Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1117070 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30589500_1.fastq.gz | Fastqsanger.gz | |||
| SRR30589500_2.fastq.gz | Fastqsanger.gz | |||
| SRR30589501_1.fastq.gz | Fastqsanger.gz | |||
| SRR30589501_2.fastq.gz | Fastqsanger.gz | |||
| SRR30589502_1.fastq.gz | Fastqsanger.gz |
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Project description:Liver receptor homolog-1 (LRH-1) is a phospholipid-sensing nuclear receptor that has shown promise as a target for alleviating intestinal inflammation and disease states characterized by metabolic dysregulation in the liver. LRH-1 contains an unusually large ligand binding pocket but generating synthetic modulators has been challenging. Leveraging a hexahydropentalene (6HP) core, we have had recent success in generating potent and efficacious agonists through two distinct strategies. We targeted residues deep within the pocket to enhance compound binding, while residues at the mouth of the pocket were targeted to mimic interactions made by endogenous phospholipids. Here, we unite these two designs into one hybrid molecule to synthesize the most potent LRH-1 agonist to date. Through a combination of global transcriptomic, biochemical, and structural studies, we show that selective modulation can be driven through contacting deep vs. surface polar regions in the pocket. While deep pocket contacts convey high-affinity, contacts with the pocket mouth dominate allostery and provide a phospholipid-like transcriptional response in cultured cells.
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Project description:Stefan2008 - calmodulin allostery
An allosteric model for calmodulin activation, in which binding to calcium facilitates the transition between a low-affinity [tense (T)] and a high-affinity [relaxed (R)] state.
This model is described in the article:
An allosteric model of calmodulin explains differential activation of PP2B and CaMKII.
Stefan MI, Edelstein SJ, Le Novère N
Proc. Natl. Acad. Sci. U.S.A. 2008 Aug; 105(31): 10768-10773
Abstract:
Calmodulin plays a vital role in mediating bidirectional synaptic plasticity by activating either calcium/calmodulin-dependent protein kinase II (CaMKII) or protein phosphatase 2B (PP2B) at different calcium concentrations. We propose an allosteric model for calmodulin activation, in which binding to calcium facilitates the transition between a low-affinity [tense (T)] and a high-affinity [relaxed (R)] state. The four calcium-binding sites are assumed to be nonidentical. The model is consistent with previously reported experimental data for calcium binding to calmodulin. It also accounts for known properties of calmodulin that have been difficult to model so far, including the activity of nonsaturated forms of calmodulin (we predict the existence of open conformations in the absence of calcium), an increase in calcium affinity once calmodulin is bound to a target, and the differential activation of CaMKII and PP2B depending on calcium concentration.
This model is hosted on BioModels Database and identified by: BIOMD0000000183.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.
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