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41.
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Using functional domain composition and support vector machines for prediction of protein subcellular location 总被引:17,自引:0,他引:17
Proteins are generally classified into the following 12 subcellular locations: 1) chloroplast, 2) cytoplasm, 3) cytoskeleton, 4) endoplasmic reticulum, 5) extracellular, 6) Golgi apparatus, 7) lysosome, 8) mitochondria, 9) nucleus, 10) peroxisome, 11) plasma membrane, and 12) vacuole. Because the function of a protein is closely correlated with its subcellular location, with the rapid increase in new protein sequences entering into databanks, it is vitally important for both basic research and pharmaceutical industry to establish a high throughput tool for predicting protein subcellular location. In this paper, a new concept, the so-called "functional domain composition" is introduced. Based on the novel concept, the representation for a protein can be defined as a vector in a high-dimensional space, where each of the clustered functional domains derived from the protein universe serves as a vector base. With such a novel representation for a protein, the support vector machine (SVM) algorithm is introduced for predicting protein subcellular location. High success rates are obtained by the self-consistency test, jackknife test, and independent dataset test, respectively. The current approach not only can play an important complementary role to the powerful covariant discriminant algorithm based on the pseudo amino acid composition representation (Chou, K. C. (2001) Proteins Struct. Funct. Genet. 43, 246-255; Correction (2001) Proteins Struct. Funct. Genet. 44, 60), but also may greatly stimulate the development of this area. 相似文献
43.
本文综述了小RNA病毒和小DNA病毒的主要结构特征,绘制出了它们的三维结构模型,从中找出了两者间的共同点和差异,为进一步研究两种病毒提供了依据。 相似文献
44.
Zenghong Ma Wei Cai Lei Wang Chenglin Du Weiwei Luo Linyu Niu Shuqing Xue Mengxin Ren Xinzheng Zhang Jingjun Xu 《Plasmonics (Norwell, Mass.)》2016,11(6):1481-1486
Magnetic hot spots, which implies confinements and enhancements of magnetic fields, are demonstrated in graphene junctions (GJs) in the mid-infrared range. The appearance of magnetic hot spots in GJs comes from the conduction currents in the junction. In further, the extinction resonance peaks suffer blue shift, along with the increases in the magnetic fields inside junction area, when the junction width reduces. In opposite to the circumstances for electric field enhancements, neither magnetic field enhancements nor resonance frequency of GJs is perturbed by the intrinsic nonlocal electronic response of graphene. Such nonlocality immunized magnetic enhancement could be explained by the polarization dependent property of nonlocal effect. 相似文献
45.
Dynamic distribution of epidermal growth factor during mouse embryo peri-implantation 总被引:6,自引:0,他引:6
Embryo implantation depends on the synchronized development of the blastocyst and the endometrium. This process is highly controlled by the coordinated action of the steroid hormones: estrogen and progesterone. By autocrine, paracrine or juxtacrine routes, some growth factors or cytokines are involved in this steroidal regulation pathway. Here we report the effects of epidermal growth factor (EGF) on embryo implantation in the mouse, the expression and distribution patterns of EGF protein in the mouse blastocyst, ectoplacental cone (EPC) and peri-implantation uterus on days 1-8 of gestation.By RT-PCR and dot blot, we found that EGF and its receptor (EGFR) are co-expressed in the blastocyst and peri-implantational uteri of pregnant days 2-8 (D2-D8) mice. Injection of EGF antibody into a uterine horn on the third day of pregnancy (D3) significantly reduced the number of mouse embryos that implanted on D8, indicating EGF have a function in the mouse embryo implantation.Further investigation by using indirect immunofluorescence and confocal microscope was made to trace EGF and EGFR protein localization during the mouse embryo implantation. EGF and EGFR are co-localized in the blastocyst, and in the secondary trophoblastic giant cells (SGC) of the EPC. At the pre-implantation stage, the distribution of EGF protein in the mouse uterus changes from epithelium to stroma. On D1 of pregnancy, EGF is mainly distributed in uterine stroma and myometrium. On D2, it is present in the uterine epithelium. On D3, it changes again from the uterine epithelium to the stroma. By D4, EGF is predominantly in the stroma. This dynamic distribution correlates with the proliferation activity of uterine cells at each period. On D6-D8 of embryo implantation, EGF 3 protein accumulates at the uterine mesometrial pole, a region that contributes to the trophoblastic invasiveness and placentation.This temporal and spatial localization of EGF protein in the mouse uterus implicates the cytokine in the regulation of trophoblastic invasiveness and uterine receptiveness. 相似文献
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The thyroid gland synthesizes thyroxine (T4), which passes through the larval tadpole's circulatory system. The enzyme type II iodothyronine deiodinase (D2) converts thyroxine (T4) to the active hormone 3,5,3'-triiodothyronine (T3) in peripheral tissues. An early response to thyroid hormone (TH) in the Xenopus laevis tadpole is the stimulation of cell division in cells that line the brain ventricles, the lumen of the spinal cord, and the limb buds. These cells express constitutively high levels of D2 mRNA. Exogenous T4 induces early DNA synthesis in brain, spinal cord, and limb buds as efficiently as T3. The deiodinase inhibitor iopanoic acid blocks T4- but not T3-induced cell division. At metamorphic climax, both TH-induced cell division and D2 expression decrease in the brain. Then D2 expression appears in late-responding tissues including the anterior pituitary, the intestine, and the tail where cell division is reduced or absent. Therefore, constitutive expression of D2 occurs in the earliest target tissues of TH that will grow and differentiate, while TH-induced expression of D2 takes place in late-responding tissues that will remodel or die. This pattern of constitutive and induced D2 expression contributes to the timing of metamorphic changes in these tissues. 相似文献
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Characterization of the carboxysomal carbonic anhydrase CsoSCA from Halothiobacillus neapolitanus 下载免费PDF全文
Heinhorst S Williams EB Cai F Murin CD Shively JM Cannon GC 《Journal of bacteriology》2006,188(23):8087-8094
In cyanobacteria and many chemolithotrophic bacteria, the CO(2)-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is sequestered into polyhedral protein bodies called carboxysomes. The carboxysome is believed to function as a microcompartment that enhances the catalytic efficacy of RubisCO by providing the enzyme with its substrate, CO(2), through the action of the shell protein CsoSCA, which is a novel carbonic anhydrase. In the work reported here, the biochemical properties of purified, recombinant CsoSCA were studied, and the catalytic characteristics of the carbonic anhydrase for the CO(2) hydration and bicarbonate dehydration reactions were compared with those of intact and ruptured carboxysomes. The low apparent catalytic rates measured for CsoSCA in intact carboxysomes suggest that the protein shell acts as a barrier for the CO(2) that has been produced by CsoSCA through directional dehydration of cytoplasmic bicarbonate. This CO(2) trap provides the sequestered RubisCO with ample substrate for efficient fixation and constitutes a means by which microcompartmentalization enhances the catalytic efficiency of this enzyme. 相似文献