Protein Data Bank: the single global archive for 3D macromolecular structure data

Autor: Masashi Yokochi, Ju Yaen Kim, Chenghua Shao, John M. Berrisford, Hongyang Yao, Miron Livny, Stephen Anyango, Abhik Mukhopadhyay, Romana Gáborová, Yi-Ping Tao, Monica Sekharan, Aleksandras Gutmanas, Jose M. Dana, Mandar Deshpande, Charmi Bhikadiya, Yannis Ioannidis, Pedro Romero, Jonathan R. Wedell, Eldon L. Ulrich, Gert-Jan Bekker, Chris Randle, Chunxiao Bi, Jeffrey C. Hoch, Nurul Nadzirin, Jaroslav Koča, Yumiko Kengaku, Jasmine Young, Cole Christie, John D. Westbrook, Naohiro Kobayashi, Alexander S. Rose, Sameer Velankar, David Sehnal, Lukáš Pravda, David R. Armstrong, Hasumi Cho, Genji Kurisu, Lora Mak, John L. Markley, Saqib Mir, Sutapa Ghosh, Ardan Patwardhan, Zukang Feng, Stephen K. Burley, Robert Lowe, David S. Goodsell, Hirofumi Suzuki, Maria Voigt, Paul Gane, Jose M. Duarte, Osman Salih, Irina Periskova, Matthew J. Conroy, Toshimichi Fujiwara, Yasuyo Ikegawa, Takahiro Kudou, Dimitri Maziuk, Typhaine Paysan-Lafosse, Brian P. Hudson, Christine Zardecki, Sreenath Nair, Gerard J. Kleywegt, Marina A. Zhuravleva, Shuchismita Dutta, Dmytro Guzenko, Kumaran Baskaran, Rachel Kramer Green, Ezra Peisach, Li Chen, Reiko Yamashita, Vladimir Guranovic, Yu-He Liang, Takeshi Iwata, Atsushi Nakagawa, Haruki Nakamura, Junko Sato, Radka Svobodová Vařeková, Helen M. Berman, Deepti Gupta, Luigi Di Costanzo, Mihaly Varadi, Yana Valasatava

Publikováno v: Nucleic Acids Research

The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an i

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::270875b3782759eb0deca83927e6993c
https://doi.org/10.1093/nar/gky949

Non-covalent forces tune the electron transfer complex between ferredoxin and sulfite reductase to optimize enzymatic activity

Autor: Takahisa Ikegami, Yuji Goto, Young-Ho Lee, Toshiharu Hase, John E. Ladbury, Chojiro Kojima, Genji Kurisu, Ju Yaen Kim, Toshihiko Sugiki, Misaki Kinoshita, Hanke Gt, Satoshi Kume

Publikováno v: Europe PubMed Central

Although electrostatic interactions between negatively charged ferredoxin (Fd) and positively charged sulfite reductase (SiR) have been predominantly highlighted to characterize complex formation, the detailed nature of intermolecular forces remains

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b3b26bfcc4810babcd3f9eb6c28fc4a6
https://doi.org/10.1042/bcj20160658

Energetic basis on interactions between ferredoxin and ferredoxin NADP

Autor: Misaki, Kinoshita, Ju Yaen, Kim, Satoshi, Kume, Yuxi, Lin, K Hun, Mok, Yosky, Kataoka, Koichiro, Ishimori, Natalia, Markova, Genji, Kurisu, Toshiharu, Hase, Young-Ho, Lee

Publikováno v: Biochemical and biophysical research communications. 482(4)

In spite of a number of studies to characterize ferredoxin (Fd):ferredoxin NADP

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::c2fe601286a6a49fd04a86aa3a4b3596
https://pubmed.ncbi.nlm.nih.gov/27894842

Biochemical and Biophysical Methods to Examine the Effects of Site-Directed Mutagenesis on Enzymatic Activities and Interprotein Interactions

Autor: Misaki Kinoshita, Yuxi Lin, Toshiharu Hase, Ju Yaen Kim, Young-Ho Lee, Natalia Markova

Publikováno v: Methods in Molecular Biology ISBN: 9781493964703

Mutations in proteins often affect interactions with partner molecules, sequentially changing their activities and functions. In order to examine mutagenic effects, we herein describe practical and detailed protocols for enzymatic activity assays usi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::467e4f628d8797a04f51d211e8986077
https://doi.org/10.1007/978-1-4939-6472-7_30

Investigation of Protein-Protein Interactions of Ferredoxin and Sulfite Reductase Under Different Sodium Chloride Concentrations by NMR Spectroscopy and Isothermal Titration Calorimetry

Autor: Young-Ho Lee, Ju Yaen Kim, Takahisa Ikegami, Toshiharu Hase, Yuji Goto

Publikováno v: Proceedings of the International Plant Sulfur Workshop ISBN: 9783319201368

Sulfite reductase (SiR) catalyzes the reduction of sulfite to sulfide by using six electrons transported from ferredoxin (Fd) for eventual sulfur assimilation. As efficient electron flows are ensured by forming a productive Fd:SiR complex, detailed c

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::fb60627c057290e6e0d03d315342d721
https://doi.org/10.1007/978-3-319-20137-5_17