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Accurate protein structure prediction: what comes next? 准确的蛋白质结构预测:下一步是什么?
BIODESIGN Pub Date : 2021-09-30 DOI: 10.34184/kssb.2021.9.3.47
Chaok Seok, M. Baek, Martin Steinegger, Hahnbeom Park, Gyu Rie Lee, Jonghun Won
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引用次数: 18
Purification and preliminary X-ray analysis of YbeY from Staphylococcus aureus 金黄色葡萄球菌YbeY的纯化及初步x线分析
BIODESIGN Pub Date : 2021-06-30 DOI: 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}
引用次数: 0
Comparative analysis of CSL-binding motifs of SMRT and KyoT2 corepressors SMRT和KyoT2共阻遏子csl结合基序的比较分析
BIODESIGN Pub Date : 2021-06-30 DOI: 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}
引用次数: 0
Purification, crystallization, and X-ray crystallographic analysis of spermidine synthase from Kluyveromyces lactis 克鲁维菌亚精胺合成酶的纯化、结晶和x射线晶体学分析
BIODESIGN Pub Date : 2021-06-30 DOI: 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}
引用次数: 1
Purification, crystallization and X-ray crystallographic analysis of methylmalonyl- CoA epimerase from Metallosphaera sedula 金属球藻甲基丙二酰辅酶a酯酶的纯化、结晶及x射线晶体学分析
BIODESIGN Pub Date : 2021-06-30 DOI: 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}
引用次数: 0
Structure-function relationships of SMC protein complexes for DNA loop extrusion DNA环挤压SMC蛋白复合物的结构-功能关系
BIODESIGN Pub Date : 2021-03-30 DOI: 10.34184/KSSB.2021.9.1.1
Hansol Lee, H. Noh, Je-Kyung Ryu
{"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}
引用次数: 4
Structural mechanism of inhibitor-resistance by ERK2 mutations ERK2突变对抑制剂耐药的结构机制
BIODESIGN Pub Date : 2021-03-30 DOI: 10.34184/KSSB.2021.9.1.14
Y. Park, Myeongbin Kim, S. Ryu
{"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}
引用次数: 0
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