Abstract：
:The dynamic structure of proteins is essential for their functions and may include large conformational transitions which can be studied by molecular dynamics (MD) simulations. However, details of these transitions are difficult to automatically track. To facilitate their analysis, we developed two scores of correlation between sidechain dihedral angles. The CIRCULAR and OMES scores are computed from, respectively, dihedral angle values and rotamer distributions. As a case study, we applied our methods to an activation-like transition of the chemokine receptor CXCR4, observed during accelerated MD simulations. The principal component analysis of the correlation matrices was consistent with the networking structure of the top ranking pairs. Both scores identify a set of residues whose "collaborative" sidechain rotamerization immediately preceded or accompanied the conformational transition of CXCR4. Detailed analysis of the sequential order of these rotamerizations suggests that an allosteric mechanism, involving the outward motion of an asparagine residue in transmembrane helix 3, might be a prerequisite to the large scale conformational transition of CXCR4. This case study provides the proof-of-concept that the correlation methods developed here are valuable exploratory techniques to help decipher complex reactional pathways.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Taddese B,Garnier A,Abdi H,Henrion D,Chabbert Mdoi
10.1038/s41598-020-72766-1subject
Has Abstractpub_date
2020-09-28 00:00:00pages
15901issue
1issn
2045-2322pii
10.1038/s41598-020-72766-1journal_volume
10pub_type
杂志文章abstract：:Ricco's area (the largest area of visual space in which stimulus area and intensity are inversely proportional at threshold) has previously been hypothesised to be a result of centre/surround antagonism in retinal ganglion cell receptive fields, but recent evidence suggests a sizeable cortical contribution. Here, Ricc...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-21620-6
更新日期：2018-03-01 00:00:00
abstract：:Magma transport through the Earth's crust occurs dominantly via sheet intrusions, such as dykes and cone-sheets, and is fundamental to crustal evolution, volcanic eruptions and geochemical element cycling. However, reliable methods to reconstruct flow direction in solidified sheet intrusions have proved elusive. Aniso...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep27635
更新日期：2016-06-10 00:00:00
abstract：:We aimed to investigate the diagnostic accuracy of contrast-enhanced ultrasound (CEUS) in evaluating blunt abdominal trauma for patients presenting to the emergency department. Electronic search of Scopus and Pubmed was performed from inception to September 2016. Human studies investigating the diagnostic accuracy of ...
journal_title：Scientific reports
pub_type： 杂志文章,meta分析
doi：10.1038/s41598-017-04779-2
更新日期：2017-06-30 00:00:00
abstract：:Specific HPV genotypes have been recognized as risk factors inducing head and neck cancers (HNC). The aim of this study was to validate a real-time PCR assay to detect accurately High Risk HPV DNA in Formalin Fixed Paraffin Embedded (FFPE) and oral cytobrush samples and compare the results with conventional PCR. Repea...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-29790-z
更新日期：2018-07-27 00:00:00
abstract：:Invariant natural killer T (iNKT) cells are a specialized subset of T cells contributing to both, the innate and adaptive immune responses. In contrast to conventional T lymphocytes they recognize lipid antigens. The aim of the project is to establish a novel model system, to study iNKT-TCR - ligand interaction. An iN...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-43529-4
更新日期：2019-05-15 00:00:00
abstract：:Psychopathic traits of conduct disorder (CD) have a core callous-unemotional (CU) component and an impulsive-antisocial component. Previous task-driven fMRI studies have suggested that psychopathic traits are associated with dysfunction of several brain areas involved in different cognitive functions (e.g., empathy, r...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-11775-z
更新日期：2017-09-12 00:00:00
abstract：:The concept of entropy connects the number of possible configurations with the number of variables in large stochastic systems. Independent or weakly interacting variables render the number of configurations scale exponentially with the number of variables, making the Boltzmann-Gibbs-Shannon entropy extensive. In syst...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-72422-8
更新日期：2020-09-23 00:00:00
abstract：:Human KHDRBS1/Sam68 is an oncogenic splicing factor involved in signal transduction and pre-mRNA splicing. We explored the molecular mechanism of KHDRBS1 to be a prognostic marker in four different cancers. Within specific cancer, including kidney renal papillary cell carcinoma (KIRP), lung adenocarcinoma (LUAD), acut...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-47558-x
更新日期：2019-07-31 00:00:00
abstract：:The fusion of villous cytotrophoblasts into the multinucleated syncytiotrophoblast is critical for the essential functions of the mammalian placenta. Using RNA-Seq gene expression and quantitative protein expression, we identified genes and their cognate proteins which are coordinately up- or down-regulated in two cel...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-23379-2
更新日期：2018-03-23 00:00:00
abstract：:Online financial markets can be represented as complex systems where trading dynamics can be captured and characterized at different resolutions and time scales. In this work, we develop a methodology based on non-negative tensor factorization (NTF) aimed at extracting and revealing the multi-timescale trading dynamic...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-29537-w
更新日期：2018-07-25 00:00:00
abstract：:Peripheral blood indices of systemic inflammation such as the neutrophil-lymphocyte ratio (NLR) have been shown to be prognostic in various cancers. We aim to investigate the clinical significance of these indices in patients with soft tissue sarcoma (STS). Seven hundred and twelve patients with available blood counts...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-30442-5
更新日期：2018-08-10 00:00:00
abstract：:Molecular imaging technique is an attractive tool to detect liver disease at early stage. This study aims to develop a simultaneous dual-isotope single photon emission computed tomography (SPECT)/CT imaging method to assist diagnosis of hepatic tumor and liver fibrosis. Animal models of liver fibrosis and orthotopic h...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep28812
更新日期：2016-07-05 00:00:00
abstract：:Methylation of histone H3-lysine 9 (H3K9) and H3K27 by the methyltransferase G9a and polycomb repressive complex 2 (PRC2) inhibits transcription of target genes. A crosstalk between G9a and PRC2 via direct physical interaction has been shown recently. Here, we demonstrate an alternative mechanism by which G9a promotes...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep18709
更新日期：2015-12-21 00:00:00
abstract：:Previous studies have documented that decompression led to endothelial dysfunction with controversial results. This study aimed to clarify the relationship between endothelial dysfunction, bubble formation and decompression rate. Rats were subjected to simulated air dives with one of four decompression rates: one slow...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep33390
更新日期：2016-09-12 00:00:00
abstract：:The D40 gene encodes a kinetochore protein that plays an essential role in kinetochore formation during mitosis. Short inhibitory RNA against D40, D40 siRNA, has been shown to deplete the D40 protein in the human cancer cell line HeLa, which harbors wild-type p53, and this activity was followed by the significant inhi...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep13676
更新日期：2015-09-08 00:00:00
abstract：:A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper. ...
journal_title：Scientific reports
pub_type： 已发布勘误
doi：10.1038/s41598-018-22372-z
更新日期：2018-03-06 00:00:00
abstract：:Overuse of antibiotics has caused serious problems, such as appearance of super bacteria, whose accumulation in the human body through the food chain is a concern. Kanamycin is a common antibiotic used to treat diverse infections; however, residual kanamycin can cause many side effects in humans. Thus, development of ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep40305
更新日期：2017-01-05 00:00:00
abstract：:Lonicera japonica Thunb, rich in chlorogenic acid (CHA), is used for viral upper respiratory tract infection treatment caused by influenza virus, parainfluenza virus, and respiratory syncytial virus, ect in China. It was reported that CHA reduced serum hepatitis B virus level and death rate of influenza virus-infected...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep45723
更新日期：2017-04-10 00:00:00
abstract：:A positive Indian Ocean Dipole (IOD) and a warm phase of the El Niño-Southern Oscillation (ENSO) reduce rainfall over the Indian subcontinent and southern Australia. However, since the 1980s, El Niño's influence has been decreasing, accompanied by a strengthening in the IOD's influence on southern Australia but a reve...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep31767
更新日期：2016-08-22 00:00:00
abstract：:Current approaches to predicting a cardiovascular disease (CVD) event rely on conventional risk factors and cross-sectional data. In this study, we applied machine learning and deep learning models to 10-year CVD event prediction by using longitudinal electronic health record (EHR) and genetic data. Our study cohort i...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-36745-x
更新日期：2019-01-24 00:00:00
abstract：:High-grade gliomas are the most aggressive malignant brain tumors. Accurate pre-operative prognosis for this cohort can lead to better treatment planning. Conventional survival prediction based on clinical information is subjective and could be inaccurate. Recent radiomics studies have shown better prognosis by using ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-37387-9
更新日期：2019-01-31 00:00:00
abstract：:Pressure therapy has been proved to be an effective treatment for hypertrophic scars in a clinical setting. However, evidence-based data are controversial and the precise mechanism of action of this technique remains unknown. The aim of this study was to investigate the potential molecular mechanisms of pressure thera...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-29840-6
更新日期：2018-08-07 00:00:00
abstract：:Recent studies have linked appearance of Paneth cells in colorectal adenomas to adenoma burden and male gender. However, the clinical importance of Paneth cells' associations with synchronous advanced adenoma (AA) and colorectal carcinoma (CRC) is currently unclear. We performed a comprehensive case-control study usin...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep26129
更新日期：2016-05-18 00:00:00
abstract：:The challenge of balancing biodiversity protection with economic growth is epitomized by the development of renewable and unconventional energy, whose adoption is aimed at stemming the impacts of global climate change, yet has outpaced our understanding of biodiversity impacts. We evaluated the potential conflict betw...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-64501-7
更新日期：2020-05-05 00:00:00
abstract：:Divalent metal-ion transporter 1 (DMT1) has been found to play an important role in the iron metabolism and hemogenesis. However, little is known about the potential role of DMT1 in the pathogenesis of anemia from patients with inflammatory bowel disease (IBD). Herein, we investigated expression of DMT1 in the intesti...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep16344
更新日期：2015-11-17 00:00:00
abstract：:The aim of this study was to investigate whether a novel physiologically relevant marker, InsuTAG (fasting insulin × fasting triglycerides) can predict insulin resistance (IR) and metabolic syndrome (MetS). Data of 618 participants from the Retirement Health and Lifestyle Study (RHLS) were evaluated for the current st...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-15460-z
更新日期：2017-11-09 00:00:00
abstract：:The Dirac materials, such as graphene and three-dimensional topological insulators, have attracted much attention because they exhibit novel quantum phenomena with their low energy electrons governed by the relativistic Dirac equations. One particular interest is to generate Dirac cone anisotropy so that the electrons...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep05385
更新日期：2014-06-20 00:00:00
abstract：:The sensitivity and accuracy of the Risk/Injury/Failure/Loss/End-stage (RIFLE) versus acute kidney injury Network (AKIN) criteria for acute kidney injury (AKI) in critically ill patients remains uncertain. Therefore, we performed a systematic review and meta-analysis to investigate the incidence and prognostic value o...
journal_title：Scientific reports
pub_type： 杂志文章,meta分析
doi：10.1038/srep17917
更新日期：2015-12-07 00:00:00
abstract：:Insects are ectothermal animals that are constrained in their survival and reproduction by external temperature fluctuations which require either active avoidance of or movement towards a given heat source. In Drosophila, different thermoreceptors and neurons have been identified that mediate temperature sensation to ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-80103-9
更新日期：2021-01-08 00:00:00
abstract：:The formation of Pb, Zn, and Cu carboxylates (soaps) has caused visible deterioration in hundreds of oil paintings dating from the 15th century to the present. Through transport phenomena not yet understood, free fatty acids in the oil binding medium migrate through the paint and react with pigments containing heavy m...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-11525-1
更新日期：2017-09-14 00:00:00
