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71.
Computer-aided model-building strategies for protein design 总被引:5,自引:0,他引:5
Model-building strategies for protein modification and design are developed. These strategies emphasize simple geometric aspects of protein structure, use local coordinate systems defined at particular residues, and systematically consider a large number of alternative sequences and conformations. We have written a computer program, PROTEUS, to implement these search methods. PROTEUS has been used to find positions where disulfide bonds could be added to the N-terminal domain of the lambda repressor and to predict how a loop on the surface of repressor could be shortened. 相似文献
72.
Characterization and partial purification of a chloride- and calcium-dependent glutamate-binding protein from rat brain 总被引:2,自引:0,他引:2
A glutamate-binding protein was solubilized from rat brain synaptic plasma membranes using sodium cholate. Its properties were characterized after addition of exogenous phospholipids and formation of proteoliposomes. Glutamate binding was dependent on calcium and chloride ions with maximal binding at concentrations of 10(-5) M calcium and 10 mM chloride ions. The effects of the two ions were synergistic rather than additive. In addition, glutamate binding was not affected by inhibitors specific for N-methyl-D-aspartate and kainate receptor subtypes, but was inhibited by quisqualate (Ki = 50 microM) and DL-2-amino-4-phosphonobutyrate (Ki = 1.3 mM). Furthermore, binding was abolished by 100 microM 4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid and 1 mM dithiothreitol. These properties resemble those of the chloride- and calcium-dependent binding site. Starting from the detergent extract, the glutamate-binding protein was purified 123-fold using fractionated ammonium sulfate precipitation, chromatography on hydroxyapatite and on DEAE-Sephacel as sequential purification steps. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified protein fraction showed two major bands migrating with Mr values of 51,000 and 105,000. The properties of the partially purified binding protein were similar to those of the detergent extract. Glutamate binding to the partially purified protein is not due to a sequestration process or product binding to N-acetylated alpha-linked dipeptidase. Thus, the functional role of the binding protein remains to be established. 相似文献
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74.
Nature of sulphated macromolecules in mouse Reichert''s membrane. Evidence for tyrosine O-sulphate in basement-membrane proteins. 总被引:10,自引:2,他引:8 下载免费PDF全文
Seven different sulphated macromolecules were detected in 6 M-guanidinium chloride extracts of metabolically [35S]sulphate-labelled mouse Reichert's membrane and were partially separated. Polypeptide bands of apparent Mr 50 000, 150 000 (tentatively identified as entactin) and 170 000 contained essentially tyrosine O-sulphate as the labelled component. Most of the radioactive sulphate was incorporated into three different proteoglycans, which could be separated by chromatography and density-gradient centrifugation before and after enzymic degradation. Enzymic analysis of glycosaminoglycans and of protein cores by immunoassays identified these components as low-density and high-density forms of heparan sulphate proteoglycan and a high-density form of chondroitin sulphate or dermatan sulphate proteoglycan. 相似文献
75.
Direct photoaffinity labeling with radioactively labeled adenosine 3'-phosphate 5'-phosphosulfate (PAPS) followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography was used to identify PAPS binding proteins in a Golgi membrane preparation of bovine adrenal medulla. [3'-32P]PAPS was synthesized from adenosine 5'-phosphosulfate (APS) and [gamma-32P]ATP using APS kinase prepared from yeast and was purified by reverse-phase ion pair high performance liquid chromatography. Upon irradiation with UV light, [3'-32P]PAPS, as well as [35S]PAPS under conditions which minimized sulfotransferase-catalyzed incorporation of 35SO4 from [35S]PAPS into proteins, bound selectively to a 34-kDa protein of the Golgi membrane preparation. PAPS binding to the 34-kDa protein was strongly inhibited by the presence of 50 microM atractyloside. The 34-kDa PAPS binding protein therefore appears to be similar to the mitochondrial ATP/ADP translocator with regard to both molecular weight and inhibition by atractyloside of adenine nucleotide binding. Photoaffinity labeling will be useful in the purification and functional identification of the 34-kDa protein. 相似文献
76.
Background
Traditional HTML interfaces for input to and output from Bioinformatics analysis on the Web are highly variable in style, content and data formats. Combining multiple analyses can therfore be an onerous task for biologists. Semantic Web Services allow automated discovery of conceptual links between remote data analysis servers. A shared data ontology and service discovery/execution framework is particularly attractive in Bioinformatics, where data and services are often both disparate and distributed. Instead of biologists copying, pasting and reformatting data between various Web sites, Semantic Web Service protocols such as MOBY-S hold out the promise of seamlessly integrating multi-step analysis. 相似文献77.
Wang Y O'Neil SV Wos JA Oppong KA Laufersweiler MC Soper DL Ellis CD Baize MW Fancher AN Lu W Suchanek MK Wang RL Schwecke WP Cruze CA Buchalova M Belkin M De B Demuth TP 《Bioorganic & medicinal chemistry》2007,15(3):1311-1322
Peptidomimetic compounds possessing a caprolactam ring constraint were prepared and evaluated as interleukin-1beta converting enzyme (ICE) inhibitors. The caprolactam ring was used to constrain the P3 region of our inhibitors. This strategy proved to be effective for the synthesis of ICE inhibitors, maintaining key hydrogen bond interactions with the enzyme and invoking a preferred conformation for binding. Several compounds exhibited IC(50) values less than 10nM in a caspase-1 enzyme assay and less than 100nM in a THP-1 whole cell assay measuring IL-1beta production. Two compounds, 13c and 13j, were found to have good oral bioavailability (>50%) in rats when administered as prodrugs. 相似文献
78.
79.
Thomas H. Suchanek 《Journal of experimental marine biology and ecology》1978,31(1):105-120
Information is given to show that Mytilus edulis L. is an important component of exposed rocky coast communities of the Western Hemisphere. It is abundant on the exposed coast of Washington State with a potential distribution extending from + 10.6 ft ( + 3.2 m) down to at least 10 m depth: it is not continuous along this entire gradient. It dominates a band from +10.6 ft down to +9.6 ft ( + 3.2 to + 2.9 m) tidal height where it usually intergrades with its congener M. californianus Conrad. Its upper limit appears to be determined by desiccation stress and the lower probably by competition and or predation.In the mid-intertidal zone, from + 5.6 to + 9.6 ft ( + 1.7 to 2.9 m), where M. californianus is dominant, M. edulis occurs in patches of cleared space which usually form in the M. californianus bed matrix in winter months. Here, it acts as an opportunistic species by colonizing quickly and growing rapidly to reproductive size. It is preyed upon by Thais spp. which prefer it to Mytilus californianus and eventually is eliminated from these patches. It also occurs, sometimes abundantly, in tufts of the red alga Endocladia muricata (Postels & Ruprect) J. Agardh at high and mid-intertidal heights.In low intertidal and subtidal regions, to ≈ 10 m depth, Mytulis edulis can be found in refuges of filamentous or intricately arranged substrata which generally offer protection from predation. These are represented by a wide variety of forms such as hydroids. bryozoans, filamentous algae, coralline algae, and kelp with convoluted holdfasts or complex stipes. 相似文献
80.