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1.
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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Biological soil crusts (BSCs, or biocrusts) have important positive ecological functions such as erosion control and soil fertility improvement, and they may also have negative effects on soil moisture in some cases. Simultaneous discussions of the two-sided impacts of BSCs are key to the rational use of this resource. This study focused on the contribution of BSCs while combining with specific types of vegetation to erosion reduction and their effects on soil moisture, and it addressed the feasibility of removal or raking disturbance. Twelve plots measuring 4 m × 2 m and six treatments (two plots for each) were established on a 15° slope in a small watershed in the Loess Plateau using BSCs, bare land (as a control, BL), Stipa bungeana Trin. (STBU), Caragana korshinskii Kom. (CAKO), STBU planted with BSCs (STBU+BSCs) and CAKO planted with BSCs (CAKO+BSCs). The runoff, soil loss and soil moisture to a depth of 3 m were measured throughout the rainy season (from June to September) of 2010. The results showed that BSCs significantly reduced runoff by 37.3% and soil loss by 81.0% and increased infiltration by 12.4% in comparison with BL. However, when combined with STBU or CAKO, BSCs only made negligible contributions to erosion control (a runoff reduction of 7.4% and 5.7% and a soil loss reduction of 0.7% and 0.3%). Generally, the soil moisture of the vegetation plots was lower in the upper layer than that of the BL plots, although when accompanied with a higher amount of infiltration, this soil moisture consumption phenomenon was much clearer when combining vegetation with BSCs. Because of the trivial contributions from BSCs to erosion control and the remaining exacerbated consumption of soil water, moderate disturbance by BSCs should be considered in plots with adequate vegetation cover to improve soil moisture levels without a significant erosion increase, which was implied to be necessary and feasible. 相似文献
4.
Wang Ting-Ting Zhu Chen-Ye Zheng Shuang Meng Cai-Cai Wang Tian-Tian Meng Dan-Hua Li Yi-Jun Zhu Hao-Miao Wang Feng-Shan Sheng Ju-Zheng 《Applied microbiology and biotechnology》2018,102(11):4785-4797
Applied Microbiology and Biotechnology - Avibacterium paragallinarum is a Gram-negative bacterium that causes infectious coryza in chicken. It was reported that the capsule polysaccharides... 相似文献
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Yibao Ma Yuanxi Xu Bryan D. Yestrepsky Roderick J. Sorenson Meng Chen Scott D. Larsen Hongmin Sun 《PloS one》2012,7(10)
Staphylococcus aureus is a major human pathogen and one of the more prominent pathogens causing biofilm related infections in clinic. Antibiotic resistance in S. aureus such as methicillin resistance is approaching an epidemic level. Antibiotic resistance is widespread among major human pathogens and poses a serious problem for public health. Conventional antibiotics are either bacteriostatic or bacteriocidal, leading to strong selection for antibiotic resistant pathogens. An alternative approach of inhibiting pathogen virulence without inhibiting bacterial growth may minimize the selection pressure for resistance. In previous studies, we identified a chemical series of low molecular weight compounds capable of inhibiting group A streptococcus virulence following this alternative anti-microbial approach. In the current study, we demonstrated that two analogs of this class of novel anti-virulence compounds also inhibited virulence gene expression of S. aureus and exhibited an inhibitory effect on S. aureus biofilm formation. This class of anti-virulence compounds could be a starting point for development of novel anti-microbial agents against S. aureus. 相似文献
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The garlic stalk is a byproduct of garlic production and normally abandoned or burned, both of which cause environmental pollution. It is therefore appropriate to determine the conditions of efficient decomposition, and equally appropriate to determine the impact of this decomposition on soil properties. In this study, the soil properties, enzyme activities and nutrient dynamics associated with the decomposition of garlic stalk at different temperatures, concentrations and durations were investigated. Stalk decomposition significantly increased the values of soil pH and electrical conductivity. In addition, total nitrogen and organic carbon concentration were significantly increased by decomposing stalks at 40°C, with a 5∶100 ratio and for 10 or 60 days. The highest activities of sucrase, urease and alkaline phosphatase in soil were detected when stalk decomposition was performed at the lowest temperature (10°C), highest concentration (5∶100), and shortest duration (10 or 20 days). The evidence presented here suggests that garlic stalk decomposition improves the quality of soil by altering the value of soil pH and electrical conductivity and by changing nutrient dynamics and soil enzyme activity, compared to the soil decomposition without garlic stalks. 相似文献
9.
Shu-Qun Liu Yan Tao Zhao-Hui Meng Yun-Xin Fu Ke-Qin Zhang 《Journal of molecular modeling》2011,17(2):289-300
The native serine protease proteinase K binds two calcium cations. It has been reported that Ca2+ removal decreased the enzyme’s thermal stability and to some extent the substrate affinity, but has discrepant effects on
catalytic activity of the enzyme. Molecular dynamics simulations were performed on the Ca2+-bound and Ca2+-free proteases to investigate the mechanism by which the calciums affect the structural stability, molecular motions, and
catalytic activity of proteinase K. Very similar structural properties were observed between these two forms of proteinase
K during simulations; and several long-lived hydrogen bonds and salt bridges common to both forms of proteinase K were found
to be crucial in maintaining the local conformations around these two Ca2+ sites. Although Ca2+ removal enhanced the overall flexibility of proteinase K, the flexibility in a limited number of segments surrounding the
substrate-binding pockets decreased. The largest differences in the equilibrium structures of the two simulations indicate
that, upon the removal of Ca2+, the large concerted motion originating from the Ca1 site can transmit to the substrate-binding regions but not to the catalytic
triad residues. In conjunction with the large overlap of the essential subspaces between the two simulations, these results
not only provide insight into the dynamics of the underlying molecular mechanism responsible for the unchanged enzymatic activity
as well as the decreased thermal stability and substrate affinity of proteinase K upon Ca2+ removal, but also complement the experimentally determined structural and biochemical data. 相似文献