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61.
The prediction of transmembrane (TM) helix and topology provides important information about the structure and function of a membrane protein. Due to the experimental difficulties in obtaining a high-resolution model, computational methods are highly desirable. In this paper, we present a hierarchical classification method using support vector machines (SVMs) that integrates selected features by capturing the sequence-to-structure relationship and developing a new scoring function based on membrane protein folding. The proposed approach is evaluated on low- and high-resolution data sets with cross-validation, and the topology (sidedness) prediction accuracy reaches as high as 90%. Our method is also found to correctly predict both the location of TM helices and the topology for 69% of the low-resolution benchmark set. We also test our method for discrimination between soluble and membrane proteins and achieve very low overall false positive (0.5%) and false negative rates (0 to approximately 1.2%). Lastly, the analysis of the scoring function suggests that the topogeneses of single-spanning and multispanning TM proteins have different levels of complexity, and the consideration of interloop topogenic interactions for the latter is the key to achieving better predictions. This method can facilitate the annotation of membrane proteomes to extract useful structural and functional information. It is publicly available at http://bio-cluster.iis.sinica.edu.tw/~bioapp/SVMtop. 相似文献
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Rodriguez-Kern A Gegelashvili M Schousboe A Zhang J Sung L Gegelashvili G 《Neurochemistry international》2003,43(4-5):363-370
64.
Kalthoum Tizaoui Jae Won Yang Keum Hwa Lee Ji Hong Kim Minseok Kim Sojung Yoon Yeonwoo Jung Joon Beom Park Kitae An Hyeok Choi Donggyu Song HyunTaek Jung Seongmin Ahn Taeho Yuh Hee Min Choi Jae Ha Ahn Younjuong Kim Sanghyun Jee Hyeongsun Lee Soohwa Jin Jun-Gu Kang Bohyun Koo Joo Yeop Lee Kyoung Min Min Wonseok Yoo Hyeong Jun Rhyu Yeonjung Yoon Min Ho Lee Sung Eun Kim Jimin Hwang Ai Koyanagi Louis Jacob Seoyeon Park Jae Il Shin Lee Smith 《International journal of biological sciences》2022,18(9):3731
YKL-40, a chitinase-3-like protein 1 (CHI3L1) or human cartilage glycoprotein 39 (HC gp-39), is expressed and secreted by various cell-types including macrophages, chondrocytes, fibroblast-like synovial cells and vascular smooth muscle cells. Its biological function is not well elucidated, but it is speculated to have some connection with inflammatory reactions and autoimmune diseases. Although having important biological roles in autoimmunity, there were only attempts to elucidate relationships of YKL-40 with a single or couple of diseases in the literature. Therefore, in order to analyze the relationship between YKL-40 and the overall diseases, we reviewed 51 articles that discussed the association of YKL-40 with rheumatoid arthritis, psoriasis, systemic lupus erythematosus, Behçet disease and inflammatory bowel disease. Several studies showed that YKL-40 could be assumed as a marker for disease diagnosis, prognosis, disease activity and severity. It is also shown to be involved in response to disease treatment. However, other studies showed controversial results particularly in the case of Behçet disease activity. Therefore, further studies are needed to elucidate the exact role of YKL-40 in autoimmunity and to investigate its potential in therapeutics. 相似文献
65.
Effects of C10‐ and C12‐chain length alkyl analogs of monochamol on attraction of longhorn pine sawyer Monochamus saltuarius (Coleoptera: Cerambycidae) 下载免费PDF全文
Sung‐Min Lee Do Kyung Hong Sei‐Heon Jang Kyeong‐Yeoll Lee ChangWoo Lee 《Entomological Research》2018,48(5):446-450
The aggregation pheromone of Monochamus (Coleoptera: Cerambycidae) beetles, 2‐(undecyloxy) ethanol (hereafter referred to as monochamol), has gained considerable attention because of its usefulness in monitoring and population control of pine sawyer beetles. The hydroxyether structural motif is conserved in pheromones of the subfamily Lamiinae of the Cerambycidae. In this study, we investigated the effects of C10‐ and C12‐chain length alkyl analogs of monochamol, 2‐(decyloxy) ethanol and 2‐(dodecyloxy) ethanol, on attracting M. saltuairus in Andong, Gyeongsangbuk‐do, Korea. The C10 and C12 analogs attracted M. saltuarius when used in combination with α‐pinene and ethanol, but the responses of these alkyl chain analogs were lower than those of monochamol. Furthermore, the addition of either C10 or C12 analog to the use of monochamol with α‐pinene and ethanol had no effect on attraction of M. saltuarius, indicating high sensitivity of M. saltuarius to monochanol. Taken together, the results of this study suggest that chemical communication within a Monochamus species depends not only on monochamol, but also on other semiochemicals. 相似文献
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Oxygenation dynamics of sepsis patients undergoing far‐infrared intervention based on near‐infrared spectroscopy 下载免费PDF全文
Kuei‐Hung Chuang Ming‐Lung Chuang Sung‐kien Sia Chia‐Wei Sun 《Journal of biophotonics》2017,10(3):360-366
Near‐infrared spectroscopy (NIRS; continuous wave type) is a noninvasive tool for detecting the relative change of oxyhemoglobin and deoxyhemoglobin. To make this change, intervention methods must be applied. This study determined the hemodynamics of 44 healthy participants and 35 patients with sepsis during exposure to FIR as a novel physical intervention approach. Local microcirculation of their brachioradialis was monitored during exposure and recovery through NIRS. The variations in blood flow and microvascular reaction were determined by conducting paired and unpaired t tests. The oxyhemoglobin levels of the healthy participants increased continuously, even during recovery. In contrast to expextations, the oxyhemoglobin levels of the patients plateaued after only 5 min of FIR illumination. The proposed method has potential applications for ensuring efficient treatment and facilitating doctors in diagnosing the functions of vessels in intensive care units.
68.
Moon Woo Chun Sung Pil Choi Myong Jung Kim Chol Joon Bae Hyung Ryong Moon Hee-Doo Kim 《Nucleosides, nucleotides & nucleic acids》2013,32(4-5):615-616
Abstract Novel 1,3-oxathiolanyl pyrimidine nucleosides with 5-hydroxymethyl substituent were synthesized starting from d-mannose and evaluated for antiviral activities against HIV-1, HSV type 1,2 and HCMV. 相似文献
69.
Regulation of protein phosphorylation in pancreatic acini by cyclic AMP-mediated secretagogues: interaction with carbamylcholine 总被引:1,自引:0,他引:1
The effects on protein phosphorylation in mouse pancreatic acini of cyclic AMP-mediated secretagogues and the Ca2+-mediated agonist carbamylcholine were compared. Under the conditions adopted for the study of protein phosphorylation, carbamylcholine (3 microM) stimulated amylase release from pancreatic acini 6-fold, whereas vasoactive intestinal polypeptide (VIP) (100 nM) and the cyclic AMP analogue 8-bromo-cyclic AMP (1 mM) caused little or no increase in secretion. However, VIP and 8-bromo-cyclic AMP, when added in combination with carbamylcholine, potentiated the stimulation of amylase release to 170-180% of that caused by carbamylcholine alone. As assessed by two-dimensional gel electrophoresis, VIP reproduced four of the ten changes in protein phosphorylation elicited by carbamylcholine, these changes being the increased phosphorylation of one soluble protein and the decreased phosphorylation of three soluble proteins. VIP enhanced the carbamylcholine-induced changes in phosphorylation for three proteins. In addition, VIP increased the phosphorylation of a unique protein of Mr 52,000 and pI 5.66 which was not affected by carbamylcholine. All of the effects on protein phosphorylation exerted by VIP in the presence or absence of carbamylcholine were mimicked by 8-bromo-cyclic AMP. Secretin also reproduced most of the changes in protein phosphorylation caused by VIP, although concentrations of secretin of at least 100-fold higher were required to elicit a maximal response. It is concluded that cyclic AMP-mediated secretagogues alter the phosphorylation of a unique protein as well as of several pancreatic proteins affected by carbamylcholine. Moreover, these effects appear to be mediated primarily by VIP-preferring receptors and may be involved in the synergistic action of VIP to promote carbamylcholine-induced amylase release. 相似文献
70.
A new type of biosorbent was developed for binding anionic precious metals through cross-linking waste biomass Corynebacterium glutamicum with polyethylenimine (PEI). This biomass was evaluated for the removal and recovery of palladium and compared to commercial adsorbents, such as Amberjet 4200 Cl, Lewatit Monoplus TP 214, SPC-100, and SPS-200. The kinetic experiments revealed that the sorption equilibrium was reached with 30 min for the PEI-modified biomass. The maximum uptake of the biosorbent was 176.8 mg/g, which was calculated using the Langmuir model. The Pd(II) maximum uptake exhibited the following order: Amberjet 4200 Cl > Lewatit Monoplus TP 214 > PEI-modified biomass > SPC-100 > SPS-200. Acidified thiourea in 1.0 M HCl was used to desorb Pd(II) from all of the sorbents examined. 相似文献