Homology of the N-terminal domain of the petH gene product from Anabaena sp. PCC 7119 to the CpcD phycobilisome linker polypeptide

The complete nucleotide sequence of the petH gene encoding ferredoxin-NADP⁺ reductase from the nitrogen-fixing cyanobacterium Anabaena sp. PCC 7119 has been determined. The encoded polypeptide is 136 amino acids longer than the enzyme obtained after purification to homogeneity. The extended N-terminal domain consists of 80 amino acids which shows homology to the CpcD phycobilisome linker polypeptide, through which FNR might be anchored to the thylakoid-bound phycobilisomes. A 56 amino acid interdomain fragment is found which could be a target for proteolysis.     

Helix orientations in membrane-associated Bcl-X<Subscript>L</Subscript> determined by <Superscript>15</Superscript>N-solid-state NMR spectroscopy

Controlled cell death is fundamental to tissue hemostasis and apoptosis malfunctions can lead to a wide range of diseases. Bcl-x_L is an anti-apoptotic protein the function of which is linked to its reversible interaction with mitochondrial outer membranes. Its interfacial and intermittent bilayer association makes prediction of its bound structure difficult without using methods able to extract data from dynamic systems. Here we investigate Bcl-x_L associated with oriented lipid bilayers at physiological pH using solid-state NMR spectroscopy. The data are consistent with a C-terminal transmembrane anchoring sequence and an average alignment of the remaining helices, i.e. including helices 5 and 6, approximately parallel to the membrane surface. Data from several biophysical approaches confirm that after removal of the C-terminus from Bcl-x_L its membrane interactions are weak. In the presence of membranes Bcl-x_L can still interact with a Bak BH3 domain peptide suggesting a model where the hydrophobic C-terminus of the protein unfolds and inserts into the membrane. During this conformational change the Bcl-x_L hydrophobic binding pocket becomes accessible for protein–protein interactions whilst the structure of the N-terminal region remains intact. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Homology modeling of the transmembrane domain of the GABA<Subscript>A</Subscript> receptor

The permeability of ion channels for ions and substances that bind inside the pore depends on the cross-sectional area of the pore. We have constructed models of the closed, open, and desensitized α₁β₂γ₂ GABA_A receptor on the basis of known structures of both prokaryotic and eukaryotic ligand-gated channels. We employed Monte Carlo energy minimization to optimize the model structures. We have found significant pore constrictions, whose diameter depends on the functional state of the receptor in the cytoplasmic, middle, and extracellular parts of the pore-forming M2 segments. It is known that the constrictions in the middle (the 9' ring of residues) and cytoplasmic (the 2' ring of residues) parts of the M2 helices form the activation and desensitization gates of the GABA_A receptor. Our computations predict that the constriction in the extracellular part of the M2 helices (the 20' ring of residues) may also serve as a gate in the GABA_A receptor, whose physiological role is still unclear. Our results imply that the structures of a number of prokaryotic and eukaryotic ligand-gated channels that have been found in bacteria and lower organisms can be used for homology modeling of the pore region of the human GABA_A receptor.     

Solid-state NMR chemical shift assignments for AL-09 V<Subscript>L</Subscript> immunoglobulin light chain fibrils

Light chain (AL) amyloidosis is a systemic disease characterized by the formation of immunoglobulin light-chain fibrils in critical organs of the body. The light-chain protein AL-09 presents one severe case of cardiac AL amyloidosis, which contains seven mutations in the variable domain (V_L) relative to its germline counterpart, κI O18/O8 V_L. Three of these mutations are non-conservative—Y87H, N34I, and K42Q—and previous work has shown that they are responsible for significantly reducing the protein’s thermodynamic stability, allowing fibril formation to occur with fast kinetics and across a wide-range of pH conditions. Currently, however, there is extremely limited structural information available which explicitly describes the residues that are involved in supporting the misfolded fibril structure. Here, we assign the site-specific ¹⁵N and ¹³C chemical shifts of the rigid residues of AL-09 V_L fibrils by solid-state NMR, reporting on the regions of the protein involved in the fibril as well as the extent of secondary structure.     

Interactions of linker proteins with the phycobiliproteins in the phycobilisome substructures of <Emphasis Type="Italic">Gloeobacter violaceus</Emphasis>

Gloeobacter violaceus PCC 7421 is a unicellular oxygenic photosynthetic organism, which precedes the diversification of cyanobacteria in the phylogenetic tree. It is the only cyanobacterium that does not contain internal membranes. The unique structure of the rods of the phycobilisome (PBS), grouped as one bundle of six parallel rods, distinguishes G. violaceus from the other PBS-containing cyanobacteria. It has been proposed that unique multidomain rod-linkers are responsible for this peculiarly organized shape. However, the localization of the multidomain linkers Glr1262 and Glr2806 in the PBS-rods remains controversial (Koyama et al. 2006, FEBS Lett 580:3457–3461; Krogmann et al. 2007, Photosynth Res 93:27–43). To further increase our understanding of the structure of the G. violaceus PBS, the identification of the proteins present in fractions obtained from sucrose gradient centrifugation and from native electrophoresis of partially dissociated PBS was conducted. The identification of the proteins, after electrophoresis, was done by spectrophotometry and mass spectrometry. The results support the localization of the multidomain linkers as previously proposed by us. The Glr1262 (92 kDa) linker protein was found to be the rod-core linker L_RC ⁹², and Glr2806 (81 kDa), a special rod linker L_R ⁸¹ that joins six disks of hexameric PC. Consequently, we propose to designate glr1262 as gene cpcGm (encoding L_RC ⁹²) and glr2806 as gene cpcJm (encoding L_R ⁸¹). We also propose that the cpeC (glr1263) gene encoding L_R ^31.8 forms the interface that binds PC to PE.     

Crystal structure of the N-terminal domain of linker L(R) and the assembly of cyanobacterial phycobilisome rods

Phycobilisomes are light‐harvesting supramolecular complexes in cyanobacteria and red algae. Linkers play a pivotal role in the assembly and energy transfer modulation of phycobilisomes. However, how linkers function remains unclear due to the lack of structural and biochemical studies of linkers, especially the N‐terminal domain of L_R (pfam00427). Here, we report the crystal structure of the pfam00427 domain of the linker L_R³⁰ from Synechocystis sp. PCC 6803 at 1.9 Å. The pfam00427 presents as a previously uncharacterized point symmetric six α‐helix bundle. To elucidate the binding style of pfam00427 in the C‐phycocyanin (C‐PC) (αβ)₆ hexamer, we fixed pfam00427 computationally into the C‐PC (αβ)₆ inner cavity using the program AutoDock. Combined with a conserved ‘C‐PC binding patch’ on pfam00427 identified, we arrived at a model for the pfam00427–C‐PC (αβ)₆ complex. This model was further optimized and evaluated as a reasonable result by a molecular dynamics simulation. In the resulting model, the pfam00427 domain is stably positioned in the central hole of the C‐PC trimer. Moreover, the L_RT (pfam01383) was docked into our pfam00427–C‐PC model to generate a complete phycobilisome rod in which the linkers join individual biliprotein hexamers.     

L<Subscript>2</Subscript>-norm multiple kernel learning and its application to biomedical data fusion

Background  

This paper introduces the notion of optimizing different norms in the dual problem of support vector machines with multiple kernels. The selection of norms yields different extensions of multiple kernel learning (MKL) such as L _∞, L ₁, and L ₂ MKL. In particular, L ₂ MKL is a novel method that leads to non-sparse optimal kernel coefficients, which is different from the sparse kernel coefficients optimized by the existing L _∞ MKL method. In real biomedical applications, L ₂ MKL may have more advantages over sparse integration method for thoroughly combining complementary information in heterogeneous data sources.     

Structural elements of the C-terminal domain of subunit E (E<Subscript>133-222</Subscript>) from the <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> V<Subscript>1</Subscript>V<Subscript>O</Subscript> ATPase determined by solution NMR spectroscopy

Subunit E of the vacuolar ATPase (V-ATPase) contains an N-terminal extended α helix (Rishikesan et al. J Bioenerg Biomembr 43:187–193, 2011) and a globular C-terminal part that is predicted to consist of a mixture of α-helices and β-sheets (Grüber et al. Biochem Biophys Res Comm 298:383–391, 2002). Here we describe the production, purification and 2D structure of the C-terminal segment E_133-222 of subunit E from Saccharamyces cerevisiae V-ATPase in solution based on the secondary structure calculation from NMR spectroscopy studies. E_133-222 consists of four β-strands, formed by the amino acids from K136-V139, E170-V173, G186-V189, D195-E198 and two α-helices, composed of the residues from R144-A164 and T202-I218. The sheets and helices are arranged as β1:α1:β2:β3:β4:α2, which are connected by flexible loop regions. These new structural details of subunit E are discussed in the light of the structural arrangements of this subunit inside the V₁- and V₁V_O ATPase.     

The roles of Bcl-x<Subscript>L</Subscript> in modulating apoptosis during development of <Emphasis Type="Italic">Xenopus laevis</Emphasis>

Background  

Apoptosis is a common and essential aspect of development. It is particularly prevalent in the central nervous system and during remodelling processes such as formation of the digits and in amphibian metamorphosis. Apoptosis, which is dependent upon a balance between pro- and anti-apoptotic factors, also enables the embryo to rid itself of cells damaged by gamma irradiation. In this study, the roles of the anti-apoptotic factor Bcl-x_L in protecting cells from apoptosis were examined in Xenopus laevis embryos using transgenesis to overexpress the XR11 gene, which encodes Bcl-x_L. The effects on developmental, thyroid hormone-induced and γ-radiation-induced apoptosis in embryos were examined in these transgenic animals.     

Plasminogen K5 activates mitochondrial apoptosis pathway in endothelial cells by regulating Bak and Bcl-x<Subscript>L</Subscript> subcellular distribution

Plasminogen Kringle 5(K5) is a proteolytic fragment of plasminogen, which displays potent anti-angiogenic activities. K5 has been shown to induce apoptosis in proliferating endothelial cells; however the exact mechanism has not been well explored. The present study was designed to elucidate the possible molecular mechanism of K5-induced endothelial cell apoptosis. Our results showed that K5 inhibited basic fibroblast growth factors activated in human umbilical vein endothelial cells (HUVECs), indicating proliferation in a dose-dependent manner and induced endothelial cell death via apoptosis. K5 exposure activated caspase 7, 8 and 9. These results suggested that both the intrinsic mitochondrial apoptosis pathway and extrinsic pathway might be involved in K5-induced apoptosis. K5 reduced mitochondrial membrane potential (MMP) of HUVECs, demonstrating mitochondrial depolarization in HUVECs. K5 increased the ratio of Bak to Bcl-x_L on mitochondria, decreased the ratio in cytosol, and had no effect on the total amounts of these proteins. K5 also did not effect on Bax/Bcl-2 distribution. K5 increased the ratio of Bak to Bcl-x_L on mitochondrial that resulted in mitochondrial depolarization, cytochrome c release and consequently the cleavage of caspase 9. These results suggested that K5 induces endothelial cell apoptosis at least in part via activating mitochondrial apoptosis pathway. The regulation of K5 on Bak and Bcl-x_L distribution may play an important role in endothelial cell apoptosis. These results provide further insight into the anti-angiogenesis roles of K5 in angiogenesis-related ocular diseases and solid tumors.     

Adenosine-induced caspase-3 activation by tuning Bcl-X<Subscript>L</Subscript>/DIABLO/IAP expression in HuH-7 human hepatoma cells

Extracellular adenosine disrupted mitochondrial membrane potentials in HuH-7 cells, a Fas-deficient human hepatoma cell line, and the effect was inhibited by the adenosine transporter inhibitor dipyridamole or by overexpressing Bcl-X_L. Adenosine downregulated the expression of mRNAs and proteins for Bcl-X_L and inhibitor of apoptosis protein 2 (IAP2) to directly inhibit caspase-3, -7, and -9, but it otherwise upregulated the expression of mRNA and protein for DIABLO, an inhibitor of IAPs. Those adenosine effects were attenuated by dipyridamole. Caspase-3 and -8 were implicated in adenosine-induced HuH-7 cell death, and adenosine actually activated caspase-3 without caspase-9 activation. The caspase-3 activation was inhibited by overexpressing Bcl-X_L or IAP2. Taken together, the results of the present study indicate that intracellularly transported adenosine activates caspase-3 by neutralizing caspase-3 inhibition due to IAP as a result of decreased IAP2 expression and reduced IAP activity in response to increased DIABLO expression and perhaps DIABLO release from damaged mitochondria, in addition to caspase-8 activation. This represents further insight into adenosine-induced HuH-7 cell apoptotic pathway.     

An <Emphasis Type="Italic">L</Emphasis><Subscript>1</Subscript>-regularized logistic model for detecting short-term neuronal interactions

Interactions among neurons are a key component of neural signal processing. Rich neural data sets potentially containing evidence of interactions can now be collected readily in the laboratory, but existing analysis methods are often not sufficiently sensitive and specific to reveal these interactions. Generalized linear models offer a platform for analyzing multi-electrode recordings of neuronal spike train data. Here we suggest an L ₁-regularized logistic regression model (L ₁ L method) to detect short-term (order of 3 ms) neuronal interactions. We estimate the parameters in this model using a coordinate descent algorithm, and determine the optimal tuning parameter using a Bayesian Information Criterion. Simulation studies show that in general the L ₁ L method has better sensitivities and specificities than those of the traditional shuffle-corrected cross-correlogram (covariogram) method. The L ₁ L method is able to detect excitatory interactions with both high sensitivity and specificity with reasonably large recordings, even when the magnitude of the interactions is small; similar results hold for inhibition given sufficiently high baseline firing rates. Our study also suggests that the false positives can be further removed by thresholding, because their magnitudes are typically smaller than true interactions. Simulations also show that the L ₁ L method is somewhat robust to partially observed networks. We apply the method to multi-electrode recordings collected in the monkey dorsal premotor cortex (PMd) while the animal prepares to make reaching arm movements. The results show that some neurons interact differently depending on task conditions. The stronger interactions detected with our L ₁ L method were also visible using the covariogram method.     

Immobilization of glucose oxidase on Fe<Subscript>3</Subscript>O<Subscript>4</Subscript>/SiO<Subscript>2</Subscript> magnetic nanoparticles

Glucose oxidase (GOD) was covalently immobilized onto Fe₃O₄/SiO₂ magnetic nanoparticles (FSMNs) using glutaraldehyde (GA). Optimal immobilization was at pH 6 with 3-aminopropyltriethoxysilane at 2% (v/v), GA at 3% (v/v) and 0.143 g GOD per g carrier. The activity of immobilized GOD was 4,570 U/g at pH 7 and 50°C. The immobilized GOD retained 80% of its initial activity after 6 h at 45°C while free enzyme retained only 20% activity. The immobilized GOD maintained 60% of its initial activity after 6 cycles of repeated use and retained 75% of its initial activity after 1 month at 4°C whereas free enzymes retained 62% of its activity.     

The encapsulated lithium effect on the first hyperpolarizability of C<Subscript>60</Subscript>Cl<Subscript>2</Subscript> and C<Subscript>60</Subscript>F<Subscript>2</Subscript>

In this paper, we report a study on the structure and first hyperpolarizability of C₆₀Cl₂ and C₆₀F₂. The calculation results show that the first hyperpolarizabilities of C₆₀Cl₂ and C₆₀F₂ were 172 au and 249 au, respectively. Compared with the fullerenes, the first hyperpolarizability of C₆₀Cl₂ increased from 0 au to 172 au, while the first hyperpolarizability of C₆₀F₂ increased from 0 au to 249 au. In order to further increase the first hyperpolarizability of C₆₀Cl₂ and C₆₀F₂, Li@C₆₀Cl₂ and Li@C₆₀F₂ were obtained by introducing a lithium atom to C₆₀Cl₂ and C₆₀F₂. The first hyperpolarizabilities of Li@C₆₀Cl₂ and Li@C₆₀F₂ were 2589 au and 985 au, representing a 15-fold and 3.9-fold increase, respectively, over those of C₆₀Cl₂ and C₆₀F₂. The transition energies of four molecules (C₆₀Cl₂, Li@C₆₀Cl₂, C₆₀F₂, Li@C₆₀F₂) were calculated, and were found to be 0.17866 au, 0.05229 au, 0.18385 au, and 0.05212 au, respectively. A two-level model explains why the first hyperpolarizability increases for Li@C₆₀Cl₂ and Li@C₆₀F₂.     

Allophycocyanin complexes of the phycobilisome from Mastigocladus laminosus. Influence of the linker polypeptide L8.9C on the spectral properties of the phycobiliprotein subunits

The following phycobiliproteins and complexes of the allophycocyanin core were isolated from phycobilisomes of the thermophilic cyanobacterium Mastigocladus laminosus: alpha AP, beta AP, (alpha AP beta AP), (alpha AP beta AP)3, (alpha AP beta AP)3L8.9C, (alpha APB alpha AP2 beta AP3)L8.9C. The six proteins and complexes were characterised spectroscopically with respect to absorption, oscillator strength, extinction coefficient, fluorescence emission, relative quantum yield, fluorescence emission polarisation and fluorescence excitation polarisation. The interpretation of the spectral data was based on the three-dimensional structure model of (alpha PC beta PC)3 (Schirmer et al. (1985) J. Mol. Biol. 184, 257-277), which is related to the allophycocyanin trimer. The absorption and CD spectra of the complexes (alpha AP beta AP)3, (alpha AP beta AP)3L8.9C and (alpha APB alpha AP2 beta AP3)L8.9C could be deconvoluted into the spectra of the phycobiliprotein subunits. The assumptions made for the deconvolution could be checked by the synthesis of the spectra of (alpha APB beta AP)3. The synthesised spectra are in good agreement with the corresponding measured spectra published by other authors. Considering the deconvoluted spectra the following influences on the chromophores could be ascribed to L8.9C: L8.9C neither influences the alpha AP nor the alpha APB chromophores. L8.9C shifts the absorption maximum of the beta AP chromophore to longer wavelength than the absorption maximum of the alpha AP chromophore in trimeric complexes. L8.9C increases the oszillator strength of the beta AP chromophores to about the value of the alpha AP chromophores in trimeric complexes. L8.9C turns the beta AP chromophores from sensitizing into weak fluorescing chromophores. By means of the hydropathy plot and the predicted secondary structure, a postulated three-fold symmetry in the tertiary structure of L8.9C could be confirmed.     

Calculations of the C<Subscript>2</Subscript> fragmentation energies of higher fullerenes C<Subscript>80</Subscript> and C<Subscript>82</Subscript>

The C₂ fragmentation energies of the most stable isolated-pentagon-rule (IPR) isomers of the C₈₀ and C₈₂ fullerenes were evaluated with second-order Møller-Plesset (MP2) theory, density-functional theory (DFT) and the semiempirical self-consistent charge density-functional tight-binding (SCC-DFTB) method. Zero-point energy, ionization energy and empirical C₂ corrections were included in the calculation of fragmentation energies for comparison with experimental C₂ fragmentation energies of the fullerene cations. In the case of the most probable Stone-Wales pathway of C₂ fragmentation of C₈₀, the calculated \(D_{0} {\left( {{\text{C}}_{{{\text{80}}}} ^{ + } } \right)}\) agree well with experimental data, whereas in the case of C₈₂ fragmentation, the calculated \(D_{0} {\left( {{\text{C}}_{{{\text{82}}}} ^{ + } } \right)}\) exceed by up to 1.2 eV the experimental ones, which suggests that other IPR isomers may be present in sufficient amounts in experimental samples. Computer-intensive MP2 calculations and DFT calculations with larger basis sets do not yield much improved C₂ fragmentation energies, compared to those reported earlier with B3LYP/3-21G. On the other hand, semiempirical approaches such as SCC-DFTB, which are orders of magnitude less intensive, yield satisfactory fragmentation energies for higher fullerenes and may become a method of choice for routine calculations of fullerenes and carbon nanotubes.

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Figure C₂ fragmentation energies of C₈₀ and C₈₂ fullerenes have been calculated with B3LYP/6-31G* model chemistry, with semiempirical self-consistent-charge density-functional tight-binding (SCC-DFTB) method and with the more rigorous MP2 method. The influence of basis set extension and level of theory on the resulting fragmentation energies is discussed

     

Effect of a commercial alcohol ethoxylate surfactant (C<Subscript>11-15</Subscript>E<Subscript>7</Subscript>) on

Biodegradation of poorly soluble polycyclic aromatic hydrocarbons (PAHs) has been a challenge in bioremediation. In recent years, surfactant-enhanced bioremediation of PAH contaminants has attracted great attention in research. In this study, biodegradation of phenanthrene as a model PAHs solubilized in saline micellar solutions of a biodegradable commercial alcohol ethoxylate nonionic surfactant was investigated. The critical micelle concentration (CMC) of the surfactant and its solubilization capacity for phenanthrene were examined in an artificial saline water medium, and a type of marine bacteria, Neptunomonas naphthovorans, was studied for the biodegradation of phenanthrene solubilized in the surfactant micellar solutions of the saline medium. It is found that the solubility of phenanthrene in the surfactant micellar solutions increased linearly with the surfactant concentrations, but, at a fixed phenanthrene concentration, the biodegradability of phenanthrene in the micellar solutions decreased with the increase of the surfactant concentrations. This was attributed to the reduced bioavailability of phenanthrene, due to its increased solubilization extent in the micellar phase and possibly lowered mass transfer rate from the micellar phase into the aqueous phase or into the bacterial cells. In addition, an inhibitory effect of the surfactant on the bacterial growth at high surfactant concentrations may also play a role. It is concluded that the surfactant largely enhanced the solubilization of phenanthrene in the saline water medium, but excess existence of the surfactant in the medium should be minimized or avoided for the biodegradation of phenanthrene by Neptunomonas naphthovorans.     

Cannabis Users Show Enhanced Expression of CB<Subscript>1</Subscript>-5HT<Subscript>2A</Subscript> Receptor Heteromers in Olfactory Neuroepithelium Cells

Cannabinoid CB1 receptors (CB₁R) and serotonergic 2A receptors (5HT_2AR) form heteromers in the brain of mice where they mediate the cognitive deficits produced by delta-9-tetrahydrocannabinol. However, it is still unknown whether the expression of this heterodimer is modulated by chronic cannabis use in humans. In this study, we investigated the expression levels and functionality of CB₁R-5HT_2AR heteromers in human olfactory neuroepithelium (ON) cells of cannabis users and control subjects, and determined their molecular characteristics through adenylate cyclase and the ERK 1/2 pathway signaling studies. We also assessed whether heteromer expression levels correlated with cannabis consumption and cognitive performance in neuropsychological tests. ON cells from controls and cannabis users expressed neuronal markers such as βIII-tubulin and nestin, displayed similar expression levels of genes related to cellular self-renewal, stem cell differentiation, and generation of neural crest cells, and showed comparable Na⁺ currents in patch clamp recordings. Interestingly, CB₁R-5HT_2AR heteromer expression was significantly increased in cannabis users and positively correlated with the amount of cannabis consumed, and negatively with age of onset of cannabis use. In addition, a negative correlation was found between heteromer expression levels and attention and working memory performance in cannabis users and control subjects. Our findings suggest that cannabis consumption regulates the formation of CB₁R-5HT_2AR heteromers, and may have a key role in cognitive processing. These heterodimers could be potential new targets to develop treatment alternatives for cognitive impairments.