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Ji Guo Su Xiao Ming Han Xiao Zhang Yan Xue Hou Jian Zhuo Zhu Yi Dong Wu 《Journal of biomolecular structure & dynamics》2016,34(3):560-571
Protein collective motions play a critical role in many biochemical processes. How to predict the functional motions and the related key residue interactions in proteins is important for our understanding in the mechanism of the biochemical processes. Normal mode analysis (NMA) of the elastic network model (ENM) is one of the effective approaches to investigate the structure-encoded motions in proteins. However, the motion modes revealed by the conventional NMA approach do not necessarily correspond to a specific function of protein. In the present work, a new analysis method was proposed to identify the motion modes responsible for a specific function of proteins and then predict the key residue interactions involved in the functional motions by using a perturbation approach. In our method, an internal coordinate that accounts for the specific function was introduced, and the Cartesian coordinate space was transformed into the internal/Cartesian space by using linear approximation, where the introduced internal coordinate serves as one of the axes of the coordinate space. NMA of ENM in this internal/Cartesian space was performed and the function-relevant motion modes were identified according to their contributions to the specific function of proteins. Then the key residue interactions important for the functional motions of the protein were predicted as the interactions whose perturbation largely influences the fluctuation along the internal coordinate. Using our proposed methods, the maltose transporter (MalFGK2) from E. Coli was studied. The functional motions and the key residue interactions that are related to the channel-gating function of this protein were successfully identified. 相似文献
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Abstract Schizosaccharomyces pombe becomes resistant to killing by high concentration of hydrogen peroxide and other severe stresses including oxidants, high temperature and high concentration of ethanol when pretreated with nonlethal levels of hydrogen peroxide. In the presence of the protein synthesis inhibitor, cycloheximide, during hydrogen peroxide pretreatment, the cell obtained partial resistance to a higher level of hydrogen peroxide. The partial resistance to hydrogen peroxide in the presence of cycloheximide was acquired within 30 min of pretreatment but complete resistance obtained with de novo protein synthesis was not attained before 45 min of pretreatment. During adaptation to hydrogen peroxide, at least 15 polypeptides are induced, as analyzed by two-dimensional gel electrophoresis. Catalase activity is induced eight-fold by treatment with a nonlethal level of hydrogen peroxide. 相似文献
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Field-measured grazing rates (ml/animal/d) of cladocerans (mostly daphniids) and diaptomids were assembled from various published
studies and plotted as a function of corresponding phytoplankton concentration (μg l−1 f.w.). Filtering rates of both zooplankton groups initially increased with seston concentration until maximal grazing rates
were observed at approximately 4 × 102 and 1 × 102 μg l−1 for cladocerans and copepods, respectively; at higher algal concentrations, filtering rates of both declined as a function
of food concentration. The shape of these curves are most consistent with Holling's (1966) Type 3 functional response.
We found little support for the Type 3 functional response in published laboratory studies of Daphnia; most investigators report either a Type 1 or Type 2 response. The one study in which the Type 3 response was observed involved
experiments where animals were acclimated at low food concentrations for 24 h, whereas those studies associated with response
Types 1 or 2 had acclimation periods of only 1 to 3 h. We therefore assembled relevant data from the literature to examine
the effect of acclimation period on the feeding rates of Daphnia at low food concentrations. In the absence of any acclimation, animals filtered at extremely low rates. After 2 h of acclimation,
however, filtering rates increased 4 to 5-fold but declined again with longer durations; after > 70 h of pre-conditioning,
filtering rates were almost as low as they had been with no acclimation.
We also found little support for the Type 3 functional response in published studies of copepods. The only study associated
with a Type 3 response involved a marine copepod that had been subjected to a starvation period of 48 h; however, an analysis
of the effects of acclimation period did not yield conclusive evidence that filtering rates of freshwater copepods (Diaptomus and Eudiaptomus) decrease significantly with acclimation duration.
The low filtering rates associated with long acclimation periods in laboratory experiments appears to be a direct result of
animals becoming emaciated from prolonged exposure to low food concentrations, a situation which renders them incapable of
high filtering rates. This may explain the Type 3 functional response for field cladocerans, since zooplankton in food-limiting
situations are constantly exposed to low food concentrations, and would therefore have low body carbon and consequently less
energy to filter-feed. We cannot, however, use this to explain the Type 3 response for field diaptomids, since copepods in
the laboratory did not appear to lose body carbon even after 72 h of feeding at very low food levels, and there was inconclusive
evidence that either Diaptomus or Eudiaptomus decrease their filtering rates with acclimation period.
Although Incipient Limiting Concentrations (ILC) for Daphnia ranged from 1 to 8.5 × 103 μg 1−1, more than half of these fell between 1 and 3 × 103 μg l−1, bracketing the value of 2.7 × 102 μg l−1 for field cladocerans. There was, however, a great deal of variation in reported maximum ingestion rates (MIR), maximum filtering
rates (MFR) and ILC values for Daphnia magna. ILC values from the few laboratory studies of freshwater copepods ranged between 0.5 to 2.8 × 103 μg 1−1, and was higher than the ILC value of approximately 0.2 × 103 μg l−1 calculated for field populations of D. minutus. Generally, there was considerable agreement among laboratory studies regarding the shape of grazing-rate and ingestion-rate
curves when data were converted to similar units and presented on standardized scales. 相似文献
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《Saudi Journal of Biological Sciences》2017,24(4):864-874
Programed cell death resembles a real nature active defense in Datura metel against TMV after three days of virus infection. This adaptive plant immune response was quantitatively assessed against Tomato Mosaic Virus infection by the following physiological markers; Chlorophyll-a (mg/g), Chlorophyll-b (mg/g), total protein (mg/g), hydrogen peroxide H2O2 (μmol/100 mg), DNA (μg/100 mg), RNA (μg/100 mg), Salicylic acid (μg/g), and Comet Assays. Parameters were assessed for asymptomatic healthy and symptomatic infected detached leaves. The results indicated H2O2 and Chlorophyll-a as the most potential parameters. Chlorophyll-a was considered the only significant predictor variant for the H2O2 dependent variant with a P value of 0.001 and R-square of 0.900. The plant immune response was measured within three days of virus infection using the cutoff value of H2O2 (⩽1.095 μmol/100 mg) and (⩽3.201 units) for the tail moment in the Comet Assay. Their percentage changes were 255.12% and 522.40% respectively which reflects the stress of virus infection in the plant. Moreover, H2O2 showed 100% specificity and sensitivity in the symptomatic infected group using the receiver-operating characteristic (ROC). All tested parameters in the symptomatic infected group had significant correlations with twenty-five positive and thirty-one negative correlations where the P value was <0.05 and 0.01. Chlorophyll-a parameter had a crucial role of highly significant correlation between total protein and salicylic acid. Contrarily, this correlation with tail moment unit was (r = −0.930, P < 0.01) where the P value was <0.01. The strongest significant negative correlation was between Chlorophyll-a and H2O2 at P < 0.01, while moderate negative significant correlation was seen for Chlorophyll-b where the P value < 0.05. The present study discloses the secret of the three days of rapid transient production of activated oxygen species (AOS) that was enough for having potential quantitative physiological parameters for defensive plant response toward the virus. 相似文献