• Bulletin of the Korean Chemical Society
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• v.30 no.7
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• pp.1567-1572
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• 2009

Conformational change of ubiquitin variant with valine to alanine mutation at sequence position 26 was studied by varying solvent pH. Fluorescence emission spectra indicated that this variant ubiquitin has some residual structures in acidic and basic solution as compared to denaturant-induced unfolded state. Far-UV circular dichroic spectra indicated that the base-denatured state had more secondary structure than the acid-denatured state. Near-UV circular dichroic spectra indicated that the aromatic side-chains were in the relatively more rigid environment in the base-denatured state than those in the acid-denatured state. Although it appears that the more tertiary structure present in the base-denatured state, refolding reactions measured by stopped-flow fluorescence device suggest that both the acid- and base-denatured states occur before the major folding transition state. The acid- and base-denatured states are considered to reflect the early event of protein folding process.

• Interdisciplinary Bio Central
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• v.5 no.1
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• pp.2.1-2.3
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• 2013

Birth and development of information biology are introduced with its definition and scientific basis. The discipline lives on the two types of nutrition, one is a huge amount of biological data on genomes, gene expressions, proteomes, protein 3D structures, protein networks, and so forth. The other is the method of using them on a computer. The scientific basis of the two is evolution. To collect genome and gene expression data form laboratories in the world, annotate and dissimilate back to researchers worldwide, they built the EMBL database in Europe in 1982, GenBank in USA in 1984 and DNA Data Bank of Japan in 1987. On the other hand, the methods of using and analyzing those data have accordingly been developed. The two aspects advance the discipline further and further.

• Bulletin of the Korean Chemical Society
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• v.34 no.2
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• pp.565-568
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• 2013

Acetyl-CoA carboxylases (ACCs) play critical roles in fatty acid synthesis and oxidation by the catalytic activity of the carboxylation of acetyl-CoA to malonyl-CoA. It is known that ACCs are inactivated through reversible phosphorylation by AMP-activated protein kinase (AMPK) and allosterically activated by citrate. Here, we determined the crystal structures of biotin carboxylase (BC) domain of human ACC2 phosphorylated by AMPK in the presence of citrate in order to elucidate the activation mechanism by citrate. This structure shows that phosphorylated Ser222 is released from the dimer interface, and thereby facilitating the dimerization or oligomerization of the BC domain allosterically. This structural explanation is coincident with the experimental result that the phosphorylated Ser222 was dephosphorylated more easily by protein phosphatase 2A (PP2A) as the citrate concentration increases.

• KSBB Journal
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• v.27 no.1
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• pp.45-50
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• 2012

In this paper, we investigated the effect of nanostructure on the cell behaviors such as adhesion and growth rate. Nanoporous structures with various diameters (30, 40, 45, 50, 60 nm) and 500 nm of the depth were fabricated using the anodizing method. The water contact angle of the surface consisting of nanopores with 30 nm diameter was 40 degree and those were 60~70 degree in cases of nanopores with over 40 nm diameter. Hela cells were cultivated on various nanoporous structure surface to investigate the cell behavior on nanostructure. As a result, Hela cells preferred 30 nm diameter nanoporous surface that has lower water contact angle. This result was confirmed by protein adsorption experiment and scanning electron microscope investigation.

• Proceeding of EDISON Challenge
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• 2016.03a
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• pp.126-130
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• 2016

Epidermal growth factor receptor(EGFR)는 HER family에 속하는 tyrosine kinase receptor로서 다양한 하류경로로 신호를 전달하여 세포 증식, 혈관 형성, 세포 사멸을 억제하는 역할을 한다. EGFR이 폐암의 형성에 중요한 역할을 하고 많은 상피세포 종양에서 비정상적으로 활성화됨에 따라 암 치료에 중요한 역할을 하고 있어 EGFR tyrosine kinase inhibitor(TKI)에 관한 많은 연구가 이루어졌다. 위와 같은 약 개발에 있어서 현재 가상 시뮬레이션을 통한 약 후보물질 개발이 진행되고 있다. 특히, Molecular docking 시뮬레이션은 기존의 실험적인 기술(X-ray crystallography, NMR)로는 연구하기가 어려웠던 protein과 ligand간의 상호작용을 예측하여 이에 대한 정보를 제공할 수 있다. 하지만, 우선적으로 Molecular docking 시뮬레이션은 정확한 validation을 기반으로 진행되어야 신뢰할 수 있는 정보를 얻을 수 있다. 따라서 이번 연구에서는 EDISON에서 제공하는 Dock 프로그램과 일반적으로 잘 알려진 Glide, Autodock 프로그램으로 protein data bank(PDB)에서 제공하는 EGFR wild type cocrystal을 redocking하는 방식을 통하여 최상위 rank pose의 RMSD 값을 통한 validation 성능을 비교함으로써 어떤 프로그램이 EGFR과 ligand 간의 결합예측을 하는데 있어서 보다 더 정확한 결과를 낼 수 있는지 알아보고자 하였고 시뮬레이션 결과 Autodock에서 가장 우수한 결과 값을 보여주었다.

• BMB Reports
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• v.51 no.12
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• pp.623-629
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• 2018

For mechanical force to induce changes in cellular behaviors, two main processes are inevitable; perception of the force and response to it. Perception of mechanical force by cells, or mechanosensing, requires mechanical force-induced conformational changes in mechanosensors. For this, at least one end of the mechanosensors should be anchored to relatively fixed structures, such as extracellular matrices or the cytoskeletons, while the other end should be pulled along the direction of the mechanical force. Alternatively, mechanosensors may be positioned in lipid bilayers, so that conformational changes in the embedded sensors can be induced by mechanical force-driven tension in the lipid bilayer. Responses to mechanical force by cells, or mechanotransduction, require translation of such mechanical force-induced conformational changes into biochemical signaling. For this, protein-protein interactions or enzymatic activities of mechanosensors should be modulated in response to force-induced structural changes. In the last decade, several molecules that met the required criteria of mechanosensors have been identified and proven to directly sense mechanical force. The present review introduces examples of such mechanosensors and summarizes their mechanisms of action.

• Mass Spectrometry Letters
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• v.10 no.1
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• pp.32-37
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• 2019

The ${\pi}-{\pi}$ interactions of the peptide-dimer and peptide-trimer complexes were investigated in the (VQIVYK + LYQLEN) and (VQIVYK + NNQQNY) mixing solutions. The results showed that tyrosine (Y) residues were critical in the formation of hetero peptide-dimers and -trimers during the early oligomerization process. We used collision-induced dissociation (CID) along with electrospray ionization mass spectroscopy (ESI-MS) to obtain the structural information of the hetero-dimers and -trimers. We chose three amyloidogenic peptides-VQIVYK, NNQQNY, and LYQLEN-from tau protein, yeast prion-like protein Sup35, and insulin chain A, respectively. Hetero-dimer, -trimer, -tetramer, and -pentamer complexes were observed in the mass spectra. The tandem mass spectrum of the hetero-dimer and hetero-trimer showed two different fragmentation patterns (covalent and non-covalent bond dissociation). Y-Y interaction structures were also proposed for the hetero-dimer and -trimer complexes.

• BMB Reports
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• v.55 no.7
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• pp.316-322
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• 2022

Ubiquitin is relatively modest in size but involves almost entire cellular signaling pathways. The primary role of ubiquitin is maintaining cellular protein homeostasis. Ubiquitination regulates the fate of target proteins using the proteasome- or autophagy-mediated degradation of ubiquitinated substrates, which can be either intracellular or foreign proteins from invading pathogens. Legionella, a gram-negative intracellular pathogen, hinders the host-ubiquitin system by translocating hundreds of effector proteins into the host cell's cytoplasm. In this review, we describe the current understanding of ubiquitin machinery from Legionella. We summarize structural and biochemical differences between the host-ubiquitin system and ubiquitin-related effectors of Legionella. Some of these effectors act much like canonical host-ubiquitin machinery, whereas others have distinctive structures and accomplish non-canonical ubiquitination via novel biochemical mechanisms.

• Journal of Sericultural and Entomological Science
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• no.11
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• pp.59-62
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• 1970

Many a fine structures of nuclear polyhedrosis virus in Lepidoptera had been described by electron microscope. In the larva of Antheraea pernyi Guerin, the leading virus causing infectious disease in Korea is disclosed nuclear polyhedrosis virus, which embed bundles of virus particles in the molecular lattice of polyhedra protein. The number of virus particles within a bundle. is on the average four particles, which are enclosed in a intimate membrane closely surrounded with developing membrane. The bundles of four virus particlesare at random embedded in the polyhedra protein, which is originated from the so-called virogenic stroma of chromosom in the infected nuclear.

• Applied Microscopy
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• v.52
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• pp.11.1-11.9
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• 2022

Zoonotic poxvirus infections pose significant threat to human health as we have witnessed recent spread of monkeypox. Therefore, insights into molecular mechanism behind poxvirus replication cycle are needed for the development of efficient antiviral strategies. Virion assembly is one of the key steps that determine the fate of replicating poxviruses. However, in-depth understanding of poxvirus assembly is challenging due to the complex nature of multi-step morphogenesis and heterogeneous virion structures. Despite these challenges, decades of research have revealed virion morphologies at various maturation stages, critical protein components and interactions with host cell compartments. Transmission electron microscopy has been employed as an indispensable tool for the examination of virion morphology, and more recently for the structure determination of protein complexes. In this review, we describe some of the major findings in poxvirus morphogenesis and the contributions of continuously advancing electron microscopy techniques.