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At least 1,423 records · Page 79Linked to original sources
PubMed1997

Erythropoietin induces tyrosine phosphorylation of the interleukin-3 receptor beta subunit (betaIL3) and recruitment of Stat5 to possible Stat5-docking sites in betaIL3.

The receptors for erythropoietin (Epo) and interleukin-3 (IL-3) both induce the ligand-dependent activation of the Jak2 tyrosine kinase. Activated Jak2 then phosphorylates these receptors and thereby recruits various signaling molecules containing the Src homology (SH)-2 domain, including Stat5, to the tyrosine phosphorylated receptors. In the present study, we demonstrate that Epo stimulation induces unidirectional cross-phosphorylation of the IL-3 receptor beta subunit (betaIL3) on tyrosines and its rapid and transient association with Stat5 in murine IL-3-dependent cell lines engineered to express the Epo receptor (EpoR). Using cell lines expressing various EpoR mutants, it was demonstrated that the Epo-induced tyrosine phosphorylation of betaIL3 is dependent on the membrane-proximal EpoR cytoplasmic region involved in the activation of Jak2, but not on the extracellular and transmembrane regions or on the carboxy-terminal 145 amino acid region containing all the intracellular tyrosine residues. It was also shown that IL-3 induces rapid and dose-dependent association of Jak2 with betaIL3. However, Epo failed to induce any detectable association of betaIL3 with Jak2 or the EpoR. The present study also demonstrates that in IL-3-stimulated cells, an ovine Stat5 mutant harboring a substitution of Tyr694 to Phe, which abolishes the tyrosine phosphorylation required for activation, fails to dimerize with endogenous Stat5, shows sustained binding with tyrosine-phosphorylated betaIL3, and inhibits the tyrosine phosphorylation of endogenous Stat5. These results suggest that betaIL3 may have Stat5 docking sites, similar to those found in the EpoR, that facilitate the activation of Stat5 by Jak2 and raise the possibility that Epo may cross-activate or transmodulate the IL-3 receptor signaling pathways.

Animals↗
PubMed1997

Structural consensus in ligand-protein docking identifies recognition peptide motifs that bind streptavidin.

Computational structure prediction of streptavidin-peptide complexes for known recognition sequences and a number of random di-, tri-, and tetrapeptides has been conducted, and mechanisms of peptide recognition with streptavidin have been investigated by a new computational protocol. The structural consensus criterion, which is computed from multiple docking simulations and measures the accessibility of the dominant binding mode, identifies recognition motifs from a set of random peptide sequences, whereas energetic analysis is less discriminatory. The predicted conformations of recognition tripeptide and tetrapeptide sequences are also in structural harmony and composed of peptide fragments that are individually unfrustrated in their bound conformation, resulting in a minimally frustrated energy landscape for recognition peptides.

Amino Acid Sequence↗
PubMed1998

Characterization of receptors with a new negative image: use in molecular docking and lead optimization.

The characterization of receptor binding sites is an important aspect of molecular docking, molecular recognition, and the structure-based design process. This characterization can take several forms: the receptor surface itself can be delineated or described, the space adjacent to the surface can be chemically mapped, or a negative image of the protein binding region can be generated. In this report, we describe a new method of constructing a negative image through generation of a set of spheres. These spheres lie along the receptor surface, and their centers represent possible ligand atom positions. By the method in which they are constructed, these spheres carry a limited amount of energetic and chemical information in addition to their primary geometric information. We test the accuracy of the image by comparing sphere positions to the positions of bound ligand atoms and propose a figure of merit for such tests. Then, we use the spheres to orient ligands in enzyme active sites and show how they can be used to generate low scoring configurations more efficiently than other approaches that search orientation space. In addition, two novel applications of these spheres are described: they are used to help identify structural differences among families of enzymes and to suggest points for ligand modification in analog design.

Algorithms↗
PubMed1998

A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking.

We analyze the contact distance distributions between nonbonded atoms in known protein structures. A complete set of van der Waals (VDW) radii for 24 protein atom types and for crystal-bound water is derived from the contact distance distributions of these atoms with a selected group of apolar atoms. In addition, a set of Coulombic radii for polar atoms is derived from their contacts with water. The contact distance distributions and the two sets of radii are derived in a systematic and self-consistent manner using an iterative procedure. The Coulombic radii for polar atoms are, on average, 0.18 A smaller than their VDW radii. The VDW radius of water is 1.7 A, which is 0.3 A larger than its Coulombic radius. We show that both the VDW and the Coulombic radii of polar atoms are needed in calculating the molecular and solvent-accessible surfaces of proteins. The VDW radii are needed to generate the apolar portions of the surface and the Coulombic radii for the polar portions. The fact that polar atoms have two apparent sizes implies that a hydrophobic cavity has to be larger than a polar cavity in order to accommodate the same number of water molecules. Most surface area calculations have used only one radius for each polar atom. As a result, unreal cavities, grooves, or pockets may be generated if the Coulombic radii of polar atoms are used. On the other hand, if the VDW radii of polar atoms are used, the details of the polar regions of the surface may be lost. The accuracy of the molecular and the solvent-accessible surfaces of proteins can be improved if the radii of polar atoms are allowed to change depending on the nature of their contacting neighbors. The surface of a protein at a protein-protein interface differs from that in solution in that it has to be generated using at least two kinds of probes, one representing a typical apolar atom and the other a typical polar atom. This observation has important implications for docking, which relies on surface complementarity at the interface.

Evaluation Studies as Topic↗
PubMed1998

Docking analysis of a series of cytochrome P-450(14) alpha DM inhibiting azole antifungals.

Binding modes of a series of structurally diverse azole antifungals belonging to triazole and imidazole classes have been studied using molecular modeling techniques. The predictive model was derived from docking experiments. The analysis of the resulting model indicated that the N3 of imidazole and N4 of triazole rings are in coordinate bond forming distances with heme iron. The aromatic ring has been found to interact with Phe87, Tyr96, Val295, Val396 and Ile395 at the hydrophobic site of the cytochrome P-450cam. In addition, the hydrogen bonding interaction between an etherial oxygen of compounds 2, 5, 8, 9 and 12 and Tyr96 OH seem to have a significant role. Solvent accessible surface area calculations suggested that the active site of the cytochrome P-450cam is highly hydrophobic. The results are in consistent with the biological activity of these compounds. The proposed active orientation model of azole antifungals could be useful for the rational design of more potent inhibitors.

Antifungal Agents↗
PubMed1998

Enhanced expression of the insulin receptor substrate-2 docking protein in human pancreatic cancer.

Insulin receptor substrate-2 (IRS-2) is a multisite docking protein implicated in mitogenic signaling after activation of the insulin and insulin-like growth factor (IGF)-I receptors. In the present study, we characterized IRS-2 expression and function in human pancreatic cancer. IRS-2 mRNA and protein were expressed in ASPC-1 and COLO-357 human pancreatic cancer cell lines. Insulin, IGF-I, and IGF-II enhanced the growth of both cell lines, stimulated tyrosine phosphorylation of IRS-2, and increased IRS-2-associated phosphatidylinositol (PI) 3-kinase activity. The mitogenic effects of insulin, IGF-I, and IGF-II were markedly attenuated by the PI 3-kinase inhibitor LY 294002. Northern blot analysis of total RNA extracted from normal and cancerous tissues revealed that IRS-2 mRNA levels were increased in the cancer tissues (P = 0.032). In the normal pancreas, IRS-2 immunoreactivity was present at low levels in some ductal and acinar cells and at moderate levels in a heterogeneous pattern in all of the endocrine islets. In the pancreatic cancers, IRS-2 was abundant in the ductal-like cancer cells. These findings indicate that IRS-2 is overexpressed in human pancreatic cancer and suggest that it may contribute to enhanced mitogenic signaling via the PI 3-kinase pathway, thereby leading to excessive growth stimulation in this malignancy.

Colonic Neoplasms↗
PubMed2003

Evaluation of the third solvent clusters fitting procedure for the prediction of protein-protein interactions based on the results at the CAPRI blind docking study.

To predict protein-protein interactions, rough or coarse handling for the induced fit problem is proposed. Our method involves the overlap of two hydrophobic interactions as "third solvent clusters fitting." Predictions for binding sites and geometric centers were acceptable, but those of the binding axes were poor. In this study, only the largest benzene cluster was used for the third solvent clusters fitting. For the next CAPRI targets, we must perform protein-protein interaction analyses, which include other smaller benzene clusters.

Benzene↗
PubMed2026

Inhibitory mechanism of anthocyanin B-ring substituents on advanced glycation end-product formation through bovine serum albumin binding: Insights from multispectral, molecular docking and proteomics approaches.

This study demonstrated that the inhibitory effect of anthocyanins on AGEs formation is highly dependent on the substitution pattern of the B-ring. Among the four anthocyanins, delphinidin-3-O-glucoside (D3G) exhibited the most potent antiglycation activity across BSA-fructose, MGO, and GO models with half-maximal inhibitory concentration (IC50) of 30.77, 200.29 and 269.97 μM. This superior performance was attributed to the presence of three hydroxyl groups on the B-ring, which facilitates a high-affinity, spontaneous binding interaction with BSA primarily through hydrophobic forces and hydrogen bonding. Spectroscopic and computational analyses revealed that D3G effectively stabilizes the protein scaffold, specifically recovering α-helix content and shielding critical subdomains (IB, IIA, and IIIA). Proteomics data are consistent with a protective binding mechanism, suggesting that D3G reduces the accessibility of key lysine and arginine residues to glycation-induced modifications. These findings provide a structural basis for developing D3G-rich extracts as targeted, structure-based functional ingredients to mitigate glycation-associated food quality degradation and related health issues.

Anthocyanins↗
PubMedDate not supplied

Automated docking of flexible ligands: applications of AutoDock.

AutoDock is a suite of C programs used to predict the bound conformations of a small, flexible ligand to a macromolecular target of known structure. The technique combines simulated annealing for conformation searching with a rapid grid-based method of energy evaluation. This paper reviews recent applications of the technique and describes the enhancements included in the current release.

Carrier Proteins↗
PubMed2001

The concept of docking and protecting groups in biohydroxylation.

The hydroxylation of unactivated carbon atoms employing methods developed in the realms of classical organic chemistry is difficult to achieve and the processes available lack the degree of chemo-, regio- and enantioselectivity required for organic synthesis. To improve this situation, the concept of docking/protecting groups should enable the organic chemist to employ biohydroxylation as an easy tool for preparative work. Similar to the common practice of using protective groups in organic chemistry, a docking/protecting (d/p) group is introduced first, then the biotransformation is performed, and finally the d/p group is removed. The aim of this concept is not only to avoid time consuming microorganism screening methods, but also to improve hydroxylation position predictability, prevent undesired side reactions, aid substrate detection, and product recovery. This approach is successfully applied to carboxylic acids, ketones, aldehydes, and alcohols.

Alcohols↗
PubMed2001

Lipopolysaccharide and ceramide docking to CD14 provokes ligand-specific receptor clustering in rafts.

The glycosylphosphatidylinositol-anchored receptor CD14 plays a major role in the inflammatory response of monocytes to lipopolysaccharide. Here, we describe that ceramide, a constituent of atherogenic lipoproteins, binds to CD14 and induces clustering of CD14 to co-receptors in rafts. In resting cells, CD14 was associated with CD55, the Fcgamma-receptors CD32 and CD64 and the pentaspan CD47. Ceramide further recruited the complement receptor 3 (CD11b/CD18) and CD36 into proximity of CD14. Lipopolysaccharide, in addition, induced co-clustering with Toll-like receptor 4, Fcgamma-RIIIa (CD16a) and the tetraspanin CD81 while CD47 was dissociated. The different receptor complexes may be linked to ligand-specific cellular responses initiated by CD14.

Antigens, CD↗