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Find video protocols related to scientific articles indexed in Pubmed.
A PH Domain in ACAP1 Possesses Key Features of the BAR Domain in Promoting Membrane Curvature.
Dev. Cell
PUBLISHED: 06-10-2014
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The BAR (Bin-Amphiphysin-Rvs) domain undergoes dimerization to produce a curved protein structure, which superimposes onto membrane through electrostatic interactions to sense and impart membrane curvature. In some cases, a BAR domain also possesses an amphipathic helix that inserts into the membrane to induce curvature. ACAP1 (Arfgap with Coil coil, Ankyrin repeat, and PH domain protein 1) contains a BAR domain. Here, we show that this BAR domain can neither bind membrane nor impart curvature, but instead requires a neighboring PH (Pleckstrin Homology) domain to achieve these functions. Specific residues within the PH domain are responsible for both membrane binding and curvature generation. The BAR domain adjacent to the PH domain instead interacts with the BAR domains of neighboring ACAP1 proteins to enable clustering at the membrane. Thus, we have uncovered the molecular basis for an unexpected and unconventional collaboration between PH and BAR domains in membrane bending.
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Molecular insights into the membrane-associated phosphatidylinositol 4-kinase II?.
Nat Commun
PUBLISHED: 03-05-2014
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Phosphatidylinositol 4-kinase II? (PI4KII?), a membrane-associated PI kinase, plays a central role in cell signalling and trafficking. Its kinase activity critically depends on palmitoylation of its cysteine-rich motif (-CCPCC-) and is modulated by the membrane environment. Lack of atomic structure impairs our understanding of the mechanism regulating kinase activity. Here we present the crystal structure of human PI4KII? in ADP-bound form. The structure identifies the nucleotide-binding pocket that differs notably from that found in PI3Ks. Two structural insertions, a palmitoylation insertion and an RK-rich insertion, endow PI4KII? with the 'integral' membrane-binding feature. Molecular dynamics simulations, biochemical and mutagenesis studies reveal that the palmitoylation insertion, containing an amphipathic helix, contributes to the PI-binding pocket and anchors PI4KII? to the membrane, suggesting that fluctuation of the palmitoylation insertion affects PI4KII?'s activity. We conclude from our results that PI4KII?'s activity is regulated indirectly through changes in the membrane environment.
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Revealing various coupling of electron transfer and proton pumping in mitochondrial respiratory chain.
Curr. Opin. Struct. Biol.
PUBLISHED: 05-07-2013
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Cellular respiration is the process that releases energy from food and supplies energy for life processes. The mitochondrial respiratory chain is the final and most important step for cellular respiration and is located on the inner membrane of mitochondrion and comprises four large trans-membrane protein complexes (respiratory chain Complexes I, II, III and IV) as well as ubiquinone between Complexes I/II and III and cytochrome c between Complexes III and IV. The function of mitochondrial respiratory chain is biological oxidation by transferring electrons from NADH and succinate to oxygen and then generating proton gradient across the inner membrane. Such proton gradient is utilized by ATP synthase (ATPase, also called as Complex V) to produce energy molecules ATP. Structural studies of mitochondrial respiratory membrane protein complexes are important to understand the mechanism of electron transfer and the redox-coupled proton translocation across the inner membrane. Here, according to the time line, we reviewed the great achievements on structural studies of mitochondrial respiratory complexes in the past twenty years as well as the recent research progresses on the structures of mitochondrial respiratory supra-complexes.
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Structural insights into the substrate specificity of human granzyme H: the functional roles of a novel RKR motif.
J. Immunol.
PUBLISHED: 12-09-2011
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Human granzyme H (GzmH) is constitutively expressed in human NK cells that have important roles in innate immune responses against tumors and viruses. GzmH is a chymotrypsin-like serine protease. Its substrate preference and its mechanism of substrate recognition are poorly understood. To provide structural insights into the substrate recognition mechanisms for GzmH, we solved the crystal structures of a D102N-GzmH mutant alone and in complex with a decapeptide substrate and an inhibitor to 2.2 Å, 2.4 Å, and 2.7 Å, respectively. The Thr(189), Gly(216), and Gly(226) specificity triad in the S1 pocket of GzmH defines its preference for bulky, aromatic residues (Tyr and Phe) at the P1 position. Notably, we discovered that an unusual RKR motif (Arg(39)-Lys(40)-Arg(41)), conserved only in GzmH, helps define the S3 and S4 binding regions, indicating the preference for acidic residues at the P3 and P4 sites. Disruption of the RKR motif or the acidic P3 and P4 residues in the substrate abolished the proteolytic activity of GzmH. We designed a tetrapeptide chloromethylketone inhibitor, Ac-PTSY-chloromethylketone, which can selectively and efficiently block the enzymatic and cytotoxic activity of GzmH, providing a useful tool for further studies on the function of GzmH.
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Thiabendazole inhibits ubiquinone reduction activity of mitochondrial respiratory complex II via a water molecule mediated binding feature.
Protein Cell
PUBLISHED: 06-29-2011
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The mitochondrial respiratory complex II or succinate: ubiquinone oxidoreductase (SQR) is a key membrane complex in both the tricarboxylic acid cycle and aerobic respiration. Five disinfectant compounds were investigated with their potent inhibition effects on the ubiquinone reduction activity of the porcine mitochondrial SQR by enzymatic assay and crystallography. Crystal structure of the SQR bound with thiabendazole (TBZ) reveals a different inhibitor-binding feature at the ubiquinone binding site where a water molecule plays an important role. The obvious inhibitory effect of TBZ based on the biochemical data (IC(50) ~100 ?mol/L) and the significant structure-based binding affinity calculation (~94 ?mol/L) draw the suspicion of using TBZ as a good disinfectant compound for nematode infections treatment and fruit storage.
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Autotransporter passenger domain secretion requires a hydrophobic cavity at the extracellular entrance of the ?-domain pore.
Biochem. J.
PUBLISHED: 02-11-2011
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Whooping cough (pertussis) is a highly contagious acute respiratory illness of humans caused by the Gram-negative bacterial pathogen Bordetella pertussis. The AT (autotransporter) BrkA (Bordetella serum-resistance killing protein A) is an important B. pertussis virulence factor that confers serum resistance and mediates adherence. In the present study, we have solved the crystal structure of the BrkA ?-domain at 3 Å (1 Å=0.1 nm) resolution. Special features are a hairpin-like structure formed by the external loop L4, which is observed fortuitously sitting inside the pore of the crystallographic adjacent ?-domain, and a previously undiscovered hydrophobic cavity formed by patches on loop L4 and ?-strands S5 and S6. This adopts a ubiquitous structure characteristic of all AT ?-domains. Mutagenesis studies have demonstrated that the hairpin-like structure and hydrophobic cavity are crucial for BrkA passenger domain (virulence effector) translocation. This structure helps in understanding the molecular mechanism of AT assembly and secretion and provides a potential target for anti-pertussis drug design.
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Crystal structure of group II chaperonin in the open state.
Structure
PUBLISHED: 06-01-2010
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Thermosomes are group II chaperonins responsible for protein refolding in an ATP-dependent manner. Little is known regarding the conformational changes of thermosomes during their functional cycle due to a lack of high-resolution structure in the open state. Here, we report the first complete crystal structure of thermosome (rATcpn?) in the open state from Acidianus tengchongensis. There is a ?30° rotation of the apical and lid domains compared with the previous closed structure. Besides, the structure reveals a conspicuous hydrophobic patch in the lid domain, and residues locating in this patch are conserved across species. Both the closed and open forms of rATcpn? were also reconstructed by electron microscopy (EM). Structural fitting revealed the detailed conformational change from the open to the closed state. Structural comparison as well as protease K digestion indicated only ATP binding without hydrolysis does not induce chamber closure of thermosome.
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Crystallization and preliminary X-ray analysis of cecropin B from Bombyx mori.
Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
PUBLISHED: 04-20-2010
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Cecropin B is a 37-residue cationic antimicrobial peptide derived from the haemolymph of Bombyx mori. The precise mechanism by which cecropins exert their antimicrobial and cytolytic activities is not well understood. Crystals of cecropin B were obtained by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipitant at 289 K. The crystal diffracted to 1.43 A resolution using X-ray radiation and belonged to the orthorhombic space group P1, with unit-cell parameters a = 15.08, b = 22.75, c = 30.20 A, alpha = 96.9, beta = 103.1, gamma = 96.5 degrees. The asymmetric unit contained only one molecule of cecropin B, with a calculated Matthews coefficient of 2.48 A(3) Da(-1) and a solvent content of 50.4%.
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The role and structure of the carboxyl-terminal domain of the human voltage-gated proton channel Hv1.
J. Biol. Chem.
PUBLISHED: 02-10-2010
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The voltage-gated proton channel Hv1 has a voltage sensor domain but lacks a pore domain. Although the C-terminal domain of Hv1 is known to be responsible for dimeric architecture of the channel, its role and structure are not known. We report that the full-length Hv1 is mainly localized in intracellular compartment membranes rather than the plasma membrane. Truncation of either the N or C terminus alone or both together revealed that the N-terminal deletion did not alter localization, but deletion of the C terminus either alone or together with the N terminus resulted in expression throughout the cell. These results indicate that the C terminus is essential for Hv1 localization but not the N terminus. In the 2.0 A structure of the C-terminal domain, the two monomers form a dimer via a parallel alpha-helical coiled-coil, in which one chloride ion binds with the Neta atom of Arg(264). A pH-dependent structural change of the protein has been observed, but it remains a dimer irrespective of pH value.
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Purification, crystallization and preliminary crystallographic analysis of very-long-chain acyl-CoA dehydrogenase from Caenorhabditis elegans.
Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
PUBLISHED: 02-08-2010
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Acyl-CoA dehydrogenase [acyl-CoA:(acceptor) 2,3-oxidoreductase; EC 1.3.99.3] catalyzes the first reaction step in mitochondrial fatty-acid beta-oxidation. Here, the very-long-chain acyl-CoA dehydrogenase from Caenorhabditis elegans (cVLCAD) has been cloned and overexpressed in Escherichia coli strain BL21 (DE3). Interestingly, unlike other very-long-chain acyl-CoA dehydrogenases, cVLCAD was found to form a tetramer by size-exclusion chromatography coupled with in-line static light-scattering, refractive-index and ultraviolet measurements. Purified cVLCAD (12 mg ml(-1)) was successfully crystallized by the hanging-drop vapour-diffusion method under conditions containing 100 mM Tris-HCl pH 8.0, 150 mM sodium chloride, 200 mM magnesium formate and 13% PEG 3350. The crystal has a tetragonal form and a complete diffraction data set was collected and processed to 1.8 A resolution. The crystal belonged to space group C2, with unit-cell parameters a = 138.6, b = 116.7, c = 115.3 A, alpha = gamma = 90.0, beta = 124.0 degrees . A self-rotation function indicated the existence of one noncrystallographic twofold axis. A preliminary molecular-replacement solution further confirmed the presence of two molecules in one asymmetric unit, which yields a Matthews coefficient V(M) of 2.76 A(3) Da(-1) and a solvent content of 55%.
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Expression, purification, crystallization and preliminary crystallographic study of the carboxyl-terminal domain of the human voltage-gated proton channel Hv1.
Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
PUBLISHED: 01-31-2009
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The voltage-gated proton channel Hv1 is essential to proton permeation and contains a voltage-sensor domain without a pore domain. It contains three predicted domains: an N-terminal acid and proline-rich domain, a transmembrane voltage-sensor domain and a C-terminal domain that is responsible for the dimeric architecture of Hv1. Here, the C-terminal domain of the human voltage-gated proton channel Hv1 (C-Hv1) was overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystals have a tetragonal form and diffraction data were collected to 2.5 A resolution in-house. The crystal belongs to space group P4(1)2(1)2, with unit-cell parameters a = b = 37.76, c = 137.52 A. Structural determination of C-Hv1 is in progress.
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Mechanistic insights into regulated cargo binding by ACAP1 protein.
J. Biol. Chem.
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Coat complexes sort protein cargoes into vesicular transport pathways. An emerging class of coat components has been the GTPase-activating proteins (GAPs) that act on the ADP-ribosylation factor (ARF) family of small GTPases. ACAP1 (ArfGAP with coiled-coil, ankyrin repeat, and PH domains protein 1) is an ARF6 GAP that also acts as a key component of a recently defined clathrin complex for endocytic recycling. Phosphorylation by Akt has been shown to enhance cargo binding by ACAP1 in explaining how integrin recycling is an example of regulated transport. We now shed further mechanistic insights into how this regulation is achieved at the level of cargo binding by ACAP1. We initially defined a critical sequence in the cytoplasmic domain of integrin ?1 recognized by ACAP1 and showed that this sequence acts as a recycling sorting signal. We then pursued a combination of structural, modeling, and functional studies, which suggest that phosphorylation of ACAP1 relieves a localized mechanism of autoinhibition in regulating cargo binding. Thus, we have elucidated a key regulatory juncture that controls integrin recycling and also advanced the understanding of how regulated cargo binding can lead to regulated transport.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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