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Docking Sites (docking + site)

Distribution by Scientific Domains
Chemistry66%

Selected Abstracts

An agonistic mAb directed to the TrkC receptor juxtamembrane region defines a trophic hot spot and interactions with p75 coreceptors

DEVELOPMENTAL NEUROBIOLOGY, Issue 3 2010
Veronique Guillemard
Abstract The D5 domain of TrkC receptors is a docking site for Neurotrophin-3 (NT-3), but other domains may be relevant for function or harmonizing signals with p75NTR coreceptors. We report a monoclonal antibody (mAb) 2B7 targeting the juxtamembrane domain of TrkC. mAb 2B7 binds to murine and human TrkC receptors and is a functional agonist that affords activation of TrkC, AKT, and MAPK. These signals result in cell survival but not in cellular differentiation. Monomeric 2B7 Fabs also affords cell survival. Binding of 2B7 mAb and 2B7 Fabs to TrkC are blocked by NT-3 in a dose-dependent manner but not by pro-NT-3. Expression of p75NTR coreceptors on the cell surface block the binding and function of mAb 2B7, whereas NT-3 binding and function are enhanced. mAb 2B7 defines a previously unknown neurotrophin receptor functional hot spot; that exclusively generates survival signals; that can be activated by non-dimeric ligands; and potentially unmasks a site for p75-TrkC interactions. © 2009 Wiley Periodicals, Inc. Develop Neurobiol, 2010. [source]

Structure, regulation and evolution of Nox-family NADPH oxidases that produce reactive oxygen species

FEBS JOURNAL, Issue 13 2008
Hideki Sumimoto
NADPH oxidases of the Nox family exist in various supergroups of eukaryotes but not in prokaryotes, and play crucial roles in a variety of biological processes, such as host defense, signal transduction, and hormone synthesis. In conjunction with NADPH oxidation, Nox enzymes reduce molecular oxygen to superoxide as a primary product, and this is further converted to various reactive oxygen species. The electron-transferring system in Nox is composed of the C-terminal cytoplasmic region homologous to the prokaryotic (and organelle) enzyme ferredoxin reductase and the N-terminal six transmembrane segments containing two hemes, a structure similar to that of cytochrome b of the mitochondrial bc1 complex. During the course of eukaryote evolution, Nox enzymes have developed regulatory mechanisms, depending on their functions, by inserting a regulatory domain (or motif) into their own sequences or by obtaining a tightly associated protein as a regulatory subunit. For example, one to four Ca2+ -binding EF-hand motifs are present at the N-termini in several subfamilies, such as the respiratory burst oxidase homolog (Rboh) subfamily in land plants (the supergroup Plantae), the NoxC subfamily in social amoebae (the Amoebozoa), and the Nox5 and dual oxidase (Duox) subfamilies in animals (the Opisthokonta), whereas an SH3 domain is inserted into the ferredoxin,NADP+ reductase region of two Nox enzymes in Naegleria gruberi, a unicellular organism that belongs to the supergroup Excavata. Members of the Nox1,4 subfamily in animals form a stable heterodimer with the membrane protein p22phox, which functions as a docking site for the SH3 domain-containing regulatory proteins p47phox, p67phox, and p40phox; the small GTPase Rac binds to p67phox (or its homologous protein), which serves as a switch for Nox activation. Similarly, Rac activates the fungal NoxA via binding to the p67phox -like protein Nox regulator (NoxR). In plants, on the other hand, this GTPase directly interacts with the N-terminus of Rboh, leading to superoxide production. Here I describe the regulation of Nox-family oxidases on the basis of three-dimensional structures and evolutionary conservation. [source]

Dok protein family members are involved in signaling mediated by the type 1 Fc, receptor

EUROPEAN JOURNAL OF IMMUNOLOGY, Issue 1 2003
Jakub Abramson
Abstract Aggregation of type 1 Fc, receptors (Fc,RI) on mast cells activates a biochemical cascade that culminates in secretion of inflammatory mediators, as well as in changes of cell morphology and adhesion properties. Some of the intracellular components involved in the early coupling events are still unidentified. Here we show that two adaptor proteins, downstream of tyrosine kinases (Dok)-1 and Dok-2, are involved in the Fc,RI coupling cascade in the rat mucosal-type mast cells of the RBL-2H3 line. Dok-1 is found to be constitutively associated with the Fc,RI, even in untreated cells, and this interaction is not affected by this receptor's aggregation. Both Dok forms undergo a fast and relatively long-term tyrosyl-phosphorylation. This modification of Dok-1 increases its association with RasGAP, suggesting that it is modulating Ras activity. Indeed, we further found that Fc,RI-mediated Ras/Raf1/Erk signaling as well as the de novo synthesis of TNF-, are markedly reduced in cells overexpressing Dok-1. Moreover, Fc,RI clustering causes both Dok-1 and Dok-2 to become docking sites for other signaling molecules including Nck, CrkL and Cas. The latter proteins have been implicated particularly in regulation of the actin-cytoskeletal reorganization. Hence Dok-1/Dok-2 may also be involved in the Fc,RI-stimulated processes of cytoskeleton rearrangement required for cell adhesion, membrane ruffling and exocytosis. [source]

CO migration pathways in cytochrome P450cam studied by molecular dynamics simulations

PROTEIN SCIENCE, Issue 5 2007
Liliane Mouawad
Abstract Previous laser flash photolysis investigations between 100 and 300 K have shown that the kinetics of CO rebinding with cytochrome P450cam(camphor) consist of up to four different processes revealing a complex internal dynamics after ligand dissociation. In the present work, molecular dynamics simulations were undertaken on the ternary complex P450cam(cam)(CO) to explore the CO migration pathways, monitor the internal cavities of the protein, and localize the CO docking sites. One trajectory of 1 nsec with the protein in a water box and 36 trajectories of 1 nsec in the vacuum were calculated. In each trajectory, the protein contained only one CO ligand on which no constraints were applied. The simulations were performed at 200, 300, and 320 K. The results indicate the presence of seven CO docking sites, mainly hydrophobic, located in the same moiety of the protein. Two of them coincide with xenon binding sites identified by crystallography. The protein matrix exhibits eight persistent internal cavities, four of which corresponding to the ligand docking sites. In addition, it was observed that water molecules entering the protein were mainly attracted into the polar pockets, far away from the CO docking sites. Finally, the identified CO migration pathways provide a consistent interpretation of the experimental rebinding kinetics. [source]

Methodology for Multi-Site Ligand,Protein Docking Identification Developed for the Optimization of Spirostenol Inhibition of , -Amyloid-Induced Neurotoxicity

CHEMISTRY & BIODIVERSITY, Issue 11 2005

Spirostenol steroids have been found to inhibit , -amyloid-induced neurotoxicity. We have evaluated in parallel experimental and molecular-modeling studies the relative effectiveness of 17 (22R)-hydroxycholesterol derivatives in binding to the target peptide. Our results support the previous evidence that , -amyloid offers multiple docking sites for these steroids. Molecular modeling allowed for the correlation of spirostenol candidate structural differences with a choice of proposed active sites. A multi-site identification technique based on a Site-Identifier Matrix (SIM) was developed that clearly showed the uniqueness of our lead (maximum neurotoxicity inhibition) candidate SP233, with a nearly equal docking affinity for two sites. [source]

Structural Identification of Spectroscopic Substates in Neuroglobin

CHEMPHYSCHEM, Issue 1 2010
Karin Nienhaus Dr.
Abstract The structural origins of infrared absorptions of photodissociated CO in murine neuroglobin (Ngb) are determined by combining Fourier transform infrared (FTIR) spectroscopy and molecular dynamics (MD) simulations. Such an approach allows to identify and characterize both the different conformations of the Ngb active site and the transient ligand docking sites. To capture the influence of the protein environment on the spectroscopy and dynamics, experiments and simulations are carried out for the wild type protein and its F28L and F28W mutants. It is found that a voluminous side chain at position 28 divides site B into two subsites, B' and B". At low temperatures, CO in wt Ngb only migrates to site B' from where it can rebind, and B" is not populated. The spectra of CO in site B' for wt Ngb from simulations and experiments are very similar in spectral shift and shape. They both show doublets, red-shifted with respect to gas-phase CO and split by,8 cm,1. The FTIR spectra of the F28L mutant show additional bands which are also found in the simulations and can be attributed to CO located in substate B". The different bands are mainly related to different orientations of the His64 side chain with respect to the CO ligand. Large red-shifts arise from strong interactions between the HistidineNH and the CO oxygen. After dissociation from the heme iron, the CO ligand visits multiple docking sites. The locations of the primary docking site B and a secondary site C, which corresponds to the Mb Xe4 cavity, could be identified unambiguously. Finally, by comparing experiment and simulations it is also possible to identify protonation of its , position (His,64 NgbCO) as the preferred heme-bound conformation in the wild type protein with a signal at 1935 cm,1. [source]