Rumi Shiba

Japan Advanced Institute of Science and Technology

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Hironari Kamikubo

Nara Institute of Science and Technology

Mikio Kataoka

Nara Institute of Science and Technology

Yoichi Yamazaki

Kwansei Gakuin University

Mariko Yamaguchi

Osaka University of Pharmaceutical Sciences

Mika Umeyama

University of Tsukuba

Masahiro Iwakura

National Institute of Advanced Industrial Science and Technology

Sayaka Tsukasa

Nara Institute of Science and Technology

Kana Fuji

The University of Tokyo

Tadaomi Furuta

Institute of Science Tokyo

Mikito Toda

Nara Women's University

Cooperative Institutions

Nara Institute of Science and Technology

Osaka University

Kyoto University

The University of Tokyo

Northwest African American Museum

Hokkaido University

RIKEN

Nara Women's University

RIKEN Center for Computational Science

Centre National de la Recherche Scientifique

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3P041 Extractoin of the regions encoded foldability and/or functionability from dihydrofolate reductase by a systematic alanine insertion(Proteins-structure and structure-function relationship,Poster Presentations)

Seibutsu Butsuri (2007)

Rumi Shiba Hironari Kamikubo Mika Umeyama Yoichi Yamazaki Masahiro Iwakura

Dihydrofolate reductase

Alanine

Structure function

10.2142/biophys.47.s213_2

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3P019 The role of the flexible loop in Staphylococcal nuclease on its catalytic activity(01A. Protein: Structure,Poster)

Seibutsu Butsuri (2013)

Rumi Shiba Hironari Kamikubo Yutaka Maruyama Junko Yunoki Keiichi Fukuyama

Deleting an internal loop of SNase substantially reduces its hydrolytic activity.In order to clarify the role of the loop, we performed crystal structure and 3D-RISM analysis on the Δ44-49 and WT.While their static structures are almost identical, but dynamical properties especially on loops were found to be different from each other.The crystal structures also showed that a water molecule involved in the catalytic reaction locates at the same position between WT and the mutant.The 3D-RISM analysis, however, revealed that the coordination of the water to the ligand is altered upon the deletion.From these results, the loops influence the dynamical properties, and in addition, the local reaction coordinate, which might be indispensable for catalytic reactions.

Nuclease

10.2142/biophys.53.s215_1

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1H1536 Classification of function element of dihydrofolate reductase by the systematic alanine insertion(Protein: Property 2,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri (2011)

Rumi Shiba Hironari Kamikubo Mika Umeyama Sayaka Tsukasa Yoichi Yamazaki

Dihydrofolate reductase

Alanine

10.2142/biophys.51.s50_3

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2P064 網羅的アラニン挿入変異解析法によるジヒドロ葉酸還元酵素の機能エレメントの分類(蛋白質-物性(安定性,折れたたみなど),第48回日本生物物理学会年会)

生物物理 (2010)

Rumi Shiba Hironari Kamikubo Mika Umeyama Sayaka Tsukasa Yoichi Yamazaki

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1H1536 網羅的アラニン挿入変異解析法によるジヒドロ葉酸還元酵素の機能エレメントの分類(蛋白質_物性 2,第49回日本生物物理学会年会)

生物物理 (2011)

Rumi Shiba Hironari Kamikubo Mika Umeyama Sayaka Tsukasa Yoichi Yamazaki

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1P063 Main-chain dynamics of staphylococcal nuclease in microsecond timescale(01C. Protein:Property,Poster)

Seibutsu Butsuri (2013)

Takahiro Matsumoto Mariko Yamaguchi Rumi Shiba Hironari Kamikubo Yoichi Yamazaki

Microsecond

Nuclease

10.2142/biophys.53.s116_3

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CYTOCHEMICAL STUDIES ON THE ENZYMES OF ASCITES HEPATOMA

Modern medicine (1965)

M. Mori Rumi Shiba

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3P-050 Extraction of the regions encoded foldability and/or functionability from Dihydrofolate reductase by the systematic alanine insertion(Protein:Property,The 47th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri (2009)

Rumi Shiba Hironari Kamikubo Mika Umeyama Sayaka Tsukasa Yoichi Yamazaki

Dihydrofolate reductase

Alanine

10.2142/biophys.49.s159_3

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2P064 Classification of the functional element of dihydrofolate reductase (DHFR) by the systematic alanine insertion(The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri (2010)

Rumi Shiba Hironari Kamikubo Mika Umeyama Sayaka Tsukasa Yoichi Yamazaki

Dihydrofolate reductase

Alanine

10.2142/biophys.50.s93_2

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3P045 Analysis of the structural fluctuation in Staphylococcal nuclease and its Δ44-49 mutant: Insight into the enzymatic activity(01B. Protein: Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri (2014)

Kana Fuji Hiroshi Fujisaki Tadaomi Furuta Rumi Shiba Mikito Toda

Antifreeze proteins (AFPs) facilitate cold-survival of the organisms living under freezing environment by inhibiting ice crystal growth.In this study, we focused on a fungal AFP denoted TisAFP secreted from a psychrophilic snow-mold fungus, Typhula ishikariensis.It reported seven isoforms of TisAFP that share a high sequence identity.Significantly, fluorescencebased ice plane affinity (FIPA) analysis showed that the ice binding specificity of TisAFP8 is quite different from the others.To clarify what determines the uniqueness of TisAFP8, we performed mutagenesis experiments on TisAFP8, especially on the residues constructing its putative ice-binding site.The data suggested an importance of inward pointing residues not just outward pointing residues of TisAFP8.

Nuclease

10.2142/biophys.54.s256_3

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