Resolved Structure Research Articles

Rotation of methane molecules in dimers and small clusters.

This work reports on the study of the internal rotation of methane molecules in small clusters containing up to about five molecules. The clusters were assembled in helium droplets at T = 0.38 K by successive capture of single methane molecules and studied by infrared laser spectroscopy of the fundamental CH4 ν3 vibration around 3030 cm(-1). The spectra demonstrate well resolved structure due to internal rotation of the constituent molecules in the clusters. The most resolved spectrum for the dimers shows characteristic splitting of the lines due to anisotropic intermolecular interaction. The magnitude of the splitting is found to be in a good quantitative agreement with the recent theoretical anisotropic intermolecular potentials.

Abstract 3653: Structure-based study to overcome cross-reactivity of novel androgen receptor inhibitors

Abstract The mutation-driven transformation of clinically used anti-androgens into agonists of human androgen receptor (AR) represents a major challenge in the current treatment of prostate cancer (PCa). To address this problem, we have developed a novel class of AR inhibitors targeting the DNA-binding domain (DBD) of the receptor, which is distanced from the mutations-prone androgen binding site (ABS) in the ligand-binding domain (LBD) of the AR, targeted by all conventional antiandrogens. While many members of the developed phenyl-thiazol-2-yl-morpholine series demonstrated potent sub-micromolar inhibition of the wild-type AR, some compounds also exhibited an undesired partial agonistic effect toward the T877A mutated form of the receptor, implying their cross-interaction with the AR ABS. To study the molecular basis of the cross-reactivity, we have solved the T877A mutated form of the AR LBD in complex with one developed compound exhibiting such unwanted partial agonism. Based on the resolved crystal structure, we have identified critical protein-ligand interactions and conformational changes in wild-type and T877A forms of AR that drive observed agonistic effects. The identified structural basis has further been used to modify the scaffold of developed AR DBD binders to eliminate their cross-reactivity toward T877A mutated AR LBD. In particular, the replacement of the phenyl ring with less hydrophobic heterocycles resulted in a series of inhibitors that did not demonstrate affinity toward ABS or exhibit an undesired agonistic effect on AR. This study provides insights into the development of AR inhibitors with high specificity, which may help overcome the mutation-driven resistance of anti-AR drugs in the treatment of PCa. Citation Format: Huifang Li, Nada Lallous, Kush Dalal, Eric Leblanc, Fuqiang Ban, Fabrice Ciesielski, Paul S. Rennie, Artem Cherkasov. Structure-based study to overcome cross-reactivity of novel androgen receptor inhibitors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3653. doi:10.1158/1538-7445.AM2015-3653

Investigation of structural, optical and electrical properties of a new cobalt phthalocyanine thin films with potential applications in perchlorate sensor

Optical, structural and electrical properties of new cobalt phthalocyanine derivatives (Co(II)Pc-AP) thin films have been investigated. The Raman spectroscopy study shows the different vibrations bands corresponding to the metallophthalocyanine. The cobalt-phthalocyanine derivative films exhibit absorption spectra with a resolved electronic structure in the UV–vis range and the energy gap was determined by the Tauc method. Electrical properties of the ITO/Co(II)Pc-AP/Al structure have been investigated by I–V characteristics and impedance spectroscopy measurements. The conduction is governed by space-charge-limited current (SCLC) mechanism. The impedance spectroscopy study showed a hopping transport process, which is a typical behavior of disordered materials. The electrical characteristics of the devices were modeled by a single parallel resistor and capacitor network in series with a resistance.

High-resolution vacuum-ultraviolet photoabsorption spectra of 1-butyne and 2-butyne

The absolute photoabsorption cross sections of 1- and 2-butyne have been recorded at high resolution by using the vacuum-ultraviolet Fourier-Transform spectrometer at the SOLEIL Synchrotron. Both spectra show more resolved structure than previously observed, especially in the case of 2-butyne. In this work, we assess the potential importance of Rydberg states with higher values of orbital angular momentum, l, than are typically observed in photoabsorption experiments from ground state molecules. We show how the character of the highest occupied molecular orbitals in 1- and 2-butyne suggests the potential importance of transitions to such high-l (l = 3 and 4) Rydberg states. Furthermore, we use theoretical calculations of the partial wave composition of the absorption cross section just above the ionization threshold and the principle of continuity of oscillator strength through an ionization threshold to support this conclusion. The new absolute photoabsorption cross sections are discussed in light of these arguments, and the results are consistent with the expectations. This type of argument should be valuable for assessing the potential importance of different Rydberg series when sufficiently accurate direct quantum chemical calculations are difficult, for example, in the n ≥ 5 manifolds of excited states of larger molecules.

Helicobacter pylori HP0377, a member of the Dsb family, is an untypical multifunctional CcmG that cooperates with dimeric thioldisulfide oxidase HP0231.

BackgroundIn the genome of H. pylori 26695, 149 proteins containing the CXXC motif characteristic of thioldisulfide oxidoreductases have been identified to date. However, only two of these proteins have a thioredoxin-like fold (i.e., HP0377 and HP0231) and are periplasm-located. We have previously shown that HP0231 is a dimeric oxidoreductase that catalyzes disulfide bond formation in the periplasm. Although HP0377 was originally described as DsbC homologue, its resolved structure and location of the hp0377 gene in the genome indicate that it is a counterpart of CcmG/DsbE.ResultsThe present work shows that HP0377 is present in H. pylori cells only in a reduced form and that absence of the main periplasmic oxidase HP0231 influences its redox state. Our biochemical analysis indicates that HP0377 is a specific reductase, as it does not reduce insulin. However, it possesses disulfide isomerase activity, as it catalyzes the refolding of scrambled RNase. Additionally, although its standard redox potential is -176 mV, it is the first described CcmG protein having an acidic pKa of the N-terminal cysteine of the CXXC motif, similar to E. coli DsbA or E. coli DsbC. The CcmG proteins that play a role in a cytochrome c-maturation, both in system I and system II, are kept in the reduced form by an integral membrane protein DsbD or its analogue, CcdA. In H. pylori HP0377 is re-reduced by CcdA (HP0265); however in E. coli it remains in the oxidized state as it does not interact with E. coli DsbD. Our in vivo work also suggests that both HP0377, which plays a role in apocytochrome reduction, and HP0378, which is involved in heme transport and its ligation into apocytochrome, provide essential functions in H. pylori.ConclusionsThe present data, in combination with the resolved three-dimensional structure of the HP0377, suggest that HP0377 is an unusual, multifunctional CcmG protein.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0471-z) contains supplementary material, which is available to authorized users.

Threshold photoelectron spectroscopy of unstable N-containing compounds: Resolution of ΔK subbands in HNCO(+) and vibrational resolution in NCO(.).

The threshold photoelectron spectra (TPES) of two unstable nitrogen-containing species, HNCO and NCO, were recorded utilizing vacuum ultraviolet synchrotron radiation. Both are intermediates in combustion processes and play a role in the removal of nitrogen oxides from exhaust gases. The rovibronic structure of the first band in the TPES of HNCO(+) was analyzed within the framework of an orbital ionization model, and the resolved structure of the origin band was assigned to ΔK subbands. An ionization energy of 11.602 ± 0.005 eV was determined and the vibrational structure of the cationic ground state was analyzed by a Franck-Condon fit. Low lying electronically excited states of HNCO(+) were also observed. In a second series of experiments, the NCO radical was generated by flash pyrolysis from chlorine isocyanate. The ionization energy to the X(+) (3)Σ(-) ground state was determined to be 11.76 ± 0.02 eV, while for the a(+) (1)Δ state, a value of 12.93 ± 0.02 eV was obtained. Vibrational structure was observed for both states, and bands were assigned by Franck-Condon simulations.

Dissecting the AGB star L2Puppis: a torus in the making

The circumstellar environment of L2 Pup, an oxygen-rich semiregular variable, was observed to understand the evolution of mass loss and the shaping of ejecta in the late stages of stellar evolution. High-angular resolution observations from a single 8 m telescope were obtained using aperture masking in the near-infrared (1.64, 2.30 and 3.74 $\rm\mu m$) on the NACO/VLT, both in imaging and polarimetric modes. The aperture-masking images of L2 Pup at 2.30 $\rm\mu m$ show a resolved structure that resembles a toroidal structure with a major axis of ~140 milliarcseconds (mas) and an east-west orientation. Two clumps can be seen on either side of the star, ~65 mas from the star, beyond the edge of the circumstellar envelope (estimated diameter is ~27 mas), while a faint, hook-like structure appear toward the northeast. The patterns are visible both in the imaging and polarimetric mode, although the latter was only used to measure the total intensity (Stokes I). The overall shape of the structure is similar at the 3.74 $\rm\mu m$ pseudo-continuum (dust emission), where the clumps appear to be embedded within a dark, dusty lane. The faint, hook-like patterns are also seen at this wavelength, extending northeast and southwest with the central, dark lane being an apparent axis of symmetry. We interpret the structure as a circumstellar torus with inner radius of 4.2 au. With a rotation velocity of 10 km s$^{-1}$ as suggested by the SiO maser profile, we estimate a stellar mass of 0.7 M$_\odot$.}

Developing a two-step retrieval method for estimating total suspended solid concentration in Chinese turbid inland lakes using Geostationary Ocean Colour Imager (GOCI) imagery

Total suspended solid (TSS) concentration is an important water quality parameter. Mapping its varying distribution using satellite images with high temporal resolution is valuable for studying suspended sediment transportation and diffusion patterns in inland lakes. A total of 255 sites were used to make remote-sensing reflectance measurements and surface water sampling at four Chinese inland lakes, i.e. Taihu Lake, Chaohu Lake, Dianchi Lake, and the Three Gorges Reservoir, at different seasons. A two-step retrieval method was then developed to estimate TSS concentration for contrasting Chinese inland lakes, which is described in this article. In the first step, a cluster method was applied for water classification using eight Geostationary Ocean Colour Imager (GOCI) channel reflectance spectra simulated by spectral reflectance measured by an Analytical Spectral Devices (ASD) Inc. spectrometer. This led to the classification of the water into three classes (1, 2, and 3), each with distinct optical characteristics. Based on the water quality, spectral absorption, and reflectance, the optical features in Class 1 were dominated by TSS, while Class 3 was dominated by chl-a and the optical characteristics of Class 2 were dominated jointly by TSS and chl-a. In the second step, class-specific TSS concentration retrieval algorithms were built. We found that the band ratio Band 8/Band 4 was suitable for Class 1, while the band ratio of Band 7/Band 4 was suitable for both Class 2 and Class 3. A comprehensive determination value, combining the spectral angle mapper and Euclidean distance, was adopted to identify the classes of image pixels when the method was applied to a GOCI image. Then, based on the pixel’s class, the class-specific retrieval algorithm was selected for each pixel. The accuracy analysis showed that the performance of this two-step method was improved significantly compared to the unclassed method: the mean absolute percentage error decreased from 38.9% to 24.3% and the root mean square error decreased from 22.1 to 16.5 mg l–1. Finally, the GOCI image acquired on 13 May 2013 was used as a demonstration to map the TSS concentration in Taihu Lake with a reasonably good accuracy and highly resolved spatial structure pattern.

Hyperfine structure in the X8, A[19.1]9 and B[21.68]8 states of HoF and X8 and A[15.6]9 state of HoCl

High resolution spectra of holmium monofluoride, HoF and holmium monochloride, HoCl, prepared in a laser ablation source, have been obtained using laser induced fluorescence. Spectra of the A[19.1]9–X8 0-0 and 1-0 and B[21.68]8–X8 0-0 bands of HoF and the A[15.6]9–X8 0-0 band of HoCl all show resolved hyperfine structure. Analysis of the spectra yielded magnetic hyperfine parameters, h=0.2240(5), 0.2210(6), 0.2177(6) and 0.2488(5)cm−1 for the X (v=0), A (v=0 and 1) and B (v=0) states of HoF and 0.2355(32) and 0.2448(29)cm−1 for the X (v=0) and A (v=0) states of HoCl, respectively. The following quadrupole coupling constants were obtained for the above six states; eQq0(HoF)=−0.0874(67), −0.0586(44), −0.0579(56), −0.0840(64)cm−1 and eQq0(HoCl)=−0.082(11), −0.060(11)cm−1. Comparison with previously determined values for HoO and HoS show that the ground state magnetic hyperfine structure in HoF and HoCl is entirely due to the Ho 4f electron and is consistent with the ground state, X8, configuration of Ho+{4f10(5I8)6s2}X− (X=F,Cl). Calculations of the ground state magnetic, h(X8), and quadrupole, eQq0(X8) hyperfine parameters from atomic hyperfine parameters are found to be consistent with the observed values for both molecules.

Na+ Inhibits the Epithelial Na+ Channel by Binding to a Site in an Extracellular Acidic Cleft

The epithelial Na(+) channel (ENaC) has a key role in the regulation of extracellular fluid volume and blood pressure. ENaC belongs to a family of ion channels that sense the external environment. These channels have large extracellular regions that are thought to interact with environmental cues, such as Na(+), Cl(-), protons, proteases, and shear stress, which modulate gating behavior. We sought to determine the molecular mechanism by which ENaC senses high external Na(+) concentrations, resulting in an inhibition of channel activity. Both our structural model of an ENaC α subunit and the resolved structure of an acid-sensing ion channel (ASIC1) have conserved acidic pockets in the periphery of the extracellular region of the channel. We hypothesized that these acidic pockets host inhibitory allosteric Na(+) binding sites. Through site-directed mutagenesis targeting the acidic pocket, we modified the inhibitory response to external Na(+). Mutations at selected sites altered the cation inhibitory preference to favor Li(+) or K(+) rather than Na(+). Channel activity was reduced in response to restraining movement within this region by cross-linking structures across the acidic pocket. Our results suggest that residues within the acidic pocket form an allosteric effector binding site for Na(+). Our study supports the hypothesis that an acidic cleft is a key ligand binding locus for ENaC and perhaps other members of the ENaC/degenerin family.

Shared structural features of the 9aaTAD family in complex with CBP.

A number of transactivation domains for transcription factors including p53, E2A/HEB, MLL, cMyb, CREB, FOXO3, Gcn4, Oaf1 and Pdr1 have been reported to interact with the KIX domain of general transcriptional mediators CBP, p300 or MED15. Most of those factors belong to the already established Nine amino acid Transactivation Domain (9aaTAD) family. By using available structural data, we found binding analogy for the 9aaTAD in the MLL-KIX and also E2A/HEB-KIX complexes. We recognized two distinct TAD formations in the KIX complex. In the E2A/HEB-KIX complex, the leucine position is determined by the prolonged helical structure including the 9aaTAD and the leucine (long-helical TAD). However in the MLL-KIX complex, the equal position of 9aaTAD and proximal leucine is achieved differently by leucine-turn-helix structural architecture. Furthermore, the FOXO3-KIX complex shares structural analogy with the E2A-KIX complex in respect of both 9aaTAD and proximal leucine. Next, from (i) sequence alignment of the identified 9aaTADs in p53, E2A/HEB and MLL proteins and (ii) the resolved structure of the MLL-KIX and E2A/HEB-KIX complexes, we generated a plausible structural model for p53 that could be used also for other members of the 9aaTAD family. The position of 9aaTADs in Oaf1-, Pdr1- and Gcn4-MED15 KIX complexes and 9aaTAD composition are in good agreement with E2A, MLL, FOXO3 and p53. Analyses of structural data in this study define fundamental structural requirements and shed more light on the ambiguous 9aaTAD domain.

QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure.

BackgroundHydrogen/deuterium exchange (HDX) coupled to mass spectrometry permits analysis of structure, dynamics, and molecular interactions of proteins. HDX mass spectrometry is confounded by deuterium exchange-associated peaks overlapping with peaks of heavy, natural abundance isotopes, such as carbon-13. Recent studies demonstrated that high-performance mass spectrometers could resolve isotopic fine structure and eliminate this peak overlap, allowing direct detection and quantification of deuterium incorporation.ResultsHere, we present a graphical tool that allows for a rapid and automated estimation of deuterium incorporation from a spectrum with isotopic fine structure. Given a peptide sequence (or elemental formula) and charge state, the mass-to-charge ratios of deuterium-associated peaks of the specified ion is determined. Intensities of peaks in an experimental mass spectrum within bins corresponding to these values are used to determine the distribution of deuterium incorporated. A theoretical spectrum can then be calculated based on the estimated distribution of deuterium exchange to confirm interpretation of the spectrum. Deuterium incorporation can also be detected for ion signals without a priori specification of an elemental formula, permitting detection of exchange in complex samples of unidentified material such as natural organic matter. A tool is also incorporated into QUDeX-MS to help in assigning ion signals from peptides arising from enzymatic digestion of proteins. MATLAB-deployable and standalone versions are available for academic use at qudex-ms.sourceforge.net and agarlabs.com.ConclusionIsotopic fine structure HDX-MS offers the potential to increase sequence coverage of proteins being analyzed through mass accuracy and deconvolution of overlapping ion signals. As previously demonstrated, however, the data analysis workflow for HDX-MS data with resolved isotopic fine structure is distinct. QUDeX-MS we hope will aid in the adoption of isotopic fine structure HDX-MS by providing an intuitive workflow and interface for data analysis.

High-resolution, vacuum-ultraviolet absorption spectrum of boron trifluoride.

In the course of investigations of thermal neutron detection based on mixtures of (10)BF3 with other gases, knowledge was required of the photoabsorption cross sections of (10)BF3 for wavelengths between 135 and 205 nm. Large discrepancies in the values reported in existing literature led to the absolute measurements reported in this communication. The measurements were made at the SURF III Synchrotron Ultraviolet Radiation Facility at the National Institute of Standards and Technology. The measured absorption cross sections vary from 10(-20) cm(2) at 135 nm to less than 10(-21) cm(2) in the region from 165 to 205 nm. Three previously unreported absorption features with resolvable structure were found in the regions 135-145 nm, 150-165 nm, and 190-205 nm. Quantum mechanical calculations, using the TD-B3LYP/aug-cc-pVDZ variant of time-dependent density functional theory implemented in Gaussian 09, suggest that the observed absorption features arise from symmetry-changing adiabatic transitions.

The effect of the dipole bound state on AgF⁻ vibrationally resolved photodetachment cross sections and photoelectron angular distributions.

The first photoelectron spectra of AgF(-) are recorded over the energy range 1.61-1.85 eV using the velocity map imaging technique. The resolved vibrational structure of the AgF X', v' ← AgF(-) X″, v″ = 0 band yields an AgF electron affinity of 1.46 ± 0.01 eV and vibrational frequency of 500 ± 40 cm(-1). For the v' = 2, 3, 4 channels, the photodetachment cross sections and angular distributions undergo rapid changes over a narrow electron kinetic energy range in the region of 50 meV (approximately 13 meV below the opening of the next vibrational channel). This is consistent with Fano-like behavior indicating autodetachment following excitation to a resonant anion state lying in the detachment continuum. EOM-CCSD calculations reveal this to be a dipole bound state. The consistency of the detachment data with the vibrational autodetachment propensity rule Δv = -1 shows that the autodetachment results from breakdown of the Born-Oppenheimer approximation, coupling the vibrational and electronic degrees of freedom.

Mechanism of enzymatic reaction and protein–protein interactions of PLD from a 3D structural model

The phospholipase D (PLD) superfamily catalyzes the hydrolysis of cell membrane phospholipids generating the key intracellular lipid second messenger phosphatidic acid. However, there is not yet any resolved structure either from a crystallized protein or from NMR of any mammalian PLDs. We propose here a 3D model of the PLD2 by combining homology and ab initio 3 dimensional structural modeling methods, and docking conformation. This model is in agreement with the biochemical and physiological behavior of PLD in cells. For the lipase activity, the N- and C-terminal histidines of the HKD motifs (His 442/His 756) form a catalytic pocket, which accommodates phosphatidylcholine head group (but not phosphatidylethanolamine or phosphatidyl serine). The model explains the mechanism of the reaction catalysis, with nucleophilic attacks of His 442 and water, the latter aided by His 756. Further, the secondary structure regions superimposed with bacterial PLD crystal structure, which indicated an agreement with the model. It also explains protein–protein interactions, such as PLD2–Rac2 transmodulation (with a 1:2 stoichiometry) and PLD2 GEF activity both relevant for cell migration, as well as the existence of binding sites for phosphoinositides such as PIP2. These consist of R236/W238 and R557/W563 and a novel PIP2 binding site in the PH domain of PLD2, specifically R210/R212/W233. In each of these, the polar inositol ring is oriented towards the basic amino acid Arginine. Since tumor-aggravating properties have been found in mice overexpressing PLD2 enzyme, the 3D model of PLD2 will be also useful, to a large extent, in developing pharmaceuticals to modulate its in vivo activity.

Validation and structural characterization of the LEDGF/p75-MLL interface as a new target for the treatment of MLL-dependent leukemia.

Mixed lineage leukemia (MLL) fusion-driven acute leukemias represent a genetically distinct subset of leukemias with poor prognosis. MLL forms a ternary complex with the lens epithelium-derived growth factor (LEDGF/p75) and MENIN. LEDGF/p75, a chromatin reader recognizing H3K36me3 marks, contributes to the association of the MLL multiprotein complex to chromatin. Formation of this complex is critical for the development of MLL leukemia. Available X-ray data represent only a partial structure of the LEDGF/p75-MLL-MENIN complex. Using nuclear magnetic resonance spectroscopy, we identified an additional LEDGF/p75-MLL interface, which overlaps with the binding site of known LEDGF/p75 interactors-HIV-1 integrase, PogZ, and JPO2. Binding of these proteins or MLL to LEDGF/p75 is mutually exclusive. The resolved structure, as well as mutational analysis, shows that the interaction is primarily sustained via two aromatic residues of MLL (F148 and F151). Colony-forming assays in MLL-AF9(+) leukemic cells expressing MLL interaction-defective LEDGF/p75 mutants revealed that this interaction is essential for transformation. Finally, we show that the clonogenic growth of primary murine MLL-AF9-expressing leukemic blasts is selectively impaired upon overexpression of a LEDGF/p75-binding cyclic peptide CP65, originally developed to inhibit the LEDGF/p75-HIV-1 integrase interaction. The newly defined protein-protein interface therefore represents a new target for the development of therapeutics against LEDGF/p75-dependent MLL fusion-driven leukemic disorders. Cancer Res; 74(18); 5139-51. ©2014 AACR.

Terbium(III) and yttrium(III) complexes with pyridine-substituted nitronyl nitroxide radical and different β-diketonate ligands. Crystal structures and magnetic and luminescence properties.

A terbium(III) complex of nitronyl nitroxide free radical 2-(2-pyridyl)-4,4,5,5-tetramethyl-4,5-dihydro1H-imidazolyl-1-oxy-3-oxide (NIT2Py), [Tb(acac)3NIT2Py]·0.5H2O (3) (acac = acetylacetonate), was synthesized for comparison with the previously reported [Tb(hfac)3NIT2Py]·0.5C7H16 (1) (hfac = hexafluoroacetylacetonate), together with their yttrium analogues [Y(hfac)3NIT2Py]·0.5C7H16 (2) and [Y(acac)3NIT2Py]·0.5H2O (4). The crystal structures show that in all complexes the nitronyl nitroxide radical acts as a chelating ligand. Magnetic studies show that 3 like 1 exhibits slow relaxation of magnetization at low temperature, suggesting single-molecule magnet behavior. The luminescence spectra show resolved vibronic structure with the main interval decreasing from 1600 cm(-1) to 1400 cm(-1) between 80 and 300 K. This effect is analyzed quantitatively using experimental Raman frequencies.

Structure of the calcium pyrophosphate monohydrate phase (Ca2P2O7·H2O): towards understanding the dehydration process in calcium pyrophosphate hydrates.

Calcium pyrophosphate hydrate (CPP, Ca(2)P(2)O(7) · nH2O) and calcium orthophosphate compounds (including apatite, octacalcium phosphate etc.) are among the most prevalent pathological calcifications in joints. Even though only two dihydrated forms of CPP (CPPD) have been detected in vivo (monoclinic and triclinic CPPD), investigations of other hydrated forms such as tetrahydrated or amorphous CPP are relevant to a further understanding of the physicochemistry of those phases of biological interest. The synthesis of single crystals of calcium pyrophosphate monohydrate (CPPM; Ca(2)P(2)O(7) · H2O) by diffusion in silica gel at ambient temperature and the structural analysis of this phase are reported in this paper. Complementarily, data from synchrotron X-ray diffraction on a CPPM powder sample have been fitted to the crystal parameters. Finally, the relationship between the resolved structure for the CPPM phase and the structure of the tetrahydrated calcium pyrophosphate β phase (CPPT-β) is discussed.

Modelling the structure of full-length Epstein–Barr virus nuclear antigen 1

Epstein-Barr virus is a clinically important human virus associated with several cancers and is the etiologic agent of infectious mononucleosis. The viral nuclear antigen-1 (EBNA1) is central to the replication and propagation of the viral genome and likely contributes to tumourigenesis. We have compared EBNA1 homologues from other primate lymphocryptoviruses and found that the central glycine/alanine repeat (GAr) domain as well as predicted cellular protein (USP7 and CK2) binding sites are present in homologues in the Old World primates, but not the marmoset, suggesting that these motifs may have co-evolved. Using the resolved structure of the C-terminal one-third of EBNA1 (homodimerization and DNA binding domain), we have gone on to develop monomeric and dimeric models in silico of the full-length protein. The C-terminal domain is predicted to be structurally highly similar between homologues, indicating conserved function. Zinc could be stably incorporated into the model, bonding with two N-terminal cysteines predicted to facilitate multimerisation. The GAr contains secondary structural elements in the models, while the protein binding regions are unstructured, irrespective of the prediction approach used and sequence origin. These intrinsically disordered regions may facilitate the diversity observed in partner interactions. We hypothesize that the structured GAr could mask the disordered regions, thereby protecting the protein from default degradation. In the dimer conformation, the C-terminal tails of each monomer wrap around a proline-rich protruding loop of the partner monomer, providing dimer stability, a feature which could be exploited in therapeutic design.

Crystal structure and encapsulation dynamics of ice II-structured neon hydrate.

Neon hydrate was synthesized and studied by in situ neutron diffraction at 480 MPa and temperatures ranging from 260 to 70 K. For the first time to our knowledge, we demonstrate that neon atoms can be enclathrated in water molecules to form ice II-structured hydrates. The guest Ne atoms occupy the centers of D2O channels and have substantial freedom of movement owing to the lack of direct bonding between guest molecules and host lattices. Molecular dynamics simulation confirms that the resolved structure where Ne dissolved in ice II is thermodynamically stable at 480 MPa and 260 K. The density distributions indicate that the vibration of Ne atoms is mainly in planes perpendicular to D2O channels, whereas their distributions along the channels are further constrained by interactions between adjacent Ne atoms.