Background: The hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago. The fold appears to have a strong association with fatty acid biosynthesis, its regulation and metabolism, as the proteins with this fold are predominantly coenzyme A-binding enzymes with a variety of substrates located at their active sites.
Sensing and responding to environmental water deficiency and osmotic stresses are essential for the growth, development, and survival of plants. Recently, an osmolality-sensing ion channel called OSCA1 was discovered that functions in sensing hyperosmolality inArabidopsis. Here, we report the cryo-electron microscopy (cryo-EM) structure and function of an OSCA1 homolog from rice (Oryza sativa; OsOSCA1.2), leading to a model of how it could mediate hyperosmolality sensing and transport pathway gating. The structure reveals a dimer; the molecular architecture of each subunit consists of 11 transmembrane (TM) helices and a cytosolic soluble domain that has homology to RNA recognition proteins. The TM domain is structurally related to the TMEM16 family of calcium-dependent ion channels and lipid scramblases. The cytosolic soluble domain possesses a distinct structural feature in the form of extended intracellular helical arms that are parallel to the plasma membrane. These helical arms are well positioned to potentially sense lateral tension on the inner leaflet of the lipid bilayer caused by changes in turgor pressure. Computational dynamic analysis suggests how this domain couples to the TM portion of the molecule to open a transport pathway. Hydrogen/deuterium exchange mass spectrometry (HDXMS) experimentally confirms the conformational dynamics of these coupled domains. These studies provide a framework to understand the structural basis of proposed hyperosmolality sensing in a staple crop plant, extend our knowledge of the anoctamin superfamily important for plants and fungi, and provide a structural mechanism for potentially translating membrane stress to transport regulation.
PCAF (KAT2B) belongs to the GNAT family of lysine acetyltransferases (KAT) and specifically acetylates the histone H3K9 residue and several nonhistone proteins. PCAF is also a transcriptional coactivator. Due to the lack of a PCAF KAT-specific small molecule inhibitor, the exclusive role of the acetyltransferase activity of PCAF is not well understood. Here, we report that a natural compound of the hydroxybenzoquinone class, embelin, specifically inhibits H3Lys9 acetylation in mice and inhibits recombinant PCAF-mediated acetylation with near complete specificity in vitro. Furthermore, using embelin, we have identified the gene networks that are regulated by PCAF during muscle differentiation, further highlighting the broader regulatory functions of PCAF in muscle differentiation in addition to the regulation via MyoD acetylation.
SummaryTriclosan, a well-known inhibitor of Enoyl Acyl Carrier Protein Reductase (ENR) from several pathogenic organisms, is a promising lead compound to design effective drugs. We have solved the X-ray crystal structures of Plasmodium falciparum ENR in complex with triclosan variants having different substituted and unsubstituted groups at different key functional locations. The structures revealed that 4 and 2 0 substituted compounds have more interactions with the protein, cofactor, and solvents when compared with triclosan. New water molecules were found to interact with some of these inhibitors. Substitution at the 2 0 position of triclosan caused the relocation of a conserved water molecule, leading to an additional hydrogen bond with the inhibitor. This observation can help in conserved water-based inhibitor design. 2 0 and 4 0 unsubstituted compounds showed a movement away from the hydrophobic pocket to compensate for the interactions made by the halogen groups of triclosan. This compound also makes additional interactions with the protein and cofactor which compensate for the lost interactions due to the unsubstitution at 2 0 and 4 0 . In cell culture, this inhibitor shows less potency, which indicates that the chlorines at 2 0 and 4 0 positions increase the ability of the inhibitor to cross multilayered membranes. This knowledge helps us to modify the different functional groups of triclosan to get more potent inhibitors.
IUBMBIUBMB Life, 62(6): [467][468][469][470][471][472][473][474][475][476] 2010
1Cryo-EM structure of OSCA1.2 from Oryza sativa: Mechanical basis of 2 hyperosmolality-gating in plants 3 4 5Abstract 46Sensing and responding to environmental water deficiency and osmotic stresses is 47 essential for the growth, development and survival of plants. Recently, sensing ion channel called OSCA1 was discovered that functions in sensing 49 hyperosmolality in Arabidopsis. Here, we report the cryo-EM structure and function of 50 an ion channel from rice (Oryza sativa; OsOSCA1.2), showing how it mediates 51 hyperosmolality sensing and ion permeability. The structure reveals a dimer; the 52 molecular architecture of each subunit consists of eleven transmembrane helices and 53 a cytosolic soluble domain that has homology to RNA recognition proteins. The 54transmembrane domain is structurally related to the TMEM16 family of calcium 55 dependent ion channels and scramblases. The cytosolic soluble domain possesses a 56 distinct structural feature in the form of extended intracellular helical arms that is 57parallel to the plasma membrane. These helical arms are well positioned to sense 58 lateral tension on the inner leaflet of the lipid bilayer caused by changes in turgor 59pressure. Computational dynamic analysis suggests how this domain couples to the 60 transmembrane portion of the molecule to open the channel. Hydrogen-deuterium 61 exchange mass spectrometry (HDXMS) experimentally confirms the conformational 62 dynamics of these coupled domains. The structure provides a framework to 63understand the structural basis of hyperosmolality sensing in an important crop plant, 64 extends our knowledge of the anoctamin superfamily important for plants and fungi, 65and provides a structural mechanism for translating membrane stress to ion transport 66 regulation. 67 68Introduction 69Hyperosmolarity and osmotic stress are among the first physiological responses to 70 changes in salinity and drought. Hyperosmolality triggers increases in cytosolic free 71Ca 2+ concentration and thereby initiates an osmotic stress-induced signal transduction 72 cascade in plants (1-3). Salinity and drought stress trigger diverse protective 73 mechanisms in plants enabling enhanced drought tolerance and reduction of water 74 loss in leaves. 75 76Ion channels have long been hypothesized as sensors of osmotic stress. A candidate 77 membrane protein named OSCA was isolated in a genetic screen for mutants that 78impair the rapid osmotic stress-induced Ca 2+ elevation in plants (1). OSCA1 encodes 79 a multi-spanning membrane protein that functions in osmotic/mechanical stress-80induced activation of ion currents. However, the underlying mechanisms and whether 81OSCA1 itself encodes an ion conducting pore specific for Ca 2+ requires further 82analysis. OSCA1 is a member of a larger gene family in Arabidopsis with 15 members 83(4), and with many homologs encoded in other plants and fungal genomes. 84Furthermore, evolutionary analyses have revealed that OSCA is distantly related to 85 the anoctamin superfamily, that includes the TMEM16 family...
The crystal structure of Rv0098, a long-chain fatty acyl-CoA thioesterase from Mycobacterium tuberculosis with bound dodecanoic acid at the active site provided insights into the mode of substrate binding but did not reveal the structural basis of substrate specificities of varying chain length. Molecular dynamics studies demonstrated that certain residues of the substrate binding tunnel are flexible and thus modulate the length of the tunnel. The flexibility of the loop at the base of the tunnel was also found to be important for determining the length of the tunnel for accommodating appropriate substrates. A combination of crystallographic and molecular dynamics studies thus explained the structural basis of accommodating long chain substrates by Rv0098 of M. tuberculosis.
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