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71.
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures 总被引:32,自引:0,他引:32
Brünger AT 《Nature》1992,355(6359):472-475
The determination of macromolecular structure by crystallography involves fitting atomic models to the observed diffraction data. The traditional measure of the quality of this fit, and presumably the accuracy of the model, is the R value. Despite stereochemical restraints, it is possible to overfit or 'misfit' the diffraction data: an incorrect model can be refined to fairly good R values as several recent examples have shown. Here I propose a reliable and unbiased indicator of the accuracy of such models. By analogy with the cross-validation method of testing statistical models I define a statistical quantity (R(free) (T) that measures the agreement between observed and computed structure factor amplitudes for a 'test' set of reflections that is omitted in the modelling and refinement process. As examples show, there is a high correlation between R(free) (T) and the accuracy of the atomic model phases. This is useful because experimental phase information is usually inaccurate, incomplete or unavailable. I expect that R(free) (T) will provide a measure of the information content of recently proposed models of thermal motion and disorder, time-averaging and bulk solvent. 相似文献
72.
M. T. Santini R. Masella A. Cantafora S. W. Peterson 《Cellular and molecular life sciences : CMLS》1992,48(1):36-39
We have recently demonstrated, using electron paramagnetic resonance (EPR) spectroscopy, that insulin receptor internalization in response to insulin incubation (down-regulation) in human erythrocytes is accompanied by a transient decrease in membrane order, as measured by the 2T order parameter. Since membrane lipids play such an important role in receptor internalization, we investigated the possible effects that an alteration of the normally-occurring lipid profile might have on down-regulation and the concomitant transient decrease in membrane order. Consequently, human erythrocytes enriched with cholesterol and erythrocytes from cirrhotic patients were examined, because both of these groups of cells have a higher cholesterol/phospholipid molar ratio (CH/PL) than controls. The 5-nitroxystearate spin label, which inserts into the lipid bilayer of cell membranes, was used to monitor changes in 2T for a 3-h period at 37°C. We report here that both cholesterol-enriched and cirrhotic erythrocytes do not down-regulate, as demonstrated by binding assays, and that they do not show the typical transient decrease in membrane order observed in controls. The results seem to indicate that a more ordered membrane inhibits internalization of the insulin receptor in erythrocytes, and that an increase in membrane disorder is necessary for insulin receptor down-regulation. 相似文献
73.
A E Davis K Aulak R B Parad H P Stecklein E Eldering C E Hack J Kramer R C Strunk J Bissler F S Rosen 《Nature genetics》1992,1(5):354-358
Heterozygosity for a mutant dysfunctional C1 inhibitor protein, a member of the serine proteinase inhibitor (serpin) superfamily, results in type II hereditary angioneurotic oedema. We identified a "hinge" region mutation in C1 inhibitor with a Val to Glu replacement at P14 Val-432. Recombinant C1 inhibitors P10 Ala-->Thr and P14Val-->Glu did not form stable complexes with fluid phase C1s or kallikrein. The P14 Val-->Glu mutant, however, was cleaved to a 96K form by C1s, while the P10 Ala-->Thr mutant was not. The recombinant P10 mutant also did not complex with C1s, kallikrein or beta-factor Xlla-Sepharose. The two mutations, therefore, result in dysfunction by different mechanisms: in one (P14 Val-->Glu), the inhibitor is converted to a substrate, while in the other (P10 Ala-->Thr), interaction with target protease is blocked. 相似文献
74.
D. Porquet M. Appel T. Fournier O. Bertaux D. Biou J. Féger 《Cellular and molecular life sciences : CMLS》1992,48(3):257-261
Both in vivo and in vitro models have certain disadvantages for the study of the chronic hepatotoxicity of drugs. The aim of this work was to evaluate a new approach based on an in vivo/in vitro model. After chronic in vivo treatment of rats with Vincamine and Vindeburnol (an eburnamenine derivative which exhibits hepatotoxic properties in man) liver cells were isolated, and functional and metabolic disorders (metabolic utilization of fructose and protein biosynthesis) were studied to determine injury. The results showed no modification of blood parameters, but a direct relationship between the dose of Vindeburnol administered in vivo and the metabolic disorders observed in vitro, evidencing the high sensitivity and reliability of this model. 相似文献
75.
76.
R. Wiesendanger B. Martinoni T. Boller D. Arigoni 《Cellular and molecular life sciences : CMLS》1986,42(2):207-209
Summary Under the action of the appropriate synthase from ripe tomatoes a 11 mixture of (3S, 4R)-[3,4-2H2] and (3R, 4S)-[3,4-2H2]-(2S)-adenosylmethionine is transformed into a 11 mixture of the two meso forms of [2H2]-1-aminocyclopropanecarboxylic acid, a result which proves the operation of an inversion mechanism and which is consistent with direct nucleophilic displacement of the leaving group in the substrate. 相似文献
77.
S. Suzuki S. Kurasawa H. Kitai M. Oba S. Komatsu K. Yoda R. Iizuka 《Cellular and molecular life sciences : CMLS》1986,42(7):795-798
Summary Porcine or human follicular fluid inhibited the spontaneous maturation of isolated hamster oocytes in vitro during the first 1.5 h of culture. Moreover, the presence of 50% follicular fluid combined with 100 M dbcAMP cooperatively reduced the incidence of germinal vesicle breakdown. The addition of FSH also inhibited the resumption of meiosis, and the presence of LH did not overcome the inhibitory effects of follicular fluid and tended to impede isolated hamster oocyte maturation in vitro. 相似文献
78.
79.
Evolution of the atmosphere and oceans 总被引:1,自引:0,他引:1
The residence times of most constituents of the atmosphere and oceans are small fractions of the age of the Earth and, in general, their rate of output has been nearly equal to their rate of input. We are disturbing a number of these dynamic equilibria quite severely. The mineralogy of marine evaporites rules out drastic changes in the composition of sea water during the last 900 Myr. The chemistry of soils formed more than 1,000 Myr ago suggests that the atmosphere then contained significantly more CO2 and less O2 than at present. Hydrogen peroxide may well have been the principal oxidant and formaldehyde the main reductant in rain water between 3,000 and 1,000 Myr ago. Major changes in atmospheric chemistry since that time are almost certainly related to the evolution of the biosphere. 相似文献
80.
Secular variation in carbon isotope ratios from Upper Proterozoic successions of Svalbard and East Greenland 总被引:12,自引:0,他引:12
Analyses of stratigraphically continuous suites of samples from Upper Proterozoic sedimentary successions of East Greenland, Spitsbergen and Nordaustlandet (Svalbard) provide an approximation to the secular variation in carbon isotope ratios during a geologically and biologically important period of change from around 900 million years ago to the beginning of the Cambrian period. Late Riphean carbonates and organic material show a stratigraphically useful pattern of enrichment in 13C relative to Phanerozoic or earlier Proterozoic samples. Isotopic compositions of isolated samples from other localities are consistent with a worldwide extended interval of enhanced organic burial and consequent net survival of oxidized material, probably O2, just before the initial radiation of metazoans. 相似文献