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131.
This study aimed to assess the anthelmintic activity of methanol extracts from Merremia vitifolia stems using a combination approach encompassing experimental, in vitro, and in silico evaluations. Despite the well-recognized pharmacological properties of M. vitifolia, its potential as an anthelmintic agent remained unexplored. This plant's anthelmintic potential was assessed on adult earthworms (Pheretima posthuma), revealing a dose-dependent reduction in spontaneous motility leading to paralysis and eventual mortality. The most effective dose of M. vitifolia (200 mg/ml) for anthelmintic effects on Pheretima posthuma was identified. Complementary in silico investigations were also conducted, employing Autodock PyRx 0.8 for docking studies of reported M. vitifolia compounds. Notably, quercetin emerged as a promising candidate with superior binding energies against β-tubulin (−8.3 Kcal/mol). Moreover, this comprehensive research underlines the anthelmintic potential of Merremia vitifolia stem extract and highlights quercetin as a noteworthy compound for further investigation in the quest for novel anthelmintic agents.  相似文献   
132.
We demonstrate the use of molecular dynamics and molecular mechanics methods to calculate properties and behavior of metal-chelate complexes that can be used as MRI contrast agents. Static and dynamic properties of several known agents were calculated and compared with experiment. We calculated the static properties such as the q-values (number of inner shell waters) and binding distances of chelate atoms to the metal ion for a set of chelates with known X-ray structure. The dynamic flexibility of the chelate arms was also calculated. These computations were extended to a series of exploratory chelate structures in order to estimate their potential as MRI contrast agents. We have also calculated for the first time the NMR relaxivity of an MRI contrast agent using a long (5 nsec) molecular dynamics simulation. Our predictions are promising enough that the method should prove useful for evaluating novel candidate compounds before they are synthesized. One novel static property, the projected area of chelate atoms onto a virtual surface centered on the metal ion (gnomonic projection), was found to give an effective measure of how well the chelate atoms use the free space around the metal ion.  相似文献   
133.
The completion of the genome sequence of the budding yeast Saccharomyces cerevisiae marks the dawn of an exciting new era in eukaryotic biology that will bring with it a new understanding of yeast, other model organisms, and human beings. This body of sequence data benefits yeast researchers by obviating the need for piecemeal sequencing of genes, and allows researchers working with other organisms to tap into experimental advantages inherent in the yeast system and learn from functionally characterized yeast gene products which are their proteins of interest. In addition, the yeast post-genome sequence era is serving as a testing ground for powerful new technologies, and proven experimental approaches are being applied for the first time in a comprehensive fashion on a complete eukaryotic gene repertoire.  相似文献   
134.
Summary The ability of time-averaged restrained molecular dynamics (TARMD) to escape local low-energy conformations and explore conformational space is compared with conventional simulated-annealing methods. Practical suggestions are offered for performing TARMD calculations with ligand-receptor systems, and are illustrated for the complex of the immunosuppressant FK506 bound to Q50R,A95H,K98I triple mutant FKBP-13. The structure of 13C-labeled FK506 bound to triple-mutant FKBP-13 was determined using a set of 87 NOE distance restraints derived from HSQC-NOESY experiments. TARMD was found to be superior to conventional simulated-annealing methods, and produced structures that were conformationally similar to FK506 bound to wild-type FKBP-12. The individual and combined effects of varying the NOE restraint force constant, using an explicit model for the protein binding pocket, and starting the calculations from different ligand conformations were explored in detail.Abbreviations DG distance geometry - dmFKBP-12 double-mutant (R42K,H87V) FKBP-12 - FKBP-12 FK506-binding protein (12 kDa) - FKBP-13 FK506-binding protein (13 kDa) - HSQC heteronuclear single-quantum coherence - KNOE force constant (penalty) for NOE-derived distance restraints - MD molecular dynamics - NOE nuclear Overhauser effect - SA simulated annealing - TARMD molecular dynamics with time-averaged restraints - tmFKBP-13 triple-mutant (Q50R,A95H,K98I) FKBP-13 - wtFKBP-12 wild-type FKBP-12  相似文献   
135.
    
Summary The IASRYDQL synthetic octapeptide (250–257) of the Leishmania major surface glycoprotein gp63 efficiently inhibits parasite attachment to the macrophage receptors in in vitro experiments, and the SRYD-containing tetrapeptide mimics antigenically and functionally the RGDS sequence of fibronectin. The conformational properties of the octapeptide were investigated in dimethylsulfoxide (DMSO) with the combined use of NMR data (vicinal coupling constants, nuclear Overhauser effects (NOEs) and temperature coefficient values), molecular modeling by energy minimization and molecular dynamics. The structure is characterized by the high occurrence, exceeding 95%, of the Arg-Asp side-chain-side-chain ionic interaction, which plays a key role in the backbone folding through a distorted type-I -turn involving the Gln256-NH to Arg253-CO hydrogen bond.  相似文献   
136.
Summary The influence of water binding on the conformational dynamics of the cyclic decapeptide antamanide dissolved in the model lipophilic environment chloroform is investigated by NMR relaxation measurements. The water-peptide complex has a lifetime of 35 s at 250 K, which is longer than typical lifetimes of water-peptide complexes reported in aqueous solution. In addition, there is a rapid intracomplex mobility that probably involves librational motions of the bound water or water molecules hopping between different binding sites. Water binding restricts the flexibility of antamanide. The experimental findings are compared with GROMOS molecular dynamics simulations of antamanide with up to eight bound water molecules. Within the simulation time of 600 ps, no water molecule leaves the complex. Additionally, the simulations show a reduced flexibility for the complex in comparison with uncomplexed antamanide. Thus, there is a qualitative agreement between the experimental NMR results and the computer simulations.  相似文献   
137.
Summary A new program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for the analysis of MD trajectories, OPAL affords high efficiency and flexibility for work with diferent force fields, and offers a user-friendly interface and extensive trajectory analysis capabilities. Salient features are computational speeds of up to 1.5 GFlops on vector supercomputers such as the NEC SX-3, ellipsoidal boundaries to reduce the system size for studies in explicit solvents, and natural treatment of the hydrostatic pressure. Practical applications of OPAL are illustrated with MD simulations of pure water, energy minimization of the NMR structure of the mixed disulfide of a mutant E. coli glutaredoxin with glutathione in different solvent models, and MD simulations of a small protein, pheromone Er-2, using either instantaneous or time-averaged NMR restraints, or no restraints.Abbreviations D diffusion constant in cm2/s - Er-2 pheromone 2 from Euplotes raikovi - GFlop one billion floating point operations per second - Grx(C14S)-SG mixed disulfide between a mutant E. coli glutaredoxin, with Cys14 replaced by Ser, and glutathione - MD molecular dynamics - NOE nuclear Overhauser enhancement - rmsd root-mean-square deviation - density in g/cm3  相似文献   
138.
A subtractive-hybridization technique, combined with differential screenings and subsequent whole mount in situ hybridization (ISH) reactions, was used to isolate novel cDNA clones representing developmentally-regulated genes of carp. Small-scale differential screenings of an oocyte and a segmentation-stage cDNA library using oocyte-specific and segmentation stage-specific enriched probes, yielded 75 positive clones. ISH screening showed that 65% (15) of the oocyte-stage clones and 50% (26) of the segmentation-stage clones were indeed stage-specific. Partial sequence analysis suggests that approximately 65% of the 41 stage-specific clones represent novel genes. In addition, an Otxl clone was isolated. Two novel clones and the Otxl clone are of special interest for developmental studies. The clones represent genes that are locally expressed during embryonic development. The expression patterns of Otxl and one of the novel clones suggest functions in specification of the anterior-posterior axis. The three clones provide molecular markers for the study of gastrulation and the patterning of the a-p axis in teleosts.  相似文献   
139.
采用逆转录聚合酶链反应(RT-PCR)从广东省一例慢性丙型肝炎病人血清中获得丙型肝炎病毒(HCV)5'端非编码区(5'NCR)302bp的cDNA片段,经补齐和提纯后插入pUC19质粒,获得的重组体pUN进行序列测定。将pUN的目的基因亚克隆进体外转录载体pSPORTI多克隆位点的EooRI和PstI切点之间,所得重组体pSN线性化后由T_7RNA多聚酶及SP6RNA多聚酶引导体外转录反应,产物经凝胶电泳及特异引物RT-PCR,证实SP6引导的是正义RNA,T7合成的是反义RNA,其大小分别力429bp和362bp。并证实所得RNA力HCV5'NCRcDNA转录而来。获得的HCV5'NCRcDNA和RNA在常规逆转录和PCR步骤中用于设立有效的模板对照,对消除假用性及评估试剂有重要意义。同时,HCV5'NCR体外转录载体的构建可用于制各RNA探针和反义RNA,改进后还可作为定量PCR的竞争性模板。  相似文献   
140.
以Wistar大鼠肝为材料,确立了一个简便的纯化鼠肝DNA甲基化酶的程序,包括:细胞的超声破碎、去内源核酸、硫酸铵盐析、磷酸纤维素亲和层析、DEAE-SephadexA-50柱层析及SephadexG-150凝胶过滤。用不同浓度聚丙烯酰胺凝胶电泳和孔梯度凝胶电泳检测,纯化后的酶已达电泳均一,且酶的比活力提高112倍。以聚丙烯酰胺孔梯度凝胶电泳测得其天然酶的分子量为365kD,以SDS-聚丙烯酰胺凝胶电泳测得该酶有两种亚基,大亚基为95kD,小亚基为85kD,推测该酶由两个大亚基和两个小亚基组成。  相似文献   
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