| 1. |
- Abrahamson, Magnus
(författare)
-
Cystatins
- 1994
-
Ingår i: Methods in Enzymology. - : Elsevier. - 0076-6879. ; 244, s. 685-700
-
Tidskriftsartikel (refereegranskat)
|
|
| 2. |
|
|
| 3. |
|
|
| 4. |
- Carlström, Göran, et al.
(författare)
-
[7] NMR studies of complex DNA structures : The holliday junction intermediate in genetic recombination
- 1995
-
Ingår i: Methods in Enzymology : Nuclear Magnetic Resonance and Nucleic Acids - Nuclear Magnetic Resonance and Nucleic Acids. - 0076-6879. - 9780121821623 ; 261, s. 163-182
-
Bokkapitel (refereegranskat)abstract
- Publisher Summary This chapter discusses the current status, of using nuclear magnetic resonance (NMR), to study the structure and dynamics of the holliday junction (HJ). Complex deoxyribonucleic acid (DNA) structures (e.g., triplexes, quadruplexes, junctions) pose difficult problems for study, by NMR, relative to the typical DNA duplexes, because they have nonstandard or distorted local conformations and higher molecular weights that give rise to large resonance linewidths and severe 1H spectral overlap. With more atoms in the system, both assignment and structure calculation become more challenging. The HJ, a four-arm DNA crossover structure, is a transient intermediate formed in the course of genetic recombination as well as during other cellular processes, such as replication and telomere resolution. A significant body of evidence has accumulated, indicating that the structure at the junction has a central role, in determining the outcome of these cellular events. For NMR studies, the titration of the four component 16-mer strands to create an equimolar mixture is critical. Gel electrophoresis has shown that titrations based on the standard ultraviolet (UV) estimates of strand concentrations result in significant amounts of residual single-strand, half-complementary duplex, and three-arm structures.
|
|
| 5. |
- Duan, Rui-Dong, et al.
(författare)
-
Sphingolipid hydrolysis enzymes in the gastrointestinal tract
- 1999
-
Ingår i: Methods in Enzymology. - 0076-6879. ; 311, s. 276-286
-
Forskningsöversikt (refereegranskat)abstract
- In the intestinal tract, there are enzymes that hydrolyze both endogenous and exogenous sphingolipids. The alkaline sphingomyelinases (SMase) of the gut and human bile have been most studied, and a major part of this chapter discusses these enzymes. It also discusses studies of ceramidase, glycosylceramidase, and the digestion of dietary sphingolipids. In the intestinal tract, a distinct enzyme that hydrolyzes SM was discovered in 1969 by Nilsson and named “alkaline SMase.” The alkaline SMase activity is localized specifically in the intestinal tract and is not detectable in other organs, including brain, kidney, lung, spleen, testis, pancreas, and stomach, or in milk and urine. The intestinal alkaline SMase is not bacterial in origin as similar activity is found in ordinary mice and germ-free mice and in meconium of human fetus as early as 26 weeks of gestation. In the intestines of different experimental animals, the highest activities were in rat, mouse, pig, and baboon, lower activity in rabbit, and little activity in the guinea pig. Whether these species differences indicate genetic variation or an influence of diet composition on the expression of the enzyme in the intestine is unknown.
|
|
| 6. |
- Hebert, Hans, et al.
(författare)
-
Two-dimensional crystallization and electron crystallography of MAPEG proteins.
- 2005
-
Ingår i: Methods in Enzymology. - 0076-6879 .- 1557-7988. ; 401, s. 161-8
-
Tidskriftsartikel (refereegranskat)abstract
- Members of the membrane-associated proteins in the eicosanoid and glutathione metabolism (MAPEG) superfamily have been subjected to two-dimensional crystallization experiments. A common denominator for successful attempts has been the use of a low lipid/protein ratio in the range of 1-9 (mol/mol). Electron crystallography demonstrated either hexagonal or orthorhombic packing of trimeric protein units. Three-dimensional structure analysis of the MAPEG member microsomal glutathione transferase 1 has shown that the monomer for this protein contains a left-handed bundle of four transmembrane helices. It is likely that this is a common structural motif for MAPEG proteins, because projection maps of all structurally characterized members are very similar.
|
|
| 7. |
- Hohmann, Stefan, 1956, et al.
(författare)
-
Yeast osmoregulation
- 2007
-
Ingår i: Methods in Enzymology. - 1557-7988 .- 0076-6879. ; 428, s. 29-45
-
Tidskriftsartikel (refereegranskat)abstract
- Osmoregulation is the active control of the cellular water balance and encompasses homeostatic mechanisms crucial for life. The osmoregulatory system in the yeast Saccharomyces cerevisiae is particularly well understood. Key to yeast osmoregulation is the production and accumulation of the compatible solute glycerol, which is partly controlled by the high osmolarity glycerol (HOG) signaling system. Genetic analyses combined with studies on protein-protein interactions have revealed the wiring scheme of the HOG signaling network, a branched mitogen-activated protein (MAP) kinase (MAPK) pathway that eventually converges on the MAPK Hog1. Hog1 is activated following cell shrinking and controls posttranscriptional processes in the cytosol as well as gene expression in the nucleus. HOG pathway activity can easily and rapidly be controlled experimentally by extracellular stimuli, and signaling and adaptation can be separated by a system of forced adaptation. This makes yeast osmoregulation suitable for studies on system properties of signaling and cellular adaptation via mathematical modeling. Computational simulations and parallel quantitative time course experimentation on different levels of the regulatory system have provided a stepping stone toward a holistic understanding, revealing how the HOG pathway can combine rigorous feedback control with maintenance of signaling competence. The abundant tools make yeast a suitable model for an integrated analysis of cellular osmoregulation. Maintenance of the cellular water balance is fundamental for life. All cells, even those in multicellular organisms with an organism-wide osmoregulation, have the ability to actively control their water balance. Osmoregulation encompasses homeostatic processes that maintain an appropriate intracellular environment for biochemical processes as well as turgor of cells and organism. In the laboratory, the osmoregulatory system is studied most conveniently as a response to osmotic shock, causing rapid and dramatic changes in the extracellular water activity. Those rapid changes mediate either water efflux (hyperosmotic shock), and hence cell shrinkage, or influx (hypoosmotic shock), causing cell swelling. The yeast S. cerevisiae, as a free-living organism experiencing both slow and rapid changes in extracellular water activity, has proven a suitable and genetically tractable experimental system in studying the underlying signaling pathways and regulatory processes governing osmoregulation. Although far from complete, the present picture of yeast osmoregulation is both extensive and detailed (de Nadal et al., 2002; Hohmann, 2002; Klipp et al., 2005). Simulations using mathematical models combined with time course measurements of different molecular processes in signaling and adaptation have allowed elucidation of the first system properties on the yeast osmoregulatory network.
|
|
| 8. |
|
|
| 9. |
- Jesorka, Aldo, 1967, et al.
(författare)
-
COMPLEX NANOTUBE-LIPOSOME NETWORKS
- 2009
-
Ingår i: Methods in Enzymology. - 1557-7988 .- 0076-6879. ; 464:C, s. 309-325
-
Tidskriftsartikel (refereegranskat)abstract
- Surfactant nanotube-vesicle networks (NVN) belong to the smallest artificial devices known to date for performing controlled chemical operations with enzymes. Newly established means for transport of chemical reactants between containers, as well as advancements in initiation and control of chemical reactions in such systems have opened pathways to new devices with a resolution down to the single-molecule level. Here, we summarize the fabrication and functionalization of complex nanotube-liposome networks for such devices, and discuss related aspects of their application for studying chemical kinetics and materials transport phenomena in ultrasmall-scale bio-mimetic environments.
|
|
| 10. |
|
|
