| 1. |
- Abazov, V. M., et al.
(författare)
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The upgraded DO detector
- 2006
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 565:2, s. 463-537
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Tidskriftsartikel (refereegranskat)abstract
- The DO experiment enjoyed a very successful data-collection run at the Fermilab Tevatron collider between 1992 and 1996. Since then, the detector has been upgraded to take advantage of improvements to the Tevatron and to enhance its physics capabilities. We describe the new elements of the detector, including the silicon microstrip tracker, central fiber tracker, solenoidal magnet, preshower detectors, forward muon detector, and forward proton detector. The uranium/liquid -argon calorimeters and central muon detector, remaining from Run 1, are discussed briefly. We also present the associated electronics, triggering, and data acquisition systems, along with the design and implementation of software specific to DO.
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| 2. |
- Ålander, J., et al.
(författare)
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Microsomal glutathione transferase 1 exhibits one-third-of-the-sites-reactivity towards glutathione
- 2009
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Ingår i: Archives of Biochemistry and Biophysics. - : Elsevier BV. - 0003-9861 .- 1096-0384. ; 487:1, s. 42-48
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Tidskriftsartikel (refereegranskat)abstract
- The trimeric membrane protein microsomal glutathione transferase 1 (MGST1) possesses glutathione transferase and peroxidase activity. Previous data indicated one active site/trimer whereas structural data suggests three GSH-binding sites. Here we have determined ligand interactions of MGST1 by several techniques. Nanoelectrospray mass spectrometry of native MGST1 revealed binding of three GSH molecules/trimer and equilibrium dialysis showed three product molecules/trimer (K(d) = 320 +/- 50 mu M). All three product molecules Could be competed out with GSH. Reinvestigation of GSH-binding showed one high affinity site per trimer, consistent with earlier data. Using single turnover stopped flow kinetic measurements, Kd could be determined for a low affinity GSH-binding site (2.5 +/- 0.5 mu M). Thus we can reconcile previous observations and show here that MGST1 contains three active sites with different affinities for GSH and that only the high affinity site is catalytically competent.
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| 3. |
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| 4. |
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| 5. |
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| 6. |
- Busenlehner, Laura S., et al.
(författare)
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Location of substrate binding sites within the integral membrane protein microsomal glutathione transferase-1
- 2007
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 46:10, s. 2812-2822
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Tidskriftsartikel (refereegranskat)abstract
- Microsomal glutathione transferase-1 (MGST1) is a trimeric, membrane-bound enzyme with both glutathione (GSH) transferase and hydroperoxidase activities. As a member of the MAPEG superfamily, MGST1 aids in the detoxication of numerous xenobiotic substrates and in cellular protection from oxidative stress through the GSH-dependent reduction of phospholipid hydroperoxides. However, little is known about the location of the different substrate binding sites, including whether the transferase and peroxidase activities overlap structurally. Although molecular density attributed to GSH has been observed in the 3.2 A resolution electron crystallographic structure of MGST1, the electrophilic and phospholipid hydroperoxide substrate binding sites remain elusive. Amide H-D exchange kinetics and H-D ligand footprinting experiments indicate that GSH and hydrophobic substrates bind within similar, but distinct, regions of MGST1. Site-directed mutagenesis, guided by the H-D exchange results, demonstrates that specific residues within the GSH footprint effect transferase activity toward 1-chloro-2,4-dinitrobenzene. In addition, cytosolic residues surrounding the chemical stress sensor C49 but not modeled in the crystal structure appear to play an important role in the formation of the binding site for hydrophobic substrates. Although the fatty acid/phospholipid binding site structurally overlaps that for GSH, it does not appear to be localized to the same region as other hydrophobic substrates. Finally, H-D exchange mass spectrometry reveals a specific conformational transition that may mediate substrate binding and/or product release. Such structural changes in MGST1 are essential for activation of the enzyme and are important for its biological function.
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| 7. |
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| 8. |
- Cheng, Kimberley, et al.
(författare)
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Rapana thomasiana hemocyanin (RtH): Comparison of the two isoforms, RtH1 and RtH2, at 19 angstrom 16 angstrom resolution
- 2006
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Ingår i: Micron. - : Elsevier BV. - 0968-4328 .- 1878-4291. ; 37:6, s. 566-576
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Forskningsöversikt (refereegranskat)abstract
- Three-dimensional (3D) reconstructions of the two 8.4 MDa Rapana thomasiana hemocyanin isoforms, RtH1 and RtH2, have been obtained by cryoelectron microscopy of molecules embedded in vitreous ice and single particle image processing. The final 3D structures of the RtH1 and RtH2 didecamers at 19 angstrom and 16 angstrom resolution, respectively, are very similar to earlier reconstructions of gastropodan hemocyanins, revealing structural features such as the obliquely oriented subunits, the five- and two-fold symmetrical axes. Three new interactions are defined; two of them connecting the arch and the wall while the third is formed between the collar and the wall. The collar-wall connection and one of the arch-wall connections are positioned between two individual subunit dimers, while the second arch-wall connection is located between two subunits within the subunit dimer. All three interactions establish connections to the first tier of the wall. Furthermore, for each interaction we have allocated two first tier functional units most likely involved in forming the connections. (
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| 9. |
- Elmlund, Hans, et al.
(författare)
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The cyclin-dependent kinase 8 module sterically blocks Mediator interactions with RNA polymerase II
- 2006
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 103:43, s. 15788-15793
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Tidskriftsartikel (refereegranskat)abstract
- CDK8 (cyclin-dependent kinase 8), along with CycC, Med12, and Med13, form a repressive module (the Cdk8 module) that prevents RNA polymerase II (pol II) interactions with Mediator. Here, we report that the ability of the Cdk8 module to prevent pol II interactions is independent of the Cdk8-dependent kinase activity. We use electron microscopy and single-particle reconstruction to demonstrate that the Cdk8 module forms a distinct structural entity that binds to the head and middle region of Mediator, thereby sterically blocking interactions with pol II.
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| 12. |
- Hebert, Hans, et al.
(författare)
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Two-dimensional crystallization and electron crystallography of MAPEG proteins.
- 2005
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Ingår i: Methods in Enzymology. - 0076-6879 .- 1557-7988. ; 401, s. 161-8
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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.
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| 13. |
- Hébert-Losier, Kim, 1985-, et al.
(författare)
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Raising the standards of the calf-raise test : a systematic review.
- 2009
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Ingår i: Journal of science and medicine in sport / Sports Medicine Australia. - : Elsevier BV. - 1878-1861 .- 1440-2440. ; 12:6, s. 594-602
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Tidskriftsartikel (refereegranskat)abstract
- The calf-raise test is used by clinicians and researchers in sports medicine to assess properties of the calf muscle-tendon unit. The test generally involves repetitive concentric-eccentric muscle action of the plantar-flexors in unipedal stance and is quantified by the number of raises performed. Although the calf-raise test appears to have acceptable reliability and face validity, and is commonly used for medical assessment and rehabilitation of injuries, no universally acceptable test parameters have been published to date. A systematic review of the existing literature was conducted to investigate the consistency as well as universal acceptance of the evaluation purposes, test parameters, outcome measurements and psychometric properties of the calf-raise test. Nine electronic databases were searched during the period May 30th to September 21st 2008. Forty-nine articles met the inclusion criteria and were quality assessed. Information on study characteristics and calf-raise test parameters, as well as quantitative data, were extracted; tabulated; and statistically analysed. The average quality score of the reviewed articles was 70.4+/-12.2% (range 44-90%). Articles provided various test parameters; however, a consensus was not ascertained. Key testing parameters varied, were often unstated, and few studies reported reliability or validity values, including sensitivity and specificity. No definitive normative values could be established and the utility of the test in subjects with pathologies remained unclear. Although adapted for use in several disciplines and traditionally recommended for clinical assessment, there is no uniform description of the calf-raise test in the literature. Further investigation is recommended to ensure consistent use and interpretation of the test by researchers and clinicians.
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| 14. |
- Hébert-Losier, Kim, et al.
(författare)
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Scientific bases and clinical utilisation of the calf-raise test.
- 2009
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Ingår i: Physical Therapy in Sport. - : Elsevier BV. - 1466-853X .- 1873-1600. ; 10:4, s. 142-9
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Athletes commonly sustain injuries to the triceps surae muscle-tendon unit. The calf-raise test (CRT) is frequently employed in sports medicine for the detection and monitoring of such injuries. However, despite being widely-used, a recent systematic review found no universal consensus relating to the test's purpose, parameters, and standard protocols. OBJECTIVES: The purpose of this paper is to provide a clinical perspective on the anatomo-physiological bases underpinning the CRT and to discuss the utilisation of the test in relation to the structure and function of the triceps surae muscle-tendon unit. DESIGN: Structured narrative review. METHODS: Nine electronic databases were searched using keywords and MESH headings related to the CRT and the triceps surae muscle-tendon unit anatomy and physiology. A hand-search of reference lists and relevant journals and textbooks complemented the electronic search. SUMMARY: There is evidence supporting the clinical use of the CRT to assess soleus and gastrocnemius, their shared aponeurosis, the Achilles tendon, and the combined triceps surae muscle-tendon unit. However, employing the same clinical test to assess all these structures and their associated functions remains challenging. CONCLUSIONS: Further refinement of the CRT for the triceps surae muscle-tendon unit is needed. This is vital to support best practice utilisation, standardisation, and interpretation of the CRT in sports medicine.
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| 15. |
- Koeck, Philip J. B., et al.
(författare)
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3D-correlation-averaging for membrane-protein-crystals
- 2008
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Ingår i: EMC 2008 14th European Microscopy Congress. - Berlin, Heidelberg : Springer Berlin Heidelberg. ; , s. 55-56
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Konferensbidrag (refereegranskat)abstract
- Few 2-dimensional protein crystals can be used to determine high-resolution structures, whereas most electron crystallography projects remain at a resolution around 10 Ångström. This might be partly due to lack of flatness of many two-dimensional crystals [1]. We have investigated this problem and suggest single particle projection matching (3D-correlation averaging) of locally averaged unit cells to improve the quality of three-dimensional maps. Theoretical considerations and tests on simulated data demonstrate the feasibility of this refinement method [2].
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| 16. |
- Koeck, Philip J. B., et al.
(författare)
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Single particle refinement in electron crystallography : A pilot study
- 2007
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Ingår i: Journal of Structural Biology. - : Elsevier BV. - 1047-8477 .- 1095-8657. ; 160:3, s. 344-352
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Tidskriftsartikel (refereegranskat)abstract
- Electron crystallography can be used to determine the structures of membrane proteins at near-atomic resolution in some cases. However, most electron crystallography projects remain at a resolution around 10 Å. This might be partly due to lack of flatness of many two-dimensional crystals. We have investigated this problem and suggest single particle processing of locally averaged unit cells to improve the quality and possibly the resolution of three-dimensional maps. Applying this method to the secondary transporter melibiose permease we have calculated a three-dimensional map that is clearer and easier to interpret than the map derived using purely electron-crystallographic methods.
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| 22. |
- Verbeeck, J., et al.
(författare)
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Optimal aperture sizes and positions for EMCD experiments
- 2008
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Ingår i: Ultramicroscopy. - : Elsevier BV. - 0304-3991 .- 1879-2723. ; 108:9, s. 865-872
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Tidskriftsartikel (refereegranskat)abstract
- The signal-to-noise ratio (SNR) in energy-loss magnetic chiral dichroism (EMCD)-the equivalent of Xray magnetic circular dichroism (XMCD) in the electron microscope-is optimized with respect to the detector shape, size and position. We show that an important increase in SNR over previous experiments can be obtained when taking much larger detector sizes. We determine the ideal shape of the detector but also show that round apertures are a good compromise if placed in their optimal position. We develop the theory for a simple analytical description of the EMCD experiment and then apply it to dynamical multibeam Bloch wave calculations and to an experimental data set. In all cases it is shown that a significant and welcome improvement of the SNR is possible.
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| 23. |
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| 24. |
- Wu, S.R., et al.
(författare)
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Turning of the receptor binding domains opens up the murine leukaemia virus Env for membrane fusion
- 2008
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Ingår i: EMBO Journal. - : Wiley. - 0261-4189 .- 1460-2075. ; 27:20, s. 2799-2808
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Tidskriftsartikel (refereegranskat)abstract
- The activity of the membrane fusion protein Env of Moloney mouse leukaemia virus is controlled by isomerization of the disulphide that couples its transmembrane (TM) and surface (SU) subunits. We have arrested Env activation at a stage prior to isomerization by alkylating the active thiol in SU and compared the structure of isomerization-arrested Env with that of native Env. Env trimers of respective form were isolated from solubilized particles by sedimentation and their structures were reconstructed from electron microscopic images of both vitrified and negatively stained samples. We found that the protomeric unit of both trimers formed three protrusions, a top, middle and a lower one. The atomic structure of the receptor-binding domain of SU fitted into the upper protrusion. This was formed similar to a bent finger. Significantly, in native Env the tips of the fingers were directed against each other enclosing a cavity below, whereas they had turned outward in isomerization-arrested Env transforming the cavity into an open well. This might subsequently guide the fusion peptides in extended TM subunits into the target membrane.
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