{"id":369,"date":"2025-11-15T15:56:32","date_gmt":"2025-11-15T15:56:32","guid":{"rendered":"https:\/\/anhkim.site\/?page_id=369"},"modified":"2025-12-03T12:07:21","modified_gmt":"2025-12-03T12:07:21","slug":"structural-biology","status":"publish","type":"page","link":"https:\/\/anhkim.site\/index.php\/structural-biology\/","title":{"rendered":"STRUCTURAL BIOLOGY"},"content":{"rendered":"
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X-ray Crystallography<\/h2>\n <\/div>\n <\/div>\n
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X-ray crystallography is a structural biology technique that determines the atomic arrangement of molecules by analyzing the diffraction patterns produced when X-rays pass through protein crystals. It offers exceptionally high-resolution\n structural information, making it a gold-standard method for studying well-ordered biomolecules. This technique enables precise visualization of active sites, ligand-binding pockets, and subtle conformational details. We applied\n X-ray crystallography to elucidate DNA-protein\u2013ligand interactions with atomic precision.<\/p>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n

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Cryo-Electron Microscopy<\/h2>\n <\/div>\n <\/div>\n
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Cryo-electron microscopy is an imaging method that captures biomolecules in near-native, vitrified states using electron beams, without requiring crystallization. Its key strength lies in visualizing large, flexible, or complex assemblies\n that are difficult to crystallize, and recent technological advances allow near-atomic resolution for many systems. We are applying CryoEM to study dynamic of macromolecular complexes and membrane proteins. <\/p>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n

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Technical developments\n
in Cryo-EM<\/h3>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n
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We are developing advanced techniques and methodologies to overcome current challenges in cryo-EM sample preparation. In addition, we are establishing new approaches to apply cryo-EM in chemical screening and in the structural determination\n of challenging targets, such as low\u2013molecular-weight proteins.<\/p>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n

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Recent Publications<\/h2>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n
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1.    Lee, J., Kim, T. and Kim, K.K., 2025. Optimizing Sample Preparation for Cryogenic Electron Microscopy. Journal of Visualized Experiments (JoVE)<\/em>, (218), p.e67237.<\/p>\n

2.    Cebi, E., Lee, J., Subramani, V.K., Bak, N., Oh, C. and Kim, K.K., 2024. Cryo-electron microscopy-based drug design. Frontiers in Molecular Biosciences<\/em>, 11<\/em>, p.1342179.Lee, J., Ryu,\n B., Kim, T. and Kim, K.K., 2024. <\/p>\n

3.    Cryo-EM structure of a 16.5-kDa small heat-shock protein from Methanocaldococcus jannaschii. International Journal of Biological Macromolecules<\/em>, 258<\/em>, p.128763.<\/p>\n

4.    Le, K., Kannappan, S., Kim, T., Lee, J.H., Lee, H.R. and Kim, K.K., 2023. Structural understanding of SARS-CoV-2 virus entry to host cells. frontiers in Molecular Biosciences<\/em>, 10<\/em>,\n p.1288686.<\/p>\n

5.    Oh, C., Kim, T.D. and Kim, K.K., 2019. Carboxylic ester hydrolases in bacteria: Active site, structure, function and application. Crystals, 9(11), p.597.<\/p>\n

6.    Kim, D., Hur, J., Han, J.H., Ha, S.C., Shin, D., Lee, S., Park, S., Sugiyama, H. and Kim, K.K., 2018. Sequence preference and structural heterogeneity of BZ junctions. Nucleic acids research<\/em>, 46<\/em>(19),\n pp.10504-10513.<\/p>\n

7.    Oh, C., Ryu, B.H., Yoo, W., Nguyen, D.D., Kim, T., Ha, S.C., Kim, T.D. and Kim, K.K., 2018. Identification and crystallographic analysis of a new carbohydrate acetylesterase (SmAcE1) from Sinorhizobium meliloti.\n Crystals, 8(1), p.12.<\/p>\n

8.    Ngo, T.D., Oh, C., Mizar, P., Baek, M., Park, K.S., Nguyen, L., Byeon, H., Yoon, S., Ryu, Y., Ryu, B.H. and Kim, T.D., 2018. Structural basis for the enantioselectivity of esterase Est-Y29 toward (S)-ketoprofen.\n ACS Catalysis, 9(1), pp.755-767.<\/p>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n <\/div>\n<\/div>","protected":false},"excerpt":{"rendered":"

X-ray Crystallography X-ray crystallography is a structural biology technique that determines the atomic arrangement of molecules by analyzing the diffraction patterns produced when X-rays pass through protein crystals. It offers exceptionally high-resolution structural information, making it a gold-standard method for studying well-ordered biomolecules. This technique enables precise visualization of active sites, ligand-binding pockets, and subtle […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-templates\/full-width-page.php","meta":{"footnotes":""},"class_list":["post-369","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/anhkim.site\/index.php\/wp-json\/wp\/v2\/pages\/369","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/anhkim.site\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/anhkim.site\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/anhkim.site\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/anhkim.site\/index.php\/wp-json\/wp\/v2\/comments?post=369"}],"version-history":[{"count":13,"href":"https:\/\/anhkim.site\/index.php\/wp-json\/wp\/v2\/pages\/369\/revisions"}],"predecessor-version":[{"id":1658,"href":"https:\/\/anhkim.site\/index.php\/wp-json\/wp\/v2\/pages\/369\/revisions\/1658"}],"wp:attachment":[{"href":"https:\/\/anhkim.site\/index.php\/wp-json\/wp\/v2\/media?parent=369"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}