• Genomics & Informatics
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• v.18 no.4
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• pp.39.1-39.8
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• 2020

Alzheimer's disease (AD) is a chronic, progressive brain disorder that slowly destroys affected individuals' memory and reasoning faculties, and consequently, their ability to perform the simplest tasks. This study investigated the hub genes of AD. Proteins interact with other proteins and non-protein molecules, and these interactions play an important role in understanding protein function. Computational methods are useful for understanding biological problems, in particular, network analyses of protein-protein interactions. Through a protein network analysis, we identified the following top 10 hub genes associated with AD: PTGER3, C3AR1, NPY, ADCY2, CXCL12, CCR5, MTNR1A, CNR2, GRM2, and CXCL8. Through gene enrichment, it was identified that most gene functions could be classified as integral to the plasma membrane, G-protein coupled receptor activity, and cell communication under gene ontology, as well as involvement in signal transduction pathways. Based on the convergent functional genomics ranking, the prioritized genes were NPY, CXCL12, CCR5, and CNR2.

• Biomolecules & Therapeutics
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• v.8 no.3
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• pp.276-280
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• 2000

In order to identify the domains of the G$_{\alpha}$16 subunit G protein that are responsible for its activation by the Interleukin-8 receptor, a serious of chimeras between G$_{\alpha}$16 and G$_{\alpha}$11 were assessed for their abilities to be activated by these receptors. Co-expression of IL-8 receptor and chimeras in which the carboxyl-terminal regions of G$_{\alpha}$11 were replaced from 30 up to 156 amino acid residues with the corresponding regions of G$_{\alpha}$16 demonstrated that C-terminal 156 amino acid residues of the G$_{\alpha}$16 were not sufficient to confer IL-8 receptor interaction specificity. Testing of a reciprocal serious of chimeras composed of G$_{\alpha}$16 sequences at the amino terminus and G$_{\alpha}$11 sequences at the carboxyl terminals revealed that sequences extending from the amino tar- minus to amino acid 209 of G$_{\alpha}$16 were sufficient to 7ndow the chimera with 75-80% of interaction specificity for 7-8-induced activation. These results suggest th,.7t combined interactions of the C-terminal 30 amino acid residues and certain domains extending from the arts.ino terminus to amino acid 209 of Gal 6 protein may be involved in its couplings to IL-8 receptor.tain domains extending from the arts.ino terminus to amino acid 209 of Gal 6 protein may be involved in its couplings to IL-8 receptor.

• Archives of Pharmacal Research
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• v.21 no.4
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• pp.423-428
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• 1998

The ligand binding signals to a wide variety of seven transmembrane cell surface receptors are transduced into intracellular signals through heterotrimeric G-proteins. Recently, there have been reports which show diverse coupling patterns of ligand-activated receptors to the members of Gq family $\alpha$ subunits. In order to shed some light on these complex signal processing networks, interactions between G$\alpha$q family of G protein and neurokinin-2 receptor as well as muscarinic M$_{1}$ receptor, which are considered to be new thearpeutic targets in asthma, were studied. Using washed membranes from Cos-7 cells co-transfected with different G.alpha.q and receptor cDNAs, the receptors were stimulated with various concentrations of carbachol and neurokinin A and the agonist-dependent release of [$^3H$]inositol phosphates through phospholipase C beta-1 activation was measured. Differential coupling of Gaq family of G-protein to muscarinic M$_{1}$ receptor and neurokinin-2 receptor was observed. The neurokinin-2 receptor shows a ligand-mediated response in membranes co-transfected with G$\alpha$q, G$\alpha$11 and G$\alpha$14 but not G$\alpha$16 and the ability of the muscarinic $M_1$ receptor to activate phospholipase C through G$\alpha$/11 but not G$\alpha$14 and G$\alpha$16 was demonstrated. Clearly G$\alpha$/11 can couple $\M_1$ and neurokinin-2 receptor to activate phospholipase C. But, there are differences in the relative coupling of the G$\alpha$14 and G$\alpha$16 subunits to these receptors.

• Journal of the Korean Vacuum Society
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• v.16 no.1
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• pp.52-57
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• 2007

The interaction force between biomolecules(DNA-DNA, antigen-antibody, ligand-receptor, protein-protein) defines not only biomolecular function, but also their mechanical properties and hence bio-sensor. Atomic force microscopy(AFM) is nowadays frequently applied to determine interaction forces between biological molecules and biomolecular force measurements, obtained for example using AFM can provide valuable molecular-level information on the interactions between biomolecules. A proper modification of an AFM tip and/or a substrate with biomolecules permits the direct measurement of intermolecular interactions, such as DNA-DNA, protein-protein, and ligand-receptor, etc. and a microcantilever-based sensor appeared as a promising approach for ultra sensitive detection of biomolecular interactions.

• BMB Reports
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• v.34 no.6
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• pp.537-543
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• 2001

In the present study, an in vitro ELISA system to assess the interaction between Src homology (SH)2 domains and phosphotyrosine that contain peptides was established using purified GST-conjugated SH2 proteins and synthetic biotinylated phosphotyrosine that contain oligopeptides. The SH2 domains bound the relevant phosphopeptides that were immobilized in the streptavidin-coated microtiter plate in a highly specific and dose-dependent manner. The epidermal growth factor receptor (EGFR)-, T antigen (T Ag)-, and platelet-derived growth factor receptor (PDGFR)-derived phosphopeptides interacted with the growth factor receptor binding protein (Grb)2/SH2, Lck/SH2, and phosphatidyl inositol 3-kinase (PI3K) p85/SH2, respectively. No cross-reactions were observed. Competitive inhibition experiments showed that a short phosphopeptide of only four amino acids was long enough to determine the binding specificity. Optimal concentrations of the GST-SH2 fusion protein and phosphopeptide in this new ELISA system for screening the binding blockers were chosen at 2nM and 500nM, respectively. When two candidate compounds were tested in our ELISA system, they specifically inhibited the Lck/SH2 and/or p85/SH2 binding to the relevant phosphopeptides. Our results indicate that this ELISA system could be used as an easy screening method for the discovery of specific binding blockers of protein-protein interactions via SH2 domains.

• Biomolecules & Therapeutics
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• v.25 no.1
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• pp.4-11
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• 2017

Heterotrimeric G proteins are key intracellular coordinators that receive signals from cells through activation of cognate G protein-coupled receptors (GPCRs). The details of their atomic interactions and structural mechanisms have been described by many biochemical and biophysical studies. Specifically, a framework for understanding conformational changes in the receptor upon ligand binding and associated G protein activation was provided by description of the crystal structure of the ${\beta}2$-adrenoceptor-Gs complex in 2011. This review focused on recent findings in the conformational dynamics of G proteins and GPCRs during activation processes.

• Molecules and Cells
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• v.38 no.12
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• pp.1111-1117
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• 2015

Toll-like receptor 5 (TLR5) is a specific receptor for microbial flagellin and is one of the most well-known receptors in the TLR family. We reported previously that TLR5 signaling is well maintained during aging and that caveolin-1 may be involved in TLR5 signaling in aged macrophages through direct interactions. Therefore, it is important to clarify whether caveolin-1/TLR5 interactions affect TLR5 expression during aging. To assess the effect of caveolin-1 on TLR5, we analyzed TLR5 expression in senescent fibroblasts and aged tissues expressing high levels of caveolin-1. As expected, TLR5 mRNA and protein expression was well maintained in senescent fibroblasts and aged tissues, whereas TLR4 mRNA and protein were diminished in those cells and tissues. To determine the mechanism of caveolin-1-dependent TLR5 expression, we examined TLR5 expression in caveolin-1 deficient mice. Interestingly, TLR5 mRNA and protein levels were decreased dramatically in tissues from caveolin-1 knockout mice. Moreover, overexpressed caveolin-1 in vitro enhanced TLR5 mRNA through the MAPK pathway and prolonged TLR5 protein half-life through direct interaction. These results suggest that caveolin-1 may play a crucial role in maintaining of TLR5 by regulating transcription systems and increasing protein half-life.

• Molecules and Cells
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• v.38 no.2
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• pp.105-111
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• 2015

The beta2-adrenergic receptor (${\beta}2AR$) belongs to the G protein coupled receptor (GPCR) family, which is the largest family of cell surface receptors in humans. Extra attention has been focused on the human GPCRs because they have been studied as important protein targets for pharmaceutical drug development. In fact, approximately 40% of marketed drugs directly work on GPCRs. GPCRs respond to various extracellular stimuli, such as sensory signals, neurotransmitters, chemokines, and hormones, to induce structural changes at the cytoplasmic surface, activating downstream signaling pathways, primarily through interactions with heterotrimeric G proteins or through G-protein independent pathways, such as arrestin. Most GPCRs, except for rhodhopsin, which contains covalently linked 11 cis-retinal, bind to diffusible ligands, having various conformational states between inactive and active structures. The first human GPCR structure was determined using an inverse agonist bound ${\beta}2AR$ in 2007 and since then, more than 20 distinct GPCR structures have been solved. However, most GPCR structures were solved as inactive forms, and an agonist bound fully active structure is still hard to obtain. In a structural point of view, ${\beta}2AR$ is relatively well studied since its fully active structure as a complex with G protein as well as several inactive structures are available. The structural comparison of inactive and active states gives an important clue in understanding the activation mechanism of ${\beta}2AR$. In this review, structural features of inactive and active states of ${\beta}2AR$, the interaction of ${\beta}2AR$ with heterotrimeric G protein, and the comparison with ${\beta}1AR$ will be discussed.

• Bulletin of the Korean Chemical Society
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• v.28 no.3
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• pp.379-385
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• 2007

Receptor-oriented pharmacophore-based in silico screening is a powerful tool for rapidly screening large number of compounds for interactions with a given protein. Inhibition of the enzyme catechol-Omethyltransferase (COMT) offers a novel possibility for treating Parkinson's disease. Bisubstrate inhibitors of COMT containing the adenine of S-adenosylmethionine (SAM) and a catechol moiety are a new class of potent and selective inhibitor. In the present study, we used receptor-oriented pharmacophore-based in silico screening to examine the interactions between the active site of human COMT and bisubstrate inhibitors. We generated 20 pharmacophore maps, of which 4 maps reproduced the docking model of hCOMT and a bisubstrate inhibitor. Only one of these four, pharmacophore map I, effectively described the common features of a series of bisubstrate inhibitors. Pharmacophore map I consisted of one hydrogen bond acceptor (to Mg2+), three hydrogen bond donors (to Glu199, Glu90, and Gln120), and one hydrophobic feature (an active site region surrounded by several aromatic and hydrophobic residues). This map represented the most essential pharmacophore for explaining interactions between hCOMT and a bisubstrate inhibitor. These results revealed a pharmacophore that should help in the development of new drugs for treating Parkinson's disease.

• Korean Journal of Biological Psychiatry
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• v.7 no.1
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• pp.21-33
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• 2000

As the clinical practice of using more than one drug at a time increase, the clinician is faced with ever-increasing number of potential drug interactions. Although many interactions have little clinical significances, some may interfere with treatment or even be life-threatening. This review provides a better understanding of drug-drug interactions often encountered in pharmacotherapy of depression. Drug interactions can be grouped into two principal subdivisions : pharmacokinetic and pharmacodynamic. These subgroups serve to focus attention on possible sites of interaction as a drug moves from the site of administration and absorption to its site of action. Pharmacokinetic processes are those that include transport to and from the receptor site and consist of absorption, distribution on body tissue, plasma protein binding, metabolism, and excretion. Pharmacodynamic interactions occur at biologically active sites. In this review, emphasis is placed on antidepressant medications, how they are metabolized by the P450 system, and how they alter the metabolism of other drugs. When prescribing antidepressant medications, the clinician must consider the drug-drug interactions that are potentially problematic.