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At least 1,459 records · Page 81Linked to original sources
PubMed1993

A protein assembly-disassembly pathway in vitro that may correspond to sequential steps of synaptic vesicle docking, activation, and fusion.

The SNARE hypothesis holds that a transport vesicle chooses its target for fusion when a soluble NSF attachment protein (SNAP) receptor on the vesicle (v-SNARE) pairs with its cognate t-SNARE at the target membrane. Three synaptosomal membrane proteins have previously been identified: syntaxin, SNAP-25 (t-SNAREs), and vesicle-associated membrane protein (VAMP) (v-SNARE); all assemble with SNAPs and NSF into 20S fusion particles. We now report that in the absence of SNAP and NSF, these three SNAREs form a stable complex that can also bind synaptotagmin. Synaptotagmin is displaced by alpha-SNAP, suggesting that these two proteins share binding sites on the SNARE complex and implying that synaptotagmin operates as a "clamp" to prevent fusion from proceeding in the absence of a signal. The alpha-SNAP-SNARE complex can bind NSF, and NSF-dependent hydrolysis of ATP dissociates the complex, separating syntaxin, SNAP-25, and VAMP. ATP hydrolysis by NSF may provide motion to initiate bilayer fusion.

Adenosine Triphosphatases↗
PubMed1994

The latch region of calcineurin B is involved in both immunosuppressant-immunophilin complex docking and phosphatase activation.

The immunosuppressants cyclosporin A and FK506, when complexed with their intracellular receptors, prevent T cell activation by directly binding to the phosphatase calcineurin. We have used molecular modeling and mutagenesis to identify sites on calcineurin important for this interaction. We have created calcineurins that are resistant to both cyclosporin A and FK506 by mutating specific residues in CnB, a calcium-binding protein that regulates the catalytic subunit, CnA. Significantly, on a model of CnB, these mutations map to the latch region, an element of tertiary structure that forms when CnB binds CnA. In addition, we show that this latch region plays an important role in activating the catalytic subunit CnA. These results suggest a molecular mechanism for suppression of calcineurin by cyclosporin A and FK506 involving their binding to the same region of CnB used for allosterically activating CnA.

Amino Acid Isomerases↗
PubMed2004

The loading dock.

Explore the source record for details and available documents.

Accidents, Traffic↗
PubMed2006

Phosphatidylinositol 3-phosphate recognition and membrane docking by the FYVE domain.

The FYVE domain is a small zinc binding module that recognizes phosphatidylinositol 3-phosphate [PtdIns(3)P], a phospholipid enriched in membranes of early endosomes and other endocytic vesicles. It is usually present as a single module or rarely as a tandem repeat in eukaryotic proteins involved in a variety of biological processes including endo- and exocytosis, membrane trafficking and phosphoinositide metabolism. A number of FYVE domain-containing proteins are recruited to endocytic membranes through the specific interaction of their FYVE domains with PtdIns(3)P. Structures and PtdIns(3)P binding modes of several FYVE domains have recently been characterized, shedding light on the molecular basis underlying multiple cellular functions of these proteins. Here, structural and functional aspects and the current mechanism of the multivalent membrane anchoring by monomeric or dimeric FYVE domain are reviewed. This mechanism involves stereospecific recognition of PtdIns(3)P that is facilitated by non-specific electrostatic contacts and modulated by the histidine switch, and is accompanied by hydrophobic insertion. Contributions of each component to the FYVE domain specificity and affinity for PtdIns(3)P-containing membranes are discussed.

Amino Acid Sequence↗
PubMed2006

Pex14p, more than just a docking protein.

After binding newly synthesized peroxisomal matrix proteins in the cytosol, the second task of Pex5p, the peroxisomal cycling receptor, is to carry these proteins to the peroxisomal membrane. Defining the nature of the events that occur at this membrane system and which ultimately result in the translocation of the cargo proteins into the matrix of the organelle and in the recycling of Pex5p back to the cytosol, is one of the major goals of the research in this field. Presently, it is generally accepted that all these steps are promoted by a large protein complex embedded in the peroxisomal membrane. This docking/translocation machinery or importomer, as it is often called, comprises many different peroxins of which one of the best characterized is Pex14p. Here, we review data regarding this membrane peroxin with emphasis on the interactions that it establishes with Pex5p. The available evidence suggests that the key to understand how folded proteins are capable of passing an apparently impermeable membrane may largely reside in this pair of peroxins.

Animals↗
PubMed2006

Pex13p: docking or cargo handling protein?

The Src homology 3 (SH3) domain-containing peroxisomal membrane protein Pex13p is an essential component of the import machinery for matrix proteins and forms a binding site for the peroxisomal targeting type I (PTS1) receptor Pex5p. The interaction between these two proteins can be described as novel in several ways. In the yeasts Saccharomyces cerevisiae and Pichia pastoris, the SH3 domain itself is responsible for the interaction but not via the typical P-x-x-P motifs that are common to SH3 ligands as Pex5p lacks such a motif. Instead, a region of Pex5p containing a W-x-x-x-F/Y motif is crucial for this binding. In mammals, again W-x-x-x-F/Y motifs appear to be important for the interaction but the SH3 domain seems not to be the site for Pex5p binding, this being located in the N-terminus of Pex13p. Despite these differences in the details of the Pex13p-Pex5p interaction, the association of the two proteins is a crucial step in Pex5p-mediated protein import into peroxisomes in both yeasts and mammals.

Amino Acid Motifs↗
PubMed2004

Molecular docking of four beta-amyloid1-42 fragments on the alpha7 nicotinic receptor: delineating the binding site of the Abeta peptides.

Three-dimensional structures of the complexes between the Abeta(1-42) fragments Abeta(1-11), Abeta(10-20), Abeta(12-28), and Abeta(22-35) and the alpha7 nicotinic receptor were obtained with the aid of the ESCHER program. Furthermore, short high-temperature molecular dynamics simulations in vacuo were employed to relax the complexes and allow the peptides to accommodate in the binding site. The final models have shown that Abeta peptides do bind on the same site, which is delineated by loop C of one subunit and the loops 62-74 and G of the adjacent subunit on the receptor. This finding is supported by previous experimental and theoretical data, and should help one to obtain a better and more detailed structural information about the activity of the Abeta peptides and their repercussion in the disorders at molecular level, which are characteristic of the Alzheimer's disease.

Amyloid beta-Peptides↗
PubMed2006

Tryptophan and tyrosine to terbium fluorescence resonance energy transfer as a method to "map" aromatic residues and monitor docking.

Fluorescent lanthanide ions, with large Stokes shifts and narrow emission bands, are excellent tools for the development of FRET-based assays. In this work, a terbium ion is tethered to a peptide which binds to the BIR3 domain of XIAP, an anti-apoptotic protein. Excitation of tryptophan and tyrosine residues in the BIR3 domain causes the peptide bound terbium ion to fluoresce relative to its distance from these aromatic residues. By developing ligands with terbium ions tethered at different residues, the relative terbium emission can be used to "map" the aromatic residues within the ligand binding pocket.

Binding Sites↗
PubMedDate not supplied

Exosome secretion and red cell maturation: Exploring molecular components involved in the docking and fusion of multivesicular bodies in K562 cells.

During reticulocyte maturation, some membrane proteins and organelles that are not required in the mature red cell are lost. These proteins are released into the extracellular medium associated with vesicles present in multivesicular bodies (MVBs). Fusion of MVBs with the plasma membrane results in secretion of the small internal vesicles, termed exosomes. By studying MVBs fusion and exosome release in K562 cells, a human erythroleukemic cell line, we have determined the functional significance of Rab11 and calcium in these events. Additionally, in the transformation process that occurs during erythrocyte maturation, intracellular organelles are likely removed as a consequence of autophagic sequestration and degradation. We propose K562 cells as a useful tool to analyze, at the molecular level, the role of autophagy in the terminal differentiation of red cells.

Autophagy↗
PubMed2005

Enantiomeric N-methyl-4-piperidyl benzilates as muscarinic receptor ligands: Radioligand binding studies and docking studies to models of the three muscarinic receptors M1, M2 and M3.

Benzilic ester derivatives with a basic moiety like N-methyl-4-piperidyl benzilates are potential drugs for the treatment of urinary incontinence, duodenal and gastric ulcers and Parkinson's disease. The effect of structural variations of chiral N-methyl-4-piperidyl benzilates was investigated using radioligand binding studies on muscarinic receptors (M1-M3). The results of the binding studies demonstrate that the absolute configuration and the aromatic substituent of benzilates have an influence on muscarinic affinity and selectivity. In this regard, (S)-configuration of benzilates and hydrophilic aromatic substituents seems to enhance muscarinic affinity. A model of the receptor ligand complex for N-methyl-4-piperidyl benzilates was obtained by molecular modelling. Both the affinity of enantiomeric benzilic esters and the subtype selectivity for muscarinic receptors are comprehensively explained by this model.

Animals↗
PubMed2006

Novel diphenyl ethers: design, docking studies, synthesis and inhibition of enoyl ACP reductase of Plasmodium falciparum and Escherichia coli.

We designed some novel diphenyl ethers and determined their binding energies for Enoyl-Acyl Carrier Protein Reductase (ENR) of Plasmodium falciparum using Autodock. Out of these, we synthesized the promising compounds and tested them for their inhibitory activity against ENRs of P. falciparum as well as Escherichia coli. Some of these compounds show nanomolar inhibition of PfENR and low micromolar inhibition of EcENR. They also exhibit low micromolar potency against in vitro cultures of P. falciparum and E. coli. The study of structure-activity relationship of these compounds paves the way for further improvements in the design of novel diphenyl ethers with improved activity against purified enzyme and the pathogens.

Animals↗
PubMed2006

Identification of some novel AHAS inhibitors via molecular docking and virtual screening approach.

Acetohydroxyacid synthase (AHAS; EC 2.2.1.6) catalyzes the first common step in branched-chain amino acid biosynthesis. This enzyme is an important target for the design of environmental-benign herbicides. Based on the crystal structure of AHAS/sulfonylurea complex, we have carried out computational screening of the ACD-3D database in order to look for novel non-sulfonylurea inhibitors of AHAS for the first time. Three novel compounds were found to inhibit plant AHAS in vitro among 14 procured compounds. One compound showed promising activity in vivo for rape root growth inhibition bioassay. This research provided useful clues for further design and discovery of AHAS inhibitors.

Acetolactate Synthase↗
PubMed2006

Paclitaxel binding to human serum albumin--automated docking studies.

A computational approach was used to study the interaction of the potent anticancer drug paclitaxel (Taxol) with human serum albumin. The primary and secondary binding sites were located at the interface of subdomains IIA and IIIA, and in the cleft between domains I and III of the protein, respectively. The C13 side chain and the baccatin core of paclitaxel were found to contribute approximately equally to the binding energy at the primary site, whereas the binding mode appears to be governed by the C13 side chain.

Antineoplastic Agents, Phytogenic↗