Hexameric Units Research Articles

Syntheses, structures and properties of two multi-iron–samarium/multi-iron substituted germanotungstates

A heterometallic hexameric germanotungstate containing iron–lanthanide cluster fragments (enH2)13HK9[Fe6Sm6(H2O)12(α-GeW10O38)6]·42H2O (1) and a hexairon substituted double sandwich-type germanotungstate (enH2)6K[HFe6(B-α-GeW9O34)2(α-GeW6O26)(H2O)2]·11H2O (2) (en = 1,2-ethylenediamine) have been hydrothermally synthesized and structurally characterized using elemental analyses, inductively coupled plasma atomic emission spectrometry, IR spectra, powder X-ray diffraction (PXRD), thermogravimetric (TG) analyses and single-crystal X-ray diffraction. The common features of 1 and 2 are that both are based on lacunary Keggin-type germanotungstate fragments. 1 is the first heterometallic hexameric germanotungstate consisting of six {Fe–(μ3-O)3–Sm} bridges, while two double sandwich-type fragments in 2 are connected together through two potassium cations forming hexameric germanotungstate units. The magnetic susceptibility measurements demonstrate the presence of antiferromagnetic interactions in both compounds.

A challenging interpretation of a hexagonally layered protein structure.

The carboxysome is a giant protein complex that acts as a metabolic organelle in cyanobacteria and some chemoautotrophs. Its outer structure is formed by the assembly of thousands of copies of hexameric shell protein subunits into a molecular layer. The structure determination of a CcmK1 shell protein mutant (L11K) from the β-carboxysome of the cyanobacterium Synechocystis PCC6803 led to challenges in structure determination. Twinning, noncrystallographic symmetry and packing of hexameric units in a special arrangement led to initial difficulties in space-group assignment. The correct space group was clarified after initial model refinement revealed additional symmetry. This study provides an instructive example in which broken symmetry requires a new choice of unit-cell origin in order to identify the highest symmetry space group. An additional observation related to the packing arrangement of molecules in this crystal suggests that these hexameric shell proteins might have lower internal symmetry than previously believed.

An unknown solvate of 1-(2,4-dichlorobenzyl)-4-[(4-methylphenyl)sulfonyl]piperazine

In the title compound, C18H20Cl2N2O2S, the piperazine ring adopts a chair conformation. The dihedral angle between the sulfonyl-bound benzene ring and the best-fit plane through the six non-H atoms of the piperazine ring is 72.22 (12)°; those between the di­chloro­benzene ring and the sulfonyl and piperazine rings are 2.44 (13) and 74.16 (2)°, respectively. In the crystal, mol­ecules are connected through weak C—H⋯O inter­actions into a hexa­meric unit generating a R 6 6(60) motif in the ab plane. The mol­ecules are also connected into C(4) chains through weak C—H⋯N inter­actions. The solvent used to grow the crystal was a mixture of di­chloro­methane and methanol, but the resulting electron density was uninter­pretable. The solvent contribution to the scattering was removed with the SQUEEZE routine in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148–155]. The formula mass and unit-cell characteristics do not take into account the disordered solvent.

New 3-D polyoxovanadoborate architectures based on [V12B18O60]16− clusters

Three new 3-D polyoxovanadoborates {[Cu(dien)(H2O)]3V12B18O54(OH)6(H2O)}·4H3O·5.5H2O (1, dien = diethylenetriamine), {[Cd(H2O)2]3V12B18O54(OH)6(H2O)}·4H3O·9.5H2O (2) and {[Na(H2O)3]4Na2V12B18O56(OH)4(H2O)}(H3dien)2 (3) have been hydrothermally synthesized and structurally characterized. Compounds 1–3 contain vanadoborate cluster [V12B18O60] constructed by two hexameric oxovanadate units [V6O9] and one puckered [B18O42] ring via sharing O atoms. The vanadoborate cage [V12B18O60] can present different degrees of protonation, namely [V12B18O60H6]10− for 1 and 2, [V12B18O60H4]12− for 3. The clusters [V12B18O60H6]10− in 1 are connected by complex cations [Cu(dien)(H2O)]2+ into a new 3-D framework via all terminal O atoms of square-pyramidal [VO5] groups, while the clusters [V12B18O60H6]10−/[V12B18O60H4]12− in 2 and 3 are linked with [Cd(H2O)2]2+ groups/the combination of [Na(H2O)3]+ and Na+ ions to give another two types of new 3-D frameworks via O atoms of [BOx] (x = 3, 4) polyhedra, respectively. Magnetic measurements illustrate that compounds 1 and 2 have antiferromagnetic exchange interactions between metal centers. The theoretical band structure of 2 has been also studied.

Protease Cleavage Leads to Formation of Mature Trimer Interface in HIV-1 Capsid

During retrovirus particle maturation, the assembled Gag polyprotein is cleaved by the viral protease into matrix (MA), capsid (CA), and nucleocapsid (NC) proteins. To form the mature viral capsid, CA rearranges, resulting in a lattice composed of hexameric and pentameric CA units. Recent structural studies of assembled HIV-1 CA revealed several inter-subunit interfaces in the capsid lattice, including a three-fold interhexamer interface that is critical for proper capsid stability. Although a general architecture of immature particles has been provided by cryo-electron tomographic studies, the structural details of the immature particle and the maturation pathway remain unknown. Here, we used cryo-electron microscopy (cryoEM) to determine the structure of tubular assemblies of the HIV-1 CA-SP1-NC protein. Relative to the mature assembled CA structure, we observed a marked conformational difference in the position of the CA-CTD relative to the NTD in the CA-SP1-NC assembly, involving the flexible hinge connecting the two domains. This difference was verified via engineered disulfide crosslinking, revealing that inter-hexamer contacts, in particular those at the pseudo three-fold axis, are altered in the CA-SP1-NC assemblies compared to the CA assemblies. Results from crosslinking analyses of mature and immature HIV-1 particles containing the same Cys substitutions in the Gag protein are consistent with these findings. We further show that cleavage of preassembled CA-SP1-NC by HIV-1 protease in vitro leads to release of SP1 and NC without disassembly of the lattice. Collectively, our results indicate that the proteolytic cleavage of Gag leads to a structural reorganization of the polypeptide and creates the three-fold interhexamer interface, important for the formation of infectious HIV-1 particles.

Crystal structure of the new organic conductor (TSeF)7[FeNO(CN)5]2 with unusual molecular packing of conducting layer

X-ray single crystal diffraction study of the new molecular conductor (TSeF)7[FeNO(CN)5]2 has been carried out at room temperature and 130 K. The crystal structure is composed by layers of π-electron donors TSeF, separated by anion layers along the a-direction. The conducting organic layer has unusual for molecular conductors arrangement of neutral monomeric and charged hexameric TSeF units orthogonally packed with respect to each other. Another specific feature of the structure is fully ordered state of the nitroprusside anion and deep penetrating of its functional NO-group into the adjacent organic layer.

N-terminal domain of αB-crystallin provides a conformational switch for multimerization and structural heterogeneity

The small heat shock protein (sHSP) αB-crystallin (αB) plays a key role in the cellular protection system against stress. For decades, high-resolution structural studies on heterogeneous sHSPs have been confounded by the polydisperse nature of αB oligomers. We present an atomic-level model of full-length αB as a symmetric 24-subunit multimer based on solid-state NMR, small-angle X-ray scattering (SAXS), and EM data. The model builds on our recently reported structure of the homodimeric α-crystallin domain (ACD) and C-terminal IXI motif in the context of the multimer. A hierarchy of interactions contributes to build multimers of varying sizes: Interactions between two ACDs define a dimer, three dimers connected by their C-terminal regions define a hexameric unit, and variable interactions involving the N-terminal region define higher-order multimers. Within a multimer, N-terminal regions exist in multiple environments, contributing to the heterogeneity observed by NMR. Analysis of SAXS data allows determination of a heterogeneity parameter for this type of system. A mechanism of multimerization into higher-order asymmetric oligomers via the addition of up to six dimeric units to a 24-mer is proposed. The proposed asymmetric multimers explain the homogeneous appearance of αB in negative-stain EM images and the known dynamic exchange of αB subunits. The model of αB provides a structural basis for understanding known disease-associated missense mutations and makes predictions concerning substrate binding and the reported fibrilogenesis of αB.

Functional Implications of an Intermeshing Cogwheel-like Interaction between TolC and MacA in the Action of Macrolide-specific Efflux Pump MacAB-TolC

Macrolide-specific efflux pump MacAB-TolC has been identified in diverse gram-negative bacteria including Escherichia coli. The inner membrane transporter MacB requires the outer membrane factor TolC and the periplasmic adaptor protein MacA to form a functional tripartite complex. In this study, we used a chimeric protein containing the tip region of the TolC α-barrel to investigate the role of the TolC α-barrel tip region with regard to its interaction with MacA. The chimeric protein formed a stable complex with MacA, and the complex formation was abolished by substitution at the functionally essential residues located at the MacA α-helical tip region. Electron microscopic study delineated that this complex was made by tip-to-tip interaction between the tip regions of the α-barrels of TolC and MacA, which correlated well with the TolC and MacA complex calculated by molecular dynamics. Taken together, our results demonstrate that the MacA hexamer interacts with TolC in a tip-to-tip manner, and implies the manner by which MacA induces opening of the TolC channel.

New insights into poly(lactic-co-glycolic acid) microstructure: using repeating sequence copolymers to decipher complex NMR and thermal behavior.

Sequence, which Nature uses to spectacular advantage, has not been fully exploited in synthetic copolymers. To investigate the effect of sequence and stereosequence on the physical properties of copolymers, a family of complex isotactic, syndiotactic, and atactic repeating sequence poly(lactic-co-glycolic acid) copolymers (RSC PLGAs) were prepared and their NMR and thermal behavior was studied. The unique suitability of polymers prepared from the bioassimilable lactic and glycolic acid monomers for biomedical applications makes them ideal candidates for this type of sequence engineering. Polymers with repeating units of LG, GLG and LLG (L = lactic, G = glycolic) with controlled and varied tacticities were synthesized by assembly of sequence-specific, stereopure dimeric, trimeric, and hexameric segmer units. Specifically labeled deuterated lactic and glycolic acid segmers were likewise prepared and polymerized. Molecular weights for the copolymers were in the range M(n) = 12-40 kDa by size exclusion chromatography in THF. Although the effects of sequence-influenced solution conformation were visible in all resonances of the (1)H and (13)C NMR spectra, the diastereotopic methylene resonances in the (1)H NMR (CDCl(3)) for the glycolic units of the copolymers proved most sensitive. An octad level of resolution, which corresponds to an astounding 31-atom distance between the most separated stereocenters, was observed in some mixed sequence polymers. Importantly, the level of sensitivity of a particular NMR resonance to small differences in sequence was found to depend on the sequence itself. Thermal properties were also correlated with sequence.

Solution structures of 2 × 6-meric and 4 × 6-meric hemocyanins of crustaceans Carcinus aestuarii, Squilla mantis and Upogebia pusilla

Arthropod hemocyanins (Hcs) are a family of large, high molecular mass, extracellular oxygen transport proteins. They form oligomeric quaternary structures based on different arrangements of a basic 6×75 kDa hexameric unit. Their complex quaternary structures present binding sites for allosteric effectors and regulate the oxygen binding process in a cooperative manner. In order to describe the functional regulation of arthropod Hcs, a detailed description of their quaternary structure is necessary. We have utilized small angle X-ray scattering to characterize the structure of three arthropod Hcs in unperturbed conditions. Two different levels of complexity are evaluated: for the 2×6-meric case, we analyzed the Hcs of the portunid crab Carcinus aestuarii and stomatopod Squilla mantis, while in the case of 4×6-meric structures, we studied the Hc of the thalassinid shrimp Upogebia pusilla. While C. aestuarii Hc presented a structure comparable to other 2×6-meric crustacean Hcs, S. mantis Hc shows a peculiar and quite unique arrangement of its building blocks, resembling a substructure of giant Hcs found among cheliceratans. For U. pusilla, the arrangement of its subunits is described as tetrahedral, in contrast to the more common square planar 4×6-meric structure found in other arthropod Hcs.

Pannexin1 and Pannexin3 Delivery, Cell Surface Dynamics, and Cytoskeletal Interactions

Pannexins (Panx) are a class of integral membrane proteins that have been proposed to exhibit characteristics similar to those of connexin family members. In this study, we utilized Cx43-positive BICR-M1R(k) cells to stably express Panx1, Panx3, or Panx1-green fluorescent protein (GFP) to assess their trafficking, cell surface dynamics, and interplay with the cytoskeletal network. Expression of a Sar1 dominant negative mutant revealed that endoplasmic reticulum to Golgi transport of Panx1 and Panx3 was mediated via COPII-dependent vesicles. Distinct from Cx43-GFP, fluorescence recovery after photobleaching studies revealed that both Panx1-GFP and Panx3-GFP remained highly mobile at the cell surface. Unlike Cx43, Panx1-GFP exhibited no detectable interrelationship with microtubules. Conversely, cytochalasin B-induced disruption of microfilaments caused a severe loss of cell surface Panx1-GFP, a reduction in the recoverable fraction of Panx1-GFP that remained at the cell surface, and a decrease in Panx1-GFP vesicular transport. Furthermore, co-immunoprecipitation and co-sedimentation assays revealed actin as a novel binding partner of Panx1. Collectively, we conclude that although Panx1 and Panx3 share a common endoplasmic reticulum to Golgi secretory pathway to Cx43, their ultimate cell surface residency appears to be independent of cell contacts and the need for intact microtubules. Importantly, Panx1 has an interaction with actin microfilaments that regulates its cell surface localization and mobility.

TRIM5α and TRIMCyp form apparent hexamers and their multimeric state is not affected by exposure to restriction-sensitive viruses or by treatment with pharmacological inhibitors

Proteins of the TRIM5 family, such as TRIM5α and the related TRIMCyp, are cytoplasmic factors that can inhibit incoming retroviruses. This type of restriction requires a direct interaction between TRIM5 proteins and capsid proteins that are part of mature, intact retroviral cores. In such cores, capsids are arranged as hexameric units. Multiple lines of evidence imply that TRIM5 proteins themselves interact with retroviral cores as multimers. Accordingly, stabilization by crosslinking agents has revealed that TRIM5α and TRIMCyp are present as trimers in mammalian cells. We report here that TRIM5 proteins seem to form dimers, trimers, hexamers and multimers of higher complexity in mammalian cells. The hexameric form in particular seems to be the most abundant multimer. Multimerization did not involve disulfide bridges and was not affected by infection with restriction-sensitive viruses or by treatment with the known TRIM5 inhibitors arsenic trioxide, MG132 and cyclosporine A. We conclude that TRIM5 multimerization results from more than one protein-protein interface and that it is seemingly not triggered by contact with retroviral cores.

Structural Convergence between Cryo-EM and NMR Reveals Intersubunit Interactions Critical for HIV-1 Capsid Function

Mature HIV-1 particles contain conical-shaped capsids that enclose the viral RNA genome and perform essential functions in the virus life cycle. Previous structural analysis of two- and three-dimensional arrays of the capsid protein (CA) hexamer revealed three interfaces. Here, we present a cryoEM study of a tubular assembly of CA and a high-resolution NMR structure of the CA C-terminal domain (CTD) dimer. In the solution dimer structure, the monomers exhibit different relative orientations compared to previous X-ray structures. The solution structure fits well into the EM density map, suggesting that the dimer interface is retained in the assembled CA. We also identified a CTD-CTD interface at the local three-fold axis in the cryoEM map and confirmed its functional importance by mutagenesis. In the tubular assembly, CA intermolecular interfaces vary slightly, accommodating the asymmetry present in tubes. This provides the necessary plasticity to allow for controlled virus capsid dis/assembly.

Potassium Tri-tert-butoxysilanethiolates: Synthesis, Properties, and Crystal and Molecular Structures of [( t BuO)3SiSK]6[THF]2· 2THF, {[( t BuO)3SiS]2K2} n , and [( t BuO)3SiSK]4[H2O]4· C6H6

The synthesis and characterization of a family of potassium silanethiolates is described. [( t BuO)3SiSK]6[THF]2· 2THF ( 1 ), {[( t BuO)3SiS]2K2} n ( 2 ), and [( t BuO)3SiSK]4[H2O]4· C6H6 ( 3 ) were synthesized by treatment of ( t BuO)3SiSH with potassium metal in various solvents. The target molecules were characterized by single crystal X-ray crystallography. Compounds 1 , 2 , and 3 form hexameric, polymeric, and tetrameric units correspondingly, in the solid state. [( t BuO)3SiSK]6[THF]2· 2THF contains three, differently coordinated potassium ions and crystallizes in the space group P21/c, a = 15.227(4), b = 14.650(5), c = 32.067(9) Å, β = 117.001(18)°, V = 6374(3) Å3. {[( t BuO)3SiS]2K2} n crystallizes in the space group P-1, a = 11.6305(14), b = 13.348(3), c = 13.531(4) Å, α = 67.27(2)°, β = 76.064(16)°, γ = 88.706(14)°, V = 1874.6(8) Å3. [( t BuO)3SiSK]4[H2O]4· C6H6 crystallizes in the space group P-4b2, a = 20.854(3), b = 20.854(3), c = 9.283(2) Å, α = β = γ = 90°, V = 4037,1(12) Å3.

Expression of connexin 26 in endometrial adenocarcinoma--analysis of correlations with some anatomoclinical features.

Alterations of gap junctional intercellular communication appear to play a role in the development and progression of cancer. Gap junction channel is composed of two connexons - hexameric units formed of transmembrane proteins called connexins (Cxs). The aim of the study was to evaluate the expression and localization of Cx26 in 73 cases of endometrial cancers and to estimate the relationships between expression of this protein and selected anatomoclinical features. The control group consisted of 20 sections of normal endometrium in various menstrual cycle phases, obtained from premenopausal women. In the normal endometrium punctate, membrane-associated immunoreactivity for Cx26 was observed. 54 of 73 endometrial cancers showed Cx26 expression, but 46/54 (85%) immunopositive sections revealed cytoplasmic localization for Cx26 with granular or occasionally diffuse immunostaining pattern. In addition, part of Cx26-positive tumours showed mixed: cytoplasmic and membranous staining pattern and focally also nuclear or perinuclear immunostaining was present. In 21/54 (39%) of Cx26-positive cases weak staining pattern was seen, however in 33/54 (61%) cancers strong reaction was noted. We did not find relationship between Cx26 expression and patients' age, histological type of cancer and histological grade, nevertheless we observed positive association between Cx26 expression and tumour size (p=0.037). In conclusion, our results suggest that transformed malignant cells continue to produce Cx26, which are probably not assembled into functional gap junction channels, but could still play other roles in endometrial cancer cells.

Characterization of SV40 T‐antigen G‐quadruplex Helicase Activity Using SPR

Simian Virus 40 (SV40) is a double stranded DNA virus helpful as a model system for eukaryotic cellular DNA replication. It encodes a Large T‐antigen (T‐ag) protein, which is essential for viral genome replication and regulation of the host cell cycle. Acting as a helicase enzyme, T‐ag is able to unwind various forms of DNA. Guanine rich sequences of DNA capable of forming G‐quadruplex knot‐like structures have been identified in several eukaryotic oncogene promoter regions, as well as in the SV40 virus genome, and may possibly influence transcription activity. T‐ag forms an active hexameric unit in the presence of ATP, and was demonstrated to bind single‐strand, duplex, and G‐quadruplex DNA using real time surface plasmon resonance (SPR). Probing with single strand binding protein (SSB) confirmed that T‐ag activity resulted in the unwinding of an intermolecular quadruplex.

Structural Analysis of the Bacterial HPr Kinase/Phosphorylase V267F Mutant Gives Insights into the Allosteric Regulation Mechanism of This Bifunctional Enzyme

The HPr kinase/phosphorylase (HPrK/P) is a bifunctional enzyme that controls the phosphorylation state of the phospho-carrier protein HPr, which regulates the utilization of carbon sources in Gram-positive bacteria. It uses ATP or pyrophosphate for the phosphorylation of serine 46 of HPr and inorganic phosphate for the dephosphorylation of Ser(P)-46-HPr via a phosphorolysis reaction. HPrK/P is a hexameric protein kinase of a new type with a catalytic core belonging to the family of nucleotide-binding protein with Walker A motif. It exhibits no structural similarity to eukaryotic protein kinases. So far, HPrK/P structures have shown the enzyme in its phosphorylase conformation. They permitted a detailed characterization of the phosphorolysis mechanism. In the absence of a structure with bound nucleotide, we used the V267F mutant enzyme to assess the kinase conformation. Indeed, the V267F replacement was found to cause an almost entire loss of the phosphorylase activity of Lactobacillus casei HPrK/P. In contrast, the kinase activity remained conserved. To elucidate the structural alterations leading to this drastic change of activity, the x-ray structure of the catalytic domain of L. casei HPrK/P-V267F was determined at 2.6A resolution. A comparison with the structure of the wild type enzyme showed that the mutation induces conformation changes compatible with the switch from phosphorylase to kinase function. Together with nucleotide binding fluorescence measurements, these results allowed us to decipher the cooperative behavior of the protein and to gain new insights into the allosteric regulation mechanism of HPrK/P.

Structural insight into filament formation by mammalian septins

Septins are GTP-binding proteins that assemble into homo- and hetero-oligomers and filaments. Although they have key roles in various cellular processes, little is known concerning the structure of septin subunits or the organization and polarity of septin complexes. Here we present the structures of the human SEPT2 G domain and the heterotrimeric human SEPT2-SEPT6-SEPT7 complex. The structures reveal a universal bipolar polymer building block, composed of an extended G domain, which forms oligomers and filaments by conserved interactions between adjacent nucleotide-binding sites and/or the amino- and carboxy-terminal extensions. Unexpectedly, X-ray crystallography and electron microscopy showed that the predicted coiled coils are not involved in or required for complex and/or filament formation. The asymmetrical heterotrimers associate head-to-head to form a hexameric unit that is nonpolarized along the filament axis but is rotationally asymmetrical. The architecture of septin filaments differs fundamentally from that of other cytoskeletal structures.

Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome.

The carboxysome is a bacterial organelle that functions to enhance the efficiency of CO2 fixation by encapsulating the enzymes ribulose bisphosphate carboxylase/oxygenase (RuBisCO) and carbonic anhydrase. The outer shell of the carboxysome is reminiscent of a viral capsid, being constructed from many copies of a few small proteins. Here we describe the structure of the shell protein CsoS1A from the chemoautotrophic bacterium Halothiobacillus neapolitanus. The CsoS1A protein forms hexameric units that pack tightly together to form a molecular layer, which is perforated by narrow pores. Sulfate ions, soaked into crystals of CsoS1A, are observed in the pores of the molecular layer, supporting the idea that the pores could be the conduit for negatively charged metabolites such as bicarbonate, which must cross the shell. The problem of diffusion across a semiporous protein shell is discussed, with the conclusion that the shell is sufficiently porous to allow adequate transport of small molecules. The molecular layer formed by CsoS1A is similar to the recently observed layers formed by cyanobacterial carboxysome shell proteins. This similarity supports the argument that the layers observed represent the natural structure of the facets of the carboxysome shell. Insights into carboxysome function are provided by comparisons of the carboxysome shell to viral capsids, and a comparison of its pores to the pores of transmembrane protein channels.

Expression of the Iron-ActivatednspAandsecYGenes inNeisseria meningitidisGroup B by Fur-Dependent and -Independent Mechanisms

Our whole-genome microarray studies of Neisseria meningitidis MC58 previously identified a set of 153 genes whose transcription was activated during growth in iron. In this study, Fur-mediated regulation of the iron-activated nspA gene was confirmed, whereas iron-activated regulation of the secY gene was demonstrated to be Fur independent. Analysis of the Fur binding sequences in the nspA gene and an additional iron-activated and Fur-regulated gene identified a hexameric (G/T)ATAAT unit in the operator regions of these genes similar to that observed in Fur- and iron-repressed genes. These studies indicate that the expression of the iron-activated nspA and secY genes in N. meningitidis occur by Fur-dependent and -independent mechanisms, respectively.