| 41. |
- Van Lun, Michiel, et al.
(författare)
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Subunit Interface Dynamics in Hexadecameric Rubisco
- 2011
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 411:5, s. 1083-1098
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Tidskriftsartikel (refereegranskat)abstract
- Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) plays an important role in the global carbon cycle as a hub for biomass. Rubisco catalyzes not only the carboxylation of RuBP with carbon dioxide but also a competing oxygenation reaction of RuBP with a negative impact on photosynthetic yield. The functional active site is built from two large (L) subunits that form a dimer. The octameric core of four L(2) dimers is held at each end by a cluster of four small (S) subunits, forming a hexadecamer. Each large subunit contacts more than one S subunit. These interactions exploit the dynamic flexibility of Rubisco, which we address in this study. Here, we describe seven different types of interfaces of hexadecameric Rubisco. We have analyzed these interfaces with respect to the size of the interface area and the number of polar interactions, including salt bridges and hydrogen bonds in a variety of Rubisco enzymes from different organisms and different kingdoms of life, including the Rubisco-like proteins. We have also performed molecular dynamics simulations of Rubisco from Chlamydomonas reinhardtii and mutants thereof. From our computational analyses, we propose structural checkpoints of the S subunit to ensure the functionality and/or assembly of the Rubisco holoenzyme. These checkpoints appear to fine-tune the dynamics of the enzyme in a way that could influence enzyme performance.
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| 42. |
- Yoon, Chun Hong, et al.
(författare)
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Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering
- 2011
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Ingår i: Optics Express. - 1094-4087. ; 19:17, s. 16542-16549
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Tidskriftsartikel (refereegranskat)abstract
- Single-particle experiments using X-ray Free Electron Lasers produce more than 10(5) snapshots per hour, consisting of an admixture of blank shots (no particle intercepted), and exposures of one or more particles. Experimental data sets also often contain unintentional contamination with different species. We present an unsupervised method able to sort experimental snapshots without recourse to templates, specific noise models, or user-directed learning. The results show 90% agreement with manual classification.
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| 43. |
- Andersson, Inger, 1964
(författare)
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Health-related quality of life after stem cell transplantation - The firs year
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Health-related quality of life after stem cell transplantation – The first year Inger Andersson Institute of Health and Care Sciences at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden Abstract High-Dose Chemotherapy (HDC) followed by Stem Cell Transplantation (SCT) has been proven to be beneficial for a variety of haematological diseases, solid tumours and immune disorders. Despite improved care and treatment, SCT continues to produce significant long-term complications with impaired functioning and distressing symptoms. In this thesis the overall aim was to improve our knowledge about how SCT patients experience different types of transplantations and the effect it may have on their Health-Related Quality of Life (HRQoL) during the first year after SCT. Semi structured interviews were performed and two questionnaires, the European Organization for Research and Treatment of Cancer Quality of Life questionnaire (EORTC QLQ-C30) and the module, High-Dose-Chemotherapy (HDC-19), were administered. Health-related quality of life after allogeneic SCT following Reduced Intensity Conditioning (RIC) and MyeloAblative Conditioning (MAC) were compared. Both groups showed a similar pattern of development over time in functioning and symptoms, albeit more severe in the MAC group. One year after SCT there were no significant differences between the groups in global Quality of Life (QoL). However, RIC patients improved in global QoL back to baseline earlier compared to MAC patients. When allogeneic and autologous patients were compared, RIC patients seemed to recover in the same way as autologous patients and these two groups were closer in their scoring compared to MAC patients. The results emphasize the need to separate the two allogeneic groups when evaluating HRQoL after SCT. Symptoms related to the digestive system like; dry mouth, sore mouth, appetite loss and change of taste together with fatigue were among the most frequent reported symptoms throughout the SCT period for all three groups. In the MAC group, symptoms of dry mouth and change of taste even increased, and one year after SCT these symptoms were more pronounced compared to baseline. Four themes emerged from the data analysis of the interviews and illustrate how the participants described their life from discharge until one year after SCT; obstacles on the road to normality, to be part of a normal life, the chance to be cured overshadow everything and new values in life. The patients described that they felt restricted in life and had problems to manage the response from family and friends. Stem cell transplantation had changed their opportunities in life, meaning that plans for the future had to be altered, sometimes in a negative way. Stem cell transplantation is a demanding procedure that affects the patients HRQoL over a long period of time. Alleviation and management of distressing symptoms and impaired functioning are some of the most important tasks for the health care providers in order to contribute to a better health and life situation for SCT survivors.
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| 44. |
- Forsgren, Nina, 1979-
(författare)
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Structural studies of the surface adhesin SspB from Streptococcus gordonii
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Surface proteins on microorganisms that build up the oral biofilm are key players in the formation of the biofilm. Antigen I/II proteins are surface adhesins found on virtually all oral streptococci and share a conserved multi-domain architecture. These adhesins bind surface components on other bacteria and on host cells. Thus, they are crucial for the development of the biofilm. The objective of this thesis work is the structural characterization of the large multi-domain Antigen I/II protein SspB from the primary colonizing commensal bacterium Streptococcus gordonii. The crystal structure of the variable domain of SspB was determined to 2.3 Å resolution. The domain comprises a β-supersandwich and a putative binding cleft stabilized by a calcium ion. Despite high similarity in the overall structure, the cleft within SspB is significantly smaller than the cleft within the homologous protein from Streptococcus mutans, indicating that different substrates may bind in the clefts. A screen for carbohydrate binding resulted in no hits for interaction with the SspB variable domain suggesting that the cleft may not be suitable for binding sugars. This thesis also presents the high resolution 1.5 Å structure of a truncated C-terminal domain of SspB, the first of an Antigen I/II C-domain. The structure contains two structurally related domains, each containing one calcium ion and one intramolecular isopeptide bond. The SspB protein shares the feature of intramoleular isopeptide bonds with other surface proteins from Gram positive bacteria, such as pili from Streptococcus pyogenes and Corynebacterium diphtheriae. Intramolecular isopeptide bonds are suggested to be a common feature for retaining stability in a harsh environment. The SspB adherence region, shown to be the recognition motif for Porphyromonas gingivalis attachment to S. gordonii, protrudes from the core protein as a handle available for recognition. In conclusion, this thesis work has provided new knowledge about the SspB protein and increased the understanding of the common structure of AgI/II proteins.
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| 45. |
- Hasse, Dirk, et al.
(författare)
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Crystallization and preliminary X-ray diffraction analyses of the homodimeric glycine decarboxylase (P-protein) from the cyanobacterium Synechocystis sp. PCC 6803.
- 2010
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Ingår i: Acta Crystallographica. Section F. - 1744-3091 .- 1744-3091. ; 66:Pt 2, s. 187-191
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Tidskriftsartikel (refereegranskat)abstract
- Glycine decarboxylase, or P-protein, is a major enzyme that is involved in the C(1) metabolism of all organisms and in the photorespiratory pathway of plants and cyanobacteria. The protein from Synechocystis sp. PCC 6803 is a homodimer with a mass of 215 kDa. Recombinant glycine decarboxylase was expressed in Escherichia coli and purified by metal-affinity, ion-exchange and gel-filtration chromatography. Crystals of P-protein that diffracted to a resolution of 2.1 A were obtained using the hanging-drop vapour-diffusion method at 291 K. X-ray diffraction data were collected from cryocooled crystals using synchrotron radiation. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 96.30, b = 135.81, c = 179.08 A.
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| 46. |
- Mackenzie, Alasdair, et al.
(författare)
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Crystal structures of an oligopeptide-binding protein from the biosynthetic pathway of the beta-lactamase inhibitor clavulanic acid.
- 2010
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 396:2
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Tidskriftsartikel (refereegranskat)abstract
- Clavulanic acid (CA) is a clinically important beta-lactamase inhibitor that is produced by fermentation of Streptomyces clavuligerus. The CA biosynthesis pathway starts from arginine and glyceraldehyde-3-phosphate and proceeds via (3S,5S)-clavaminic acid, which is converted to (3R,5R)-clavaldehyde, the immediate precursor of (3R,5R)-CA. Open reading frames 7 (orf7) and 15 (orf15) of the CA biosynthesis cluster encode oligopeptide-binding proteins (OppA1 and OppA2), which are essential for CA biosynthesis. OppA1/2 are proposed to be involved in the binding and/or transport of peptides across the S. clavuligerus cell membrane. Peptide binding assays reveal that recombinant OppA1 and OppA2 bind di-/tripeptides containing arginine and certain nonapeptides including bradykinin. Crystal structures of OppA2 in its apo form and in complex with arginine or bradykinin were solved to 1.45, 1.7, and 1.7 A resolution, respectively. The overall fold of OppA2 consists of two lobes with a deep cavity in the center, as observed for other oligopeptide-binding proteins. The large cavity creates a peptide/arginine binding cleft. The crystal structures of OppA2 in complex with arginine or bradykinin reveal that the C-terminal arginine of bradykinin binds similarly to arginine. The results are discussed in terms of the possible roles of OppA1/2 in CA biosynthesis.
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| 47. |
- Seibert, M. Marvin, et al.
(författare)
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Femtosecond diffractive imaging of biological cells
- 2010
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Ingår i: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 43:19, s. 194015-
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Tidskriftsartikel (refereegranskat)abstract
- In a flash diffraction experiment, a short and extremely intense x-ray pulse illuminates the sample to obtain a diffraction pattern before the onset of significant radiation damage. The over-sampled diffraction pattern permits phase retrieval by iterative phasing methods. Flash diffractive imaging was first demonstrated on an inorganic test object (Chapman et al 2006 Nat. Phys. 2 839-43). We report here experiments on biological systems where individual cells were imaged, using single, 10-15 fs soft x-ray pulses at 13.5 nm wavelength from the FLASH free-electron laser in Hamburg. Simulations show that the pulse heated the sample to about 160 000 K but not before an interpretable diffraction pattern could be obtained. The reconstructed projection images return the structures of the intact cells. The simulations suggest that the average displacement of ions and atoms in the hottest surface layers remained below 3 angstrom during the pulse.
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| 48. |
- Wikström Hultdin, Ulrika, 1977-
(författare)
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Structural studies of FocB and Transthyretin
- 2010
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The molecular structure of a protein decides its function, its way to interact with other molecules. Using X-ray crystallography methods, a 3-dimensional, atomic model of a macromolecule can be determined. In this thesis work, the X-ray structures of two different proteins involved in human diseases were studied: FocB, which is associated with urinary tract infections, and transthyretin, which is the causative of hereditary systemic transthyretin amyloidosis. FocB is a 12 kDa protein which binds DNA in an oligomeric fashion. It is involved in the regulation of the expression of bacterial surface organelles (fimbriae), responsible for the adhesion to specific receptors in host tissue. Specifically, FocB regulates the expression of one fimbrial type found in uropathogenic E. coli (UPEC): F1C. Our FocB structure revealed it to be an all-alpha helical protein with an atypical helix-turn-helix (HTH) motif. Residues previously found important for DNA-binding in the FocB homologue PapB, were not located in the putative “recognition helix” of the HTH-motif. FocB was also found to bind to the minor groove of the DNA. Together with homology searches showing that the DNA-interactions possible for FocB are greatly diversified, these findings indicated a DNA-interaction different from the typical DNA-interaction of a HTH-protein. Transthyretin (TTR) is a plasma protein involved in transport of thyroxin (T4) and retinol. Mutated TTR is also the cause of the neurodegenerative disease hereditary systemic transthyretin amyloidosis, which is characterized by systemic deposition of TTR amyloid fibrils. The amyloid occurs through a process of TTR tetramer destabilization and partial unfolding. A common way to inhibit amyloid formation is to design small molecules that bind unoccupied thyroxin binding sites and stabilize the tetrameric form of the protein. The structural characterization of the binding of chloride and iodide ions to TTR revealed that two of three previously identified halogen binding pockets in the T4-binding site were just as optimal for halide binding. In addition, a third halide-binding site, bridging two TTR subunits, was found. In biochemical experiments, chloride and iodide ions were shown to stabilize the TTR structure and inhibit the TTR aggregation and/or amyloid formation, with iodide ions doing so more efficiently than the chloride ions. In the search for new TTR amyloid-inhibiting drugs, the identified halide-binding sites in the T4-binding pocket are possible starting points for structure-based drug design.
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| 49. |
- Andersson, Inger, 1964, et al.
(författare)
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Health-related quality of life in patients undergoing allogeneic stem cell
- 2009
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Ingår i: Cancer Nursing. - 0162-220X. ; 32:4
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this prospective study was to describe health-related quality of life (HRQOL) in patients during the first year after stem cell transplantation (SCT) who were undergoing reduced intensive conditioning (RIC) compared with patients undergoing myeloablative conditioning (MAC). Fifty-seven patients (25 for MAC and 32 for RIC) were enrolled in the study. HRQOL was assessed at 6 occasions during the first year after SCT using European Organization for Research and Treatment of Cancer Quality of Life Questionnaire and the 19-item treatment-specific module High-Dose Chemotherapy. Both groups reported most symptoms and worst functioning 1 month after SCT, but there were substantial differences. The MAC group deteriorated considerably in 20 symptom scales compared with 8 in the RIC group (score differences <10; P values ranged from .001 to .05). Dry mouth, sore mouth, appetite loss, and change of taste were among the most frequent symptoms in both groups. Thereafter, the functioning improved and the symptom scores decreased and returned to baseline in both groups, except dry mouth, which remained a worse problem for the MAC group. Overall, the RIC group regained health and QOL faster than the MAC group did. However, there were no significant differences in global QOL between the groups 1 year after SCT.
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| 50. |
- Andersson, Inger
(författare)
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Catalysis and regulation in Rubisco.
- 2008
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Ingår i: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 59:7, s. 1555-1568
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Tidskriftsartikel (refereegranskat)abstract
- Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the incorporation of inorganic CO(2) into the organic molecules of life. Rubisco is extremely inefficient as a catalyst and its carboxylase activity is compromised by numerous side-reactions including oxygenation of its sugar phosphate substrate by atmospheric O(2). The reduction in the catalytic efficiency as a result of these processes has implications for crop yield, nitrogen and water usage, and for the global carbon cycle. Several aspects of Rubisco including its complex biosynthesis and multi-step catalytic reaction are subject to tight control involving light, cellular metabolites, and molecular chaperones. Numerous high-resolution crystal structures of different forms of Rubisco are now available, including structures of mutant enzymes. These provide a molecular framework for the understanding of these processes at the molecular level.
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