170 research outputs found
Conformational recognition of an intrinsically disordered protein
No full textThere is a growing interest in understanding the properties of intrinsically disordered proteins (IDPs); however, the characterization of these states remains an open challenge. IDPs appear to have functional roles that diverge from those of folded proteins and revolve around their ability to act as hubs for protein-protein interactions. To gain a better understanding of the modes of binding of IDPs, we combined statistical mechanics, calorimetry, and NMR spectroscopy to investigate the recognition and binding of a fragment from the disordered protein Gab2 by the growth factor receptor-bound protein 2 (Grb2), a key interaction for normal cell signaling and cancer development. Structural ensemble refinement by NMR chemical shifts, thermodynamics measurements, and analysis of point mutations indicated that the population of preexisting bound conformations in the free-state ensemble of Gab2 is an essential determinant for recognition and binding by Grb2. A key role was found for transient polyproline II (PPII) structures and extended conformations. Our findings are likely to have very general implications for the biological behavior of IDPs in light of the evidence that a large fraction of these proteins possess a specific propensity to form PPII and to adopt conformations that are more extended than the typical random-coil states. © 2014 Biophysical Society
Self-organization of intrinsically disordered proteins with folded N-termini
No full textThousands of human proteins lack recognizable tertiary structure in most of their chains. Here we hypothesize that some use their structured N-terminal domains (SNTDs) to organise the remaining protein chain via intramolecular interactions, generating partially structured proteins. This model has several attractive features: as protein chains emerge, SNTDs form spontaneously and serve as nucleation points, creating more compact shapes. This reduces the risk of protein degradation or aggregation. Moreover, an interspersed pattern of SNTD-docked regions and free loops can coordinate assembly of sub-complexes in defined loop-sections and enables novel regulatory mechanisms, for example through posttranslational modifications of docked regions
Conformational Recognition of an Intrinsically Disordered Protein
No full textAbstractThere is a growing interest in understanding the properties of intrinsically disordered proteins (IDPs); however, the characterization of these states remains an open challenge. IDPs appear to have functional roles that diverge from those of folded proteins and revolve around their ability to act as hubs for protein-protein interactions. To gain a better understanding of the modes of binding of IDPs, we combined statistical mechanics, calorimetry, and NMR spectroscopy to investigate the recognition and binding of a fragment from the disordered protein Gab2 by the growth factor receptor-bound protein 2 (Grb2), a key interaction for normal cell signaling and cancer development. Structural ensemble refinement by NMR chemical shifts, thermodynamics measurements, and analysis of point mutations indicated that the population of preexisting bound conformations in the free-state ensemble of Gab2 is an essential determinant for recognition and binding by Grb2. A key role was found for transient polyproline II (PPII) structures and extended conformations. Our findings are likely to have very general implications for the biological behavior of IDPs in light of the evidence that a large fraction of these proteins possess a specific propensity to form PPII and to adopt conformations that are more extended than the typical random-coil states
sj-docx-1-wso-10.1177_17474930211062478 – Supplemental material for MRI and CT imaging biomarkers of cerebral amyloid angiopathy in lobar intracerebral hemorrhage
No full textSupplemental material, sj-docx-1-wso-10.1177_17474930211062478 for MRI and CT imaging biomarkers of cerebral amyloid angiopathy in lobar intracerebral hemorrhage by Ghil Schwarz, Gargi Banerjee, Isabel C Hostettler, Gareth Ambler, David J Seiffge, Hatice Ozkan, Simone Browning, Robert Simister, Duncan Wilson, Hannah Cohen, Tarek Yousry, Rustam Al-Shahi Salman, Gregory Y H Lip, Martin M Brown, Keith W Muir, Henry Houlden, Rolf Jäger and David J Werring in International Journal of Stroke</p
The effectiveness of interventions to treat severe acute malnutrition in young children: a systematic review
No full textSevere acute malnutrition (SAM) arises as a consequence of a sudden period of food shortage and is associated with loss of a person’s body fat and wasting of their skeletal muscle. Many of those affected are already undernourished and are often susceptible to disease. Infants and young children are the most vulnerable as they require extra nutrition for growth and development, have comparatively limited energy reserves and depend on others. Undernutrition can have drastic and wide-ranging consequences for the child’s development and survival in the short and long term. Despite efforts made to treat SAM through different interventions and programmes, it continues to cause unacceptably high levels of mortality and morbidity. Uncertainty remains as to the most effective methods to treat severe acute malnutrition in young children.ObjectivesTo evaluate the effectiveness of interventions to treat infants and children aged < 5 years who have SAM.Data sourcesEight databases (MEDLINE, EMBASE, MEDLINE In-Process & Other Non-Indexed Citations, CAB Abstracts Ovid, Bioline, Centre for Reviews and Dissemination, EconLit EBSCO and The Cochrane Library) were searched to 2010. Bibliographies of included articles and grey literature sources were also searched. The project expert advisory group was asked to identify additional published and unpublished references.Review methodsPrior to the systematic review, a Delphi process involving international experts prioritised the research questions. Searches were conducted and two reviewers independently screened titles and abstracts for eligibility. Inclusion criteria were applied to the full texts of retrieved papers by one reviewer and checked independently by a second. Included studies were mapped to the research questions. Data extraction and quality assessment were undertaken by one reviewer and checked by a second reviewer. Differences in opinion were resolved through discussion at each stage. Studies were synthesised through a narrative review with tabulation of the results.ResultsA total of 8954 records were screened, 224 full-text articles were retrieved, and 74 articles (describing 68 studies) met the inclusion criteria and were mapped. No evidence focused on treatment of children with SAM who were human immunodeficiency virus sero-positive, and no good-quality or adequately reported studies assessed treatments for SAM among infants < 6 months old. One randomised controlled trial investigated fluid resuscitation solutions for shock, with none adequately treating shock. Children with acute diarrhoea benefited from the use of hypo-osmolar oral rehydration solution (H-ORS) compared with the standard World Health Organization-oral rehydration solution (WHO-ORS). WHO-ORS was not significantly different from rehydration solution for malnutrition (ReSoMal), but the safety of ReSoMal was uncertain. A rice-based ORS was more beneficial than glucose-based ORSs, and provision of zinc plus a WHO-ORS had a favourable impact on diarrhoea and need for ORS. Comparisons of different diets in children with persistent diarrhoea produced conflicting findings. For treating infection, comparison of amoxicillin with ceftriaxone during inpatient therapy, and routine provision of antibiotics for 7 days versus no antibiotics during outpatient therapy of uncomplicated SAM, found that neither had a significant effect on recovery at the end of follow-up. No evidence mapped to the next three questions on factors that affect sustainability of programmes, long-term survival and readmission rates, the clinical effectiveness of management strategies for treating children with comorbidities such as tuberculosis and Helicobacter pylori infection and the factors that limit the full implementation of treatment programmes. Comparison of treatment for SAM in different settings showed that children receiving inpatient care appear to do as well as those in ambulatory or home settings on anthropometric measures and response time to treatment. Longer-term follow-up showed limited differences between the different settings. The majority of evidence on methods for correcting micronutrient deficiencies considered zinc supplements; however, trials were heterogeneous and a firm conclusion about zinc was not reached. There was limited evidence on either supplementary potassium or nicotinic acid (each produced some benefits), and nucleotides (not associated with benefits). Evidence was identified for four of the five remaining questions, but not assessed because of resource limitation.LimitationsThe systematic review focused on key questions prioritised through a Delphi study and, as a consequence, did not encompass all elements in the management of SAM. In focusing on evidence from controlled studies with the most rigorous designs that were published in the English language, the systematic review may have excluded other forms of evidence. The systematic review identified several limitations in the evidence base for assessing the effectiveness of interventions for treating young children with severe acute malnutrition, including a lack of studies assessing the different interventions; limited details of study methods used; short follow-up post intervention or discharge; and heterogeneity in participants, interventions, settings, and outcome measures affecting generalisability.ConclusionsFor many of the most highly ranked questions evidence was lacking or inconclusive. More research is needed on a range of topic areas concerning the treatment of infants and children with SAM. Further research is required on most aspects of the management of SAM in children < 5 years, including intravenous resuscitation regimens for shock, management of subgroups (e.g. infants < 6 months old, infants and children with SAM who are human immunodeficiency virus sero-positive) and on the use of antibiotics.FundingThe National Institute for Health Research Technology Assessment programme.<br/
Key Learning Statements for persistent pain education: an iterative analysis of consumer, clinician and researcher perspectives and development of public messaging
No full textData source: Supplementary data, https://doi.org/10.1016/j.jpain.2022.07.008Over the last decade, the content, delivery and media of pain education have been adjusted in line with scientific discovery in pain and educational sciences, and in line with consumer perspectives. This paper describes a decade-long process of exploring consumer perspectives on pain science education concepts to inform clinician-derived educational updates (undertaken by the authors). Data were collected as part of a quality audit via a series of online surveys in which consent (non-specific) was obtained from consumers for their data to be used in published research. Consumers who presented for care for a persistent pain condition and were treated with a pain science education informed approach were invited to provide anonymous feedback about their current health status and pain journey experience 6, 12 or 18 months after initial assessment. Two-hundred eighteen consumers reported improvement in health status at follow-up. Results of the surveys from three cohorts of consumers that reported improvement were used to generate iterative versions of 'Key Learning Statements'. Early iteration of these Key Learning Statements was used to inform the development of Target Concepts and associated community-targeted pain education resources for use in public health and health professional workforce capacity building initiatives. Perspective This paper reflects an explicit interest in the insights of people who have been challenged by persistent pain and then recovered, to improve pain care. Identifying pain science concepts that consumers valued learning provided valuable information to inform resources for clinical interactions and community-targeted pain education campaigns.Hayley B. Leake, Amelia Mardon, Tasha R. Stanton, Daniel S. Harvie, David S. Butler, Emma L. Karran, Dianne Wilson, JohnBooth, Trevor Barker, Pene Wood, Kal Fried, Chris Hayes, Lissanthea Taylor, Melanie Macoun, Amanda Simister, G. Lorimer Moseley, Carolyn Berryma
The crystal structure of PEBP-2, a homologue of the PEBP/RKIP family
No full textProteins from the PEBP (phosphatidylethanolamine-binding protein) family have been identified in a wide variety of species and are thought to regulate a range of intracellular signalling cascades. The rat homologue (known as RKIP; Raf-1 kinase inhibitor protein) has been shown to negatively regulate the MAP kinase pathway through formation of inhibitory complexes with Raf-1 and MEK. The crystal structure of a new, murine member of the PEBP family, termed mPEBP-2, has been determined. On the basis of amino-acid homology, mPEBP-2 belongs to a distinct subset of the mammalian PEBP proteins. Nonetheless, mPEBP-2 is seen to be very similar in structure to other PEBP proteins from human, bovine and plant sources. Regions of distinctive sequence associated with the PEBP-2 subset are discussed with reference to this structure.</p
Research progresses in understanding the pathophysiology of moyamoya disease
No full textBackground: The pathogenesis of moyamoya disease (MMD) is still unknown. The detection of inflammatory molecules such as cytokines, chemokines and growth factors in MMD patients' biological fluids supports the hypothesis that an abnormal angiogenesis is implicated in MMD pathogenesis. However, it is unclear whether these anomalies are the consequences of the disease or rather causal factors as well as these mechanisms remain insufficient to explain the pathophysiology of MMD. The presence of a family history in about 9-15% of Asian patients, the highly variable incidence rate between different ethnic and sex groups and the age of onset support the role of genetic factors in MMD pathogenesis. However, although some genetic loci have been associated with MMD, few of them have been replicated in independent series. Recently, RNF213 gene was shown to be strongly associated with MMD occurrence with a founder effect in East Asian patients. However, the mechanisms leading from RNF213 mutations to MMD clinical features are still unknown. Summary: The research on pathogenic mechanism of MMD is in its infancy. MMD is probably a complex and heterogeneous disorder, including different phenotypes and genotypes, in which more than a single factor is implicated. Key Message: Since the diagnosis of MMD is rapidly increasing worldwide, the development of more efficient stratifying risk systems, including both clinical but also biological drivers became imperative to improve our ability of predict prognosis and to develop mechanism-tailored interventions
Phylogenetic inference of <i>Actinobacteria</i> 16S rRNA genes.
No full text<p>The modified ARB database generated by Simister et al., <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053029#pone.0053029-Simister1" target="_blank">[34]</a> used long sequences (≥1200 bp) to infer the phylogeny and shorter sequences were added using the ARB parsimony interactive tool. Sequences from the sponge-specific cluster 22 (SC22) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053029#pone.0053029-Simister1" target="_blank">[34]</a> along with sequences closely related to band 1 and outgroup sequences were selected for further phylogenetic analysis. The Maximum Likelihood tree (-ln likelihood: 4501,317092) is shown, with sequences retrieved in this study highlighted in bold. Numbers at tree nodes are bootstrap values and posterior probabilities calculated in Maximum Likelihood and MCMC Bayesian analyses, respectively, and values above 70/0.95 are shown.</p
LOX-PP reduces CIN85 mono-ubiquitination and ability to interact with c-Cbl.
No full text<p>(<b>A</b>) GST or LOX-PP-GST (PP-GST) was expressed in ZR-75 (left panel) or Hs578T (right panel) cells. GST and associated proteins were precipitated as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077288#pone-0077288-g001" target="_blank">Fig. 1B</a> and subjected to WB for CIN85 (Upstate Biotechnology and Calbiochem antibodies for ZR-75 and Hs578T cells, respectively), CD2AP (H-290), c-Cbl, AMAP1, EGFR, p130Cas and GST. Input, 4%. (<b>B–C</b>) HEK293T cells were transfected with AMAP1-FLAG, CIN85, HA-c-Cbl, HA-ubiquitin and LOX-PP-GST (PP-GST) as indicated and subjected to a ubiquitination assay. FLAG-tagged AMAP1 was immunoprecipitated and total whole cell extracts were subjected to WB with an HA antibody (upper panel), or the indicated antibodies (lower panel). (B). Data were quantified and relative mono-ubiquitination of AMAP1 with and without LOX-PP was determined by averaging the results of three independent experiments (C). <i>P</i> value was calculated using Student's <i>t</i>-test. *, P<0.03. (<b>D</b>) FLAG-CIN85 was expressed in Hs578T (left panel) or MCF-7 (right panel) cells. After lysis, the indicated amount of recombinant LOX-PP-myc-His was added and the mixture incubated at 4°C for 2 h. Proteins were then immunoprecipitated with a FLAG antibody and subjected to WB with FLAG and c-Cbl antibodies. (L Exp, longer exposure).</p
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