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Article ; Online: Novel approaches to targeting BRD4.

Kharenko, Olesya A / Hansen, Henrik C

Drug discovery today. Technologies

2017 Volume 24, Page(s) 19–24

Abstract: Inhibition of bromo and extra-terminal (BET) bromodomains, including BRD4, has emerged as a new exciting epigenetic target for oncology, in particular. Recently, novel alternatives to the traditional use of reversible small molecules have emerged, ... ...

Abstract	Inhibition of bromo and extra-terminal (BET) bromodomains, including BRD4, has emerged as a new exciting epigenetic target for oncology, in particular. Recently, novel alternatives to the traditional use of reversible small molecules have emerged, including proteolytic targeting BET agents and irreversible binding inhibitors. These alternatives to reversible inhibitors may offer some advantage and can be used as tools to further decipher the underlying biology. Supportive pre-clinical data have these novel approaches bound for clinical development in the near future.
MeSH term(s)	Animals ; Drug Discovery ; Humans ; Nuclear Proteins/antagonists & inhibitors ; Nuclear Proteins/metabolism ; Proteins/antagonists & inhibitors ; Proteins/metabolism ; Transcription Factors/antagonists & inhibitors ; Transcription Factors/metabolism
Chemical Substances	BRD4 protein, human ; Nuclear Proteins ; Proteins ; Transcription Factors ; bromodomain and extra-terminal domain protein, human
Language	English
Publishing date	2017-10-28
Publishing country	England
Document type	Journal Article ; Review
ISSN	1740-6749
ISSN (online)	1740-6749
DOI	10.1016/j.ddtec.2017.10.003
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Article ; Online: Synthesis of NVS-BPTF-1 and evaluation of its biological activity.

Mélin, Léa / Calosing, Cyrus / Kharenko, Olesya A / Hansen, Henrik C / Gagnon, Alexandre

Bioorganic & medicinal chemistry letters

2021 Volume 47, Page(s) 128208

Abstract: BPTF (bromodomain and PHD finger containing transcription factor) is a multidomain protein that plays essential roles in transcriptional regulation, T-cell homeostasis and stem cell pluripotency. As part of the chromatin remodeling complex hNURF ( ... ...

Abstract	BPTF (bromodomain and PHD finger containing transcription factor) is a multidomain protein that plays essential roles in transcriptional regulation, T-cell homeostasis and stem cell pluripotency. As part of the chromatin remodeling complex hNURF (nucleosome remodeling factor), BPTF epigenetic reader subunits are particularly important for BPTF cellular function. Here we report the synthesis of NVS-BPTF-1, a previously reported highly potent and selective BPTF-bromodomain inhibitor. Evaluation of the impact of the inhibition of BPTF-bromodomain using NVS-BPTF-1 on selected proteins involved in the antigen processing pathway revealed that exclusively targeting BPTF-bromodomain is insufficient to observe an increase of PSMB8, PSMB9, TAP1 and TAP2 proteins.
MeSH term(s)	Antigens, Nuclear ; Dose-Response Relationship, Drug ; Humans ; Molecular Structure ; Nerve Tissue Proteins/antagonists & inhibitors ; Structure-Activity Relationship ; Transcription Factors/antagonists & inhibitors
Chemical Substances	Antigens, Nuclear ; Nerve Tissue Proteins ; Transcription Factors ; fetal Alzheimer antigen
Language	English
Publishing date	2021-06-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1063195-1
ISSN	1464-3405 ; 0960-894X
ISSN (online)	1464-3405
ISSN	0960-894X
DOI	10.1016/j.bmcl.2021.128208
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Article ; Online: Combination of ZEN-3694 with CDK4/6 inhibitors reverses acquired resistance to CDK4/6 inhibitors in ER-positive breast cancer.

Kharenko, Olesya A / Patel, Reena G / Calosing, Cyrus / van der Horst, Edward H

Cancer gene therapy

2021 Volume 29, Issue 6, Page(s) 859–869

Abstract: CDK4/6 inhibitors significantly prolong progression-free survival in patients with advanced hormone receptor-positive (HR+) HER2-negative breast cancer. Despite recent successes, patients acquire resistance, necessitating the development of additional ... ...

Abstract	CDK4/6 inhibitors significantly prolong progression-free survival in patients with advanced hormone receptor-positive (HR+) HER2-negative breast cancer. Despite recent successes, patients acquire resistance, necessitating the development of additional novel therapeutic strategies. Bromodomain and extra-terminal domain (BET) proteins are key epigenetic regulators that interact with acetylated lysine (AcLys) residues of histones or transcription factors. BET proteins are directly involved in modulating estrogen receptor (ER) signaling and the cell cycle. Therefore, BET inhibitors can potentially offer new strategies in the treatment of advanced ER+ breast cancer. ZEN-3694 is an orally bioavailable small molecule BET inhibitor currently being evaluated in Phase 1/2 clinical trials (NCT03901469). To assess a potential combination strategy in a CDK4/6i resistant breast cancer population, we investigated the mechanism of action of ZEN-3694 combined with CDK4/6 inhibitors in the ER+ cell lines resistant to palbociclib or abemaciclib. Here, we describe that the combination of ZEN-3694 with CDK4/6i potently inhibits proliferation and induces apoptosis in CDK4/6i resistant cell lines. The resistance to both palbociclib and abemaciclib was associated with the strong upregulation of CDK6 and CCND1 protein levels, which was reversed by the ZEN-3694 treatment. Furthermore, RNAseq data and pathway analysis elucidated the combinatorial effects of ZEN-3694 with CDK4/6 inhibitors through significant downregulation of multiple pathways involved in cell cycle regulation, cellular growth, proliferation, apoptosis, inflammation, and cellular immune response. Our data indicate that ZEN-3694 has therapeutic potential in combination with CDK4/6 inhibitors in patients with advanced ER+ breast resistant to CDK4/6 inhibitors.
MeSH term(s)	Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Breast Neoplasms/drug therapy ; Breast Neoplasms/genetics ; Breast Neoplasms/metabolism ; Cell Proliferation ; Clinical Trials, Phase I as Topic ; Clinical Trials, Phase II as Topic ; Cyclin-Dependent Kinase 4/metabolism ; Cyclin-Dependent Kinase 4/therapeutic use ; Female ; Humans ; Protein Kinase Inhibitors/pharmacology ; Protein Kinase Inhibitors/therapeutic use
Chemical Substances	Antineoplastic Agents ; Protein Kinase Inhibitors ; CDK4 protein, human (EC 2.7.11.22) ; Cyclin-Dependent Kinase 4 (EC 2.7.11.22)
Language	English
Publishing date	2021-08-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1212513-1
ISSN	1476-5500 ; 0929-1903
ISSN (online)	1476-5500
ISSN	0929-1903
DOI	10.1038/s41417-021-00375-9
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Article ; Online: Design and Synthesis of LM146, a Potent Inhibitor of PB1 with an Improved Selectivity Profile over SMARCA2.

Mélin, Léa / Gesner, Emily / Attwell, Sarah / Kharenko, Olesya A / van der Horst, Edward H / Hansen, Henrik C / Gagnon, Alexandre

ACS omega

2021 Volume 6, Issue 33, Page(s) 21327–21338

Abstract: PB1 is a bromodomain-containing protein hypothesized to act as the nucleosome-recognition subunit of the PBAF complex. Although PB1 is a key component of the PBAF chromatin remodeling complex, its exact role has not been elucidated due to the lack of ... ...

Abstract	PB1 is a bromodomain-containing protein hypothesized to act as the nucleosome-recognition subunit of the PBAF complex. Although PB1 is a key component of the PBAF chromatin remodeling complex, its exact role has not been elucidated due to the lack of potent and selective inhibitors. Chemical probes that target specific bromodomains within the complex would constitute highly valuable tools to characterize the function and therapeutic pertinence of PB1 and of each of its bromodomains. Here, we report the design and synthesis of lead compound
Language	English
Publishing date	2021-08-09
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.1c01555
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Article ; Online: Breaking boundaries: Pan BETi disrupt 3D chromatin structure, BD2-selective BETi are strictly epigenetic transcriptional regulators.

Tsujikawa, Laura M / Kharenko, Olesya A / Stotz, Stephanie C / Rakai, Brooke D / Sarsons, Christopher D / Gilham, Dean / Wasiak, Sylwia / Fu, Li / Sweeney, Michael / Johansson, Jan O / Wong, Norman C W / Kulikowski, Ewelina

Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie

2022 Volume 152, Page(s) 113230

Abstract: Background: Bromodomain and extraterminal proteins (BETs) are more than just epigenetic regulators of transcription. Here we highlight a new role for the BET protein BRD4 in the maintenance of higher order chromatin structure at Topologically ... ...

Abstract	Background: Bromodomain and extraterminal proteins (BETs) are more than just epigenetic regulators of transcription. Here we highlight a new role for the BET protein BRD4 in the maintenance of higher order chromatin structure at Topologically Associating Domain Boundaries (TADBs). BD2-selective and pan (non-selective) BET inhibitors (BETi) differentially support chromatin structure, selectively affecting transcription and cell viability. Methods: Using RNA-seq and BRD4 ChIP-seq, the differential effect of BETi treatment on the transcriptome and BRD4 chromatin occupancy of human aortic endothelial cells from diabetic patients (dHAECs) stimulated with TNFα was evaluated. Chromatin decondensation and DNA fragmentation was assessed by immunofluorescence imaging and quantification. Key dHAEC findings were verified in proliferating monocyte-like THP-1 cells using real time-PCR, BRD4 co-immunoprecipitation studies, western blots, proliferation and apoptosis assays. Findings: We discovered that 1) BRD4 co-localizes with Ying-Yang 1 (YY1) at TADBs, critical chromatin structure complexes proximal to many DNA repair genes. 2) BD2-selective BETi enrich BRD4/YY1 associations, while pan-BETi do not. 3) Failure to support chromatin structures through BRD4/YY1 enrichment inhibits DNA repair gene transcription, which induces DNA damage responses, and causes widespread chromatin decondensation, DNA fragmentation, and apoptosis. 4) BD2-selective BETi maintain high order chromatin structure and cell viability, while reducing deleterious pro-inflammatory transcription. Interpretation: BRD4 plays a previously unrecognized role at TADBs. BETi differentially impact TADB stability. Our results provide translational insight for the development of BETi as therapeutics for a range of diseases including CVD, chronic kidney disease, cancer, and COVID-19.
MeSH term(s)	COVID-19 ; Cell Cycle Proteins/metabolism ; Chromatin ; Endothelial Cells/metabolism ; Epigenesis, Genetic ; Humans ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Transcription Factors/metabolism
Chemical Substances	BRD4 protein, human ; Cell Cycle Proteins ; Chromatin ; Nuclear Proteins ; Transcription Factors
Language	English
Publishing date	2022-06-07
Publishing country	France
Document type	Journal Article
ZDB-ID	392415-4
ISSN	1950-6007 ; 0753-3322 ; 0300-0893
ISSN (online)	1950-6007
ISSN	0753-3322 ; 0300-0893
DOI	10.1016/j.biopha.2022.113230
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Article: Abscisic acid binds to recombinant Arabidopsis thaliana G-protein coupled receptor-type G-protein 1 in Sacaromycese cerevisiae and in vitro

Kharenko, Olesya A / Choudhary, Pooja / Loewen, Michele C

Plant physiology and biochemistry. 2013 July, v. 68

2013

Abstract: The G-protein coupled receptor-type G-proteins (GTG) 1 and 2 from Arabidopsis thaliana have been proposed to function in the modulation of abscisic acid (ABA) mediated responses to stress and development. In particular it has been suggested that they ... ...

Abstract	The G-protein coupled receptor-type G-proteins (GTG) 1 and 2 from Arabidopsis thaliana have been proposed to function in the modulation of abscisic acid (ABA) mediated responses to stress and development. In particular it has been suggested that they function as ABA receptors based on in planta and in vitro analyses. However a recent independent report was inconsistent with this, suggesting that there is no link between the GTGs and ABA in planta. Here we provide an independent assessment of the ability of ABA to bind to recombinant GTG1 in vitro and in vivo in Sacaromycese cerevisiae. Radio-labelled binding assays on enriched lipid-reconstituted recombinant GTG1, demonstrated specific concentration dependent binding of [³H]-ABA with a dissociation constant (KD) of 80 nM, corroborating previous reports. Assessment of the binding of [³H]-ABA to intact GTG1 expressing yeast, showed GTG1-dependent binding in vivo, yielding a physiologically relevant KD of 0.6 μM. Together these results provide independent evidence of a binding-interaction between ABA and GTG1 in vitro and in vivo, in support of the previously proposed possibility of a biologically relevant interaction between GTG1 and ABA.
Keywords	Arabidopsis thaliana ; G-proteins ; abscisic acid ; dissociation ; radiolabeling ; receptors ; stress response ; yeasts
Language	English
Dates of publication	2013-07
Size	p. 32-36.
Publishing place	Elsevier Masson SAS
Document type	Article
ZDB-ID	742978-2
ISSN	1873-2690 ; 0981-9428
ISSN (online)	1873-2690
ISSN	0981-9428
DOI	10.1016/j.plaphy.2013.03.025
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Article ; Online: Abscisic acid binds to recombinant Arabidopsis thaliana G-protein coupled receptor-type G-protein 1 in Sacaromycese cerevisiae and in vitro.

Kharenko, Olesya A / Choudhary, Pooja / Loewen, Michele C

Plant physiology and biochemistry : PPB

2013 Volume 68, Page(s) 32–36

Abstract	The G-protein coupled receptor-type G-proteins (GTG) 1 and 2 from Arabidopsis thaliana have been proposed to function in the modulation of abscisic acid (ABA) mediated responses to stress and development. In particular it has been suggested that they function as ABA receptors based on in planta and in vitro analyses. However a recent independent report was inconsistent with this, suggesting that there is no link between the GTGs and ABA in planta. Here we provide an independent assessment of the ability of ABA to bind to recombinant GTG1 in vitro and in vivo in Sacaromycese cerevisiae. Radio-labelled binding assays on enriched lipid-reconstituted recombinant GTG1, demonstrated specific concentration dependent binding of [(3)H]-ABA with a dissociation constant (KD) of 80 nM, corroborating previous reports. Assessment of the binding of [(3)H]-ABA to intact GTG1 expressing yeast, showed GTG1-dependent binding in vivo, yielding a physiologically relevant KD of 0.6 μM. Together these results provide independent evidence of a binding-interaction between ABA and GTG1 in vitro and in vivo, in support of the previously proposed possibility of a biologically relevant interaction between GTG1 and ABA.
MeSH term(s)	Abscisic Acid/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Receptors, G-Protein-Coupled/genetics ; Receptors, G-Protein-Coupled/metabolism ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism
Chemical Substances	Arabidopsis Proteins ; Receptors, G-Protein-Coupled ; Recombinant Proteins ; Abscisic Acid (72S9A8J5GW) ; GTG1 protein, Arabidopsis (EC 3.6.1.-)
Language	English
Publishing date	2013-04-12
Publishing country	France
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	742978-2
ISSN	1873-2690 ; 0981-9428
ISSN (online)	1873-2690
ISSN	0981-9428
DOI	10.1016/j.plaphy.2013.03.025
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Article ; Audio / Video: Characterization of the ATP-translocating properties of the predicted Arabidopsis thaliana mitochondrial adenine nucleotide translocator 2

Kharenko, Olesya A / Loewen, Michele C

Botany. 2010 July, v. 88, no. 7

2010

Keywords	Arabidopsis thaliana ; transport proteins ; adenosine triphosphate ; mitochondrial DNA ; recombinant proteins ; active transport ; lipid bodies ; amino acid sequences ; gene expression ; Saccharomyces cerevisiae ; cytochemistry ; cell membranes ; kinetics ; binding sites
Language	English
Dates of publication	2010-07
Size	p. 685-690.
Document type	Article ; Audio / Video
Note	Summary in French.
ZDB-ID	2467208-7
ISSN	1916-2804 ; 1916-2790
ISSN (online)	1916-2804
ISSN	1916-2790
DOI	10.1139/B10-037
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Article: Metal-induced folding of a designed metalloprotein.

Kharenko, Olesya A / Ogawa, Michael Y

Journal of inorganic biochemistry

2004 Volume 98, Issue 11, Page(s) 1971–1974

Abstract: The metal-induced assembly of a designed peptide-based rubredoxin model is described. The C16C19-GGY peptide has the sequence Ac-K(IEALEGK)(2)(CEACEGK)(IEALEGK)GGY-amide in which the presence of the Cys-X-X-Cys metal binding domain of rubredoxin was used ...

Abstract	The metal-induced assembly of a designed peptide-based rubredoxin model is described. The C16C19-GGY peptide has the sequence Ac-K(IEALEGK)(2)(CEACEGK)(IEALEGK)GGY-amide in which the presence of the Cys-X-X-Cys metal binding domain of rubredoxin was used to place cysteine residues at the hydrophobic "a" and "d" positions upon formation of a homodimeric alpha-helical coiled-coil. Circular dichroism spectroscopy shows that the apopeptide exists as a random coil and assembles into a coiled-coil in the presence of Cd(2+). Metal binding is monitored by the appearance of a new LMCT band at 238 nm. UV-Vis titrations and SDS-PAGE experiments are used to show that this designed metalloprotein exists as a metal-bridged coiled-coil dimer.
MeSH term(s)	Amino Acid Sequence ; Cadmium ; Computer Simulation ; Cysteine ; Dimerization ; Metalloproteins/chemistry ; Metalloproteins/drug effects ; Metalloproteins/metabolism ; Metals/chemistry ; Metals/pharmacology ; Models, Molecular ; Molecular Sequence Data ; Peptides/chemistry ; Protein Conformation ; Protein Folding
Chemical Substances	Metalloproteins ; Metals ; Peptides ; Cadmium (00BH33GNGH) ; Cysteine (K848JZ4886)
Language	English
Publishing date	2004-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	162843-4
ISSN	1873-3344 ; 0162-0134
ISSN (online)	1873-3344
ISSN	0162-0134
DOI	10.1016/j.jinorgbio.2004.07.015
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Article ; Online: Molecular mechanisms in the activation of abscisic acid receptor PYR1.

Dorosh, Lyudmyla / Kharenko, Olesya A / Rajagopalan, Nandhakishore / Loewen, Michele C / Stepanova, Maria

PLoS computational biology

2013 Volume 9, Issue 6, Page(s) e1003114

Abstract: The pyrabactin resistance 1 (PYR1)/PYR1-like (PYL)/regulatory component of abscisic acid (ABA) response (RCAR) proteins comprise a well characterized family of ABA receptors. Recent investigations have revealed two subsets of these receptors that, in the ...

Abstract	The pyrabactin resistance 1 (PYR1)/PYR1-like (PYL)/regulatory component of abscisic acid (ABA) response (RCAR) proteins comprise a well characterized family of ABA receptors. Recent investigations have revealed two subsets of these receptors that, in the absence of ABA, either form inactive homodimers (PYR1 and PYLs 1-3) or mediate basal inhibition of downstream target type 2C protein phosphatases (PP2Cs; PYLs 4-10) respectively in vitro. Addition of ABA has been shown to release the apo-homodimers yielding ABA-bound monomeric holo-receptors that can interact with PP2Cs; highlighting a competitive-interaction process. Interaction selectivity has been shown to be mediated by subtle structural variations of primary sequence and ligand binding effects. Now, the dynamical contributions of ligand binding on interaction selectivity are investigated through extensive molecular dynamics (MD) simulations of apo and holo-PYR1 in monomeric and dimeric form as well as in complex with a PP2C, homology to ABA insensitive 1 (HAB1). Robust comparative interpretations were enabled by a novel essential collective dynamics approach. In agreement with recent experimental findings, our analysis indicates that ABA-bound PYR1 should efficiently bind to HAB1. However, both ABA-bound and ABA-extracted PYR1-HAB1 constructs have demonstrated notable similarities in their dynamics, suggesting that apo-PYR1 should also be able to make a substantial interaction with PP2Cs, albeit likely with slower complex formation kinetics. Further analysis indicates that both ABA-bound and ABA-free PYR1 in complex with HAB1 exhibit a higher intra-molecular structural stability and stronger inter-molecular dynamic correlations, in comparison with either holo- or apo-PYR1 dimers, supporting a model that includes apo-PYR1 in complex with HAB1. This possibility of a conditional functional apo-PYR1-PP2C complex was validated in vitro. These findings are generally consistent with the competitive-interaction model for PYR1 but highlight dynamical contributions of the PYR1 structure in mediating interaction selectivity suggesting added degrees of complexity in the regulation of the competitive-inhibition.
MeSH term(s)	Abscisic Acid/metabolism ; Arabidopsis/metabolism ; Arabidopsis Proteins/metabolism ; Kinetics ; Ligands ; Membrane Transport Proteins/metabolism ; Molecular Dynamics Simulation ; Protein Binding
Chemical Substances	Arabidopsis Proteins ; Ligands ; Membrane Transport Proteins ; Pyr1 protein, Arabidopsis ; Abscisic Acid (72S9A8J5GW)
Language	English
Publishing date	2013-06-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1003114
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