Ion pairs in non-redundant protein structures

Ion pairs contribute to several functions including the activity of catalytic triads, fusion of viral membranes, stability in thermophilic proteins and solvent-protein interactions. Furthermore, they have the ability to affect the stability of protein structures and are also a part of the forces that act to hold monomers together. This paper deals with the possible ion pair combinations and networks in 25% and 90% non-redundant protein chains. Different types of ion pairs present in various secondary structural elements are analysed. The ion pairs existing between different subunits of multisubunit protein structures are also computed and the results of various analyses are presented in detail. The protein structures used in the analysis are solved using X-ray crystallography, whose resolution is better than or equal to 1.5 A and R-factor better than or equal to 20%. This study can, therefore, be useful for analyses of many protein functions. It also provides insights into the better understanding of the architecture of protein structure.     

Outcrossing increases infection success in the holoparasitic mistletoe <Emphasis Type="Italic">Tristerix aphyllus</Emphasis> (Loranthaceae)

Most studies on the fitness advantage of outbreeding in host–parasite systems have been assessed from the host rather than the parasite perspective. Here, we performed experimental pollination treatments to evaluate the consequences of outbreeding on fitness-related traits in the holoparasitic mistletoe Tristerix aphyllus in a 2-year field study. Results indicate that self-pollinated plants had a lower fruit production than outcrossed plants (20.4% and 29.5% reduction in 2002 and 2003, respectively), and resulting inbred fruits were smaller than outcrossed fruits in both years. No effect was detected for seed mass. The percentage of germination of inbred seeds was 15.1% and 6.0% lower than outcrossed seeds in 2002 and 2003, respectively. Inbred seedlings had shorter radicles, which translated to a 71.6% and 60.0% reduction in infection success compared with outcrossed plants in 2002 and 2003, respectively. Overall, our results revealed significant inbreeding depression on almost every trait that was examined. Although the mean value of traits varied from a year to another, the magnitude of inbreeding depression did not change significantly between years. Our findings constitute the first evidence that outcrossing increases infection success and probably virulence in parasitic plant populations.     

Macrophage inflammatory protein-1α (MIP-1α) enhances a receptor activator of nuclear factor κB ligand (RANKL) expression in mouse bone marrow stromal cells and osteoblasts through MAPK and PI3K/Akt pathways

Osteolytic lesions are rapidly progressive during the terminal stages of myeloma, and the bone pain or bone fracture that occurs at these lesions decreases the patients’ quality of life to a notable degree. In relation to the etiology of this bone destruction, it has been reported recently that MIP-1α, produced in large amounts in myeloma patients, acts indirectly on osteoclastic precursor cells, and activates osteoclasts by way of bone-marrow stromal cells or osteoblasts, although the details of this process remain obscure. In the present study, our group investigated the mechanism by which RANKL expression is induced by MIP-1α and the effects of MIP-1α on the activation of osteoclasts. RANKL mRNA and RANKL protein expressions increased in both ST2 cells and MC3T3–E1 cells in a MIP-1α concentration-dependent manner. RANKL mRNA expression began to increase at 1 h after the addition of MIP-1α; the increase became remarkable at 2 h, and continuous expression was observed subsequently. Both ST2 and MC3T3-E1 cells showed similar levels of increased RANKL protein expression at 1, 2, and 3 days after the addition of MIP-1α. After the addition of MIP-1α, the amount of phosphorylated ERK1/2 and Akt protein expressions showed an increase, as compared to the corresponding amount in the control group. On the other hand, the amount of phosphorylated p38MAPK protein expression showed a decrease from the amount in the control group after the addition of MIP-1α. U0126 (a MEK1/2 inhibitor) or LY294002 (a PI3K inhibitor) was added to ST2 and MC3T3-E1 cells, and was found to inhibit RANKL mRNA and RANKL protein expression in these cells. When SB203580, a p38MAPK inhibitor, was added, RANKL mRNA and RANKL protein expression were increased in these cells. MIP-1α was found to promote osteoclastic differentiation of C7 cells, an osteoclastic precursor cell line, in a MIP-1α concentration-dependent manner. MIP-1α promoted differentiation into osteoclasts more extensively in C7 cells incubated together with ST2 and MC3T3-E1 cells than in C7 cells incubated alone. These results suggested that MIP-1α directly acts on the osteoclastic precursor cells and induces osteoclastic differentiation. This substance also indirectly induces osteoclastic differentiation through the promotion of RANKL expression in bone-marrow stromal cells and osteoblasts. The findings of this investigation suggested that activation of the MEK/ERK and the PI3K/Akt pathways and inhibition of p38MAPK pathway were involved in RANKL expression induced by MIP-1α in bone-marrow stromal cells and osteoblasts. This finding may be useful in the development of an osteoclastic inhibitor that targets intracellular signaling factors.     

Investigations on unconventional hydrogen bonds in RNA binding proteins: the role of CH...O=C interactions

We have investigated the roles played by C-H...O=C interactions in RNA binding proteins. There was an average of 78 CH...O=C interactions per protein and also there was an average of one significant CH...O=C interactions for every 6 residues in the 59 RNA binding proteins studied. Main chain-Main chain (MM) CH...O=C interactions are the predominant type of interactions in RNA binding proteins. The donor atom contribution to CH...O=C interactions was mainly from aliphatic residues. The acceptor atom contribution for MM CH...O=C interactions was mainly from Val, Phe, Leu, Ile, Arg and Ala. The secondary structure preference analysis of CH...O=C interacting residues showed that, Arg, Gln, Glu and Tyr preferred to be in helix, while Ala, Asp, Cys, Gly, Ile, Leu, Lys, Met, Phe, Trp and Val preferred to be in strand conformation. Most of the CH...O=C interacting polar amino acid residues were solvent exposed while, majority of the CH...O=C interacting non polar residues were excluded from the solvent. Long and medium-range CH...O=C interactions are the predominant type of interactions in RNA binding proteins. More than 50% of CH...O=C interacting residues had a higher conservation score. Significant percentage of CH...O=C interacting residues had one or more stabilization centers. Sixty-six percent of the theoretically predicted stabilizing residues were also involved in CH...O=C interactions and hence these residues may also contribute additional stability to RNA binding proteins.     

Bacterial lipopolysaccharide induces osteoclast formation in RAW 264.7 macrophage cells

Lipopolysaccharide (LPS) is a potent bone resorbing factor. The effect of LPS on osteoclast formation was examined by using murine RAW 264.7 macrophage cells. LPS-induced the formation of multinucleated giant cells (MGC) in RAW 264.7 cells 3 days after the exposure. MGCs were positive for tartrate-resistant acid phosphatase (TRAP) activity. Further, MGC formed resorption pits on calcium-phosphate thin film that is a substrate for osteoclasts. Therefore, LPS was suggested to induce osteoclast formation in RAW 264.7 cells. LPS-induced osteoclast formation was abolished by anti-tumor necrosis factor (TNF)-alpha antibody, but not antibodies to macrophage-colony stimulating factor (M-CSF) and receptor activator of nuclear factor (NF)-kappaB ligand (RANKL). TNF-alpha might play a critical role in LPS-induced osteoclast formation in RAW 264.7 cells. Inhibitors of NF-kappaB and stress activated protein kinase (SAPK/JNK) prevented the LPS-induced osteoclast formation. The detailed mechanism of LPS-induced osteoclast formation is discussed.     

Differential expression of TRAIL and its receptors relative to calcification in AAA

Abdominal aortic aneurysm (AAA) is commonly associated with atherosclerosis. Human AAA tissue displays cells undergoing all stages of apoptosis. Tumour necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) induces apoptosis in tumour cells but not in normal cells. It has death receptors and decoy receptors. An inhibitor of TRAIL, osteoprotegerin (OPG), is involved in osteogenesis and vascular calcification. We investigated TRAIL and its receptors in AAA compared within normal aorta (NA). Both qualitative and quantitative analyses of calcification in AAA walls were determined using Von Kossa staining and pre-operation computer tomography (CT) scans. There was a significant difference in calcification level at different locations in the AAA wall (p <0.05). Apoptosis was confirmed in AAA by TUNEL assay. A significant difference in TRAIL and its receptor expression was observed between normal aortae and AAA (p<0.05). Significant differences were also observed between tissues displaying different extents of calcification for TRAIL mRNA (p<0.05) by RT-PCR examination and OPG protein (p<0.01) by protein blotting examination. We propose that this pattern of expression of TRAIL and its receptors may contribute to AAA formation and calcification in the AAA wall.     

A review of research on the interactions between dugongs (<Emphasis Type="Italic">Dugong dugon</Emphasis> Müller 1776) and intertidal seagrass beds in Indonesia

Research on dugong–seagrass interactions in Indonesia was done during the period 1990 until 2005 in respectively East Aru, Maluku Province and East Kalimantan, Indonesia. This research investigated intensive rotational grazing by dugongs in intertidal inshore Halodule univervis seagrass meadows, dugong movements in relation to these grazing swards, and analyses of parameters explaining the temporal and spatial patterns of grazing in these meadows. In this paper, we report the findings of this long-term study. The patterns of movement and the results of snorkelling surveys confirmed a practice of regular recropping of restricted grazing swards by small feeding assemblages of dugongs. Dugong grazing showed a significant correlation with carbohydrate content of the below-ground biomass and no significant relation with total N. The timing of dugong grazing in these intertidal meadows coincides with high below-ground biomass and high carbohydrate content in the rhizomes of H. uninervis in the upper 0–4 cm sediment layer. Our findings support the hypothesis that temporal dugong grazing is ruled by carbohydrate content in below-ground biomass. The mechanisms of rotational grazing in restricted grazing swards are not yet well understood, and the maximisation of carbohydrates does not fully explain this phenomenon. Our research confirms that intertidal H. univervis seagrass meadows form a crucial resource for dugong survival. These relatively unknown biotopes need therefore more attention in research and conservation programmes.     

Photooxidation of wetland and riverine dissolved organic matter: altered copper complexation and organic composition

In natural waters, the uptake of transition metals such as copper (Cu) by aquatic biota depends on the activity of the free cupric ion ({Cu²⁺}) rather than on total Cu concentration. Thus, an important ecological function of dissolved organic matter (DOM) in aquatic ecosystems is Cu–DOM complexation, which greatly decreases the {Cu²⁺}. However, Cu bioavailability is greatly modified by source and environmental history of DOM because DOM affinity for Cu varies by orders of magnitude among DOM sources; moreover, DOM is photochemically unstable. During 72-h irradiation experiments at intensities approximating sunlight with DOM from a palustrine wetland and a third-order river, we investigated photooxidative effects on DOM complexation of Cu as well as spectral and chemical changes in DOM that might explain altered Cu complexation. Irradiation decreased Cu complexation by riverine DOM, but unexpectedly increased Cu complexation by wetland DOM, resulting in 150% greater {Cu²⁺} in riverine DOM at the same dissolved organic carbon concentrations. The specific ultraviolet absorption (SUVa) and humic substances tracked photochemical changes in the conditional stability constants of Cu–DOM complexes, suggesting that the aromaticity of DOM influences its affinity for Cu. Carbonyl concentration in ¹³C nuclear magnetic resonance spectra (¹³C-NMR) covaried directly with Cu binding-site densities in DOM. However, no aspect of Cu–DOM complexation consistently covaried with fluorophores (i.e., the fluorescence index) or low molecular weight organic acids. Our results suggest that global increases in UV radiation will affect Cu–DOM complexation and subsequent Cu toxicity depending on light regime as well as DOM source. Handling editor: K. Martens     

Synthesis and structure of products of interaction of H[AuCl4] with H2DMG and pyridine

Two complexes of gold of the compositions [Au(DMG)ClPy] (1) and [AuCl₂Py₂][AuCl₄] · 2[AuCl₃Py] (2), where H₂DMG was dimethylglyoxime, were synthesized as the products of interaction of H[AuCl₄] · 4H₂O with H₂DMG in the presence of pyridine and characterized by X-ray structural analysis. It was shown that depending on the synthetic conditions, the final product represents a molecular complex 1 or an ionic complex 2, in the latter one the charged and neutral species being combined via Au?Cl or Au?Au interactions.