• Macromolecular Research
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• v.17 no.3
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• pp.192-196
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• 2009

Recently, the multi-screening of target materials has been made possible by the development of the surface plasmon resonance (SPR) imaging method. To adapt this method to biochemical analysis, the multi-patterning technology of protein microarrays is required. Among the different methods of fabricating protein microarrays, the microfluidic platform was selected due to its various advantages over other techniques. Microfluidic devices were designed and fabricated with polydimethylsiloxane (PDMS) by the replica molding method. These devices were designed to operate using only capillary force, without the need for additional flow control equipment. With these devices, multiple protein-patterned sensor surfaces were made, to support the two-dimensional detection of various protein-protein interactions with SPR. The fabrication technique of protein microarrays can be applied not only to SPR imaging, but also to other biochemical analyses.

• Genomics & Informatics
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• v.21 no.3
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• pp.41.1-41.11
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• 2023

The Dengue virus M protein is a 75 amino acid polypeptide with two helical transmembranes (TM). The TM domain oligomerizes to form an ion channel, facilitating viral release from the host cells. The M protein has a critical role in the virus entry and life cycle, making it a potent drug target. The oligomerization of the monomeric protein was studied using ab initio modeling and molecular dynamics simulation in an implicit membrane environment. The representative structures obtained showed pentamer as the most stable oligomeric state, resembling an ion channel. Glutamic acid, threonine, serine, tryptophan, alanine, isoleucine form the pore-lining residues of the pentameric channel, conferring an overall negative charge to the channel with approximate length of 51.9 Å. Residue interaction analysis for M protein shows that Ala94, Leu95, Ser112, Glu124, and Phe155 are the central hub residues representing the physicochemical interactions between domains. The virtual screening with 165 different ion channel inhibitors from the ion channel library shows monovalent ion channel blockers, namely lumacaftor, glipizide, gliquidone, glisoxepide, and azelnidipine to be the inhibitors with high docking scores. Understanding the three-dimensional structure of M protein will help design therapeutics and vaccines for Dengue infection.

• IMMUNE NETWORK
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• v.2 no.3
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• pp.125-132
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• 2002

In the past, bioinformatics was often regarded as a difficult and rather remote field, practiced only by computer scientists and not a practical tool available to biologists. However, the various on-going genome projects have had a serious impact on biological sciences in various ways and now there is little doubt that bioinformatics is an essential part of the research environment, with a wealth of biological information to analyze and predict. Fully sequenced genomes made us to have additional insights into the functional properties of the encoded proteins and made it possible to develop new tools and schemes for functional biology on a proteomic scale. Among those are the yeast two-hybrid system, mass spectrometry and microarray: the technology of choice to detect protein-protein interactions. These functional insights emerge as networks of interacting proteins, also known as "pathway informatics" or "interactomics". Without exception it is no longer possible to make advances in the signaling/regulatory pathway studies without integrating information technologies with experimental technologies. In this paper, we will introduce the databases of protein interaction worldwide and discuss several challenging issues regarding the actual implementation of databases.

• BMB Reports
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• v.43 no.2
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• pp.103-109
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• 2010

Modification of proteins by the reversible covalent addition of the small ubiquitin like modifier (SUMO) protein has important consequences affecting target protein stability, sub-cellular localization, and protein-protein interactions. SUMOylation involves a cascade of enzymatic reactions, which resembles the process of ubiquitination. In this study, we characterized the SUMOylation system from an important crop plant, rice, and show that it responds to cold, salt and ABA stress conditions on a protein level via the accumulation of SUMOylated proteins. We also characterized the transcriptional regulation of individual SUMOylation cascade components during stress and development. During stress conditions, majority of the SUMO cascade components are transcriptionally down regulated. SUMO conjugate proteins and SUMO cascade component transcripts accumulated differentially in various tissues during plant development with highest levels in reproductive tissues. Taken together, these data suggest a role for SUMOylation in rice development and stress responses.

• 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.

• BMB Reports
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• v.42 no.1
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• pp.1-5
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• 2009

Synaptic vesicles (SVs) are key structures for synaptic transmission in neurons. Numerous membrane-associated proteins are sorted from the Golgi complex to the axon and the presynaptic terminal. Protein-protein and protein-lipid interactions are involved with SV targeting in neurons. Interestingly, many SV proteins have lipid binding capability, primarily with either cholesterol or phosphoinositides (PIs). As examples, the major SV protein synaptophysin can bind to cholesterol, a major lipid component in SVs, while several other SV proteins, including synaptotagmin, can bind to PIs. Thus, lipid-protein binding plays a key role for the SV targeting of synaptic proteins. In addition, numerous SV proteins can be palmitoylated. Palmitoylation is thought to be another synaptic targeting signal. Here, we briefly describe the relationship between lipid binding and SV targeting.

• Journal of Microbiology and Biotechnology
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• v.9 no.5
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• pp.562-567
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• 1999

Single-stranded DNA binding protein (SSB) is well-characterized as having a helix-destabilizing activity. The helix-destabilizing capability of SSB has been re-examined in this study. The results of restriction endonuclease protection assays and titration experiments suggest that the stimulatory effect of SSB on strand exchange acts by melting out the secondary structure which is inaccessible to RecA protein binding; however, SSB is excluded from regions of secondary structure present in native single-stranded DNA. Complexes of SSB and RecA protein are required for eliminating the secondary structure barriers under optimal conditions for strand exchange.

• Journal of Integrative Natural Science
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• v.10 no.1
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• pp.14-19
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• 2017

Neuromedin, a neuropeptide, which is involved in various functions that include contractile activity on smooth muscle, controlling the blood flow and ion transport in the intestine, increased blood pressure and regulation of adrenocortical function. It is involved in the pathophysiology of various immune mediated inflammatory diseases like asthma. In this study, we have performed protein-protein docking analysis of neuromedin U - neuromedin U receptor 1 complex. We have developed homology models of neuromedin U, and selected a reliable model using model validation. The model was docked with the receptor model, to analyse the crucial interactions of the complex. This study could be helpful as a tool in developing novel and potent drugs for the diseases related with neuromedin U receptor 1.

• Proceedings of the Korean Biophysical Society Conference
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• 2001.06a
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• pp.56-56
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• 2001

Increasing evidence suggests that protein-protein interaction is essential in many biological processes including epithelial transport. In this report, we present the significance of protein interactions to HCO$_3$$^{-10}$ secretion in pancreatic duct cells. In pancreatic ducts HCO$_3$$^{-10}$ secretion is mediated by CFTR-activated luminal CUHCO$_3$$^{-10}$ exchange activity and HCO$_3$$^{-10}$ absorption is achieved by Na$^{＋}$-dependent mechanism including NHE3.(omitted)

• Proceedings of the Korean Biophysical Society Conference
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• 2001.06a
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• pp.21-21
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• 2001

PDZ domains are molecular-recognition elements that mediate protein-protein interactions. The PDZ domain was discovered originally as a common motif present in three structurally related proteins： PSD-95 (postsynaptic density protein), Dlg (discs-large protein) and ZQ-1 (zonula occludens-1). The PDZ domain is globular domain, containing about 80-100 amino acids, and a conserved motif with two alpha helices and six beta strands. Most of them bind selectively to the C-termini of the interacting proteins at the complexes of signaling molecules and membrane associated receptors.(omitted)