bluuebunny/crossref_metadata_2025 huggingface dataset:
Interaction of the Lys3614–Asn3643 calmodulin-binding domain with the Cys4114-Asn4142 region of the type 1 ryanodine receptor is involved in the mechanism of Ca2+/agonist-induced channel activation
Authors: Gangopadhyay Jaya P. , Ikemoto Noriaki
Published: March 2008

In the present study we show that the interaction of the CaM (calmodulin)-binding domain (Lys3614–Asn3643) with the Cys4114–Asn4142 region (a region included in the CaM-like domain) serves as an intrinsic regulator of the RyR1 (type-1 ryanodine receptor). We tested the effects of antibodies raised against the two putative key regions of RyR1 [anti-(Lys3614–Asn3643) and anti-(Cys4114–Asn4142) antibodies]. Both antibodies produced significant inhibition of [3H]ryanodine-binding activity of RyR1. This suggests that the inter-domain interaction between the two domains, Lys3614–Asn3643 and Cys4114–Asn4142, activates the channel, and that the binding of antibody to either side of the interacting domain pair interfered with the formation of a ‘channel-activation link’ between the two regions. In order to spectroscopically monitor the mode of interaction of these domains, the site of inter-domain interaction was fluorescently labelled with MCA [(7-methoxycoumarin-4-yl)acetyl] in a site-directed manner. The accessibility of the bound MCA to a large molecular mass fluorescence quencher, BSA-QSY (namely, the size of a gap between the interacting domains) decreased with an increase of [Ca2+] in a range of 0.03–2.0 μM, as determined by Stern–Volmer fluorescence quenching analysis. The Ca2+-dependent decrease in the quencher accessibility was more pronounced in the presence of 150 μM 4-CmC (4-chlorometacresol), and was reversed by 1 mM Mg2+ (a well-known inhibitor of Ca2+/agonist-induced channel activation). These results suggest that the Lys3614–Asn3643 and Cys4114–Asn4142 regions of RyR1 interact with each other in a Ca2+- and agonist-dependent manner, and this serves as a mechanism of Ca2+- and agonist-dependent activation of the RyR1 Ca2+ channel.
Structural and functional consequences of the replacement of proximal residues Cys172 and Cys192 in the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from Chlamydomonas reinhardtii
Authors: García-Murria María-Jesús , Karkehabadi Saeid , Marín-Navarro Julia , Satagopan Sriram , Andersson Inger , Spreitzer Robert J. , Moreno Joaquín
Published: March 2008

Proximal Cys172 and Cys192 in the large subunit of the photosynthetic enzyme Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39) are evolutionarily conserved among cyanobacteria, algae and higher plants. Mutation of Cys172 has been shown to affect the redox properties of Rubisco in vitro and to delay the degradation of the enzyme in vivo under stress conditions. Here, we report the effect of the replacement of Cys172 and Cys192 by serine on the catalytic properties, thermostability and three-dimensional structure of Chlamydomonas reinhardtii Rubisco. The most striking effect of the C172S substitution was an 11% increase in the specificity factor when compared with the wild-type enzyme. The specificity factor of C192S Rubisco was not altered. The Vc (Vmax for carboxylation) was similar to that of wild-type Rubisco in the case of the C172S enzyme, but approx. 30% lower for the C192S Rubisco. In contrast, the Km for CO2 and O2 was similar for C192S and wild-type enzymes, but distinctly higher (approximately double) for the C172S enzyme. C172S Rubisco showed a critical denaturation temperature approx. 2 °C lower than wild-type Rubisco and a distinctly higher denaturation rate at 55 °C, whereas C192S Rubisco was only slightly more sensitive to temperature denaturation than the wild-type enzyme. X-ray crystal structures reveal that the C172S mutation causes a shift of the main-chain backbone atoms of β-strand 1 of the α/β-barrel affecting a number of amino acid side chains. This may cause the exceptional catalytic features of C172S. In contrast, the C192S mutation does not produce similar structural perturbations.
A comprehensive model of purine uptake by the malaria parasite Plasmodium falciparum: identification of four purine transport activities in intraerythrocytic parasites
Authors: Quashie Neils B. , Dorin-Semblat Dominique , Bray Patrick G. , Biagini Giancarlo A. , Doerig Christian , Ranford-Cartwright Lisa C. , De Koning Harry P.
Published: March 2008

Plasmodium falciparum is incapable of de novo purine biosynthesis, and is absolutely dependent on transporters to salvage purines from the environment. Only one low-affinity adenosine transporter has been characterized to date. In the present study we report a comprehensive study of purine nucleobase and nucleoside transport by intraerythrocytic P. falciparum parasites. Isolated trophozoites expressed (i) a high-affinity hypoxanthine transporter with a secondary capacity for purine nucleosides, (ii) a separate high-affinity transporter for adenine, (iii) a low-affinity adenosine transporter, and (iv) a low-affinity/high-capacity adenine carrier. Hypoxanthine was taken up with 12-fold higher efficiency than adenosine. Using a parasite clone with a disrupted PfNT1 (P. falciparum nucleoside transporter 1) gene we found that the high-affinity hypoxanthine/nucleoside transport activity was completely abolished, whereas the low-affinity adenosine transport activity was unchanged. Adenine transport was increased, presumably to partly compensate for the loss of the high-affinity hypoxanthine transporter. We thus propose a model for purine salvage in P. falciparum, based on the highly efficient uptake of hypoxanthine by PfNT1 and a high capacity for purine nucleoside uptake by a lower affinity carrier.
TRPC3-interacting triadic proteins in skeletal muscle
Authors: Woo Jin Seok , Kim Do Han , Allen Paul D. , Lee Eun Hui
Published: March 2008

The expression of TRPC3 (canonical-type transient receptor potential cation channel type 3) is tightly regulated during skeletal muscle cell differentiation, and a functional interaction between TRPC3 and RyR1 [(ryanodine receptor type 1), an SR (sarcoplasmic reticulum) Ca2+-release channel] regulates the gain of SR Ca2+ release during EC (excitation–contraction) coupling. However, it has not been possible to demonstrate direct protein–protein interactions between TRPC3 and RyR1. To identify possible candidate(s) for a linker protein(s) between TRPC3 and RyR1 in skeletal muscle, in the present study we performed MALDI–TOF (matrix-assisted laser-desorption ionization–time-of-flight) MS analysis of a cross-linked triadic protein complex from rabbit skeletal triad vesicles and co-immunoprecipitation assays using primary mouse skeletal myotubes. From these studies, we found that six triadic proteins, that are known to regulate RyR1 function and/or EC coupling [TRPC1, JP2 (junctophilin 2), homer, mitsugumin 29, calreticulin and calmodulin], interacted directly with TRPC3 in a Ca2+-independent manner. However we again found no direct interaction between TRPC3 and RyR1. TRPC1 was identified as a potential physical link between TRPC3 and RyR1, as it interacted with both TRPC3 and RyR1, and JPs showed subtype-specific interactions with both RyR1 and TRPC3 (JP1–RyR1 and JP2–TRPC3). These results support the hypothesis that TRPC3 and RyR1 are functionally engaged via linker proteins in skeletal muscle.
Lamellipodin proline rich peptides associated with native plasma butyrylcholinesterase tetramers
Authors: Li He , Schopfer Lawrence M. , Masson Patrick , Lockridge Oksana
Published: March 2008

BChE (butyrylcholinesterase) protects the cholinergic nervous system from organophosphorus nerve agents by scavenging these toxins. Recombinant human BChE produced from transgenic goat to treat nerve agent intoxication is currently under development. The therapeutic potential of BChE relies on its ability to stay in the circulation for a prolonged period, which in turn depends on maintaining tetrameric quaternary configuration. Native human plasma BChE consists of 98% tetramers and has a half-life (t½) of 11–14 days. BChE in the neuromuscular junctions and the central nervous system is anchored to membranes through interactions with ColQ (AChE-associated collagen tail protein) and PRiMA (proline-rich membrane anchor) proteins containing proline-rich domains. BChE prepared in cell culture is primarily monomeric, unless expressed in the presence of proline-rich peptides. We hypothesized that a poly-proline peptide is an intrinsic component of soluble plasma BChE tetramers, just as it is for membrane-bound BChE. We found that a series of proline-rich peptides was released from denatured human and horse plasma BChE. Eight peptides, with masses from 2072 to 2878 Da, were purified by HPLC and sequenced by electrospray ionization tandem MS and Edman degradation. All peptides derived from the same proline-rich core sequence PSPPLPPPPPPPPPPPPPPPPPPPPLP (mass 2663 Da) but varied in length at their N- and C-termini. The source of these peptides was identified through database searching as RAPH1 [Ras-associated and PH domains (pleckstrin homology domains)-containing protein 1; lamellipodin, gi:82581557]. A proline-rich peptide of 17 amino acids derived from lamellipodin drove the assembly of human BChE secreted from CHO (Chinese-hamster ovary) cells into tetramers. We propose that the proline-rich peptides organize the 4 subunits of BChE into a 340 kDa tetramer, by interacting with the C-terminal BChE tetramerization domain.
Redox regulation of methylthioadenosine phosphorylase in liver cells: molecular mechanism and functional implications
Authors: Fernández-Irigoyen Joaquín , Santamaría Mónica , Sánchez-Quiles Virginia , Latasa Maria U. , Santamaría Enrique , Muñoz Javier , Sánchez Del Pino Manuel M. , Valero María L. , Prieto Jesús , Ávila Matías A. , Corrales Fernando J.
Published: March 2008

MTAP (5′-methylthioadenosine phosphorylase) catalyses the reversible phosphorolytic cleavage of methylthioadenosine leading to the production of methylthioribose-1-phosphate and adenine. Deficient MTAP activity has been correlated with human diseases including cirrhosis and hepatocellular carcinoma. In the present study we have investigated the regulation of MTAP by ROS (reactive oxygen species). The results of the present study support the inactivation of MTAP in the liver of bacterial LPS (lipopolysaccharide)-challenged mice as well as in HepG2 cells after exposure to t-butyl hydroperoxide. Reversible inactivation of purified MTAP by hydrogen peroxide results from a reduction of Vmax and involves the specific oxidation of Cys136 and Cys223 thiols to sulfenic acid that may be further stabilized to sulfenyl amide intermediates. Additionally, we found that Cys145 and Cys211 were disulfide bonded upon hydrogen peroxide exposure. However, this modification is not relevant to the mediation of the loss of MTAP activity as assessed by site-directed mutagenesis. Regulation of MTAP by ROS might participate in the redox regulation of the methionine catabolic pathway in the liver. Reduced MTA (5′-deoxy-5′-methylthioadenosine)-degrading activity may compensate for the deficient production of the precursor S-adenosylmethionine, allowing maintenance of intracellular MTA levels that may be critical to ensure cellular adaptation to physiopathological conditions such as inflammation.
Neuropilins: structure, function and role in disease
Authors: Pellet-Many Caroline , Frankel Paul , Jia Haiyan , Zachary Ian
Published: March 2008

NRPs (neuropilins) are co-receptors for class 3 semaphorins, polypeptides with key roles in axonal guidance, and for members of the VEGF (vascular endothelial growth factor) family of angiogenic cytokines. They lack a defined signalling role, but are thought to mediate functional responses as a result of complex formation with other receptors, such as plexins in the case of semaphorins and VEGF receptors (e.g. VEGFR2). Mutant mouse studies show that NRP1 is essential for neuronal and cardiovascular development, whereas NRP2 has a more restricted role in neuronal patterning and lymphangiogenesis, but recent findings indicate that NRPs may have additional biological roles in other physiological and disease-related settings. In particular, NRPs are highly expressed in diverse tumour cell lines and human neoplasms and have been implicated in tumour growth and vascularization in vivo. However, despite the wealth of information regarding the probable biological roles of these molecules, many aspects of the regulation of cellular function via NRPs remain uncertain, and little is known concerning the molecular mechanisms through which NRPs mediate the functions of their various ligands in different cell types.
New insights into PKC family affairs: three novel phosphorylation sites in PKCϵ and at least one is regulated by PKCα
Authors: Larsson Christer
Published: March 2008

PKCϵ (protein kinase Cϵ) is a serine/threonine kinase, and a member of the PKC family of isoforms. The different PKC isoforms regulate many cellular processes of importance for disease. It is therefore desirable to obtain tools to specifically modulate the activity of the individual isoforms and to develop markers of PKC activity. The paper by Durgan et al. in this issue of the Biochemical Journal has taken us some steps further towards these goals. In the paper they identify three previously unknown phosphorylation sites in PKCϵ. All of them are specific for the ϵ isoform, evolutionarily conserved and tightly regulated. The phosphorylation of one site is critical for the binding of PKCϵ to 14-3-3β, suggesting it is of functional importance. The results provide important novel findings that uncover new aspects of PKCϵ regulation and reveal new possibilities for detecting PKCϵ activity in situ.
Transcription factors that behave as master regulators during mammalian embryogenesis function as molecular rheostats
Authors: Rizzino Angie
Published: March 2008

Three transcription factors, Sox2, Oct-3/4 and Nanog, have been identified as master regulators that orchestrate mammalian embryogenesis as well as the self-renewal and pluripotency of ES (embryonic stem) cells. Efforts to understand how these transcription factors function have shown that they have a special property in common. Small changes in the expression of any one of these factors dramatically alter the self-renewal and pluripotency of ES cells. In this way, each functions as a molecular rheostat to control the behaviour of ES cells. Recent studies have begun to examine the molecular mechanisms that regulate the levels of these transcription factors. In this issue of the Biochemical Journal, Mullin and co-workers report that Nanog can self-associate to form dimers. Importantly, they also show that the domain responsible for dimerization is also needed for Nanog to sustain the self-renewal of ES cells in the absence of the cytokine LIF (leukaemia inhibitory factor). On the basis of their studies, they propose a novel mechanism for regulating the interactions between Nanog and other nuclear proteins.
Tourism Sustainability, Resiliency and Dynamics: Towards a More Comprehensive Perspective
Authors: Tyrrell Timothy J. , Johnston Robert J.
Published: March 2008

This paper uses insights from a basic but formal model of tourism dynamics to frame a discussion of sustainability in tourism planning, with a particular focus on the role of dynamic resilience — or the ability of social, economic or ecological systems to recover from tourism-induced stress. The paper presents a theoretical approach to model resiliency in the ecological-environmental quality, economic-fiscal quality and social-cultural quality of tourist destinations. The model also formalises the difference between actual and perceived changes in these vectors. The specific goals of the paper are to characterise a more quantitative approach towards tourism sustainability and resilience, to summarise results in the tourism literature that might contribute to initial empirical implementation of such quantitative models, and to stimulate debate regarding the potential role of such approaches in guiding tourism policy.
SNP-specific array-based allele-specific expression analysis
Authors: Bjornsson Hans T. , Albert Thomas J. , Ladd-Acosta Christine M. , Green Roland D. , Rongione Michael A. , Middle Christina M. , Irizarry Rafael A. , Broman Karl W. , Feinberg Andrew P.
Published: March 2008

We have developed an optimized array-based approach for customizable allele-specific gene expression (ASE) analysis. The central features of the approach are the ability to select SNPs at will for detection, and the absence of need to PCR amplify the target. A surprisingly long probe length (39–49 nt) was needed for allelic discrimination. Reconstitution experiments demonstrate linearity of ASE over a broad range. Using this approach, we have discovered at least two novel imprinted genes, NLRP2, which encodes a member of the inflammasome, and OSBPL1A, which encodes a presumed oxysterol-binding protein, were both preferentially expressed from the maternal allele. In contrast, ERAP2, which encodes an aminopeptidase, did not show preferential parent-of-origin expression, but rather, cis-acting nonimprinted differential allelic control. The approach is scalable to the whole genome and can be used for discovery of functional epigenetic modifications in patient samples.
Molecular and crystalline structure of cycloheptanespiro-3′(4′H)-6′,7′,8′,9′-tetrahydrocyclohexa[b][1,4]thiazole-2′(5′H)-thione from powder synchrotron X-ray diffraction data
Authors: Avila Edward E. , Mora Asiloé J. , Delgado Gerzon E. , Contreras Ricardo R. , Fitch Andrew N. , Brunelli Michela
Published: March 2008

A series of bidentate nitrogen–sulfur pro-ligands has been designed and synthesized with the purpose of introducing a structural modification that favours the tetrahedral site distortions of metalloprotein systems with metallic centers surrounded by ligands containing two N atoms and two S atoms as donor groups. Some of these new pro-ligands were obtained only as powders. Here we present the molecular and crystalline structure of cycloheptanespiro-3′(4′H)-6′,7′,8′,9′-tetrahydrocyclohexa[b][1,4]thiazole-2′(5′H)-thione (I) solved and refined from powder synchrotron X-ray diffraction data. Two independent molecules comprising a total of 36 non-H atoms were obtained from the direct-methods solution and refined against the powder X-ray diffraction data using the Rietveld method. The molecular conformations of the heterocyclic benzothiazine ring, the fused heptenyl ring and the heptanyl spiro ring are thoroughly discussed and compared with VASP theoretical calculations and other related structures. The packing of molecules in (I) is based on hydrogen bonds of the type N—H...S and hydrophobic C—H interactions.
Conformations of substituted benzophenones
Authors: Cox Philip J. , Kechagias Dimitrios , Kelly Orla
Published: March 2008

The inclination of the two aryl rings (ring twists) in a series of benzophenone molecules has been examined. For each structure the dihedral angle (between the planes of the two sets of six aromatic C atoms) relates to both the steric considerations of the single molecule and the packing forces related to the crystal structure. Six new benzophenone structures are incorporated into the study including 2,2′-dihydroxy-4,4′-dimethoxybenzophenone (I), C15H14O5, that appears to have the smallest reported twist angle, 37.85 (5)°, of any substituted benzophenone reported to date. Three further benzophenones, 4,4′-bis(diethylamino)benzophenone (II), C21H28N2O, 3,4-dihydroxybenzophenone (III), C13H10O3, and 3-hydroxybenzophenone (IV), C13H10O2, have similar ring twists [49.83 (5), 49.84 (5) and 51.61 (5)°, respectively] that are comparable with the value of 54° found for the orthorhombic form of unsubstituted benzophenone. 4-Chloro-4′-hydroxybenzophenone (V), C13H9ClO2, has a ring twist of 64.66 (8)° that is close to the value of 65° found in the metastable monoclinic form of unsubstituted benzophenone and 2-amino-2′,5-dichlorobenzophenone (VI), C13H9Cl2NO2, has a large ring twist of 83.72 (6)°. Comparisons with a further 98 substituted benzophenone molecules from the Cambridge Structural Database (CSD) have been made.
Disordered misfit [Ca2CoO3][CoO2]1.62 structure revisited via a new intrinsic modulation
Authors: Muguerra Hervé , Grebille Dominique , Bourée Françoise
Published: March 2008

The structure of the thermoelectric lamellar misfit cobalt oxide [Ca2CoO3][CoO2]1.62 was refined again using single-crystal X-ray diffraction data. A new commensurate intrinsic modulation was observed involving a modulation vector orthogonal to the misfit direction (⅔,0,−⅓). The five-dimensional superspace group is C2/m(1δ0)(α0γ)gm and the structure was solved using a commensurate approximation. A new model is given involving an occupation modulation of the split sites of the [CoO] layer. This [CoO] layer can be described by triple chains running along b. The residual disorder along b can then be explained by the assumption of a local ordering with two types of clusters: CoO2 and Co5O4. A powder neutron diffraction experiment confirmed the ordering evidenced by the single-crystal X-ray diffraction study, but was not sufficient by itself to deal with this double modulated scheme. The new intrinsic modulation is destroyed by partial metal substitutions in the [CoO] layer. The structural modifications of this layer directly influence the physical properties which are related to the electronic structure of the [CoO2] layers.
KSm(MoO4)2, an incommensurately modulated and partially disordered scheelite-like structure
Authors: Arakcheeva Alla , Pattison Philip , Chapuis Gervais , Rossell Marta , Filaretov Andrey , Morozov Vladimir , Van Tendeloo Gustaaf
Published: March 2008

The incommensurately modulated scheelite-like KSm(MoO4)2 structure has been refined in the monoclinic superspace group I2/b(αβ0)00 by the Rietveld method on the basis of synchrotron radiation powder diffraction data. The systematic broadening of satellite reflections has been accounted for by applying anisotropic microstrain line-broadening. The microstructure has been studied by transmission electron microscopy (TEM). The partial disorder of the K and Sm cations in the A position is best approximated by a combination of harmonic and complex crenel functions with (0.952Sm + 0.048K) and (0.952K + 0.048Sm) atomic domains. This combination yields a compositional wave distribution from {KMoO4} to {SmMoO4} observed in the ab structure projection along q. The specific features of KSm(MoO4)2 and degree of the A-cation ordering are discussed in comparison with the previously reported structure of KNd(MoO4)2.
Kaolin polytypes revisited ab initio
Authors: Mercier Patrick H. J. , Le Page Yvon
Published: March 2008

The well known 36 distinguishable transformations between adjacent kaolin layers are split into 20 energetically distinguishable transformations (EDT) and 16 enantiomorphic transformations, hereafter denoted EDT*. For infinitesimal energy contribution of interactions between non-adjacent layers, the lowest-energy models must result from either (a) repeated application of an EDT or (b) alternate application of an EDT and its EDT*. All modeling, quantum input preparation and interpretation was performed with Materials Toolkit, and quantum optimizations with VASP. Kaolinite and dickite are the lowest-energy models at zero temperature and pressure, whereas nacrite and HP-dickite are the lowest-enthalpy models under moderate pressures based on a rough enthalpy/pressure graph built from numbers given in the supplementary tables. Minor temperature dependence of this calculated 0 K graph would explain the bulk of the current observations regarding synthesis, diagenesis and transformation of kaolin minerals. Other stackings that we list have energies so competitive that they might crystallize at ambient pressure. A homometric pair of energetically distinguishable ideal models, one of them for nacrite, is exposed. The printed experimental structure of nacrite correctly corresponds to the stable member of the pair. In our opinion, all recent literature measurements of the free energy of bulk kaolinite are too negative by ∼ 15 kJ mol−1 for some unknown reason.
Pseudopolymorphism of N-acetyl-L-phenylalanine methyl ester
Authors: Janik Alicja , Jarocha Monika , Stadnicka Katarzyna
Published: March 2008

The structures of two pseudopolymorphs of N-acetyl-L-phenylalanine methyl ester, L-AcFOMe, were determined at both 293 (2) and 150 (2) K. At room temperature, the orthorhombic phase C12H15NO3 (I), with space group P212121, converts into the tetragonal phase C12H15NO3·0.5H2O (II), with space group P41212, in the presence of water. In the structures of both pseudopolymorphs, alternating layers of hydrophilic and hydrophobic intermolecular interaction can be distinguished. In the hydrophilic layers the structures are stabilized by moderate hydrogen bonds of the type N—H...O for the anhydrous L-AcFOMe and of types N—H...O and O—H...O for the hemihydrate. Weak C—H...π interactions are observed within the hydrophobic layers: for (I) they are of type III [Malone et al. (1997). J. Chem. Soc. Faraday Trans.
93, 3429–3436], whereas typical type I edge-to-face interactions are present for (II). The differences between the hydrogen-bonding networks of (I) and (II) are discussed in terms of graph-set analysis.
Sr4 + n
Mn3+
4Mn4+

n
O10 + 3n
: a new homologous series of oxygen-vacancy-ordered perovskites built from Mn3+O5 pyramids and Mn4+O6 octahedra
Authors: Suescun Leopoldo , Dabrowski Bogdan
Published: March 2008

A new homologous series of oxygen-vacancy-ordered perovskites with the formula Sr_{4+n}Mn^{3+}_4Mn^{4+}_nO_{10+3n} is proposed based on the structural trends found for the recently described Sr4Mn4O10, Sr5Mn5O13 and Sr7Mn7O19 compounds. These compounds correspond to n = 0 (Sr4Mn^{3+}_4O10), n = 1 (Sr5Mn^{3+}_4Mn4+O13) and n = 3 (Sr7Mn^{3+}_4Mn^{4+}_3O19) members of the series. A linear set of four Mn3+O5 pyramids placed on the ab plane and pointing along the +x, -y, +y, -x directions defines the n = 0 building block for the series. The nth members can be constructed from blocks containing four pyramids and n Mn4+O6 octahedra with 2/m symmetry. Compounds in the related systems CaMnO
x
and LaCuO
x
, containing Mn3+ and Cu2+ pyramids and Mn4+ and Cu3+ octahedra have also been found to be members of the series. The size and charge of the A-site cation and the apical distortion of the pyramidally coordinated B-site cation are shown to be important factors in the stabilization of certain members of the series. A qualitative explanation for the absence of some of the possible members of the series is presented based on these factors.
Crystal architecture of R
2SnS5 (R = Pr, Nd, Gd and Tb): crystal structure relationships in chalcogenides
Authors: Daszkiewicz Marek , Gulay Lubomir D. , Shemet Vasylyna Ya.
Published: March 2008

The crystal structure of the R
2SnS5 (R = Pr, Nd, Gd and Tb) compounds has been investigated using X-ray single-crystal diffraction. Crystal architecture and structural relationships among U3S5, Y2HfS5, R
2SnS5 compounds are discussed and a structural origin is determined. It is shown that the complex architecture of the crystal structure of Eu5Sn3S12 is a result of interweaving of the simple crystal structures. The location of the copper ions in the non-stoichiometric compound Y2Cu0.20Sn0.95S5 is proposed on the basis of comparative analysis of the R—S interatomic distances in the R
2SnS5 series of compounds.
Structures of mono-unsaturated triacylglycerols. IV. The highest melting β′-2 polymorphs of trans-mono-unsaturated triacylglycerols and related saturated TAGs and their polymorphic stability
Authors: van Mechelen Jan B. , Peschar Rene , Schenk Henk
Published: March 2008

The β_1^{\prime}-2 crystal structures of a series of mixed-chain saturated and trans-mono-unsaturated triacylglycerols containing palmitoyl, stearoyl and elaidoyl acyl chains have been solved from high-resolution powder diffraction data, from synchrotron as well as laboratory X-ray sources. The structures crystallized in the space group I2 with two independent molecules forming a dimer in the asymmetric unit, and packed in double-chain length layers. Unlike the corresponding β-2 structures the solved β_1^{\prime}-2 structures have different molecular conformations for the symmetric and the asymmetric mixed triacylglycerols, both with the sn-2 chain in a leg position of the chair-shaped conformation. A transformation to the β-2 structure with the sn-2 chain in the back position is complicated and unlikely to take place in the solid state. A novel β′-2 polymorph of PSS has been crystallized and its structure has been solved. The melting point (239 K) of this so-called β_0^{\prime}-2 polymorph is 2 K above that of the β_1^{\prime}-2 polymorph and almost equal to that of the β-2 polymorph of PSS. The difference in packing of the β_0^{\prime}-2 versus β_1^{\prime}-2 structure explains the slow β_1^{\prime}-2 to β_0^{\prime}-2 phase transition. The transition is strikingly similar to the β2-3 to β1-3 transition in cis-mono-unsaturated triacylglycerols.
Structures of 6H perovskites Ba3CaSb2O9 and Ba3SrSb2O9 determined by synchrotron X-ray diffraction, neutron powder diffraction and ab initio calculations
Authors: Rowda Budwy , Avdeev Maxim , Lee Peter L. , Henry Paul F. , Ling Chris D.
Published: March 2008

The structures of the 6H perovskites Ba3
B
2+Sb5+
2O9, B = Ca and Sr, have been solved and refined using synchrotron X-ray and neutron powder diffraction data. Ba3CaSb2O9 and Ba3SrSb2O9 have monoclinic C2/c and triclinic P\bar 1 space-group symmetries, respectively, while Ba3MgSb2O9 has ideal hexagonal P63/mmc space-group symmetry. The symmetry-lowering distortions are a consequence of internal `chemical pressure' owing to the increasing effective ionic radius of the alkaline-earth cation in the perovskite B site from Mg2+ (0.72 Å) to Ca2+ (1.00 Å) to Sr2+ (1.18 Å). Increasing the effective ionic radius further to Ba2+ (1.35 Å) leads to decomposition at room temperature. The driving force behind the transition from P63/mmc to C2/c is the need to alleviate underbonding of Ba2+ cations in the perovskite A site via octahedral rotations, while the transition from C2/c to P\bar 1 is driven by the need to regularize the shape of the Sb2O9 face-sharing octahedral dimers. Ab initio geometry-optimization calculations were used to find a triclinic starting model for Ba3SrSb2O9.
Cis/trans isomers of PtX
2
L
2 (X = halogen, L = neutral ligand); the crystal structures of two polymorphs of cis-dichlorobis(dibenzyl sulfido-κS)platinum(II) in the temperature range 100–295 K
Authors: Hansson Christian , Lindqvist Maria , Oskarsson Åke
Published: March 2008

The structures of two polymorphs, one triclinic and one monoclinic, of cis-dichlorobis(dibenzyl sulfido-κS)platinum(II), cis-PtCl2(Bz2S)2, have been determined at 295, 250, 200, 150 and 100 K. In both polymorphs the complex has a structure where platinum(II) coordinates two dibenzyl sulfide molecules and two chloro ligands, forming a complex with pseudo-square-planar coordination geometry. The triclinic polymorph shows disorder at all temperatures. Both polymorphs have a packing arrangement involving centrosymmetric structural dimers. cis-PtCl2(Bz2S)2 belongs to a group of complexes with the general formula PtX
2
L
2, where X is a halogen and L is a ligand with a donor atom from groups 14, 15 or 16. The distribution of structural classes among 173 cis-PtX
2
L
2 compounds found in the Cambridge Structural Database (CSD, Version 5.28, November 2006) has been investigated. The predominant structural class [notation according to Belsky & Zorkii (1977). Acta Cryst. A33, 1004–1006] among the cis compounds is P21/c, Z = 4 (1) (73 structures, 42%), followed by P\bar 1, Z = 2 (1) (33 structures, 19%). Inversion centres combined with the screw-axis/glide plane are the dominating packing operators (56%) followed by the inversion centre (21%). The cis and trans influence in cis/trans-PtCl2
L
2 compounds has been investigated using data from the CSD. The cis influence is small for donor atoms in groups 15 and 16. The trans influence is small for group 16 donor atoms and for nitrogen, but for phosphorus it is significantly greater than the other donor atoms studied.
Transmembrane helices that form two opposite homodimeric interactions: An asparagine scan study of αM and β2 integrins
Authors: Parthasarathy Krupakar , Lin Xin , Tan Suet Mien , Law S.K. Alex , Torres Jaume
Published: March 2008

Integrins are α/β heterodimers, but recent in vitro and in vivo experiments also suggest an ability to associate through their transmembrane domains to form homomeric interactions. While the results of some in vitro experiments are consistent with an interaction mediated by a GxxxG‐like motif, homo‐oligomers observed after in vivo cross‐linking are consistent with an almost opposite helix–helix interface. We have shown recently that both models of interaction are compatible with evolutionary conservation data, and we predicted that the α‐helices in both models would have a similar rotational orientation. Herein, we have tested our prediction using in vitro asparagine scan of five consecutive residues along the GxxxG‐like motif of the transmembrane domain of α and β integrins, αM and β2. We show that Asn‐mediated dimerization occurs twice for every turn of the helix, consistent with two almost opposite forms of interaction as suggested previously for αIIb and β3 transmembrane domains. The orientational parameters helix tilt and rotational orientation of each of these two Asn‐stabilized dimers were measured by site‐specific infrared dichroism (SSID) in model lipid bilayers and were found to be consistent with our predicted computational models. Our results highlight an intrinsic tendency for integrin transmembrane α‐helices to form two opposite types of homomeric interaction in addition to their heteromeric interactions and suggest that integrins may form complex and specific networks at the transmembrane domain during function.
Contribution of dipole–dipole interactions to the stability of the collagen triple helix
Authors: Improta Roberto , Berisio Rita , Vitagliano Luigi
Published: March 2008

Unveiling sequence–stability and structure–stability relationships is a major goal of protein chemistry and structural biology. Despite the enormous efforts devoted, answers to these issues remain elusive. In principle, collagen represents an ideal system for such investigations due to its simplified sequence and regular structure. However, the definition of the molecular basis of collagen triple helix stability has hitherto proved to be a difficult task. Particularly puzzling is the decoding of the mechanism of triple helix stabilization/destabilization induced by imino acids. Although the propensity‐based model, which correlates the propensities of the individual imino acids with the structural requirements of the triple helix, is able to explicate most of the experimental data, it is unable to predict the rather high stability of peptides embedding Gly–Hyp–Hyp triplets. Starting from the available X‐ray structures of this polypeptide, we carried out an extensive quantum chemistry analysis of the mutual interactions established by hydroxyproline residues located at the X and Y positions of the Gly–X–Y motif. Our data clearly indicate that the opposing rings of these residues establish significant van der Waals and dipole–dipole interactions that play an important role in triple helix stabilization. These findings suggest that triple helix stabilization can be achieved by distinct structural mechanisms. The interplay of these subtle but recurrent effects dictates the overall stability of this widespread structural motif.
N15 Cro and λ Cro: Orthologous DNA‐binding domains with completely different but equally effective homodimer interfaces
Authors: Dubrava Matthew S. , Ingram Wendy M. , Roberts Sue A. , Weichsel Andrzej , Montfort William R. , Cordes Matthew H.J.
Published: March 2008

Bacteriophage Cro proteins bind to target DNA as dimers but do not all dimerize with equal strength, and differ in fold in the region of the dimer interface. We report the structure of the Cro protein from Enterobacteria phage N15 at 1.05 Å resolution. The subunit fold contains five α‐helices and is closely similar to the structure of P22 Cro (1.3 Å backbone room mean square difference over 52 residues), but quite different from that of λ Cro, a structurally diverged member of this family with a mixed α‐helix/β‐sheet fold. N15 Cro crystallizes as a biological dimer with an extensive interface (1303 Å2 change in accessible surface area per dimer) and also dimerizes in solution with a Kd of 5.1 ± 1.5 μM. Its dimerization is much stronger than that of its structural homolog P22 Cro, which does not self‐associate detectably in solution. Instead, the level of self‐association and interfacial area for N15 Cro is similar to that of λ Cro, even though these two orthologs do not share the same fold and have dimer interfaces that are qualitatively different in structure. The common Cro ancestor is thought to be an all‐helical monomer similar to P22 Cro. We propose that two Cro descendants independently developed stronger dimerization by entirely different mechanisms.
Structure and ion channel activity of the human respiratory syncytial virus (hRSV) small hydrophobic protein transmembrane domain
Authors: Gan Siok Wan , Ng Lifang , Lin Xin , Gong Xiandi , Torres Jaume
Published: March 2008

The small hydrophobic (SH) protein from the human respiratory syncytial virus (hRSV) is a glycoprotein of ∼64 amino acids with one putative α‐helical transmembrane domain. Although SH protein is important for viral infectivity, its exact role during viral infection is not clear. Herein, we have studied the secondary structure, orientation, and oligomerization of the transmembrane domain of SH (SH‐TM) in the presence of lipid bilayers. Only one oligomer, a pentamer, was observed in PFO‐PAGE. Using polarized attenuated total reflection‐Fourier transform infrared (PATR‐FTIR) spectroscopy, we show that the SH‐TM is α‐helical. The rotational orientation of SH‐TM was determined by site‐specific infrared dichroism (SSID) at two consecutive isotopically labeled residues. This orientation is consistent with that of an evolutionary conserved pentameric model obtained from a global search protocol using 13 homologous sequences of RSV. Conductance studies of SH‐TM indicate ion channel activity, which is cation selective, and inactive below the predicted pKa of histidine. Thus, our results provide experimental evidence that the transmembrane domain of SH protein forms pentameric α‐helical bundles that form cation‐selective ion channels in planar lipid bilayers. We provide a model for this pore, which should be useful in mutagenesis studies to elucidate its role during the virus cycle.
Correspondences between low‐energy modes in enzymes: Dynamics‐based alignment of enzymatic functional families
Authors: Zen Andrea , Carnevale Vincenzo , Lesk Arthur M. , Micheletti Cristian
Published: March 2008

Proteins that show similarity in their equilibrium dynamics can be aligned by identifying regions that undergo similar concerted movements. These movements are computed from protein native structures using coarse‐grained elastic network models. We show the existence of common large‐scale movements in enzymes selected from the main functional and structural classes. Alignment via dynamics does not require prior detection of sequence or structural correspondence. Indeed, a third of the statistically significant dynamics‐based alignments involve enzymes that lack substantial global or local structural similarities. The analysis of specific residue–residue correspondences of these structurally dissimilar enzymes in some cases suggests a functional relationship of the detected common dynamic features. Including dynamics‐based criteria in protein alignment thus provides a promising avenue for relating and grouping enzymes in terms of dynamic aspects that often, though not always, assist or accompany biological function.
A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein–water interface as a determinant of pKavalues
Authors: Harms Michael J. , Schlessman Jamie L. , Chimenti Michael S. , Sue Gloria R. , Damjanović Ana , García‐Moreno E. Bertrand
Published: March 2008

Previously we reported that Lys, Asp, and Glu residues at positions 66 and 92 in staphylococcal nuclease (SNase) titrate with pKa values shifted by up to 5 pKa units in the direction that promotes the neutral state. In contrast, the internal Lys‐38 in SNase titrates with a normal pKa. The crystal structure of the L38K variant shows that the side chain of Lys‐38 is buried. The ionizable moiety is ∼7 Å from solvent and ion paired with Glu‐122. This suggests that the pKa value of Lys‐38 is normal because the energetic penalty for dehydration is offset by a favorable Coulomb interaction. However, the pKa of Lys‐38 was also normal when Glu‐122 was replaced with Gln or with Ala. Continuum electrostatics calculations were unable to reproduce the pKa of Lys‐38 unless the protein was treated with an artificially high dielectric constant, consistent with structural reorganization being responsible for the normal pKa value of Lys‐38. This reorganization must be local because circular dichroism and NMR spectroscopy indicate that the L38K protein is native‐like under all conditions studied. In molecular dynamics simulations, the ion pair between Lys‐38 and Glu‐122 is unstable. The simulations show that a minor rearrangement of a loop is sufficient to allow penetration of water to the amino moiety of Lys‐38. This illustrates both the important roles of local flexibility and water penetration as determinants of pKa values of ionizable groups buried near the protein–water interface, and the challenges faced by structure‐based pKa calculations in reproducing these effects.
Structural basis for the NAD‐hydrolysis mechanism and the ARTT‐loop plasticity of C3 exoenzymes
Authors: Ménétrey Julie , Flatau Gilles , Boquet Patrice , Ménez André , Stura Enrico A.
Published: March 2008

C3‐like exoenzymes are ADP‐ribosyltransferases that specifically modify some Rho GTPase proteins, leading to their sequestration in the cytoplasm, and thus inhibiting their regulatory activity on the actin cytoskeleton. This modification process goes through three sequential steps involving NAD‐hydrolysis, Rho recognition, and binding, leading to Rho ADP‐ribosylation. Independently, three distinct residues within the ARTT loop of the C3 exoenzymes are critical for each of these steps. Supporting the critical role of the ARTT loop, we have shown previously that it adopts a distinct conformation upon NAD binding. Here, we present seven wild‐type and ARTT loop‐mutant structures of C3 exoenzyme of Clostridium botulinum free and bound to its true substrate, NAD, and to its NAD‐hydrolysis product, nicotinamide. Altogether, these structures expand our understanding of the conformational diversity of the C3 exoenzyme, mainly within the ARTT loop.
Crystallographic and biochemical studies revealing the structural basis for antizyme inhibitor function
Authors: Albeck Shira , Dym Orly , Unger Tamar , Snapir Zohar , Bercovich Zippy , Kahana Chaim
Published: March 2008

Antizyme inhibitor (AzI) regulates cellular polyamine homeostasis by binding to the polyamine‐induced protein, Antizyme (Az), with greater affinity than ornithine decarboxylase (ODC). AzI is highly homologous to ODC but is not enzymatically active. In order to understand these specific characteristics of AzI and its differences from ODC, we determined the 3D structure of mouse AzI to 2.05 Å resolution. Both AzI and ODC crystallize as a dimer. However, fewer interactions at the dimer interface, a smaller buried surface area, and lack of symmetry of the interactions between residues from the two monomers in the AzI structure suggest that this dimeric structure is nonphysiological. In addition, the absence of residues and interactions required for pyridoxal 5′‐phosphate (PLP) binding suggests that AzI does not bind PLP. Biochemical studies confirmed the lack of PLP binding and revealed that AzI exists as a monomer in solution while ODC is dimeric. Our findings that AzI exists as a monomer and is unable to bind PLP provide two independent explanations for its lack of enzymatic activity and suggest the basis for its enhanced affinity toward Az.
Miranda cargo‐binding domain forms an elongated coiled‐coil homodimer in solution: Implications for asymmetric cell division in Drosophila
Authors: Yousef Mohammad S. , Kamikubo Hironari , Kataoka Mikio , Kato Ryuichi , Wakatsuki Soichi
Published: March 2008

Miranda is a multidomain adaptor protein involved in neuroblast asymmetric division in Drosophila melanogaster. The central domain of Miranda is necessary for cargo binding of the neural transcription factor Prospero, the Prospero‐mRNA carrier Staufen, and the tumor suppressor Brat. Here, we report the first solution structure of Miranda central “cargo‐binding” domain (residues 460–660) using small‐angle X‐ray scattering. Ab initio modeling of the scattering data yields an elongated “rod‐like” molecule with a maximum linear dimension (Dmax) of ∼22 nm. Moreover, circular dichroism and cross‐linking experiments indicate that the cargo‐binding domain is predominantly helical and forms a parallel coiled‐coil homodimer in solution. Based on the results, we modeled the full‐length Miranda protein as a double‐headed, double‐tailed homodimer with a long central coiled‐coil region. We discuss the cargo‐binding capacity of the central domain and propose a structure‐based mechanism for cargo release and timely degradation of Miranda in developing neuroblasts.
The C3 domain ofPasteurella multocidatoxin is the minimal domain responsible for activation of Gq‐dependent calcium and mitogenic signaling
Authors: Aminova Leila R. , Luo Shuhong , Bannai Yuka , Ho Mengfei , Wilson Brenda A.
Published: March 2008

The large 1285‐amino‐acid protein toxin fromPasteurella multocida(PMT) is a multifunctional single‐chain polypeptide that binds to and enters eukaryotic cells and acts intracellularly to promote Gqand G12/13protein‐dependent calcium and mitogenic signal transduction. Previous studies indicated that the intracellular activity domain responsible for PMT action was located within the C‐terminal 600–700 amino acids. In this study, we have exogenously expressed a series of N‐ and C‐terminal PMT fragments directly in mammalian cells and have used the dual luciferase reporter system to assay for toxin‐mediated activation of calcium‐calcineurin‐NFAT signaling (NFAT‐luciferase) and mitogenic serum response signaling (SRE‐luciferase). Using this approach, we have defined the last 180 amino acids, which encompass the C3 domain in the crystal structure, as the minimum domain sufficient to activate both NFAT and SRE signaling pathways.
Reduction in sodium chloride intake: effects on urinary Na, K and aldosterone output in healthy free‐living adults
Authors: Mathers J. C.
Published: March 2008

Eleven healthy free‐living adults (six women, five men) weighed and recorded all food and drink consumed and collected all urine for two non‐consecutive 7‐day periods whilst eating their usual diet (Period 1) and attempting to reduce salt intake (Period 2). Bread (including pitta bread) provided on average a quarter of total Na intake of subjects in Period 1 so that wholemeal bread made without added salt was made available in Period 2. All subjects achieved substantial reductions (mean 65%) in Na intake in Period 2 with no change in K intake so that the Na:K molar ratio fell from 1.3 to 0.5. Urinary Na output closely followed intakes and there was a large increase (mean 11.2 μg/d) in aldosterone excretion with a non‐significant increase in K output. Simple linear relationships which allow prediction of Na and K intake from the more easily measured urinary output were derived.