• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.294-299
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• 2005

We have studied unbound docking for 12 protein-protein complexes using conformational space annealing (CSA) combined along with statistical pair potentials. The CSA, a powerful global optimization tool, is used to search the conformational space represented by a translational vector and three Euler amgles between two proteins. The energy function consists of three statistical pair-wise energy terms; one from the distance-scaled finite ideal-gas reference state (DFIRE) approach by Zhou and the other two derived from residue-residue contacts. The residue-residue contact terms describe both attractive and repulsive interactions between two residues in contact. The performance of the CSA docking is compared with that of ZDOCK, a well-established protein-protein docking method. The results show that the application of CSA to the protein-protein docking is quite successful, indicating that the CSA combined with a good scoring function is a promising method for the study of protein-protein interaction.

• Molecules and Cells
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• v.26 no.1
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• pp.61-66
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• 2008

Cyclic AMP receptor protein (CRP) is allosterically activated by cAMP and functions as a global transcription regulator in enteric bacteria. Structural information on CRP in the absence of cAMP (apo-CRP) is essential to fully understand its allosteric behavior. In this study we demonstrated interdomain interactions in apo-CRP, using a comparative thermodynamic approach to the intact protein and its isolated domains, which were prepared either by limited proteolysis or using recombinant DNA. Thermal denaturation of the intact apo-CRP, monitored by differential scanning calorimetry, revealed an apparently single cooperative transition with a slight asymmetry. Combined with circular dichroism and fluorescence analysis, the thermal denaturation of apo-CRP could be interpreted as a coupled process involving two individual transitions, each attributable to a structural domain. When isolated individually, both of the domains exhibited significantly altered thermal behavior, thus pointing to the existence of non-covalent interdomain interactions in the intact apo-CRP. These observations suggest that the allosteric conformational change of CRP upon binding to cAMP is achieved by perturbing or modifying pre-existing interdomain interactions. They also underline the effectiveness of a comparative approach using calorimetric and structural probes for studying the thermodynamics of a protein.

• Journal of Animal Science and Technology
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• v.62 no.4
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• pp.533-542
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• 2020

The objective of this study was to observe the interactions between salt-soluble proteins extracted from beef and elephant foot yam (Amorphophallus campanulatus) flour in heat-induced gel matrix development. The effect of salt concentration; 0.5%, 1.0%, 1.5%, and 2.0% in weight/weight basis (w/w), during protein extraction on pH, salt-soluble protein concentration and myofibril fractions of beef extract was determined firstly, and no significant effect was found. The beef salt-soluble proteins extracted using salt solution at different concentrations were then added with elephant foot yam flour at 5%, 10%, and 15% w/w, gelatinized at 90℃ for 20 min, and cooled down at 4℃ for 12 h. The interactions between beef salt-soluble proteins and elephant foot yam flour resulted in an improved gel strength (p < 0.01) and the addition level of elephant foot yam flour affected the pH, instrumental color, moisture, crude protein, and ash content significantly. The addition of elephant foot yam flour also reduced the size of the pores in the gel matrix as shown by scanning electron microscope (SEM) photographs. These suggest that elephant foot yam flour well interacts with beef salt-soluble proteins to form gel matrix.

• BMB Reports
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• v.50 no.9
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• pp.478-483
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• 2017

Budding yeast has dozens of prions, which are mutually dependent on each other for the de novo prion formation. In addition to the interactions among prions, transmissions of prions are strictly dependent on two chaperone systems: the Hsp104 and the Hsp70/Hsp40 (J-protein) systems, both of which cooperatively remodel the prion aggregates to ensure the multiplication of prion entities. Since it has been postulated that prions and the remodeling factors constitute complex networks in cells, a quantitative approach to describe the interactions in live cells would be required. Here, the researchers applied dual-color fluorescence cross-correlation spectroscopy to investigate the molecular network of interaction in single live cells. The findings demonstrate that yeast prions and remodeling factors constitute a network through heterogeneous protein-protein interactions.

• Biomolecules & Therapeutics
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• v.24 no.5
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• pp.517-522
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• 2016

${\beta}$-Arrestins are one of the protein families that interact with G protein-coupled receptors (GPCRs). The roles of ${\beta}$-arrestins are multifaceted, as they mediate different processes including receptor desensitization, endocytosis, and G protein-independent signaling. Thus, determining the GPCR regions involved in the interactions with ${\beta}$-arrestins would be a preliminary step in understanding the molecular mechanisms involved in the selective direction of each function. In the current study, we determined the roles of the N-terminus, intracellular loops, and C-terminal tail of a representative GPCR in the interaction with ${\beta}$-arrestin2. For this, we employed dopamine $D_2$ and $D_3$ receptors ($D_2R$ and $D_3R$, respectively), since they display distinct agonist-induced interactions with ${\beta}$-arrestins. Our results showed that the second and third intracellular loops of $D_2R$ are involved in the agonist-induced translocation of ${\beta}$-arrestins toward plasma membranes. In contrast, the N- and C-termini of $D_2R$ exerted negative effects on the basal interaction with ${\beta}$-arrestins.

• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.299-299
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• 2005

• Journal of Applied Biological Chemistry
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• v.44 no.3
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• pp.125-130
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• 2001

A putative protein encoded by Arabidopsis AtMTN3 gene, a homologue of Medicago truncatula MTN3, consists of 285 amino acid residues, and has a predicted molecular mass of 31.5 kDa and a calculated pI of 9.1. Primary amino acid sequence analyses have revealed that the protein contains seven putative transmembrane regions with N-terminus oriented to the outside of the membrane. The AtMTN3 protein shows overall 16.4% of amino acid identity with the rat GALR3 protein, known to be a G-protein-coupled receptor. The gene is present as a single copy in the Arabidopsis genome, and expressed in aerial parts but not in roots of Arabidopsis. Therefore, AtMTN3 appears not to be specifically involved in Rhizobium-induced nodule development, as was predicted for the MTN3 gene. These proteins possibly mediate signal transmission through G-protein-coupled pathways during general interactions between plants and symbiotic or pathogenic microbes.

• Molecules and Cells
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• v.39 no.9
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• pp.692-698
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• 2016

Advances in next generation sequencing (NGS) technologies have enabled population-level studies for many animals to unravel the relationships between genotypic differences and traits of specific populations. The objective of this study was to perform evolutionary analysis of single nucleotide polymorphisms (SNP) in genes of Korean native cattle Hanwoo in comparison to SNP data from four other cattle breeds (Jersey, Simmental, Angus, and Holstein) and four related species (pig, horse, human, and mouse) obtained from public databases through NGS-based resequencing. We analyzed population structures and differentiation levels for the five cattle breeds and estimated species-specific SNPs with their origins and phylogenetic relationships among species. In addition, we identified Hanwoo-specific genes and proteins, and determined distinct changes in protein-protein interactions among five species (cattle, pig, horse, human, mouse) in the STRING network database by additionally considering indirect protein interactions. We found that the Hanwoo population was clearly different from the other four cattle populations. There were Hanwoo-specific genes related to its meat trait. Protein interaction rewiring analysis also confirmed that there were Hanwoo-specific protein-protein interactions that might have contributed to its unique meat quality.

• Proceedings of the Korean Society of Potoscience Conference
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• spring
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• pp.58-68
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• 2003

• The Microorganisms and Industry
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• v.17 no.1
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• pp.10-18
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• 1991

A phylogenetic comparison of homologous protein can often supplement genetic and biochemical analysis by revealing conserved structures that are critical for function(Waugh et al., 1989). I therefore isolated a secY homologue from B. subtilis, a gram positive bacterium evolutionary distant from E. coli. The comparison and interplay between these two bacterial systems should contribute greatly to our understanding of the functions and interactions within systems evolved for protein translocation in both prokaryotic and eukaryotic organisms.