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71.
Phosphoserine phosphatase (PSP) catalyzes the final and irreversible step of L‐serine synthesis by hydrolyzing phosphoserine to produce L ‐serine and inorganic phosphate. Developing a therapeutic drug that interferes with serine production is of great interest to regulate the pathogenicity of some bacteria and control D ‐serine levels in neurological diseases. We determined the crystal structure of PSP from the hyperthermophilic archaeon Thermococcus onnurineus at 1.8 Å resolution, revealing an NDSB ligand bound to a novel site that is located in a fissure between the catalytic domain and the CAP module. The structure shows a half‐open conformation of the CAP 1 module with a unique protruding loop of residues 150–155 that possesses a helical conformation in other structures of homologous PSPs. Activity assays indicate that the enzyme exhibits marginal PSP activity at low temperature but a sharp increase in the kcat/KM value, approximately 22 fold, when the temperature is increased. Structural and biochemical analyses suggest that the protruding loop in the active site might be an essential component for the regulation of the activity of PSP from hyperthermophilic T. onnurineus. Identification of this novel binding site distantly located from the catalytic site may be exploited for the development of effective therapeutic allosteric inhibitors against PSP activity. © Proteins 2013. © 2012 Wiley Periodicals, Inc. 相似文献
72.
Jeong Won Kang Young Gyu Choi Jun Ha Lee Oh Kuen Kwon Ho Jung Hwang 《Molecular simulation》2013,39(9):829-835
Pure carbon nanotube (CNT) oscillators are compared to the corresponding CNT oscillators encapsulating copper nanowires (Cu@CNTs) by molecular dynamics simulations. The classical oscillation theory provides a fairly good estimate of the mass dependence of the operating frequency when the CNT surface is not deformed by the Cu nanowire. The structural deformations of the CNT induced by the encapsulated copper nanowire have a greater effect on the oscillation frequency than the mass of the copper nanowire. The excess forces of the Cu@CNT oscillator are slightly higher than those of the CNT oscillator and the excess van der Waals forces induced by the inter-wall interactions are 17 times higher than the excess forces induced by the Cu nanowire–CNT interactions. 相似文献
73.
Abstract DNA-drug complexes are important because of their pharmacological interest but, in addition, they provide a useful model to study the essential aspects of DNA recognition processes. In order to investigate the influence of ligand binding on the dynamic properties of DNA we have carried out normal mode analysis for complexes with drugs of two types: a typical intercalator, 9-aminoacridine, and a typical groove binder, netropsin. Normal modes are analysed in terms of helicoidal parameter variations with special attention being paid to global deformations of the double helix. The results show that the influence of these two drugs is very different. Intercalation of 9-aminoacridine leads to an increase in the flexibility of the intercalated dinucleotide step, with notably larger vibrational amplitudes for both roll and twist parameters compared to free DNA. In contrast, the groove binding of netropsin induces a stiffening of the DNA segment which is in contact with the drug reflected by decreased vibrational amplitudes for backbone angles and inter base pair helicoidal parameters and an increase in vibrations for adjacent base pairs in terms of buckle and propeller twist. 相似文献
74.
Ye Sol Oh Jin Ha Park Sung Wook Han 《Journal of biomolecular structure & dynamics》2013,31(12):3035-3046
Meso-tetrakis(N-methyl pyridinium-4-yl)porphyrin (TMPyP) intercalates between the base-pairs of DNA at a low [TMPyP]/[DNA base] ratio in aqueous solutions and molecular crowding conditions, which is induced by the addition of Poly(ethylene glycol) (PEG). Studied DNA-binding drugs, including TMPyP, 9-aminoacridine, ethidium bromide, and DAPI (4′,6-diamidino-2-phenylindole) showed similar binding properties in the presence or absence of PEG molecules which is examined by circular and linear dichroism. According to the LDr (reduced linear dichroism) results of the binding drugs examined in this work, PEG molecules induced no significant change compared to their binding properties in aqueous buffering systems. These results suggest that the transition moments are not expected to be perturbed significantly by PEG molecules. In this study, the experimental conditions of PEG 8000 were maintained at 35% (v/v) of total reaction volume, which is equal to the optimal molar concentration (0.0536 M as final concentration for PEG 8000) to maintain suitable cell-like conditions. Therefore, there was no need to focus on the conformational changes of the DNA helical structure, such as forming irregular aggregate structures, induced by large quantities of molecular crowding media itself at this stage. 相似文献
75.
Doo Byoul Lee Keun Hyung Choi Ho Kyung Ha Eun Jin Yang Sang Heon Lee SangHoon Lee Hyoung Chul Shin 《Polar Biology》2013,36(8):1215-1230
The rapid melting of glaciers as well as the loss of sea ice in the Amundsen Sea makes it an ideal environmental setting for the investigation of the impacts of climate change in the Antarctic on the distribution and production of mesozooplankton. We examined the latitudinal distribution of mesozooplankton and their grazing impacts on phytoplankton in the Amundsen Sea during the early austral summer from December 27, 2010 to January 13, 2011. Mesozooplankton followed a latitudinal distribution in relation to hydrographic and environmental features, with copepods dominating in the oceanic area and euphausiids dominating in the polynya. Greater Euphausia crystallorophias biomass in the polynya was associated with lower salinity and higher food concentration (chlorophyll a, choanoflagellates, and heterotrophic dinoflagellates). The grazing impact of three copepods (Rhincalanus gigas, Calanoides acutus, and Metridia gerlachei) on phytoplankton was low, with the consumption of 3 % of phytoplankton standing stock and about 4 % of daily primary production. Estimated daily carbon rations for each of the three copepods were also relatively low (<10 %), barely enough to cover metabolic demands. This suggests that copepods may rely on food other than phytoplankton and that much of the primary production is channeled through microzooplankton. Daily carbon rations for E. crystallorophias were high (up to 49 %) with the grazing impact accounting for 17 % of the phytoplankton biomass and 84 % of primary production. The presence of E. crystallorophias appears to be a critical factor regulating phytoplankton blooms and determining the fate of fixed carbon in the coastal polynyas of the Amundsen Sea. 相似文献
76.
77.
D. A. Pavlov N. G. Emel’yanova Vo Thi Ha Luong Thi Bich Thuan 《Journal of Ichthyology》2013,53(7):478-485
The growth of individuals is analyzed in the mass tropical species manybar goatfish Parupeneus multifasciatus from the Nha Trang Bay of the South China Sea. The relationship between the body weight and body length is determined for the females and males. Among the fishes larger 180 mm fork length (FL), the males prevail. Linear growth of the sagitta is characterized by negative allometry in relation to body length, and sagitta growth in length is faster than in width. Age of fish assessed based on the analysis of daily increments on the sagitta does not exceed three years, and the majority of individuals reach the first sexual maturity by the age of one year. The growth rate of the fish is characterized by a large individual variation. 相似文献
78.
Ge Bai Da-Hai Yang Yang Zhao Si Ha Fen Yang Jun Ma Xiao-Shu Gao Zhi-Min Wang Jian-Kang Zhu 《Plant molecular biology》2013,83(6):651-664
The plant hormone abscisic acid (ABA) plays important roles in regulating plant growth, development, and responses to environmental stresses. Proteins in the PYR/PYL/RCAR family (hereafter referred to as PYLs) are known as ABA receptors. Since most studies thus far have focused on Arabidopsis PYLs, little is known about PYL homologs in crop plants. We report here the characterization of 21 PYL homologs (GmPYLs) in soybean. Twenty-three putative GmPYLs can be found from soybean genome sequence and categorized into three subgroups. GmPYLs interact with AtABI1 and two GmPP2Cs in diverse manners. A lot of the subgroup I GmPYLs interact with PP2Cs in an ABA-dependent manner, whereas most of the subgroup II and III GmPYLs bind to PP2Cs in an ABA-independent manner. The subgroup III GmPYL23, which cannot interact with any of the tested PP2Cs, differs from other GmPYLs. The CL2/gate domain is crucial for GmPYLs-PP2Cs interaction, and a mutation in the conserved proline (P109S) abolishes the interaction between GmPYL1 and AtABI1. Furthermore, the ABA dependence of GmPYLs-PP2Cs interactions are partially correlated with two amino acid residues preceding the CL2/gate domain of GmPYLs. We also show that GmPYL1 interacts with AtABI1 in an ABA-dependent manner in plant cells. Three GmPYLs differentially inhibit AtABI1 and GmPP2C1 in an ABA-dependent or -enhanced manner in vitro. In addition, ectopically expressing GmPYL1 partially restores ABA sensitivity of the Arabidopsis triple mutant pyr1/pyl1/pyl4. Taken together, our results suggest that soybean GmPYLs are ABA receptors that function by interacting and inhibiting PP2Cs. 相似文献
79.
Tae-Wook Chung Hee-Jung Choi Ji-Yeon Lee Han-Sol Jeong Cheorl-Ho Kim Myungsoo Joo Jun-Yong Choi Chang-Woo Han So-Yeon Kim Jae-Sue Choi Ki-Tae Ha 《Biochemical and biophysical research communications》2013
Metastasis is major cause of malignant cancer-associated mortality. Fucoxanthin has effect on various pharmacological activities including anti-cancer activity. However, the inhibitory effect of fucoxanthin on cancer metastasis remains unclear. Here, we show that fucoxanthin isolated from brown alga Saccharina japonica has anti-metastatic activity. To check anti-metastatic properties of fucoxanthin, in vitro models including assays for invasion, migration, actin fiber organization and cancer cell–endothelial cell interaction were used. Fucoxanthin inhibited the expression and secretion of MMP-9 which plays a critical role in tumor invasion and migration, and also suppressed invasion of highly metastatic B16-F10 melanoma cells as evidenced by transwell invasion assay. In addition, fucoxanthin diminished the expressions of the cell surface glycoprotein CD44 and CXC chemokine receptor-4 (CXCR4) which play roles in migration, invasion and cancer–endothelial cell adhesion. Fucoxanthin markedly suppressed cell migration in wound healing assay and inhibited actin fiber formation. The adhesion of B16-F10 melanoma cells to the endothelial cells was significantly inhibited by fucoxanthin. Moreover, in experimental lung metastasis in vivo assay, fucoxanthin resulted in significant reduction of tumor nodules. Taken together, we demonstrate, for the first time, that fucoxanthin suppresses metastasis of highly metastatic B16-F10 melanoma cells in vitro and in vivo. 相似文献
80.