| 1. |
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| 2. |
- Thomas, HS, et al.
(författare)
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- 2019
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swepub:Mat__t
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| 3. |
- Abdelhady, Wael Awad
(författare)
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Glypican-1: Structural and functional analysis of the N-glycosylated human protein
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Glypicans are multifunctional cell surface heparan sulphate proteoglycans co-regulating numerous signalling pathways, and are thereby involved in the control of cellular division, differentiation, and morphogenesis. The heparan sulphate (HS) chains are responsible for many of those biological functions; nevertheless recent studies suggest functional roles for the glypican core proteins in mediating the signalling of various growth factors. Glypican-1 (GPC1) is the predominant HS proteoglycan in the developing and adult human brain. In addition, GPC1 is involved in Alzheimer’s disease and scrapie, among others. There is a shortage of detailed structural knowledge regarding the GPC1 core protein and accordingly, we proposed in this thesis to structurally and functionally characterize the human GPC1 core protein and to elucidate its overall topology with respect to the membrane. First, we determined the crystal structure of the human N-glycosylated GPC1 core protein by the two-wavelength MAD method on a SeMet-substituted protein crystal. The GPC1 structure revealed a quite rigid, cylindrical single-domain all α-helical fold with three substantial loops. Shortly afterwards, we achieved improvements of GPC1 crystal diffraction properties by controlled crystal dehydration using a humidity control device (HC1b) and generated better electron density for crystals of GPC1, allowing the building of previously disordered parts of the structure. Using small angle X-ray scattering and other biophysical approaches, we found that the GPC1 core protein lies on the membrane in a transverse orientation, directing a surface evolutionarily conserved in GPC1 orthologues towards the membrane, where it can interact with enzymes involved in HS substitution in the Golgi apparatus. Furthermore, the N-linked glycans are shown to extend the protein stability and lifetime by protection against proteolysis and aggregation. The EXTL3 protein, a member of the exostosin family, functions mainly as an initiator for HS assembly on the glypicans. We have investigated the spectroscopic and structural characteristics of the catalytic region of EXTL3, which exhibits a quite stable extended monomeric structure with two functional domains containing a majority of β sheets. Additionally, it was found that catalytic EXTL3 is occupied with N-glycans at least at two sites and these N-glycans seem critical for proper EXTL3 biosynthesis. To precisely determine how the GPC1 core protein regulates HS assembly through interactions with EXTL3, investigations of the GPC1-EXTL3 complexes are ongoing, and some preliminary results are presented here.
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| 4. |
- Abdelhady, Wael Awad, et al.
(författare)
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GPC1 (glypican 1)
- 2014
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Ingår i: Atlas of Genetics and Cytogenetics in Oncology and Haematology. - : INIST-CNRS. - 1768-3262. ; 18:7, s. 461-464
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Tidskriftsartikel (refereegranskat)abstract
- Review on GPC1, with data on DNA/RNA, on the protein encoded and where the gene is implicated.
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| 5. |
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| 6. |
- Awad, Wael, et al.
(författare)
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Improvements in the order, isotropy and electron density of glypican-1 crystals by controlled dehydration.
- 2013
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Ingår i: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; 69:Pt 12, s. 2524-2533
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Tidskriftsartikel (refereegranskat)abstract
- The use of controlled dehydration for improvement of protein crystal diffraction quality is increasing in popularity, although there are still relatively few documented examples of success. A study has been carried out to establish whether controlled dehydration could be used to improve the anisotropy of crystals of the core protein of the human proteoglycan glypican-1. Crystals were subjected to controlled dehydration using the HC1 device. The optimal protocol for dehydration was developed by careful investigation of the following parameters: dehydration rate, final relative humidity and total incubation time Tinc. Of these, the most important was shown to be Tinc. After dehydration using the optimal protocol the crystals showed significantly reduced anisotropy and improved electron density, allowing the building of previously disordered parts of the structure.
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| 7. |
- Awad, Wael, et al.
(författare)
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Structural and Biophysical Characterization of Human EXTL3 : Domain Organization, Glycosylation, and Solution Structure
- 2018
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 57:7, s. 1166-1177
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Tidskriftsartikel (refereegranskat)abstract
- Heparan sulfate proteoglycans are proteins substituted with one or more heparan sulfate (HS) polysaccharides, found in abundance at cell surfaces. HS chains influence the activity of many biologically important molecules involved in cellular communication and signaling. The exostosin (EXT) proteins are glycosyltransferases in the Golgi apparatus that assemble HS chains on HSPGs. The EXTL3 enzyme mainly works as an initiator in HS biosynthesis. In this work, human lumenal N-glycosylated EXTL3 (EXTL3ΔN) was cloned, expressed in human embryonic kidney cells, and purified. Various biophysical and biochemical approaches were then employed to elucidate the N-glycosylation sites and the function of their attached N-glycans. Furthermore, the stability and conformation of the purified EXTL3ΔN protein in solution have been analyzed. Our data show that EXTL3ΔN has N-glycans at least at two positions, Asn290 and Asn592, which seem to be critical for proper protein folding and/or release. EXTL3ΔN is quite stable, as high temperature (∼59 °C) was required for denaturation. Deconvolution of the EXTL3ΔN far-UV CD spectrum revealed a substantial fraction of β sheets (25%) with a minor proportion of α-helices (14%) in the secondary structure. Solution small-angle X-ray scattering and dynamic light scattering revealed an extended structure suggestive of a dimeric arrangement and consisting of two distinct regions, narrow and broad, respectively. This is consistent with bioinformatics analyses suggesting a 3-domain structure with two glycosyltransferase domains and a coiled-coil domain.
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| 8. |
- Awad, Wael, et al.
(författare)
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Structural Basis for YjbH Adaptor-Mediated Recognition of Transcription Factor Spx
- 2019
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Ingår i: Structure. - : Elsevier BV. - 0969-2126. ; 27:6, s. 6-936
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Tidskriftsartikel (refereegranskat)abstract
- YjbH is a bacterial adaptor protein required for efficient proteolysis of the RNA polymerase-binding transcription factor Spx by the ClpXP protease. We report the structure of YjbH in complex with Spx. YjbH comprises a DsbA-like thioredoxin domain connected via a linker to a C-terminal domain reminiscent of the winged helix-turn-helix fold. The interaction between YjbH and Spx involves a large surface area. Binding to YjbH stabilizes the C-terminal ClpX recognition region of Spx. We show that mutation of critical YjbH contact residues abrogates Spx recognition. Small-angle X-ray scattering and hydrogen-deuterium exchange mass spectrometry analyses determined the existence of a stable heterodimeric complex in solution and provide evidence that binding of Spx to YjbH reduces the overall conformational flexibility of Spx. Our findings provide insights into the molecular basis for Spx recognition and suggest a model for how YjbH stabilizes Spx and displays the C terminus of Spx for engagement by ClpXP. Awad et al. determined the crystal structure of the ClpXP adaptor protein YjbH in complex with the transcription factor Spx. Structural dynamics of the complex were investigated by hydrogen-deuterium exchange mass spectrometry. The insights provided in this work add molecular details to the recognition of Spx by YjbH.
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| 9. |
- Danielsson, Jens, et al.
(författare)
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Global structural motions from the strain of a single hydrogen bond
- 2013
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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. ; 110:10, s. 3829-3834
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Tidskriftsartikel (refereegranskat)abstract
- The origin and biological role of dynamic motions of folded enzymes is not yet fully understood. In this study, we examine the molecular determinants for the dynamic motions within the beta-barrel of superoxide dismutase 1 (SOD1), which previously were implicated in allosteric regulation of protein maturation and also pathological misfolding in the neurodegenerative disease amyotrophic lateral sclerosis. Relaxation-dispersion NMR, hydrogen/deuterium exchange, and crystallographic data show that the dynamic motions are induced by the buried H43 side chain, which connects the backbones of the Cu ligand H120 and T39 by a hydrogen-bond linkage through the hydrophobic core. The functional role of this highly conserved H120-H43-T39 linkage is to strain H120 into the correct geometry for Cu binding. Upon elimination of the strain by mutation H43F, the apo protein relaxes through hydrogen-bond swapping into a more stable structure and the dynamic motions freeze out completely. At the same time, the holo protein becomes energetically penalized because the twisting back of H120 into Cu-bound geometry leads to burial of an unmatched backbone carbonyl group. The question then is whether this coupling between metal binding and global structural motions in the SOD1 molecule is an adverse side effect of evolving viable Cu coordination or plays a key role in allosteric regulation of biological function, or both?
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| 10. |
- Drake, TM, et al.
(författare)
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Surgical site infection after gastrointestinal surgery in children: an international, multicentre, prospective cohort study
- 2020
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Ingår i: BMJ global health. - : BMJ. - 2059-7908. ; 5:12
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Tidskriftsartikel (refereegranskat)abstract
- Surgical site infection (SSI) is one of the most common healthcare-associated infections (HAIs). However, there is a lack of data available about SSI in children worldwide, especially from low-income and middle-income countries. This study aimed to estimate the incidence of SSI in children and associations between SSI and morbidity across human development settings.MethodsA multicentre, international, prospective, validated cohort study of children aged under 16 years undergoing clean-contaminated, contaminated or dirty gastrointestinal surgery. Any hospital in the world providing paediatric surgery was eligible to contribute data between January and July 2016. The primary outcome was the incidence of SSI by 30 days. Relationships between explanatory variables and SSI were examined using multilevel logistic regression. Countries were stratified into high development, middle development and low development groups using the United Nations Human Development Index (HDI).ResultsOf 1159 children across 181 hospitals in 51 countries, 523 (45·1%) children were from high HDI, 397 (34·2%) from middle HDI and 239 (20·6%) from low HDI countries. The 30-day SSI rate was 6.3% (33/523) in high HDI, 12·8% (51/397) in middle HDI and 24·7% (59/239) in low HDI countries. SSI was associated with higher incidence of 30-day mortality, intervention, organ-space infection and other HAIs, with the highest rates seen in low HDI countries. Median length of stay in patients who had an SSI was longer (7.0 days), compared with 3.0 days in patients who did not have an SSI. Use of laparoscopy was associated with significantly lower SSI rates, even after accounting for HDI.ConclusionThe odds of SSI in children is nearly four times greater in low HDI compared with high HDI countries. Policies to reduce SSI should be prioritised as part of the wider global agenda.
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| 11. |
- Khanji, Mohammed Y., et al.
(författare)
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Management of aortic stenosis : A systematic review of clinical practice guidelines and recommendations
- 2021
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Ingår i: European Heart Journal - Quality of Care and Clinical Outcomes. - : Oxford University Press (OUP). - 2058-5225 .- 2058-1742. ; 7:4, s. 340-353
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Forskningsöversikt (refereegranskat)abstract
- Multiple guidelines exist for the management of aortic stenosis (AS). We systematically reviewed current guidelines and recommendations, developed by national or international medical organizations, on management of AS to aid clinical decision-making. Publications in MEDLINE and EMBASE between 1 June 2010 and 15 January 2021 were identified. Additionally, the International Guideline Library, National Guideline Clearinghouse, National Library for Health Guidelines Finder, Canadian Medical Association Clinical Practice Guidelines Infobase, and websites of relevant organizations were searched. Two reviewers independently screened titles and abstracts. Two reviewers assessed rigour of guideline development and extracted the recommendations. Of the seven guidelines and recommendations retrieved, five showed considerable rigour of development. Those rigourously developed, agreed on the definition of severe AS and diverse haemodynamic phenotypes, indications and contraindications for intervention in symptomatic severe AS, surveillance intervals in asymptomatic severe AS, and the importance of multidisciplinary teams (MDTs) and shared decision-making. Discrepancies exist in age and surgical risk cut-offs for recommending surgical aortic valve replacement (SAVR) vs. transcatheter aortic valve implantation (TAVI), the use of biomarkers and complementary multimodality imaging for decision-making in asymptomatic patients and surveillance intervals for non-severe AS. Contemporary guidelines for AS management agree on the importance of MDT involvement and shared decision-making for individualized treatment and unanimously indicate valve replacement in severe, symptomatic AS. Discrepancies exist in thresholds for age and procedural risk used in choosing between SAVR and TAVI, role of biomarkers and complementary imaging modalities to define AS severity and risk of progression in asymptomatic patients.
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| 12. |
- Ricci, Fabrizio, et al.
(författare)
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Tricuspid regurgitation management : a systematic review of clinical practice guidelines and recommendations
- 2022
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Ingår i: European heart journal. Quality of care & clinical outcomes. - : Oxford University Press (OUP). - 2058-1742 .- 2058-5225. ; 8:3, s. 238-248
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Tidskriftsartikel (refereegranskat)abstract
- Tricuspid regurgitation (TR) is a highly prevalent condition and an independent risk factor for adverse outcomes. Multiple clinical guidelines exist for the diagnosis and management of TR, but the recommendations may sometimes vary. We systematically reviewed high-quality guidelines with a specific focus on areas of agreement, disagreement, and gaps in evidence. We searched MEDLINE and EMBASE (1 January 2011 to 30 August 2021), the Guidelines International Network International, Guideline Library, National Guideline Clearinghouse, National Library for Health Guidelines Finder, Canadian Medical Association Clinical Practice Guidelines Infobase, Google Scholar, and websites of relevant organizations for contemporary guidelines that were rigorously developed (as assessed by the Appraisal of Guidelines for Research and Evaluation II tool). Three guidelines were finally retained. There was consensus on a TR grading system, recognition of isolated functional TR associated with atrial fibrillation, and indications for valve surgery in symptomatic vs. asymptomatic patients, primary vs. secondary TR, and isolated TR forms. Discrepancies exist in the role of biomarkers, complementary multimodality imaging, exercise echocardiography, and cardiopulmonary exercise testing for risk stratification and clinical decision-making of progressive TR and asymptomatic severe TR, management of atrial functional TR, and choice of transcatheter tricuspid valve intervention (TTVI). Risk-based thresholds for quantitative TR grading, robust risk score models for TR surgery, surveillance intervals, population-based screening programmes, TTVI indications, and consensus on endpoint definitions are lacking.
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| 13. |
- Saber, Abeer, et al.
(författare)
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Adapting the pre-trained convolutional neural networks to improve the anomaly detection and classification in mammographic images
- 2023
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Ingår i: Scientific Reports. - : NATURE PORTFOLIO. - 2045-2322. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Mortality from breast cancer (BC) is among the top causes of cancer death in women. BC can be effectively treated when diagnosed early, improving the likelihood that a patient will survive. BC masses and calcification clusters must be identified by mammography in order to prevent disease effects and commence therapy at an early stage. A mammography misinterpretation may result in an unnecessary biopsy of the false-positive results, lowering the patients odds of survival. This study intends to improve breast mass detection and identification in order to provide better therapy and reduce mortality risk. A new deep-learning (DL) model based on a combination of transfer-learning (TL) and long short-term memory (LSTM) is proposed in this study to adequately facilitate the automatic detection and diagnosis of the BC suspicious region using the 80-20 method. Since DL designs are modelled to be problem-specific, TL applies the knowledge gained during the solution of one problem to another relevant problem. In the presented model, the learning features from the pre-trained networks such as the squeezeNet and DenseNet are extracted and transferred with the features that have been extracted from the INbreast dataset. To measure the proposed model performance, we selected accuracy, sensitivity, specificity, precision, and area under the ROC curve (AUC) as our metrics of choice. The classification of mammographic data using the suggested model yielded overall accuracy, sensitivity, specificity, precision, and AUC values of 99.236%, 98.8%, 99.1%, 96%, and 0.998, respectively, demonstrating the models efficacy in detecting breast tumors.
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| 14. |
- Svensson Birkedal, Gabriel, et al.
(författare)
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Crystal structure of N-glycosylated human glypican-1 core protein: Structure of two loops evolutionarily conserved in vertebrate glypican-1.
- 2012
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Ingår i: Journal of Biological Chemistry. - 1083-351X. ; 287:17, s. 14040-14051
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Tidskriftsartikel (refereegranskat)abstract
- Glypicans are a family of cell-surface proteoglycans that regulate Wnt, hedgehog, bone morphogenetic protein and fibroblast growth factor signaling. Loss-of-function mutations in glypican core proteins and in glycosaminoglycan synthezing enzymes have revealed that glypican core proteins and their glycosaminoglycan chains are important in shaping animal development. Glypican core proteins consist of a stable alpha-helical domain containing 14 conserved Cys residues followed by a glycosaminoglycan attachment domain that becomes exclusively substituted with heparan sulfate (HS) and presumably adopts a random coil conformation. Removal of the alpha-helical domain results in almost exclusive addition of the glycosaminoglycan chondroitin sulfate, suggesting that factors in the alpha-helical domain promote assembly of HS. Glypican-1 is involved in brain development and is one of six members of the vertebrate family of glypicans. We expressed and crystallized N-glycosylated human glypican-1 lacking HS and N-glycosylated glypican-1 lacking the HS attachment domain. The crystal structure of glypican-1 was solved using crystals of selenomethionine labelled glypican-1 core protein lacking the HS domain. No additional electron density was observed for crystals of glypican-1 containing the HS attachment domain, and CD spectra of the two protein species were highly similar. The crystal structure of N- glycosylated human glypican-1 core protein at 2.5 Å, the first crystal structure of a vertebrate glypican, reveals the complete disulfide bond arrangement of the conserved Cys residues, and also extends the structural knowledge of glypicans for one alpha helix and two long loops. Importantly, the loops are evolutionarily conserved in vertebrate glypican-1 and one of them is involved in glycosaminoglycan class determination.
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