodating either the pyridine–pyrazole (BTRX-246040) or the isoquinoline (AT-076) moiety of the ligand, in turn allowing the protonated piperidine nitrogen to maximize interaction (salt-bridge) with residue D1303,32 of the NOP, and the aromatic head to be sandwiched in optimal π-stacking between Y1313,33 and M1343,36. The QM/MM optimization after the MF-docking procedure has provided the more likely conformations for the binding to the NOP receptor of BTRX-246040 and AT-076, based on different pharmacophores and exhibiting different selectivity profiles. While the high selectivity for NOP of BTRX-246040 can be explained by interactions with NOP specific residues, the lack of selectivity of AT-076 could be associated to its ability to penetrate into the deep hydrophobic pocket of NOP, while retaining a conformation very similar to the one assumed by the antagonist JDTic into the K-opioid receptor. The proposed binding geometries fit better the binding pocket environment providing clues for experimental studies aimed to design selective or multifunctional opioid drugs.

Nonsyndromic craniosynostosis (NCS) is the premature ossification of skull sutures, without associated clinical features. Mutations in several genes account for a small number of NCS patients; thus, the molecular etiopathogenesis of NCS remains largely unclear. Our study aimed at characterizing the molecular signaling implicated in the aberrant ossification of sutures in NCS patients. Comparative gene expression profiling of NCS patient sutures identified a fused suture-specific signature, including 17 genes involved in primary cilium signaling and assembly. Cells from fused sutures displayed a reduced potential to form primary cilia compared to cells from control patent sutures of the same patient. We identified specific upregulated splice variants of the Bardet Biedl syndrome-associated gene 9 (BBS9), which encodes a structural component of the ciliary BBSome complex. BBS9 expression increased during in vitro osteogenic differentiation of suture-derived mesenchymal cells of NCS patients. Also, Bbs9 expression increased during in vivo ossification of rat sutures. BBS9 functional knockdown affected the expression of primary cilia on patient suture cells and their osteogenic potential. Computational modeling of the upregulated protein isoforms (observed in patients) predicted that their binding affinity within the BBSome may be affected, providing a possible explanation for the aberrant suture ossification in NCS.

Nucleophosmin (NPM1) is a nucleocytoplasmic shuttling protein, mainly localized at nucleoli, that plays a number of functions in ribosome biogenesis and export, cell cycle control, and response to stress stimuli. NPM1 is the most frequently mutated gene in acute myeloid leukemia; mutations map to the C-terminal domain of the protein and cause its denaturation and aberrant cytoplasmic translocation. NPM1 C-terminal domain binds G-quadruplex regions at ribosomal DNA and at gene promoters, including the well characterized sequence from the nuclease-hypersensitive element III region of the c-MYC promoter. These activities are lost by the leukemic variant. Here we analyze the NPM1/G-quadruplex interaction, focusing on residues belonging to both the NPM1 terminal three-helix bundle and a lysine-rich unstructured tail, which has been shown to be necessary for high affinity recognition. We performed extended site-directed mutagenesis and measured binding rate constants through surface plasmon resonance analysis. These data, supported by molecular dynamics simulations, suggest that the unstructured tail plays a double role in the reaction mechanism. On the one hand, it facilitates the formation of an encounter complex through long range electrostatic interactions; on the other hand, it directly contacts the G-quadruplex scaffold through multiple and transient electrostatic interactions, significantly enlarging the contact surface.

In the opportunistic pathogen Pseudomonas aeruginosa the denitrification process is triggered by nitric oxide (NO) and plays a crucial role for the survival in chronic infection sites as a microaerobic-anaerobic biofilm. This respiratory pathway is transcriptionally induced by DNR, an heme-based gas sensor which positively responds to NO. Molecular details of the NO sensing mechanism employed by DNR are now emerging: we recently reported an in vitro study which dissected, for the first time, the heme-iron environment and identified one of the heme axial ligand (i.e. His187), found to be crucial to respond to NO. Nevertheless, the identification of the second heme axial ligand has been unsuccessful, given that a peculiar phenomenon of ligand switching around the heme-iron presumably occurs in DNR. The unusual heme binding properties of DNR could be due to the remarkable flexibility in solution of DNR itself, which, in turns, is crucial for the sensing activity; protein flexibility and dynamics indeed represent a common strategy employed by heme-based redox sensors, which present features deeply different from those of "canonical" hemeproteins. The capability of DNR to deeply rearrange around the heme-iron as been here demonstrated by means of spectroscopic characterization of the H167A/H187A DNR double mutant, which shows unusual kinetics of binding of NO and CO. Moreover, we show that the alteration (such as histidines mutations) of the distal side of the heme pocket is perceived by the proximal one, possibly via the DNR protein chain.

A systematic study is presented on a set of vanadium-bearing model compounds, representative of the most common V coordination geometries and oxidation states, analysed by means of vanadiumK-edge X-ray absorption near-edge spectroscopy calculations in the full multiple scattering (FMS) framework. Analysis and calibration of the free parameters of the theory under the muffin-tin approximation (muffin-tin overlap and interstitial potential) have been carried out by fitting the experimental spectra using theMXANprogram. The analysis shows a correlation of the fit parameters with the V coordination geometry and oxidation state. By making use of this correlation it is possible to approach the study of unknown V-bearing compounds with useful preliminary information.

International audience; AIMS: In the opportunistic pathogen Pseudomonas aeruginosa, nitric oxide (NO) triggers the respiration of nitrate (denitrification), thus allowing survival in chronic infection sites as a microaerobic-anaerobic biofilm. The NO-dependent induction of denitrification is mediated by the dissimilative nitrate respiration regulator (DNR), a transcription factor forming a stable complex with heme, which is required to sense the physiological messenger (i.e., NO). The molecular details of NO sensing in DNR and, more in general, in this class of sensors are largely unknown, and a study aimed at integrating microbiology and biochemistry is needed. RESULTS: Here we present a comprehensive study, including in vivo results and spectroscopy, kinetics, and protein engineering, that demonstrates the direct involvement of a histidine residue in heme iron coordination. Moreover, a peculiar phenomenon of ligand switching around heme iron, which hampers the identification of the second heme axial ligand, is also suggested. These results indicate that DNR is characterized by a remarkable flexibility in solution, as observed for other cAMP receptor protein/fumarate and nitrate reductase regulators (CRP-FNR) to which DNR belongs. INNOVATION: The present work represents one of the few studies focused on the biochemistry of NO sensing by bacterial transcriptional regulators. The data presented demonstrate that structural plasticity of DNR is crucial for the sensing activity and confers to the protein unusual heme binding properties. CONCLUSIONS: Protein flexibility and dynamics is a key structural feature essential to explain the evolutionary success and adaptability of CRP-FNR, and may represent a common strategy employed by heme-based redox sensors, which presents features deeply different from those of canonical hemeproteins.

The effect of structural disorder on the X-ray absorption near-edge structure (XANES) spectrum of a heme protein has been investigated using the dynamical description of the system derived from molecular dynamics (MD) simulations. The XANES spectra of neuroglobin (Ngb) and carbonmonoxy-neuroglobin (NgbCO) have been quantitatively reproduced, starting from the MD geometrical configurations, without carrying out any optimization in the structural parameter space. These results provide an important experimental validation of the reliability of the potentials used in the MD simulations and accordingly corroborate the consistency of the structural dynamic information on the metal center, related to its biological function. This analysis allowed us to demonstrate that the configurational disorder associated with the distortion of the heme plane and with the different orientations of the axial ligands can affect the XANES features at very low energy. Neglecting configurational disorder in the XANES quantitative analysis of heme proteins is a source of systematic errors in the determination of Fe coordination geometry. The combined use of XANES and MD is a novel strategy to enhance the resolution and reliability of the structural information obtained on metalloproteins, making the combination of these techniques powerful for metalloprotein investigations.

Polarized Fe K-edge X-ray absorption near-edge structure (XANES) spectra of murine carbonmonoxy-neuroglobin (NgbCO) single crystals have been collected and compared with a number of derivatives of sperm whale myoglobin (Mb), that is, the nitrosyl (MbNO) and deoxy (Mb) derivatives, the previously reported cyanomet (MbCN) and carbonmonoxy (MbCO) derivatives, and the cryogenic photoproduct of MbCO (Mb·CO). The single crystals under study exhibit a strong XANES angular dichroism which allows the heme geometry of each sample to be analyzed with extremely high accuracy via the full multiple scattering (MS) approach. The results of two alternative methods to undergo the MS analysis have been compared with high resolution X-ray diffraction (XRD) data and with X-ray absorption spectroscopy (XAS) data in solution. As a result of the present analysis, the Fe-heme structure in solution and in the cryo-trapped NgbCO single crystal (which cracks at room temperature) are the same. Accordingly, the residual energy involved in the protein relaxation responsible of crystal cracking at room temperature after CO binding does not reside in the heme pocket. A combined approach (polarized XANES and XRD) is suggested to be applied on the same single crystals of metalloproteins at opportunely equipped synchrotron beamlines.

A full quantitative analysis of Fe K-edge X-ray absorption spectra has been performed for hemes in two porphynato complexes, that is, iron(III) tetraphenylporphyrin chloride (Fe(III)TPPCl) and iron(III) tetraphenylporphyrin bis(imidazole) (Fe(III)TPP(Imid)2), in two protein complexes whose X-ray structure is known at atomic resolution (1.0 A), that is, ferrous deoxy-myoglobin (Fe(II)Mb) and ferric aquo-myoglobin (Fe(III)MbH2O), and in ferric cyano-myoglobin (Fe(III)MbCN), whose X-ray structure is known at lower resolution (1.4 A). The analysis has been performed via the multiple scattering approach, starting from a muffin tin approximation of the molecular potential. The Fe-heme structure has been obtained by analyzing independently the Extended X-ray Absorption Fine Structure (EXAFS) region and the X-ray Absorption Near Edge Structure (XANES) region. The EXAFS structural results are in full agreement with the crystallographic values of the models, with an accuracy of +/- 0.02 A for Fe-ligand distances, and +/-6 degrees for angular parameters. All the XANES features above the theoretical zero energy (in the lower rising edge) are well accounted for by single-channel calculations, for both Fe(II) and Fe(III) hemes, and the Fe-N p distance is determined with the same accuracy as EXAFS. XANES evaluations of Fe-5th and Fe-6th ligand distances are determined with 0.04-0.07 A accuracy; a small discrepancy with EXAFS (0.01 to 0.05 A beyond the statistical error), is found for protein compounds. Concerns from statistical correlation among parameters and multiple minima in the parameter space are discussed. As expected, the XANES accuracy is slightly lower than what was found for polarized XANES on Fe(III)MbCN single crystal (0.03-0.04 A), and states the actual state-of-the-art of XANES analysis when used to extract heme-normal parameters in a solution spectrum dominated by heme-plane scattering.

The conversion of the prion protein (PrPC) into prions plays a key role in transmissible spongiform encephalopathies. Despite the importance for pathogenesis, the mechanism of prion formation has escaped detailed characterization due to the insoluble nature of prions. PrPC interacts with copper through octarepeat and non-octarepeat binding sites. Copper coordination to the non-octarepeat region has garnered interest due to the possibility that this interaction may impact prion conversion. We used X-ray absorption spectroscopy to study copper coordination at pH 5.5 and 7.0 in human PrPC constructs, either wild-type (WT) or carrying pathological mutations. We show that mutations and pH cause modifications of copper coordination in the non-octarepeat region. In the WT at pH 5.5, copper is anchored to His96 and His111, while at pH 7 it is coordinated by His111. Pathological point mutations alter the copper coordination at acidic conditions where the metal is anchored to His111. By using in vitro approaches, cell-based and computational techniques, we propose a model whereby PrPC coordinating copper with one His in the non-octarepeat region converts to prions at acidic condition. Thus, the non-octarepeat region may act as the long-sought-after prion switch, critical for disease onset and propagation.

A general procedure to compute X-ray absorption near-edge structure (XANES) spectra within multiple-scattering theory starting from molecular dynamics (MD) structural data has been developed and applied to the study of a Ni(2+) aqueous solution. This method allows one to perform a quantitative analysis of the XANES spectra of disordered systems using a proper description of the thermal and structural fluctuations. The XANES spectrum of Ni(2+) in aqueous solution has been calculated using the structural information obtained from the MD simulations without carrying out any minimization in the structural parameter space. A very good reproduction of the experimental data was obtained including the second-shell water molecules in the calculation, thus showing that the second hydration shell provides a detectable contribution to the XANES spectra of ionic solutions. The analysis including the first-shell cluster only permitted us to quantitatively determine the effect of disorder on the amplitude of the XANES spectra for molecular complexes. These results simultaneously confirm the reliability of the procedure and the structural results obtained from MD simulations. The combination of MD and XANES is found to be very helpful to get important new insights into the quantitative estimation of structural properties of disordered systems.

Folate receptor α (FRα) is a cell surface, glycophosphatidylinositol-anchored protein which has focussed attention as a therapeutic target and as a marker for the diagnosis of cancer. It has a high affinity for the dietary supplemented folic acid (FOL), carrying out endocytic transport across the cell membrane and delivering the folate at the acidic pH of the endosome. Starting from the recently reported X-ray structure at pH 7, 100 ns classical molecular dynamics simulations have been carried out on the FRα-FOL complex; moreover, the ligand dissociation process has been studied by metadynamics, a recently reported method for the analysis of free-energy surfaces (FES), providing clues on the intermediate states and their energy terms. Multiple dissociation runs were considered to enhance the configurational sampling; a final clustering of conformations within the averaged FES provides the representative structures of several intermediate states, within an overall barrier for ligand escape of about 75 kJ/mol. Escaping of FOL to solvent occurs while only minor changes affect the FRα conformation of the binding pocket. During dissociation, the FOL molecule translates and rotates around a turning point located in proximity of the receptor surface. FOL at this transition state assumes an "L" shaped conformation, with the pteridin ring oriented to optimize stacking within W102 and W140 residues, and the negatively charged glutamate tail, outside the receptor, interacting with the positively charged R103 and R106 residues, that contrary to the bound state, are solvent exposed. We show that metadynamics method can provide useful insights at the atomistic level on the effects of point-mutations affecting functionality, thus being a very promising tool for any study related to folate-targeted drug delivery or cancer therapies involving folate uptake.

Francesca Bugli,1 Valeria Caprettini,2 Margherita Cacaci,1 Cecilia Martini,1 Francesco Paroni Sterbini,1 Riccardo Torelli,1 Stefano Della Longa,3 Massimiliano Papi,4 Valentina Palmieri,4 Bruno Giardina,5 Brunella Posteraro,1 Maurizio Sanguinetti,1 Alessandro Arcovito5 1Istituto di Microbiologia, Università Cattolica del Sacro Cuore, 2Dipartimento di Fisica, Sapienza Università di Roma, Rome, 3Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell’Ambiente, Università dell’Aquila, L’Aquila, 4Istituto di Fisica, 5Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Rome, Italy Abstract: In order to deliver low-cost viral capsomeres from a large amount of soluble viral VP6protein from human rotavirus, we developed and optimized a biotechnological platform in Escherichia coli. Specifically, three different expression protocols were compared, differing in their genetic constructs, ie, a simple native histidine-tagged VP6sequence, VP6fused to thioredoxin, and VP6obtained with the newly described small ubiquitin-like modifier (SUMO) fusion system. Our results demonstrate that the histidine-tagged protein does not escape the accumulation in the inclusion bodies, and that SUMO is largely superior to the thioredoxin-fusion tag in enhancing the expression and solubility of VP6protein. Moreover, the VP6protein produced according to the SUMO fusion tag displays well-known assembly properties, as observed in both transmission electron microscopy and atomic force microscopy images, giving rise to either VP6trimers,60nm spherical virus-like particles, or nanotubes a few micron long. This different quaternary organization of VP6shows a higher level of immunogenicity for the elongated structures with respect to the spheres or the protein trimers. Therefore, the expression and purification strategy presented here – providing a large amount of the viral capsid protein in the native form with relatively simple, rapid, and economical procedures – opens a new route toward large-scale production of a more efficient antigenic compound to be used as a vaccination tool or as an adjuvant, as well as represents a top-quality biomaterial to be further modified for biotechnological purposes. Keywords: Virus-like particles, protein-based nanotubes, SUMO fusion tag, human rotavirus vaccine

The Fe site structure in the recombinant wild-type and T72I mutant of the cooperative homodimeric hemoglobin (HbI) of the mollusc Scapharca inaequivalvis has been investigated by measuring the Fe K-edge X-ray absorption near edge structure (XANES) spectra of their oxy, deoxy and carbonmonoxy derivatives, and the cryogenic photoproducts of the carbonmonoxy derivatives at T=12 K. According to our results, the Fe site geometry in T72I HbI-CO is quite similar to that of human carbonmonoxy hemoglobin (HbA-CO), while in native HbI-CO it seems intermediate between that of HbA-CO and sperm whale MbCO. The XANES spectra of oxy and deoxy derivatives are similar to the homologous spectra of human HbA, except for T72I HbI, for which the absorption edge is blue-shifted (about +1 eV) towards the spectrum of the oxy form. XANES spectra of the cryogenic photoproducts of HbA-CO (HbA*), HbI-CO (HbI*) and mutant HbI-CO (T72I HbI*) were acquired under continuous illumination at 12 K. The Fe-heme structures of the three photoproducts are similar; however, while in the case of HbA* and HbI* the data indicate incomplete structural relaxation of the Fe-heme towards its deoxy-like (T) form, the relaxation in T72I HbI* is almost completely towards the proposed "high affinity" Fe-heme structure of T72I HbI. This evidence suggests that minor tertiary restraints affect the Fe-heme dynamics of T72I HbI, corresponding to a reduction of the energy necessary for the T→R structural transition, which can contribute to the observed dramatic enhancement in oxygen affinity of this hemoprotein, and the decreased cooperativity.

The effect of allosteric effectors, such as inositol hexakisphosphate and/or bezafibrate, has been investigated on the unliganded human adult hemoglobin both spectroscopically (employing electronic absorption, circular dichroism, resonance Raman, and x-ray absorption near-edge spectroscopies) and functionally (following the kinetics of the first CO binding step up to a final 4% ligand saturation degree). All data indicate that the unliganded T-state is not perturbed by the interaction with either one or both effectors, suggesting that their functional influence is only exerted when a ligand molecule is bound to the heme. This is confirmed by the observation that CO dissociation from partially liganded hemoglobin ( Y ¯ ≤ 0.04) is strongly altered by the presence of either effector, and the effect is enhanced whenever the two effectors are simultaneously present. Altogether, these data are a direct demonstration of the occurrence of a strain induced by the presence of a ligand molecule bound to the heme, and for the first time there is a clear indication that the expression of the functional heterotropic effect by these non-heme ligands requires this strain, which is not present in the unliganded molecule.

The Cu K-edge X-ray Absorption Near Edge Structure (XANES) spectra of hemocyanin (Hc) in its deoxy- form has been simulated by the multiple scattering approach in the real space of coordinates. The features of the experimental spectra are related to structural parameters such as bond lenghts and the overall simmetry at the Cu site(s), whose changes are directly linked to the ligand binding dynamics. The experimental spectrum is compared with that of deoxy-tyrosinase, for which diffraction data are still unavailable, and the structure of its copper site(s) is inferred. These calculations, together to the previously reported ones on oxy-Hc [1], provide new theoretical support to any XANES investigation of the oxygen binding dynamics in Hc and its related proteins.

Folate receptor α (FRα) is a cell surface, glycophosphatidylinositol (GPI)-anchored protein with a high affinity for its ligand partner, which is highly expressed in malignant cells and has been selected as a therapeutic target and marker for the diagnosis of cancer. No direct structural information is available from either X-ray diffraction or NMR on the post-translational structure of this disulfide-rich protein. Three-dimensional models of the FRα structure have been derived with the recent homology modeling packages, using the crystal structure of the riboflavin-binding protein (RfBP) as a template. Molecular dynamics trajectories have been exploited allowing successfully the formation of a full disulfide bridge network, which was expected based on the similarities between FRα and RfBP. After the selection of the best model, a folic acid molecule was docked "in silico" onto the putative binding site and its binding mode was compared with that of vintafolide, a much larger molecule designed as a chemotherapy agent targeting specifically FRα. In both cases, a 40ns molecular dynamics trajectory was calculated, providing suggestions regarding the key structural determinants driving the affinity and specificity of FRα for folic acid with respect to other folate homologues. Moreover, some other crucial experimental results related to the structure of the receptor are discussed, such as the expected location/accessibility of known immune epitopes, the set of N-linked glycosylation sites and the effect of point mutations on the impairment of folate binding. Our results may provide useful insights for studies related to folate-targeted drug delivery or cancer therapies involving folate uptake.

A former spectroscopic study of Cu(II) coordination by the 13-membered ring cyclic tetrapeptide c(Lys-dHis-βAla-His) (DK13), revealed the presence, at alkaline pH, of a stable peptide/Cu(III) complex formed in solution by atmospheric dioxygen oxidation. To understand the nature of this coordination compound and to investigate the role of the His residues in the Cu(III) species formation, Cu K-edge XANES, and EXAFS spectra have been collected for DK13 and two other 13-membered cyclo-peptides: the diastereoisomer c(Lys-His-βAla-His) (LK13), and c(Gly-βAla-Gly-Lys) (GK13), devoid of His residues. Comparison of pre-edge peak features with those of Cu model compounds, allowed us to get information on copper oxidation state in two of the three peptides, DK13 and GK13: DK13 contains only Cu(III) ions in the experimental conditions, while GK13 binds only with Cu(II). For LK13/Cu complex, EXAFS spectrum suggested and UV-vis analysis confirmed the presence of a mixture of Cu(II) and Cu(III) coordinated species. Theoretical XANES spectra have been calculated by means of the MXAN code. The good agreement between theoretical and experimental XANES data collected for DK13, suggests that the refined structure, at least in the first coordination shell around Cu, is a good approximation of the DK13/Cu(III) coordination species present at strongly alkaline pH. All the data are consistent with a slightly distorted pyramidal CuN(4) unit, coming from the peptide bonds. Surprisingly, the His side-chains seemed not involved in the final, stable, Cu(III) scaffold.

X-ray absorption near edge structure (XANES) spectroscopy is a synchrotron radiation technique sensitive to the local structure and dynamics around the metal site of a heme containing protein. Advances in detection techniques and theoretical/computational platforms in the last 15 years allowed the use of XANES as a quantitative probe of the key structural determinants driving functional changes, both in a concerted way with protein crystallography and EXAFS (extended X-ray absorption fine structure), or as a stand-alone method to apply in the crystal state as well as in solution. Moreover, the local dynamics of the heme site has been deeply investigated, on one hand, coupling XANES to classical photolysis experiments at cryogenic temperatures; on the other hand, the intrinsic property of the synchrotron radiation to induce radiolysis events, has been exploited to investigate specific cryotrapped intermediates, using X-rays both as a pump and a probe. Insights on the XANES method and some specific examples are presented to illustrate these topics.

Prion diseases are a class of fatal neurodegenerative disorders characterized by brain spongiosis, synaptic degeneration, microglia and astrocytes activation, neuronal loss and altered redox control. These maladies can be sporadic, iatrogenic and genetic. The etiological agent is the prion, a misfolded form of the cellular prion protein, PrP(C). PrP(C) interacts with metal ions, in particular copper and zinc, through the octarepeat and non-octarepeat binding sites. The physiological implication of this interaction is still unclear, as is the role of metals in the conversion. Since prion diseases present metal dyshomeostasis and increased oxidative stress, we described the copper-binding site located in the human C-terminal domain of PrP-HuPrP(90-231), both in the wild-type protein and in the protein carrying the pathological mutation Q212P. We used the synchrotron-based X-ray absorption fine structure technique to study the Cu(II) and Cu(I) coordination geometries in the mutant, and we compared them with those obtained using the wild-type protein. By analyzing the extended X-ray absorption fine structure and the X-ray absorption near-edge structure, we highlighted changes in copper coordination induced by the point mutation Q212P in both oxidation states. While in the wild-type protein the copper-binding site has the same structure for both Cu(II) and Cu(I), in the mutant the coordination site changes drastically from the oxidized to the reduced form of the copper ion. Copper-binding sites in the mutant resemble those obtained using peptides, confirming the loss of short- and long-range interactions. These changes probably cause alterations in copper homeostasis and, consequently, in redox control.

Under prolonged X-ray irradiation, the ferrous heme of nitrosylated human adult hemoglobin derivative (HbNO) undergoes a reversible transition generating a 5-coordinate species, due to release of the Fe-NO bond. The overall process can be investigated using X-ray absorption near edge structure (XANES) spectroscopy. In this work, Fe K-edge XANES spectra were measured at T15 K, pH 9.2, i.e., on a high-affinity state (R-HbNO) where all the hemes are 6-coordinate, and at pH 6.5 in the presence of inositol hexakis-phosphate (IHP), i.e., on a low-affinity ligated state (T-HbNO) where the iron-hemes of the α-chains are 5-coordinate due to breaking of the Fe-proximal histidine bond. Under X-ray irradiation, 5-coordinate Fe-hemes are populated in both R-HbNO and T-HbNO, the Fe-NO bond lysis induced in T-HbNO involving rebinding of the proximal histidine to the transiently populated 4-coordinate hemes of the α-chains. A detailed analysis of the spectra confirms that different intermediate states in the ligand binding cooperative process of hemoglobin can be populated by X-ray irradiation, and that the part of the energy associated to the R-T quaternary transition, that is transmitted to the heme site, can be monitored by XANES spectroscopy.

By using X-ray absorption near edge structure (XANES) spectroscopy, we show that under prolonged exposure to Synchrotron X-rays, at T10 K, the Fe-heme in carbonmonoxy-myoglobin (MbCO) undergoes a slow two-state transition process. The final spectrum is nearly identical to that of the classical photoproduct (Mb*CO) obtained by UV-visible light illumination at 15 K. By increasing the temperature, the starting spectrum of MbCO is recovered at T100 K, demonstrating that the process is reversible and no damage occurred at the heme site in the time course of the experiment. Thus, the overall X-ray-induced process at low temperature is identical to the well-known (light-induced) photolysis of CO-hemeproteins.

The polarized E\ensuremath{\perp}c oxygen K-edge x-ray-absorption near-edge structure (XANES) spectrum of ${\mathrm{Bi}}_{2}$${\mathrm{Sr}}_{2}$${\mathrm{CaCu}}_{2}$${\mathrm{O}}_{8+\mathrm{\ensuremath{\delta}}}$ (Bi 2:2:1:2) has been calculated by a multiple-scattering approach and compared with experimental data. The symmetry of the conduction bands over a range of 15 eV above the Fermi level has been studied by a combined analysis of five different polarized x-ray-absorption spectra at the following edges: O K edge, Cu K edge, and Cu ${\mathit{L}}_{3}$ edge. Information on the partial density of states of the conduction bands, ${\mathit{scrD}}_{\mathit{X}(\mathit{l},}$${\mathit{m}}_{\mathit{l}}$), projected on the atomic site X (Cu and O) with selected orbital angular momentum l, and its projection ${\mathit{m}}_{\mathit{l}}$ along the c axis (${\mathit{scrD}}_{\mathrm{Cu}(2,0)}$, ${\mathit{scrD}}_{\mathrm{C}\mathrm{u}(2,\ifmmode\pm\else\textpm\fi{}1)}$, and ${\mathit{scrD}}_{\mathrm{C}\mathrm{u}(2,\ifmmode\pm\else\textpm\fi{}2)}$ for the Cu site; ${\mathit{scrD}}_{\mathrm{O}(1,0)}$ and ${\mathit{scrD}}_{\mathrm{O}(1,\ifmmode\pm\else\textpm\fi{}1)}$ for the oxygen site) have been obtained. The symmetry of the itinerant states induced by doping at the Fermi level is deduced to be a mixture of 3d holes with ${\mathit{m}}_{\mathit{l}}$=\ifmmode\pm\else\textpm\fi{}2 and ${\mathit{m}}_{\mathit{l}}$=0 orbital angular momenta and holes on planar oxygen in the molecular-orbital combination of local ${\mathit{b}}_{1}$ and ${\mathit{a}}_{1}$ symmetry [the ligand holes L(${\mathit{b}}_{1}$) and L(${\mathit{a}}_{1}$)].

Multiple Scattering (MS) theory, via the MXAN package, is able to reproduce the experimental XANES data of aqua ions, small molecules, and metal sites in biomolecules from the edge up to 150–200 eV. In this paper we present the last advances of the method, including the potential description and optimization. Improved parameterization also includes new routines to handle the structural determinants via generalized degrees of freedom. Examples will be presented to illustrate the method.

Experimental investigations on protein dynamics are usually carried out in solution; however, in most cases, the determination of protein structure is done by crystallography that relies on the diffraction properties of the protein arranged in a three-dimensional lattice. X-ray Absorption Spectroscopy (XAS) is an ideal tool to investigate the deep relationships between structure and dynamics, on a wide class of metal containing proteins, including hemeproteins. In fact, this technique can be used either as a structural refinement of X-ray diffraction on the same crystal, or as an independent tool to study structural dynamic properties both in crystal and solution. Different examples will be presented and discussed, with particular emphasis onto the original contribution due to the application of the MXAN software package to the analysis of XANES spectra.

The linearly polarized Cu K-edge x-ray-absorption near-edge structure (XANES) of ${\mathrm{Bi}}_{2}$${\mathrm{Sr}}_{2}$${\mathrm{CaCu}}_{2}$${\mathrm{O}}_{8+\mathrm{\ensuremath{\delta}}}$ (Bi 2:2:1:2) has been measured, and the spectra are interpreted by the multiple-scattering approach in real space. The polarized spectra can be predicted in terms of a one-electron dipole (\ensuremath{\Delta}l=+1) transition Cu 1s\ensuremath{\rightarrow}\ensuremath{\epsilon}p, probing the unoccupied p-like (l=1) density of states projected on the Cu site with orbital angular momentum ${\mathit{m}}_{\mathit{l}}$=0 in the E\ensuremath{\parallel}z spectra, and the ${\mathit{m}}_{\mathit{l}}$=1 in the E\ensuremath{\perp}c spectra. Therefore we show that the electronic structure of the high-energy conduction bands, beyond the Cu 3d band, are well described in terms of the one-electron approximation. Final-state effects induced by the core hole have been studied and calculated. A satellite 7 eV above the main K-XANES peak in both polarizations is shown to be a multielectron shake-up excitation, and it is enhanced going into the insulating phase. Structural information on the copper site in ${\mathrm{Bi}}_{2}$${\mathrm{Sr}}_{2}$${\mathrm{CaCu}}_{2}$${\mathrm{O}}_{8+\mathrm{\ensuremath{\delta}}}$ and in ${\mathrm{Bi}}_{2}$${\mathrm{Sr}}_{2}$${\mathrm{YCu}}_{2}$${\mathrm{O}}_{8+\mathrm{\ensuremath{\delta}}}$ has been extracted from XANES spectra, providing evidence for the decrease of the Cu-O distance in the metallic phase.

The symmetry of the conduction bands over a range of 15 eV above the Fermi level in La2CuO4 has been studied by the joint analysis of the polarized X-ray absorption spectra at several edges: O K-edge, Cu K-edge, and Cu L3-edge. The partial density of states of the conduction bands DX (l, ml) projected on the atomic site X (Cu and O) with selected orbital angular momentum l, and its projection ml along the c-axis have been obtained. The oxygen K-edge X-ray absorption near edge structure (XANES) spectrum has been calculated by multiple scattering approach. A good agreement between the one-electron calculations in the fully relaxed final state potential and the experimental spectra for the final states in the high energy conduction bands has been found.

The polarized Cu K-edge X-ray Absorption Near Edge Structure (XANES) of La2CuO4 has been interpreted by the multiple scattering approach. The size of the cluster of neighbouring atoms having good agreement with the XANES experimental data is determined by 45 atoms surrounding the absorbing Cu. The polarized spectra can be predicted in term of a one-electron dipole (Δl=+1) transition Cu 1s→ϵp, probing the unoccupied p-like (l=1) density of states projected on a Cu site with orbital angular momentum ml=0 in the E∥z spectra, and the ml=1 for the E⊤c spectra. Thus we show that the electronic structure of the high energy conduction bands, beyond the Cu 3d band, of La2CuO4 are well described in terms of the one-electron approximation. It is shown that XANES spectra are consistent with the contraction of the Cu-apex oxygen distance with doping. Final state effects induced by the core hole have been indentified: (i) the core transitions take place in the fully relaxed potential, (ii) the satellite at 7 eV above the main K-XANES peak in both polarizations is assigned to a multielectron shake up excitation. Finally the shoulder on the rising absorption edge, present in many Cu compounds and usually assigned to a shake down multi-electron excitation, is shown to be due to a one-electron transition to a state delocalized over a large cluster.

Neuroglobin (Ngb) is a member of the globin family expressed in the vertebrate brain, whose function is still under debate. A combined approach of X-ray Diffraction (XRD) on single crystal, together with Extended X-ray Absorption Fine Structure (EXAFS) and X-ray Absorption Near Edge Structure (XANES) in solution, has been undertaken to unequivocally establish the oxidation state of the heme iron in the crystal state, and to determine the fine structural details of the active site both in the bis-histidine and the CO-bound (NgbCO) states. The crystal structure of dithionite reduced mouse Ngb (at T=100K) has been compared with that of the ferric derivative previously reported (Vallone et al. 2004); no significant changes between the two were detected. Since the Fe K-edge X-ray Absorption Spectroscopy (XAS) method is sensitive to the oxidation state of the heme iron, we collected spectra in solution at 15K; moreover we acquired XANES data on a ferric bis-imidazole model compound, for comparison. The XAS data demonstrate that under X-ray the heme iron is photoreduced fairly rapidly. We conclude that the previously reported X-ray structure, which was collected on a crystal of ferric Ngb, very likely refers to a photoreduced species indistinguishable from the dithionite reduced protein. Results from the XAS analysis of NgbCO in solution are in good agreement with XRD data on the crystal, providing detailed parameters for the Fe-CO ligand binding geometry and pointing toward an 0.1-0.2 A increase of the Fe-proximal histidine bond relative to the ferrous bis-histidine state of the protein. However prolonged exposure of NgbCO to the X-ray beam is associated to XANES changes indicating rupture of the Fe-CO bond, probably due to secondary absorption events induced by X-rays. This result paves the way to novel experiments aimed at the structural characterization of the pentacoordinate state of ferrous Ngb, which is the only species competent in binding external ligands such as O2, CO or NO. Reference: Vallone, B., Nienhaus, K., Brunori, M., and G. U. Nienhaus. 2004. The structure of murine neuroglobin: Novel pathways for ligand migration and binding. Proteins. 56:85-92.

X-ray absorption spectroscopy is exquisitely sensitive to the coordination geometry of an absorbing atom and therefore allows bond distances and angles of the surrounding atomic cluster to be measured with atomic resolution. By contrast, the accuracy and resolution of metalloprotein active sites obtainable from x-ray crystallography are often insufficient to analyze the electronic properties of the metals that are essential for their biological functions. Here, we demonstrate that the combination of both methods on the same metalloprotein single crystal yields a structural model of the protein with exceptional active-site resolution. To this end, we have collected an x-ray diffraction data set to 1.4-angstrom resolution and Fe K-edge polarized x-ray absorption near edge structure (XANES) spectra on the same cyanomet sperm whale myoglobin crystal. The XANES spectra were quantitatively analyzed by using a method based on the multiple scattering approach, which yielded Fe-heme structural parameters with +/-(0.02-0.07)-angstrom accuracy on the atomic distances and +/- 7 degrees on the Fe-CN angle. These XANES-derived parameters were subsequently used as restraints in the crystal structure refinement. By combining XANES and x-ray diffraction, we have obtained an cyanomet sperm whale myoglobin structural model with a higher precision of the bond lengths and angles at the active site than would have been possible with crystallographic analysis alone.

The key structural features that define the reaction mechanism of the binuclear copper enzyme Tyrosinase (Ty) from Streptomyces antibioticus were investigated by X-ray absorption spectroscopy. The data for the met form, the halide bound derivative and the adduct with the competitive inhibitor and transition state analogue Kojic acid were analysed using the recently developed MXAN package. This analysis permitted the definition of structural clusters that include all atoms within 5 A from the metal ions of the active site. The data obtained for the different forms provide validation of the structural models previously proposed on the basis of the magnetic properties investigated by both pulsed EPR and paramagnetic NMR spectroscopies. The structural model of the reaction center obtained in this solution study is compared with the crystallographic structures recently proposed for several derivatives of bacterial Ty to suggest that only one of these structures is relevant to solution conditions.

A quite unexpected sevenfold coordination of the hydrated Hg(II) complex in aqueous solution is revealed by an extensive study combining X-ray absorption spectroscopy (XAS) and quantum mechanics/molecular dynamics (QM/MD) calculations. As a matter of fact, the generally accepted octahedral solvation of Hg(II) ion cannot be reconciled with XAS results. Next, refined QM computations point out the remarkable stability of a heptacoordinated structure with C 2 symmetry, and long-time MD simulations by new interaction potentials including many-body effects reveal that the hydrated complex has a quite flexible structure, corresponding for most of the time to heptacoordinated species. This picture is fully consistent with X-ray absorption near-edge structure experimental data which unambiguously show the preference for a sevenfold instead of a sixfold coordination.

Recently, a new method (MXAN) of extracting the local structural information available in the XANES spectra has been developed in the framework of the multiple scattering theory and successfully applied to the analysis of several system, both in solid and liquid state, In this paper we show the progress we have done in the MXAN procedure, in particular for what concerns the phenomenological broadening and the electronic charge fitting. We have also implemented parallelization on MXAN code by MPI library for both energy points and annealing for no‐structure parameters. This approach reduce the computer time of a factor ≈ 10 ( our cluster contains 14 nodes but the computer times scales with the number of nodes ) and at the same time increase the accuracy of the method. The new version of the program will be discussed on the basis of several examples.

Recently, we have shown that multiple scattering (MS) theory, via the MXAN package, is able to reproduce the experimental X‐ray absorption near edge structure (XANES) data of biological samples, in particular hemeproteins, from the rising edge up to ∼150–200 eV above the edge. In the present work, we illustrate how XANES can be used either as an independent tool to provide bond‐lengths and bond‐angles for a metalloprotein active site in solution, or in combination with X‐ray Diffraction for structural determinations of ligand binding geometry of the same diffracting protein crystal, providing atomic precision even for crystallographic structures solved at > 1.2 A resolution. At low temperature, XANES can be applied to provide the Fe‐heme structure of trapped intermediate conformations of light triggered processes, and some aspects of the ligand binding dynamics. Very recently, XANES difference spectra have been analyzed to provide the Fe‐heme structure of multiple intermediates of carbonmonoxy‐myoglobin, obtained under different photolysis protocols in solution state.

A full multiple theoretical model (MXAN) is applied to fit picosecond difference X-ray absorption spectra at the ruthenium L(3) edge upon photoexcitation of aqueous [RuII(bpy)3]2+. We show that fitting difference spectra allows an increase in sensitivity, such that slight structural changes can be retrieved, which are not detected in fitting full spectra. The Ru-N bond distances of the excited complex in the (3)MLCT state are in good agreement with recently published values. The implementation of the present approach to L-edge spectra and its high sensitivity opens opportunities for its extension to a large class of experiments where difference X-ray absorption spectra are recorded.