Pub Date : 2021-09-30DOI: 10.34184/kssb.2021.9.3.47
Chaok Seok, M. Baek, Martin Steinegger, Hahnbeom Park, Gyu Rie Lee, Jonghun Won
{"title":"Accurate protein structure prediction: what comes next?","authors":"Chaok Seok, M. Baek, Martin Steinegger, Hahnbeom Park, Gyu Rie Lee, Jonghun Won","doi":"10.34184/kssb.2021.9.3.47","DOIUrl":"https://doi.org/10.34184/kssb.2021.9.3.47","url":null,"abstract":"","PeriodicalId":153406,"journal":{"name":"BIODESIGN","volume":"61 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122556805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-30DOI: 10.34184/kssb.2021.9.2.41
Jinwook Lee, Aeran Kown, N. Ha
{"title":"Purification and preliminary X-ray analysis of YbeY from Staphylococcus aureus","authors":"Jinwook Lee, Aeran Kown, N. Ha","doi":"10.34184/kssb.2021.9.2.41","DOIUrl":"https://doi.org/10.34184/kssb.2021.9.2.41","url":null,"abstract":"","PeriodicalId":153406,"journal":{"name":"BIODESIGN","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131513771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-30DOI: 10.34184/kssb.2021.9.2.25
Gwang Sik Kim, Y. C. Lee
{"title":"Comparative analysis of CSL-binding motifs of SMRT and KyoT2 corepressors","authors":"Gwang Sik Kim, Y. C. Lee","doi":"10.34184/kssb.2021.9.2.25","DOIUrl":"https://doi.org/10.34184/kssb.2021.9.2.25","url":null,"abstract":"","PeriodicalId":153406,"journal":{"name":"BIODESIGN","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123957956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-30DOI: 10.34184/kssb.2021.9.2.36
Seongjin Kim, G. T. Nguyen, J. Chang
{"title":"Purification, crystallization, and X-ray crystallographic analysis of spermidine synthase from Kluyveromyces lactis","authors":"Seongjin Kim, G. T. Nguyen, J. Chang","doi":"10.34184/kssb.2021.9.2.36","DOIUrl":"https://doi.org/10.34184/kssb.2021.9.2.36","url":null,"abstract":"","PeriodicalId":153406,"journal":{"name":"BIODESIGN","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116723683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-30DOI: 10.34184/kssb.2021.9.2.32
S. Joo, Seul Hoo Lee, Donghoon Lee, Kyung-Jin Kim
{"title":"Purification, crystallization and X-ray crystallographic analysis of methylmalonyl- CoA epimerase from Metallosphaera sedula","authors":"S. Joo, Seul Hoo Lee, Donghoon Lee, Kyung-Jin Kim","doi":"10.34184/kssb.2021.9.2.32","DOIUrl":"https://doi.org/10.34184/kssb.2021.9.2.32","url":null,"abstract":"","PeriodicalId":153406,"journal":{"name":"BIODESIGN","volume":"48 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121903198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-03-30DOI: 10.34184/KSSB.2021.9.1.1
Hansol Lee, H. Noh, Je-Kyung Ryu
Structural Maintenance of Chromosome (SMC) complexes are vital for chromosome organization. They extrude DNA loops to compact 2 meters of DNA into a micrometer-sized chromosome structure. The DNA loop extrusion process is believed to be a universal mechanism of SMC complexes for spatiotemporal chromosome organization conserved in almost all species from prokaryotes to eukaryotes. However, the molecular mechanism of DNA loop extrusion by SMC complexes is under debate; various tentative mechanistic models have been suggested, but there is no clear consensus. Here, we review the structural studies of various SMC complexes from prokaryotes to eukaryotes to understand the structurefunction relationships of SMC complexes involved in DNA loop extrusion. We introduce controversial observations of the conformations of SMC complexes based on previous reports and discuss various proposed mechanisms of DNA loop extrusion suggested by experimental observations of the conformations of diverse SMC complexes. P 1-13 MINI REVIEW https://doi.org/10.34184/kssb.2021.9.1.1
{"title":"Structure-function relationships of SMC protein complexes for DNA loop extrusion","authors":"Hansol Lee, H. Noh, Je-Kyung Ryu","doi":"10.34184/KSSB.2021.9.1.1","DOIUrl":"https://doi.org/10.34184/KSSB.2021.9.1.1","url":null,"abstract":"Structural Maintenance of Chromosome (SMC) complexes are vital for chromosome organization. They extrude DNA loops to compact 2 meters of DNA into a micrometer-sized chromosome structure. The DNA loop extrusion process is believed to be a universal mechanism of SMC complexes for spatiotemporal chromosome organization conserved in almost all species from prokaryotes to eukaryotes. However, the molecular mechanism of DNA loop extrusion by SMC complexes is under debate; various tentative mechanistic models have been suggested, but there is no clear consensus. Here, we review the structural studies of various SMC complexes from prokaryotes to eukaryotes to understand the structurefunction relationships of SMC complexes involved in DNA loop extrusion. We introduce controversial observations of the conformations of SMC complexes based on previous reports and discuss various proposed mechanisms of DNA loop extrusion suggested by experimental observations of the conformations of diverse SMC complexes. P 1-13 MINI REVIEW https://doi.org/10.34184/kssb.2021.9.1.1","PeriodicalId":153406,"journal":{"name":"BIODESIGN","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132988968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-03-30DOI: 10.34184/KSSB.2021.9.1.14
Y. Park, Myeongbin Kim, S. Ryu
Extracellular signal-regulated kinase (ERK) is a serine-threonine kinase that is involved in the regulation of cellular signals. ERK inhibitors have been developed to treat cancers with B-Raf proto-oncogene mutations. However, the use of these inhibitors in disease settings induces ERK mutations resistant to the inhibitors, which poses major difficulties in effective cancer treatment. Here, we present the crystal structures of the ERK Y36H and G37C mutants that occur in cancer cells resistant to ERK inhibitors. The structures revealed mechanisms by which these mutations confer inhibitor-resistance to ERK. The Y36H mutant structure revealed a resistance mechanism that involves rotations of the His36 residue in the Gly-rich loop and the Tyr64 residue in the helix C, which blocks the entrance of inhibitors to the ATP-binding pocket. Furthermore, the G37C mutant structure exhibited that the mutation-induced rigidity in dihedral angles plays a major role in inducing inhibitor-resistance. Detailed structural information on the resistance mechanism suggests strategy for designing of novel inhibitors that can circumvent mutation-induced inhibitor resistance. P 14-18 ARTICLE https://doi.org/10.34184/kssb.2021.9.1.14
{"title":"Structural mechanism of inhibitor-resistance by ERK2 mutations","authors":"Y. Park, Myeongbin Kim, S. Ryu","doi":"10.34184/KSSB.2021.9.1.14","DOIUrl":"https://doi.org/10.34184/KSSB.2021.9.1.14","url":null,"abstract":"Extracellular signal-regulated kinase (ERK) is a serine-threonine kinase that is involved in the regulation of cellular signals. ERK inhibitors have been developed to treat cancers with B-Raf proto-oncogene mutations. However, the use of these inhibitors in disease settings induces ERK mutations resistant to the inhibitors, which poses major difficulties in effective cancer treatment. Here, we present the crystal structures of the ERK Y36H and G37C mutants that occur in cancer cells resistant to ERK inhibitors. The structures revealed mechanisms by which these mutations confer inhibitor-resistance to ERK. The Y36H mutant structure revealed a resistance mechanism that involves rotations of the His36 residue in the Gly-rich loop and the Tyr64 residue in the helix C, which blocks the entrance of inhibitors to the ATP-binding pocket. Furthermore, the G37C mutant structure exhibited that the mutation-induced rigidity in dihedral angles plays a major role in inducing inhibitor-resistance. Detailed structural information on the resistance mechanism suggests strategy for designing of novel inhibitors that can circumvent mutation-induced inhibitor resistance. P 14-18 ARTICLE https://doi.org/10.34184/kssb.2021.9.1.14","PeriodicalId":153406,"journal":{"name":"BIODESIGN","volume":"58 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132585695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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