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21.
An accurate solvation model is essential for computer modeling of protein folding and other biomolecular self-assembly processes. Compared to explicit solvent models, implicit solvent models, such as the Poisson-Boltzmann (PB) with solvent accessible surface area model (PB/SA), offer a much faster speed—the most compelling reason for the popularity of these implicit solvent models. Since these implicit solvent models typically use empirical parameters, such as atomic radii and the surface tensions, an optimal fit of these parameters is crucial for the final accuracy of properties such as solvation free energy and folding free energy. In this paper, we proposed a combined approach, namely SD/GA, which takes the advantage of both local optimization with the steepest descent (SD), and global optimization with the genetic algorithm (GA), for parameters optimization in multi-dimensional space. The SD/GA method is then applied to the optimization of solvation parameters in the non-polar cavity term of the PB/SA model. The results show that the newly optimized parameters from SD/GA not only increase the accuracy in the solvation free energies for ~200 organic molecules, but also significantly improve the free energy landscape of a β-hairpin folding. The current SD/GA method can be readily applied to other multi-dimensional parameter space optimization as well. 相似文献
22.
Andrew P. Norgan Brian A. Davies Ishara F. Azmi Andreas S. Schroeder Johanna A. Payne Gregory M. Lynch Zhaohui Xu David J. Katzmann 《The Journal of biological chemistry》2013,288(36):26147-26156
The endosomal sorting complexes required for transport (ESCRTs) impact multiple cellular processes including multivesicular body sorting, abscission, and viral budding. The AAA-ATPase Vps4 is required for ESCRT function, and its full activity is dependent upon the co-factor Vta1. The Vta1 carboxyl-terminal Vta1 SBP1 Lip5 (VSL) domain stimulates Vps4 function by facilitating oligomerization of Vps4 into its active state. Here we report the identification of the Vps4 stimulatory element (VSE) within Vta1 that is required for additional stimulation of Vps4 activity in vitro and in vivo. VSE activity is autoinhibited in a manner dependent upon the unstructured linker region joining the amino-terminal microtubule interacting and trafficking domains and the carboxyl-terminal VSL domain. The VSE is also required for Vta1-mediated Vps4 stimulation by ESCRT-III subunits Vps60 and Did2. These results suggest that ESCRT-III binding to the Vta1 microtubule interacting and trafficking domains relieves linker region autoinhibition of the VSE to produce maximal activation of Vps4 during ESCRT function. 相似文献
23.
Single-Molecule Force Spectroscopy Study on the Mechanism of RNA Disassembly in Tobacco Mosaic Virus
Ningning Liu Ying Chen Bo Peng Yuan Lin Qian Wang Zhaohui Su Wenke Zhang Hongbin Li Jiacong Shen 《Biophysical journal》2013,105(12):2790-2800
To explore the disassembly mechanism of tobacco mosaic virus (TMV), a model system for virus study, during infection, we have used single-molecule force spectroscopy to mimic and follow the process of RNA disassembly from the protein coat of TMV by the replisome (molecular motor) in vivo, under different pH and Ca2+ concentrations. Dynamic force spectroscopy revealed the unbinding free-energy landscapes as that at pH 4.7 the disassembly process is dominated by one free-energy barrier, whereas at pH 7.0 the process is dominated by one barrier and that there exists a second barrier. The additional free-energy barrier at longer distance has been attributed to the hindrance of disordered loops within the inner channel of TMV, and the biological function of those protein loops was discussed. The combination of pH increase and Ca2+ concentration drop could weaken RNA-protein interactions so much that the molecular motor replisome would be able to pull and disassemble the rest of the genetic RNA from the protein coat in vivo. All these facts provide supporting evidence at the single-molecule level, to our knowledge for the first time, for the cotranslational disassembly mechanism during TMV infection under physiological conditions. 相似文献
24.
L Xiaoping Y Zhibin L Wenjuan W Zeyou X Gang L Zhaohui Z Ying W Minghua L Guiyuan 《Cell death & disease》2013,4(6):e675
Epigenetic mechanisms have important roles in carcinogenesis. We certified that the mRNA translation-related gene cytoplasmic polyadenylation element-binding protein 1 (CPEB1) is hypomethylated and overexpressed in glioma cells and tissues. The knockdown of CPEB1 reduced cell senescence by regulating the expression or distribution of p53 in glioma cells. CPEB1 is also regulated directly by the tumor suppressor miR-101, a potential marker of glioma. It is known that the histone methyltransferase enhancer of zeste homolog 2 (EZH2) and embryonic ectoderm development (EED) are direct targets of miR-101. We demonstrated that miR-101 downregulated the expression of CPEB1 through reversing the methylation status of the CPEB1 promoter by regulating the presence on the promoter of the methylation-related histones H3K4me2, H3K27me3, H3K9me3 and H4K20me3. The epigenetic regulation of H3K27me3 on CPEB1 promoter is mediated by EZH2 and EED. EZH2 has a role in the regulation of H3K4me2. Furthermore, the downregulation of CPEB1 induced senescence in a p53-dependent manner. 相似文献
25.
26.
Paecilomyces variotii extracts (ZNC) enhance plant immunity and promote plant growth 总被引:1,自引:0,他引:1
Lu Chongchong Liu Haifeng Jiang Depeng Wang Lulu Jiang Yanke Tang Shuya Hou Xuwen Han Xinyi Liu Zhiguang Zhang Min Chu Zhaohui Ding Xinhua 《Plant and Soil》2019,445(1-2):383-396
Plant and Soil - There are growing concerns regarding the restoration of karst rocky desertification (KRD) areas. However, the soil conditions and its residing microorganisms, which are essential... 相似文献
27.
Nian Wei Yan Zhang Fan Wu Ziwei Shen Huijun Ru Ling Liu Zhaohui Ni 《Zeitschrift fur angewandte Ichthyologie》2019,35(3):789-792
The length–weight relationships (LWRs) for 15 fish species from the Three Gorges Reservoir (TGR) were described in this paper. Specimens were collected using gill nets (mesh size: 6, 8, 10, 12 cm), cage net (mesh size: 1 cm), benthic fyke net (mesh size: 1 cm), hook longlines (80 m long, 3 barbless hooks per meter line) and electrofishing (power: 1,500 w; distance of electrodes: 1–2 m; water depth: 0.2–1.0 m; water area: 1–2 m2; catch by dip net [mesh size: 0.4 cm]) at four sections of the TGR, monthly in June–August and October–November in 2017 and 2018. The first LWR reference for Zacco acutipinnis (Bleeker, 1871), Discogobio brachyphysallidos Huang, 1989, Squalidus nitens (Günther, 1873), Leptobotia pellegrini Fang, 1936, Sinibotia reevesae (Chang, 1944), Pseudobagrus tenuifurcatus (Nichols, 1931), Pseudobagrus medianalis (Regan, 1904), Liobagrus marginatoides (Wu, 1930), Glyptothorax fokiensis (Rendahl, 1925), and Ctenogobius szechuanensis (Liu, 1940) and new maximum total length for 12 species are provided. 相似文献
28.
Shanglun Xie Shanshan Han Zhen Qu Fei Liu Jingzhen Li Shanshan Yu James Reilly Jiayi Tu Xiliang Liu Zhaojing Lu Xuebin Hu Tinsae Assefa Yimer Yayun Qin Yuwen Huang Yuexia Lv Tao Jiang Xinhua Shu Zhaohui Tang Mugen Liu 《生物化学与生物物理学报:疾病的分子基础》2019,1865(6):1273-1283
Mutations in the photoreceptor cell-specific nuclear receptor gene Nr2e3 increased the number of S-cone photoreceptors in human and murine retinas and led to retinal degeneration that involved photoreceptor and non-photoreceptor cells. The mechanisms underlying these complex phenotypes remain unclear. In the hope of understanding the precise role of Nr2e3 in photoreceptor cell fate determination and differentiation, we generated a line of Nr2e3 knockout zebrafish using CRISPR technology. In these Nr2e3-null animals, rod precursors undergo terminal mitoses but fail to differentiate as rods. Rod-specific genes are not expressed and the outer segment (OS) fails to form. Formation and differentiation of cone photoreceptors is normal. Specifically, there is no increase in the number of UV-cone or S-cone photoreceptors. Laminated retinal structure is maintained. After normal development, L-/M-cones selectively degenerate, with progressive shortening of OS that starts at age 1 month. The amount of cone phototransduction proteins is concomitantly reduced, whereas UV- and S-cones have normal OS lengths even at age 10 months. In vitro studies show Nr2e3 synergizes with Crx and Nrl to enhance rhodopsin gene expression. Nr2e3 does not affect cone opsin expression. Our results extend the knowledge of Nr2e3's roles and have specific implications for the interpretation of the phenotypes observed in human and murine retinas. Furthermore, our model may offer new opportunities in finding treatments for enhanced S-cone syndrome (ESCS) and other retinal degenerative diseases. 相似文献
29.
30.
Jun Ren Zhaohui Pei Xiyao Chen Melissa J. Berg Khalid Matrougui Qing-hua Zhang Yingmei Zhang 《生物化学与生物物理学报:疾病的分子基础》2019,1865(1):206-217
Insulin resistance leads to myocardial contractile dysfunction and deranged autophagy although the underlying mechanism or targeted therapeutic strategy is still lacking. This study was designed to examine the impact of inhibition of the cytochrome P450 2E1 (CYP2E1) enzyme on myocardial function and mitochondrial autophagy (mitophagy) in an Akt2 knockout model of insulin resistance. Adult wild-type (WT) and Akt2?/? mice were treated with the CYP2E1 inhibitor diallyl sulfide (100?mg/kg/d, i.p.) for 4?weeks. Cardiac geometry and function were assessed using echocardiographic and IonOptix systems. Western blot analysis was used to evaluate autophagy, mitophagy, inducible NOS (iNOS), and the NLRP3 inflammasome, a multi-protein intracellular pattern recognition receptor complex. Akt2 deletion triggered insulin resistance, compromised cardiac contractile and intracellular Ca2+ property, mitochondrial ultrastructural damage, elevated O2– production, as well as suppressed autophagy and mitophagy, accompanied with elevated levels of NLRP3 and iNOS, the effects of which were significantly attenuated or ablated by diallyl sulfide. In vitro studies revealed that the NLRP3 activator nigericin nullified diallyl sulfide-offered benefit against Akt2 knockout on cardiomyocyte mechanical function and mitophagy (using Western blot and colocalization of GFP-LC3 and MitoTracker Red). Moreover, inhibition of iNOS but not mitochondrial ROS production attenuated Akt2 deletion-induced activation of NLRP3, substantiating a role for iNOS-mediated NLRP3 in insulin resistance-induced changes in mitophagy and cardiac dysfunction. In conclusion, these data depict that insulin resistance through CYP2E1 may contribute to the pathogenesis of myopathic changes including myocardial contractile dysfunction, oxidative stress and mitochondrial injury, possibly through activation of iNOS and NLRP3 signaling. 相似文献