当前位置： SCI文献检索 > Scientific Reports期刊下所有文献 > Exploring the PXR ligand binding mechanism with advanced Molecular Dynamics methods.

Exploring the PXR ligand binding mechanism with advanced Molecular Dynamics methods.

Abstract：

:The Pregnane X Receptor (PXR) is a ligand-activated transcription factor belonging to the nuclear receptor family. PXR can bind diverse drugs and environmental toxicants with different binding modes, making it an intriguing target for drug discovery. Here we investigated the binding mechanism of the SR12813 ligand to elucidate the significant steps, from the ligand entrance pathway into the binding cavity, to the ligand-induced conformational changes, and to the exploration of its alternative binding geometries. We used the advanced Molecular Dynamics-based methods implemented in the BiKi suite and developed specific methodological approaches to overcome the complexity induced by the buried and flexible binding cavity. The adopted methods provided a full dynamic description of the binding event and allowed rationalization of the observed multiple binding modes. These results suggest that the same approach could be exploited for the study of other binding processes with similar characteristics.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Motta S,Callea L,Giani Tagliabue S,Bonati L

doi

10.1038/s41598-018-34373-z

subject

Has Abstract

pub_date

2018-11-01 00:00:00

pages

16207

issue

1

issn

2045-2322

pii

10.1038/s41598-018-34373-z

journal_volume

8

pub_type

杂志文章

相关文献

Scientific Reports文献大全
  • The effect of fluorescent nanodiamonds on neuronal survival and morphogenesis.

    abstract：:Nanodiamond (ND) has emerged as a promising carbon nanomaterial for therapeutic applications. In previous studies, ND has been reported to have outstanding biocompatibility and high uptake rate in various cell types. ND containing nitrogen-vacancy centers exhibit fluorescence property is called fluorescent nanodiamond...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep06919

    authors： Huang YA,Kao CW,Liu KK,Huang HS,Chiang MH,Soo CR,Chang HC,Chiu TW,Chao JI,Hwang E

    更新日期：2014-11-05 00:00:00

  • Form and function of the human and chimpanzee forefoot: implications for early hominin bipedalism.

    abstract：:During bipedal walking, modern humans dorsiflex their forefoot at the metatarsophalangeal joints (MTPJs) prior to push off, which tightens the plantar soft tissues to convert the foot into a stiff propulsive lever. Particular features of metatarsal head morphology such as "dorsal doming" are thought to facilitate this...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep30532

    authors： Fernández PJ,Holowka NB,Demes B,Jungers WL

    更新日期：2016-07-28 00:00:00

  • Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei.

    abstract：:Nitrification directly contributes to the ammonia removal in sponges, and it plays an indispensable role in sponge-mediated nitrogen cycle. Previous studies have demonstrated genomic evidences of nitrifying lineages in the sponge Theonella swinhoei. However, little is known about the transcriptional activity of nitrif...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep24966

    authors： Feng G,Sun W,Zhang F,Karthik L,Li Z

    更新日期：2016-04-26 00:00:00

  • Publisher Correction: Impaired oxidative stress response characterizes HUWE1-promoted X-linked intellectual disability.

    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/s41598-018-24189-2

    authors： Bosshard M,Aprigliano R,Gattiker C,Palibrk V,Markkanen E,Backe PH,Pellegrino S,Raymond FL,Froyen G,Altmeyer M,Bjørås M,Dianov GL,Loon BV

    更新日期：2018-04-12 00:00:00

  • Semi-quantized Spin Pumping and Spin-Orbit Torques in Topological Dirac Semimetals.

    abstract：:We study the time-development processes of spin and charge transport phenomena in a topological Dirac semimetal attached to a ferromagnetic insulator with a precessing magnetization. Compared to conventional normal metals, topological Dirac semimetals manifest a large inverse spin Hall effect when a spin current is pu...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-55802-7

    authors： Misawa T,Nomura K

    更新日期：2019-12-23 00:00:00

  • Confirmation of GLRA3 as a susceptibility locus for albuminuria in Finnish patients with type 1 diabetes.

    abstract：:Urinary albumin excretion is an early sign of diabetic kidney disease, affecting every third individual with diabetes. Despite substantial estimated heritability, only variants in the GLRA3 gene have been genome-wide significantly associated (p-value < 5 × 10-8) with diabetic albuminuria, in Finnish individuals with t...

    journal_title：Scientific reports

    pub_type： 杂志文章,meta分析

    doi：10.1038/s41598-018-29211-1

    authors： Sandholm N,Haukka JK,Toppila I,Valo E,Harjutsalo V,Forsblom C,Groop PH

    更新日期：2018-08-17 00:00:00

  • Quantum gates by periodic driving.

    abstract：:Topological quantum computation has been extensively studied in the past decades due to its robustness against decoherence. One way to realize the topological quantum computation is by adiabatic evolutions-it requires relatively long time to complete a gate, so the speed of quantum computation slows down. In this work...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep22077

    authors： Shi ZC,Wang W,Yi XX

    更新日期：2016-02-25 00:00:00

  • ITCH modulates SIRT6 and SREBP2 to influence lipid metabolism and atherosclerosis in ApoE null mice.

    abstract：:Atherosclerosis is a chronic inflammatory disease characterized by the infiltration of pro-inflammatory macrophages into a lipid-laden plaque. ITCH is an E3 ubiquitin ligase that has been shown to polarize macrophages to an anti-inflammatory phenotype. We therefore investigated the effect of ITCH deficiency on the dev...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep09023

    authors： Stöhr R,Mavilio M,Marino A,Casagrande V,Kappel B,Möllmann J,Menghini R,Melino G,Federici M

    更新日期：2015-03-17 00:00:00

  • In situ structural characterization of early amyloid aggregates in Alzheimer's disease transgenic mice and Octodon degus.

    abstract：:Amyloid plaques composed of Aβ amyloid peptides and neurofibrillary tangles are a pathological hallmark of Alzheimer's disease. In situ identification of early-stage amyloid aggregates in Alzheimer's disease is relevant for their importance as potential targets for effective drugs. Synchrotron-based infrared imaging i...

    journal_title：Scientific reports

    pub_type： 杂志文章,收录出版

    doi：10.1038/s41598-020-62708-2

    authors： Benseny-Cases N,Álvarez-Marimon E,Aso E,Carmona M,Klementieva O,Appelhans D,Ferrer I,Cladera J

    更新日期：2020-04-03 00:00:00

  • Predictors for development of denosumab-induced hypocalcaemia in cancer patients with bone metastases determined by ordered logistic regression analysis.

    abstract：:This retrospective study was undertaken to identify predictors for the development of hypocalcaemia even with prophylactic administration of calcium and vitamin D, and to help guide future strategies to improve the safety, efficacy, and QOL of patients receiving denosumab. Between January 2016 and February 2020, a tot...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-80243-y

    authors： Kanbayashi Y,Sakaguchi K,Hongo F,Ishikawa T,Tabuchi Y,Ukimura O,Takayama K,Taguchi T

    更新日期：2021-01-13 00:00:00

  • Flood-conditioned place aversion as a novel non-pharmacological aversive learning procedure in mice.

    abstract：:The place conditioning paradigm is an efficient, widely-used method to study mechanisms that underlie appetitive or aversive learning and memory processes. However, pharmacological agents used to induce conditioned place preference (CPP) or aversion (CPA) can per se interfere with learning and memory processing, hence...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-25568-5

    authors： Goltseker K,Barak S

    更新日期：2018-05-08 00:00:00

  • Changes in the population and community structure of corals during recent disturbances (February 2016-October 2017) on Maldivian coral reefs.

    abstract：:Climate change is the greatest threat to coral reef ecosystems. In particular, increasing ocean temperatures are causing severe and widespread coral bleaching, contributing to extensive coral loss and degradation of coral reef habitats globally. Effects of coral bleaching are not however, equally apportioned among dif...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-44809-9

    authors： Pisapia C,Burn D,Pratchett MS

    更新日期：2019-06-10 00:00:00

  • Early detection and late cognitive control of emotional distraction by the prefrontal cortex.

    abstract：:Unpleasant emotional distraction can impair the retention of non-emotional information in working memory (WM). Research links the prefrontal cortex with the successful control of such biologically relevant distractors, although the temporal changes in this brain mechanism remain unexplored. We use magnetoencephalograp...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep10046

    authors： García-Pacios J,Garcés P,Del Río D,Maestú F

    更新日期：2015-06-12 00:00:00

  • Studies of the oligomerisation mechanism of a cystatin-based engineered protein scaffold.

    abstract：:Engineered protein scaffolds are an alternative to monoclonal antibodies in research and drug design due to their small size, ease of production, versatility, and specificity for chosen targets. One key consideration when engineering such proteins is retaining the original scaffold structure and stability upon inserti...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-45565-6

    authors： Zalar M,Indrakumar S,Levy CW,Tunnicliffe RB,Peters GHJ,Golovanov AP

    更新日期：2019-06-21 00:00:00

  • Solar thermal polymerase chain reaction for smartphone-assisted molecular diagnostics.

    abstract：:Nucleic acid-based diagnostic techniques such as polymerase chain reaction (PCR) are used extensively in medical diagnostics due to their high sensitivity, specificity and quantification capability. In settings with limited infrastructure and unreliable electricity, however, access to such devices is often limited due...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep04137

    authors： Jiang L,Mancuso M,Lu Z,Akar G,Cesarman E,Erickson D

    更新日期：2014-02-20 00:00:00

  • Development of an embedded multimodality imaging platform for onco-pharmacology using a smart anticancer prodrug as an example.

    abstract：:Increasingly, in vivo imaging holds a strategic position in bio-pharmaceutical innovation. We will present the implementation of an integrated multimodal imaging setup enabling the assessment of multiple, complementary parameters. The system allows the fusion of information provided by: Near infrared fluorescent bioma...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-59561-8

    authors： Raes F,Badiane SM,Renoux B,Papot S,Lerondel S,Le Pape A

    更新日期：2020-02-14 00:00:00

  • Peroxisomes are platforms for cytomegalovirus' evasion from the cellular immune response.

    abstract：:The human cytomegalovirus developed distinct evasion mechanisms from the cellular antiviral response involving vMIA, a virally-encoded protein that is not only able to prevent cellular apoptosis but also to inhibit signalling downstream from mitochondrial MAVS. vMIA has been shown to localize at mitochondria and to tr...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep26028

    authors： Magalhães AC,Ferreira AR,Gomes S,Vieira M,Gouveia A,Valença I,Islinger M,Nascimento R,Schrader M,Kagan JC,Ribeiro D

    更新日期：2016-05-16 00:00:00

  • A Probabilistic Model for Estimating the Depth and Threshold Temperature of C-fiber Nociceptors.

    abstract：:The subjective experience of thermal pain follows the detection and encoding of noxious stimuli by primary afferent neurons called nociceptors. However, nociceptor morphology has been hard to access and the mechanisms of signal transduction remain unresolved. In order to understand how heat transducers in nociceptors ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep17670

    authors： Dezhdar T,Moshourab RA,Fründ I,Lewin GR,Schmuker M

    更新日期：2015-12-07 00:00:00

  • Unprecedented Microbial Conversion of Biliverdin into Bilirubin-10-sulfonate.

    abstract：:Biliverdin (BV) possesses antioxidant and anti-inflammatory properties, with previous reports identifying protection against oxidant and inflammatory injury in animal models. Recent reports indicate that intra-duodenal administration of BV results in the formation of an uncharacterised metabolite, which is potently ab...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-39548-w

    authors： Shiels RG,Vidimce J,Pearson AG,Matthews B,Wagner KH,Battle AR,Sakellaris H,Bulmer AC

    更新日期：2019-02-27 00:00:00

  • Spin-dependent manipulating of vector beams by tailoring polarization.

    abstract：:We examine the spin-dependent manipulating of vector beams by tailoring the inhomogeneous polarization. The spin-dependent manipulating is attributed to the spin-dependent phase gradient in vector beams, which can be regarded as the intrinsic feature of inhomogeneous polarization. The desired polarization can be obtai...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep34276

    authors： Zhou J,Zhang W,Liu Y,Ke Y,Liu Y,Luo H,Wen S

    更新日期：2016-09-28 00:00:00

  • IRGM1 enhances B16 melanoma cell metastasis through PI3K-Rac1 mediated epithelial mesenchymal transition.

    abstract：:Melanoma is one of the most aggressive skin cancers and is well known for its high metastatic rate. Studies have shown that epithelial mesenchymal transition (EMT) is essential for melanoma cell metastasis. However, the molecular mechanisms underlying EMT are still not fully understood. We have shown that IRGM1, a mem...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep12357

    authors： Tian L,Li L,Xing W,Li R,Pei C,Dong X,Fu Y,Gu C,Guo X,Jia Y,Wang G,Wang J,Li B,Ren H,Xu H

    更新日期：2015-07-23 00:00:00

  • Influence of estrogen-related receptor γ (ESRRG) rs1890552 A > G polymorphism on changes in fasting glucose and arterial stiffness.

    abstract：:To determine the effects of the estrogen-related receptor γ (ESRRG) rs1890552 A > G polymorphism on dietary advice-mediated changes in fasting glucose and arterial stiffness, 374 subjects with normal fasting glucose (NFG; control group, no treatment) and 142 subjects with impaired fasting glucose (IFG group, dietary a...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-10192-6

    authors： Kim M,Yoo HJ,Kim M,Seo H,Chae JS,Lee SH,Lee JH

    更新日期：2017-08-29 00:00:00

  • JavaCyte, a novel open-source tool for automated quantification of key hallmarks of cardiac structural remodeling.

    abstract：:Many cardiac pathologies involve changes in tissue structure. Conventional analysis of structural features is extremely time-consuming and subject to observer bias. The possibility to determine spatial interrelations between these features is often not fully exploited. We developed a staining protocol and an ImageJ-ba...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-76932-3

    authors： Winters J,von Braunmuhl ME,Zeemering S,Gilbers M,Brink TT,Scaf B,Guasch E,Mont L,Batlle M,Sinner M,Hatem S,Mansour MK,Fabritz L,Sommerfeld LC,Kirchhof P,Isaacs A,Stoll M,Schotten U,Verheule S

    更新日期：2020-11-18 00:00:00

  • Author Correction: Computer keyboard interaction as an indicator of early Parkinson's disease.

    abstract：:A correction has been published and is appended to both the HTML and PDF versions of this paper. The error has not been fixed in the paper. ...

    journal_title：Scientific reports

    pub_type： 已发布勘误

    doi：10.1038/s41598-018-32121-x

    authors： Giancardo L,Sánchez-Ferro A,Arroyo-Gallego T,Butterworth I,Mendoza CS,Montero P,Matarazzo M,Obeso JA,Gray ML,Estépar RSJ

    更新日期：2018-10-16 00:00:00

  • Low immunogenicity of mouse induced pluripotent stem cell-derived neural stem/progenitor cells.

    abstract：:Resolving the immunogenicity of cells derived from induced pluripotent stem cells (iPSCs) remains an important challenge for cell transplant strategies that use banked allogeneic cells. Thus, we evaluated the immunogenicity of mouse fetal neural stem/progenitor cells (fetus-NSPCs) and iPSC-derived neural stem/progenit...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-13522-w

    authors： Itakura G,Ozaki M,Nagoshi N,Kawabata S,Nishiyama Y,Sugai K,Iida T,Kashiwagi R,Ookubo T,Yastake K,Matsubayashi K,Kohyama J,Iwanami A,Matsumoto M,Nakamura M,Okano H

    更新日期：2017-10-11 00:00:00

  • The corticosteroid compounds prednisolone and vamorolone do not alter the nociception phenotype and exacerbate liver injury in sickle cell mice.

    abstract：:Clinicians often hesitate prescribing corticosteroids to treat corticosteroid-responsive conditions in sickle cell disease (SCD) patients because their use can be associated with complications (increased hospital readmission, rebound pain, strokes, avascular necrosis, acute chest syndrome). Consequently, SCD patients ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-24274-6

    authors： Almeida LEF,Damsker JM,Albani S,Afsar N,Kamimura S,Pratt D,Kleiner DE,Quezado M,Gordish-Dressman H,Quezado ZMN

    更新日期：2018-04-17 00:00:00

  • Inferring Temporal Information from a Snapshot of a Dynamic Network.

    abstract：:The problem of reverse-engineering the evolution of a dynamic network, known broadly as network archaeology, is one of profound importance in diverse application domains. In analysis of infection spread, it reveals the spatial and temporal processes underlying infection. In analysis of biomolecular interaction network...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-38912-0

    authors： Sreedharan JK,Magner A,Grama A,Szpankowski W

    更新日期：2019-02-28 00:00:00

  • Detailed classification of swimming paths in the Morris Water Maze: multiple strategies within one trial.

    abstract：:The Morris Water Maze is a widely used task in studies of spatial learning with rodents. Classical performance measures of animals in the Morris Water Maze include the escape latency, and the cumulative distance to the platform. Other methods focus on classifying trajectory patterns to stereotypical classes representi...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep14562

    authors： Gehring TV,Luksys G,Sandi C,Vasilaki E

    更新日期：2015-10-01 00:00:00

  • Surface modification of microparticles causes differential uptake responses in normal and tumoral human breast epithelial cells.

    abstract：:The use of micro- and nanodevices as multifunctional systems for biomedical applications has experienced an exponential growth during the past decades. Although a large number of studies have focused on the design and fabrication of new micro- and nanosystems capable of developing multiple functions, a deeper understa...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep11371

    authors： Patiño T,Soriano J,Barrios L,Ibáñez E,Nogués C

    更新日期：2015-06-12 00:00:00

  • Adherence to the Mediterranean diet is associated with a higher BMD in middle-aged and elderly Chinese.

    abstract：:Previous studies showed that better adherence to the Mediterranean diet (MD) is associated with lower risk of chronic diseases, but limited data are available on bone health. We investigated the association of the MD with bone mineral density (BMD) in Chinese adults. We included 2371 participants aged 40-75 years in t...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep25662

    authors： Chen GD,Dong XW,Zhu YY,Tian HY,He J,Chen YM

    更新日期：2016-05-09 00:00:00