Multiple-wavelength Anomalous Diffraction Research Articles

Heterotrimetallic Mixed‐Valent Molecular Precursors Containing Periodic Table Neighbors: Assignment of Metal Positions and Oxidation States

A known trinuclear structure was used to design the heterobimetallic mixed-valent, mixed-ligand molecule [CoII (hfac)3 -Na-CoIII (acac)3 ] (1). This was used as a template structure to develop heterotrimetallic molecules [CoII (hfac)3 -Na-FeIII (acac)3 ] (2) and [NiII (hfac)3 -Na-CoIII (acac)3 ] (3) via isovalent site-specific substitution at either of the cobalt positions. Diffraction methods, synchrotron resonant diffraction, and multiple-wavelength anomalous diffraction were applied beyond simple structural investigation to provide an unambiguous assignment of the positions and oxidation states for the periodic table neighbors in the heterometallic assemblies. Molecules of 2 and 3 are true heterotrimetallic rather than a statistical mixture of two heterobimetallic counterparts. Trinuclear platform 1 exhibits flexibility in accommodating a variety of di- and trivalent metals, which can be further utilized in the design of molecular precursors for the NaMM'O4 functional oxide materials.

Remote Ligand Modifications Tune Electronic Distribution and Reactivity in Site-Differentiated, High-Spin Iron Clusters: Flipping Scaling Relationships.

We report the synthesis, characterization, and reactivity of [LFe3O(RArIm)3Fe][OTf]2, the first Hammett series of a site-differentiated cluster. The cluster reduction potentials and CO stretching frequencies shift as expected on the basis of the electronic properties of the ligand: electron-donating substituents result in more reducing clusters and weaker C-O bonds. However, unusual trends in the energetics of their two sequential CO binding events with the substituent σp parameters are observed. Specifically, introduction of electron-donating substituents suppresses the first CO binding event (ΔΔH by as much as 7.9 kcal mol-1) but enhances the second (ΔΔH by as much as 1.9 kcal mol-1). X-ray crystallography, including multiple-wavelength anomalous diffraction, Mössbauer spectroscopy, and SQUID magnetometry, reveal that these substituent effects result from changes in the energetic penalty associated with electronic redistribution within the cluster, which occurs during the CO binding event.

Exposing the inadequacy of redox formalisms by resolving redox inequivalence within isovalent clusters

In this report we examine a family of trinuclear iron complexes by multiple-wavelength, anomalous diffraction (MAD) to explore the redox load distribution within cluster materials by the free refinement of atomic scattering factors. Several effects were explored that can impact atomic scattering factors within clusters, including 1) metal atom primary coordination sphere, 2) M-M bonding, and 3) redox delocalization in formally mixed-valent species. Complexes were investigated which vary from highly symmetric to fully asymmetric by 57Fe Mössbauer and X-ray diffraction to explore the relationship between MAD-derived data and the data available from these widely used characterization techniques. The compounds examined include the all-ferrous clusters [ n Bu4N][(tbsL)Fe3(μ3-Cl)] (1) ([tbsL]6- = [1,3,5-C6H9(NC6H4-o-NSi t BuMe2)3]6-]), (tbsL)Fe3(py) (2), [K(C222)]2[(tbsL)Fe3(μ3-NPh)] (4) (C222 = 2,2,2-cryptand), and the mixed-valent (tbsL)Fe3(μ3-NPh) (3). Redox delocalization in mixed-valent 3 was explored with cyclic voltammetry (CV), zero-field 57Fe Mössbauer, near-infrared (NIR) spectroscopy, and X-ray crystallography techniques. We find that the MAD results show an excellent correspondence to 57Fe Mössbauer data; yet also can distinguish between subtle changes in local coordination geometries where Mössbauer cannot. Differences within aggregate oxidation levels are evident by systematic shifts of scattering factor envelopes to increasingly higher energies. However, distinguishing local oxidation levels in iso- or mixed-valent materials can be dramatically obscured by the degree of covalent intracore bonding. MAD-derived atomic scattering factor data emphasize in-edge features that are often difficult to analyze by X-ray absorption near edge spectroscopy (XANES). Thus, relative oxidation levels within the cluster were most reliably ascertained from comparing the entire envelope of the atomic scattering factor data.

Electron Cartography in Clusters

Deconvoluting the atom-specific electron density within polynuclear systems remains a challenge. A multiple-wavelength anomalous diffraction study on four clusters that share the same [Co6Se8] core was performed. Two cluster types were designed, one having a symmetric ligand sphere and the other having an asymmetric ligand sphere. It was found that in the neutral, asymmetric, CO-bound cluster, the Co−CO site is more highly oxidized than the other five Co atoms; when an electron is removed, the hole is distributed among the Se atoms. In the neutral, symmetric cluster, the Co atoms divide by electron population into two sets of three, each set being meridional; upon removal of an electron, the hole is distributed among all the Co atoms. This ligand-dependent tuning of the electron/hole distribution relates directly to the performance of clusters in biological and synthetic systems.

Electron Cartography in Clusters.

Deconvoluting the atom-specific electron density within polynuclear systems remains a challenge. A multiple-wavelength anomalous diffraction study on four clusters that share the same [Co6 Se8 ] core was performed. Two cluster types were designed, one having a symmetric ligand sphere and the other having an asymmetric ligand sphere. It was found that in the neutral, asymmetric, CO-bound cluster, the Co-CO site is more highly oxidized than the other five Co atoms; when an electron is removed, the hole is distributed among the Se atoms. In the neutral, symmetric cluster, the Co atoms divide by electron population into two sets of three, each set being meridional; upon removal of an electron, the hole is distributed among all the Co atoms. This ligand-dependent tuning of the electron/hole distribution relates directly to the performance of clusters in biological and synthetic systems.

Pteridine glycosyltransferase from Chlorobium tepidum: crystallization and X-ray analysis.

The pteridine glycosyltransferase (PGT) found in Chlorobium tepidum (CtPGT) catalyzes the conversion of L-threo-tetrahydrobiopterin to 1-O-(L-threo-biopterin-2'-yl)-β-N-acetylglucosamine using UDP-N-acetylglucosamine. The gene for CtPGT was cloned, and selenomethionine-derivatized protein was overexpressed and purified using various chromatographic techniques. The protein was crystallized by the hanging-drop vapour-diffusion method using 0.24 M triammonium citrate pH 7.0, 14%(w/v) PEG 3350 as a reservoir solution. Multiple-wavelength anomalous diffraction data were collected to 2.15 Å resolution from a single CtPGT crystal. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a = 189.61, b = 79.98, c=105.92 Å, β=120.5°.

Crystal structure analysis of c4763, a uropathogenic Escherichia coli-specific protein.

Urinary-tract infections (UTIs), which are some of the most common infectious diseases in humans, can cause sepsis and death without proper treatment. Therefore, it is necessary to understand their pathogenicity for proper diagnosis and therapeutics. Uropathogenic Escherichia coli, the major causative agents of UTIs, contain several genes that are absent in nonpathogenic strains and are therefore considered to be relevant to UTI pathogenicity. c4763 is one of the uropathogenic E. coli-specific proteins, but its function is unknown. To investigate the function of c4763 and its possible role in UTI pathogenicity, its crystal structure was determined at a resolution of 1.45 Å by a multiple-wavelength anomalous diffraction method. c4763 is a homodimer with 129 residues in one subunit that contains a GGCT-like domain with five α-helices and seven β-strands. c4763 shows structural similarity to the C-terminal domain of allophanate hydrolase from Kluyveromyces lactis, which is involved in the degradation of urea. These results suggest that c4763 might be involved in the utilization of urea, which is necessary for bacterial survival in the urinary tract. Further biochemical and physiological investigation will elucidate its functional relevance in UTIs.

Experimenting S-SAD on BM14-2 at the ESRF

Bending Magnet beamline 14 (BM14) at the European Synchrotron Radiation Facility (ESRF, Grenoble, France) is dedicated to macromolecular crystallography (MX). This experimental station has been designed specifically to produce MX diffraction data using the methods of Single- or Multiple-wavelength Anomalous Diffraction (SAD or MAD) (www.bm14.eu). From 1994 to 2000, BM14 operated as an ESRF public beamline. Then from 2001 to 2009 the beamline was acquired and operated as an UK Medical Research Council Collaborative Research Group beamline. Since 2010, it is now back an ESRF beamline operated by a consortium between the ESRF, the EMBL Grenoble Outstation and the Indian Department of Biotechnology for the benefit of both the European and Indian MX communities. During 2011 and 2012, the beamline optics' hutch was fully upgraded (hence the new denomination BM14-2). As a consequence the upgrade produced a four-time increase in beam brilliance with the concomitant reduction in average exposure time (~5 s today versus 20 s for BM14), leading to a substantial gain in the beamline screening capacity and in scientific productivity. Moreover, in addition to the new optical elements, the new channel-cut crystal was equipped with a second crystal pusher to reject high-energy harmonics. This latter device turned to be crucial for sulphur-SAD experiment success rate as it is very efficient in "cleaning up" the spectral purity of the low energy beams. We will illustrate the benefit of rejecting harmonics in terms of data quality and phasing power, critical for S-SAD experiments. We will also explicit our multiple-kappa orientation approach to enhance multiplicity as well as to optimise scaling protocols, both also very important for the success rate of these very low anomalous signal experiments. Nota Bene: European users may apply for direct access to the beamline via the Biostruct-X European program (www.biostruct-x.eu). Users from India are encouraged to apply from http://process.mbu.iisc.ernet.in/BM14/index.jsp

Alternative phasing method in macromolecular crystallography

Selenium is the most widely used heavy atom for experimental phasing, either by single anomalous scattering (SAD) or multiple-wavelength anomalous diffraction (MAD) procedures. The use of the single isomorphous replacement (SIR) or single isomorphous replacement with anomalous scattering (SIRAS) phasing procedure with selenomethionine (Mse) containing proteins is not so commonly used, as it requires isomorphous native data. Several non-redundant X-ray diffraction data sets from various Mse derivatised protein crystals were collected at energies far below the absorption edge before and after exposing the crystal to ultraviolet (UV) radiation with 266 nm lasers. A detailed analysis revealed that significant changes in diffracted intensities were induced by ultraviolet irradiation whilst retaining crystal isomorphism. These intensity changes allowed the crystal structures to be solved by the radiation damage-induced phasing (RIP) technique [1]. These can be coupled with the anomalous signal from the dataset collected at the selenium absorption edge to obtain SIRAS phases in a UV-RIPAS phasing experiment [2]. Inspection of the crystal structures and electron-density maps demonstrated that covalent bonds between selenium and carbon at all sites located in the core of the proteins or in a hydrophobic environment were much more susceptible to UV radiation-induced cleavage than other bonds typically present in Mse proteins. The rapid UV radiation-induced bond cleavage opens a reliable new paradigm for phasing at synchrotron [1,2] and at in-house X-ray source [3].

ANODE: anomalous and heavy-atom density calculation

The new program ANODE estimates anomalous or heavy-atom density by reversing the usual procedure for experimental phase determination by methods such as single- and multiple-wavelength anomalous diffraction and single isomorphous replacement anomalous scattering. Instead of adding a phase shift to the heavy-atom phases to obtain a starting value for the native protein phase, this phase shift is subtracted from the native phase to obtain the heavy-atom substructure phase. The required native phase is calculated from the information in a Protein Data Bank file of the structure. The resulting density enables even very weak anomalous scatterers such as sulfur to be located. Potential applications include the identification of unknown atoms and the validation of molecular replacement solutions.

A Combined <I>In Situ</I> Grazing Incidence Small Angle X-Ray Scattering and Grazing Incidence X-Ray Diffraction Study of the Growth of Ge Islands on Pit-Patterned Si(001) Substrates

The growth of Ge islands on a pit-patterned Si(001) template is investigated in situ, combining grazing incidence diffraction, multiple wavelength anomalous diffraction, and small angle scattering. This allows monitoring in situ the detailed structural and morphological evolutions of the pits, of the wetting-layer and of the nucleated islands on the pit-patterned Si(001) substrate. It is shown that after Si regrowth, the Si substrate displays {107} and {1 1 11} facets. During the very first stages of Ge growth, the preliminary facets of the Si substrate are energetically unfavourable, and the pit facets break up into a rather complex pattern of {10n} and {11m} facets with n > 7 and m > 11. At 5 and 6 ML, intensity rods from {105} and {113}-type facets appear in the GISAXS images revealing the formation of pyramids and domes, respectively. The degree of ordering, the shape, strain and composition of the islands are characterized during the growth process to provide a detailed evolution of their structure and morphology.

Crystal Structure of the Ubiquitin-associated (UBA) Domain of p62 and Its Interaction with Ubiquitin

p62/SQSTM1/A170 is a multimodular protein that is found in ubiquitin-positive inclusions associated with neurodegenerative diseases. Recent findings indicate that p62 mediates the interaction between ubiquitinated proteins and autophagosomes, leading these proteins to be degraded via the autophagy-lysosomal pathway. This ubiquitin-mediated selective autophagy is thought to begin with recognition of the ubiquitinated proteins by the C-terminal ubiquitin-associated (UBA) domain of p62. We present here the crystal structure of the UBA domain of mouse p62 and the solution structure of its ubiquitin-bound form. The p62 UBA domain adopts a novel dimeric structure in crystals, which is distinctive from those of other UBA domains. NMR analyses reveal that in solution the domain exists in equilibrium between the dimer and monomer forms, and binding ubiquitin shifts the equilibrium toward the monomer to form a 1:1 complex between the UBA domain and ubiquitin. The dimer-to-monomer transition is associated with a structural change of the very C-terminal end of the p62 UBA domain, although the UBA fold itself is essentially maintained. Our data illustrate that dimerization and ubiquitin binding of the p62 UBA domain are incompatible with each other. These observations reveal an autoinhibitory mechanism in the p62 UBA domain and suggest that autoinhibition plays a role in the function of p62.

Crystallization and preliminary X-ray crystallographic studies of the ice-binding protein from the Antarctic yeastLeucosporidiumsp. AY30

Freezing is dangerous to cellular organisms because it causes an increase in the concentration of ions and other solutes in the plasma, denatures biomolecules and ruptures cell membranes. Some cold-adapted organisms can survive at subzero temperatures by producing proteins that bind to and inhibit the growth of ice crystals. To better understand the structure and function of these proteins, the ice-binding protein from Leucosporidium sp. AY30 (LeIBP) was overexpressed, purified and crystallized. The native crystal belonged to space group P4(3)2(1)2, with unit-cell parameters a=b=98.05, c=106.13 Å. Since LeIBP lacks any cysteine or methionine residues, two leucine residues (Leu69 and Leu155) were substituted by methionine residues in order to obtain selenomethionine-substituted LeIBP for use in multiple-wavelength anomalous diffraction (MAD) phasing. The selenomethionine-substituted mutant crystallized in the same space group as the native protein.

Recent advances in theCRANKsoftware suite for experimental phasing

For its first release in 2004, CRANK was shown to effectively detect and phase anomalous scatterers from single-wavelength anomalous diffraction data. Since then, CRANK has been significantly improved and many more structures can be built automatically with single- or multiple-wavelength anomalous diffraction or single isomorphous replacement with anomalous scattering data. Here, the new algorithms that have been developed that have led to these substantial improvements are discussed and CRANK's performance on over 100 real data sets is shown. The latest version of CRANK is freely available for download at http://www.bfsc.leidenuniv.nl/software/crank/ and from CCP4 (http://www.ccp4.ac.uk/).

Update on the tutorial for learning and teaching macromolecular crystallography

Two new experiments (single isomorphous replacement including anomalous-scattering effects and radiation damage-induced phasing) have been designed to complement the five experiments (sulfur single-wavelength anomalous diffraction, multiple-wavelength anomalous diffraction, molecular replacement, ion binding and ligand binding) of the first edition of the previously described tutorial for learning and teaching macromolecular crystallography [Faust, Panjikar, Mueller, Parthasarathy, Schmidt, Lamzin & Weiss (2008). J. Appl. Cryst. 41, 1161–1172]. Furthermore, the tutorial has been re-organized and in part re-written to reflect the comments and suggestions of users. The most significant overhaul was applied to the data-processing part of the tutorial. Nevertheless, the convenient features that all of the utilized proteins used are commercially available and that they can be easily and reproducibly crystallized and mounted for diffraction data collection have been retained. Also, for all of the seven experiments the raw diffraction images and the processed data are provided for illustrating and teaching the steps of data processing and structure determination.

Crystal Structure of Chiral γPNA with Complementary DNA Strand: Insights into the Stability and Specificity of Recognition and Conformational Preorganization

We have determined the structure of a PNA-DNA duplex to 1.7 A resolution by multiple-wavelength anomalous diffraction phasing method on a zinc derivative. This structure represents the first high-resolution 3D view of a hybrid duplex containing a contiguous chiral PNA strand with complete gamma-backbone modification ("gammaPNA"). Unlike the achiral counterpart, which adopts a random-fold, this particular gammaPNA is already preorganized into a right-handed helix as a single strand. The new structure illustrates the unique characteristics of this modified PNA, possessing conformational flexibility while maintaining sufficient structural integrity to ultimately adopt the preferred P-helical conformation upon hybridization with DNA. The unusual structural adaptability found in the gammaPNA strand is crucial for enabling the accommodation of backbone modifications while constraining conformational states. In conjunction with NMR analysis characterizing the structures and substructures of the individual building blocks, these results provide unprecedented insights into how this new class of chiral gammaPNA is preorganized and stabilized, before and after hybridization with a cDNA strand. Such knowledge is crucial for the future design and development of PNA for applications in biology, biotechnology, and medicine.

Enhancing MADFAdata for substructure determination

Heavy-atom substructure determination is a critical step in phasing an unknown macromolecular structure. Dual-space (Shake-and-Bake) recycling is a very effective procedure for locating the substructure (heavy) atoms using F(A) data estimated from multiple-wavelength anomalous diffraction. However, the estimated F(A) are susceptible to the accumulation of errors in the individual intensity measurements at several wavelengths and from inaccurate estimation of the anomalous atomic scattering corrections f' and f''. In this paper, a new statistical and computational procedure which merges multiple F(A) estimates into an averaged data set is used to further improve the quality of the estimated anomalous amplitudes. The results of 18 Se-atom substructure determinations provide convincing evidence in favor of using such a procedure to locate anomalous scatterers.

The structural basis for peptide selection by the transport receptor OppA

Oligopeptide-binding protein A (OppA) from Lactococcus lactis binds peptides of an exceptionally wide range of lengths (4-35 residues), with no apparent sequence preference. Here, we present the crystal structures of OppA in the open- and closed-liganded conformations. The structures directly explain the protein's phenomenal promiscuity. A huge cavity allows binding of very long peptides, and a lack of constraints for the position of the N and C termini of the ligand is compatible with binding of peptides with varying lengths. Unexpectedly, the peptide's amino-acid composition (but not the exact sequence) appears to have a function in selection, with a preference for proline-rich peptides containing at least one isoleucine. These properties can be related to the physiology of the organism: L. lactis is auxotrophic for branched chain amino acids and favours proline-rich caseins as a source of amino acids. We propose a new mechanism for peptide selection based on amino-acid composition rather than sequence.

Crystal structure of KorA bound to operator DNA: insight into repressor cooperation in RP4 gene regulation

KorA is a global repressor in RP4 which regulates cooperatively the expression of plasmid genes whose products are involved in replication, conjugative transfer and stable inheritance. The structure of KorA bound to an 18-bp DNA duplex that contains the symmetric operator sequence and incorporates 5-bromo-deoxyuridine nucleosides has been determined by multiple-wavelength anomalous diffraction phasing at 1.96-Å resolution. KorA is present as a symmetric dimer and contacts DNA via a helix–turn–helix motif. Each half-site of the symmetric operator DNA binds one copy of the protein in the major groove. As confirmed by mutagenesis, recognition specificity is based on two KorA side chains forming hydrogen bonds to four bases within each operator half-site. KorA has a unique dimerization module shared by the RP4 proteins TrbA and KlcB. We propose that these proteins cooperate with the global RP4 repressor KorB in a similar manner via this dimerization module and thus regulate RP4 inheritance.

Structure of mannosyl-3-phosphoglycerate phosphatase fromPyrococcus horikoshii

Mannosyl-3-phosphoglycerate phosphatase (MPGP) catalyzes the dephosphorylation of alpha-mannosyl-3-phosphoglycerate (MPG) to produce alpha-mannosylglycerate (MG). In the hyperthermophile Pyrococcus horikoshii, MPGP plays a role in a series of enzyme reactions that are involved in the MG-biosynthesis pathway, which is important for maintaining life under conditions of high salt concentration. Crystal structures of P. horikoshii MPGP (PhoMPGP) in the holo form and in the apo form lacking the magnesium ion were determined by the multiple-wavelength anomalous diffraction method using SeMet-substituted PhoMPGP. PhoMPGP consists of two domains: a core domain that is conserved in the haloacid dehalogenase superfamily and a cap domain that is specific to the C2B cap subclass of the superfamily. Apo-form crystals contain two PhoMPGP molecules: one in the open conformation and the other in the closed conformation. In holo-form crystals both of the two molecules are in the closed conformation with phosphate and magnesium ions. PhoMPGP has a specific hairpin loop that is bent towards the active site in the closed conformation of both the apo and holo forms. PhoMPGP has a cavity between the two domains which is considered to be the substrate-binding site as a phosphate ion is located in the cavity, mimicking the binding manner of the phosphate group of MPG. The cavity is sequestered in the closed conformation such that a conformational change is indispensable for the release of products. A salt bridge from the general acid/base Asp10 to Arg170 is observed in the holo-form PhoMPGP which is not present in the open form. The importance of the conformational change in the activity of PhoMPGP is discussed.