Search PubMed⌕ Search
Home/Archive/PubMed

PubMed · 10739918

Bulk-solvent correction in direct-methods phasing.

D Y Guo·R H Blessing·D A Langs
View original source ↗Export metadata ↓

Abstract

It is shown that for crystals of large proteins at low diffraction resolution, with N approximately 10 000 independent non-H protein atoms and d(min) approximately 8 A, a simple bulk-solvent correction yields the Sayre equation in its classical form, F(h) = q summation operator(k)F(k)F(h - k). In the low-resolution protein case, the proportionality factor becomes q = 1/[( - rho(S))V], where V is the unit-cell volume, rho(S) is the assumed constant electron density in the solvent regions of the crystal and is the average electron density in the protein regions. The classical form of the tangent formula follows from the bulk-solvent-corrected Sayre equation and its validity at low resolution is verified in empirical calculations.

Explore related subjects

AdenosylhomocysteinaseCrystallography, X-RayFourier AnalysisGlyceraldehyde-3-Phosphate DehydrogenasesHydrolasesModels, TheoreticalProbabilityProteinsSolventsJournal ArticleResearch Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

D Y Guo, R H Blessing, D A Langs. 2000. Bulk-solvent correction in direct-methods phasing.. https://doi.org/10.1107/s0907444900000573

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2001

S-adenosylmethionine reverses ilimaquinone's vesiculation of the Golgi apparatus: a fluorescence study on the cellular interactions of ilimaquinone.

The marine sponge metabolite ilimaquinone has a wide range of biological activities, including vesiculation of the Golgi apparatus and interference with intracellular protein trafficking. Some of these activities may arise from ilimaquinone's influence on the activated methyl cycle. To visualize the morphological effects of ilimaquinone on the Golgi apparatus, NRK (normal rat kidney) cells were labeled with fluorescent wheat germ agglutinin and treated with ilimaquinone in the presence and absence of the methylating agent S-adenosylmethionine (SAMe). While ilimaquinone alone fragments the Golgi apparatus, the organelle remains intact when SAMe is included in the incubation mixture. This observation supports ilimaquinone's interaction with methylation enzymes as the cause of Golgi vesiculation. The examination of a fluorescently labeled ilimaquinone analogue in NRK cells suggests that the cellular interactions of ilimaquinone are not localized to the Golgi apparatus.

Adenosylhomocysteinase↗
PubMed2001

E1 mice epilepsy shows genetic polymorphism for S-Adenosyl-L-homocysteine hydrolase.

E1 mice are an animal model of human epilepsy (idiopathic complex partial seizures). We have previously demonstrated abrupt poly(A)(+) RNA expression in liver from 1-day-old E1 mouse [Mita et al., 1991. Devl. Brain Res. 64, 27-35]. In the present study, we constructed a cDNA library of the poly(A)(+) RNA. By analyzing cDNA clones and nucleotide sequences, we found a clone that was homologous to a rat gene of S-adenosyl-L-homocysteine hydrolase (EC 3.3.1.1.) (SAHH) (a key enzyme in the active methyl transfer pathway) and showed the gene polymorphism/RFLP(PstI) between the epileptic strain, E1, and the non-epileptic mother strain, ddY, as indicated in a gel electrophoresis by cleaving 2.6 kb with PstI into 1.9 kb and 0.7 kb fragment bands. F1(E1xddY) showed the heterozygosity. An attempt to determine the mutation on the genomic SAHH gene in the E1 disclosed a single nucleotide polymorphism indicated by a C-->T transition in the 8th intron, by which the PstI site was created. SAHH enzymatic activity in the liver in 1-day-old E1 mice was slight (approximately 10%), and in fact was significantly lower than that of the control ddY. Results suggested that the abrupt primary mRNA transcribed on the SAHH gene in the liver of 1-day-old E1 mice was processed partially or incompletely because of the presence of the point mutation in the intron. Accordingly, poor energy supply by the insufficient SAHH enzymatic activity in the brain postnatally may be responsible for epileptogenesis in this animal model. It is concluded that a single nucleotide SAHH gene polymorphism may be associated with epilepsy in E1 mice.

Adenosylhomocysteinase↗
PubMed2001

Induction of drug metabolism-related enzymes by methylcholanthrene and phenobarbital in transgenic mice carrying human prototype c-Ha-ras gene and their wild type littermates.

Transgenic mice hemizygously carrying human c-Ha-ras proto-oncogene, Tg-rasH2 show very sensitive and facilitated carcinogenicity to various carcinogens. In this study, activities of certain enzymes related to drug metabolism and energy metabolism were measured in microsome and cytosol fractions of livers of Tg-rasH2 mice and their wild type littermates with both sexes treated with 3-methylcholanthrene (MC) and phenobarbital (PB). Aminopyrine N-demethylase activities increased significantly in livers of all mice treated with PB. MC and PB treatments induced significant increases in activities of UDP-glucuronosyltransferase and S-adenosyl homocysteinase compared to those in the non-treated groups in microsome fractions from all mice. In cytosol fractions of livers of all mice, glutathione S-transferase activity was significantly induced in the PB treated groups. There were no significant differences in activities of lactate dehydrogenase, glucose 6-phosphate dehydrogenase, pyruvate kinase and glucose 6-phosphatase related to energy metabolism in livers and kidneys among all mice. Tg-rasH2 mice showed stable activities of enzymes related to drug detoxication and energy metabolism similar to those of non-transgenic mice. These results suggest that the human c-Ha-ras transgene may not affect drug metabolism-related enzymes, and the facilitated carcinogenic response in the Tg-rasH2 mouse is not due to these enzymatic disorders.

Adenosylhomocysteinase↗