Development of a protein glycosylation prediction method considering the sugar types, and construction of a glycoplotein database

• Project/Area Number: 26330332
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Life / Health / Medical informatics
• Research Institution: Meiji University
• Principal Investigator: Yuri Mukai-Ikeda 明治大学, 理工学部, 専任准教授 (30371082)
• Research Collaborator: ETCHUYA Kenji ; OGAWA Tsubasa ; TAKACHIO Naoyuki ; NAGASHIMA Keiya ; HAMADA Kota ; SUGITA Hiromu ; TAKAHASHI Daiki ; YAMAGUCHI Takuya ; UCHIKAI Takayuki ; KIKEGAWA Tatsuki ; KITADA Yohei
• Project Period (FY): 2014-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000); Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2014: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
• Keywords: バイオインフォマティクス / タンパク質 / アミノ酸配列 / 二次構造 / 立体構造 / 細胞内局在 / 糖鎖修飾 / 予測法 / 配列解析 / 実験検証 / 翻訳後修飾 / 糖鎖 / 細胞分子生物学実験 / データベース / PSSM

Outline of Final Research Achievements

A protein glycosylation prediction method considering the modified sugar types was developed in this research. The sugar type specificities of the sequence, structure and subcellular localization of the sugar modified proteins in the Uniprot and PDB databases were extracted by the statistical analysis. The factors which were available as the parameters of the sugar type discrimination were found. A sugar discrimination method with high accuracy was developed using the protein sequence and subcellular localization.

Research Products

• [Journal Article] Correlation between physicochemical properties of protein signal sequence variation and subcellular transportation (2016)
  • Author(s): Tatsuki Kikegawa, Tomonao Iibuchi, Kenji Etchuya, Makoto Ohta, Noritaka Kato, Yuri Mukai
  • Journal Title: Proceedings of the sixteenth International Symposium on Advanced Fluid Information (AFI 2016) Volume: - Pages: 88-89
  • Peer Reviewed / Open Access
• [Journal Article] Correlation between protein subcellular localization and sugar variation (2016)
  • Author(s): Kenji Etchuya, Tatsuki Kikegawa, Yuri Mukai
  • Journal Title: Proceedings of the thirteenth International Conference on Flow Dynamics (ICFD 2016) Volume: - Pages: 306-307
  • Peer Reviewed / Open Access
• [Journal Article] Secondary Structure of GPI Attachment Signal Region Monitored by Circular Dichroism (2016)
  • Author(s): Yuri Mukai, Daiki Takahashi, Keiya Inoue, Hiromu Sugita, Tatsuki Kikegawa, Kenji Etchuya
  • Journal Title: Chemistry Letters Volume: 45 Issue: 10 Pages: 1153-1155
  • DOI: 10.1246/cl.160551
  • NAID: 130006837287
  • ISSN: 0366-7022, 1348-0715
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Study of molecular recognition mechanism in protein GPI modification: a bioinformatics analysis of interaction between GPI-anchored proteins and modification enzyme (2016)
  • Author(s): Yuri Mukai, Daiki Takahashi, Tsubasa Ogawa, Kota Hamada, Kenji Etchuya
  • Journal Title: Journal of Biomechanical Science and Engineering Volume: 11 Issue: 1 Pages: 15-00361-15-00361
  • DOI: 10.1299/jbse.15-00361
  • NAID: 130005157935
  • ISSN: 1880-9863
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Structural characteristics around <i>O</i>-glycosylation sites in mammalian proteins (2015)
  • Author(s): Kenji Etchuya, Yuri Mukai
  • Journal Title: Journal of Biomechanical Science and Engineering Volume: 10 Issue: 1 Pages: 14-00249-14-00249
  • DOI: 10.1299/jbse.14-00249
  • NAID: 130004695335
  • ISSN: 1880-9863
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] 一回膜貫通型タンパク質のアミノ酸出現傾向と細胞内局在の相関 (2016)
  • Author(s): 亀卦川樹, 加藤徳剛, 向井有理
  • Organizer: 第39回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2016-11-30
• [Presentation] 細胞の形態変化に影響を与えるタンパク質の網羅的検出 (2016)
  • Author(s): 北田 洋平1、寺崎 武夫1、向井 有理1 (1.明大・院理工・電気工学)
  • Organizer: 第39回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2016-11-30
• [Presentation] GPIアタッチメントシグナル領域の二次構造解析 (2016)
  • Author(s): 井上慶也, 高橋大輝, 亀卦川樹, 越中谷賢治, 向井有理
  • Organizer: 第54回生物物理学会年会
  • Place of Presentation: つくば
  • Year and Date: 2016-11-25
• [Presentation] 糖転移酵素の糖選択性とタンパク質認識に関わるアミノ酸の解析 (2016)
  • Author(s): 宮坂豪、越中谷賢治、向井有理
  • Organizer: 第54回日本生物物理学会年会
  • Place of Presentation: つくば
  • Year and Date: 2016-11-25
• [Presentation] Correlation between physicochemical properties of protein signal sequence variation and subcellular transportation (2016)
  • Author(s): Tatsuki Kikegawa, Tomonao Iibuchi, Kenji Etchuya, Makoto Ohta, Noritaka Kato, Yuri Mukai
  • Organizer: the sixteenth International Symposium on Advanced Fluid Information (AFI 2016)
  • Place of Presentation: Sendai, Japan
  • Year and Date: 2016-10-11
• [Presentation] Identification of the subcellular localization factors of transmembrane proteins (2016)
  • Author(s): Tatsuki Kikegawa, Hiromu Sugita, Ryohei Nambu, Noritaka Kato, Yuri Mukai
  • Organizer: 15th European Conference on Computational Biology (ECCB 2016)
  • Place of Presentation: The Hague, Netherlands
  • Year and Date: 2016-09-04
• [Presentation] Environment factor depending on each sugar type around O-glycosylation sites in mammalian proteins, (2016)
  • Author(s): Kenji Etchuya and Yuri Mukai
  • Organizer: The 15th European Conference on Computational Biology (ECCB 2016)
  • Place of Presentation: The Hague, Netherlands
  • Year and Date: 2016-09-04
• [Presentation] omega-site 近傍の構造に着目したGPI 修飾機構の解明 (2016)
  • Author(s): 髙橋 大輝、杉田 大夢、小川 翼、濱田 康太、越中谷 賢治、向井 有理
  • Organizer: 第5回日本生物物理学会関東支部会
  • Place of Presentation: 桐生、群馬
  • Year and Date: 2016-03-09
• [Presentation] Comparative study of the sequences and structures around O-glycosylation sites between each sugar type in mammalian proteins (2016)
  • Author(s): Kenji Etchuya, Yuri Mukai
  • Organizer: Pacific Symposium on Biocomputing 2016 (PSB 2016)
  • Place of Presentation: Hawaii, USA
  • Year and Date: 2016-01-04
  • Int'l Joint Research
• [Presentation] Comparative analysis of GPI modificatiob mechanisms between human and plant proteins focusing on signal-peptides (2016)
  • Author(s): Hiromu Sugita, Naoyuki Takachio, Noritaka Kato, Hanae Kaku, Yuri Mukai
  • Organizer: Pacific Symposium on Biocomputing 2016 (PSB 2016)
  • Place of Presentation: Hawaii, USA
  • Year and Date: 2016-01-04
  • Int'l Joint Research
• [Presentation] Interaction between GPI-anchored proteins and GPI transamidase (2016)
  • Author(s): Daiki Takahashi, Hiromu Sugita, Tsubasa Ogawa, Kota Hamada, Kenji Etchuya, Yuri Mukai
  • Organizer: Pacific Symposium on Biocomputing 2016 (PSB 2016)
  • Place of Presentation: Hawaii, USA
  • Year and Date: 2016-01-04
  • Int'l Joint Research
• [Presentation] タンパク質のGPI修飾に関連したシグナル領域の機能解析と生物種間比較 (2015)
  • Author(s): 杉田 大夢、高知尾 尚志、加藤 徳剛、向井 有理、賀来 華江、早船 真広
  • Organizer: 第38回日本分子生物学会年会
  • Place of Presentation: 神戸
  • Year and Date: 2015-12-01
• [Presentation] GPIアタッチメントシグナルの二次構造の解析 (2015)
  • Author(s): 髙橋 大輝、小川 翼、越中谷 賢治、濱田 康太、向井 有理
  • Organizer: 第38回日本分子生物学会年会
  • Place of Presentation: 神戸
  • Year and Date: 2015-12-01
• [Presentation] Protein Recognition Mechanism for GPI Modification (2015)
  • Author(s): Daiki Takahashi , Tsubasa Ogawa, Kenji Etchuya, Kota Hamada, Yuri Mukai
  • Organizer: 12th International Conference on Flow Dynamics (ICFD 2015)
  • Place of Presentation: Sendai, Japan
  • Year and Date: 2015-10-26
  • Int'l Joint Research
• [Presentation] Mammal and plant GPI modification mechanism (2015)
  • Author(s): Hiromu Sugita, Naoyuki Takachio, Noritaka Kato, Hanae Kaku, Makoto Ohta, Yuri Muka
  • Organizer: 12th International Conference on Flow Dynamics (ICFD 2015)
  • Place of Presentation: Sendai, Japan
  • Year and Date: 2015-10-26
  • Int'l Joint Research
• [Presentation] Interaction analysis between sugar chain and aromatic residue in mammalian protein (2015)
  • Author(s): Kenji Etchuya, Yuri Mukai
  • Organizer: 40th Congress of the Federation of the European Biochemical (FEBS)
  • Place of Presentation: Berlin, Germany
  • Year and Date: 2015-07-04 – 2015-07-09
• [Presentation] Interaction analysis between sugar chain and aromatic residue in mammalian protein (2015)
  • Author(s): Kenji Etchuya, Yuri Mukai
  • Organizer: 40th FEBS Congress
  • Place of Presentation: Berlin, Germany
  • Year and Date: 2015-07-04
  • Int'l Joint Research
• [Presentation] Comparative study between mammal and plant GPI modification mechanism (2015)
  • Author(s): Hiromu Sugita, Naoyuki Takachio, Noritaka Kato, Hanae Kaku, Makoto Ohta, Yuri Mukai
  • Organizer: 40th FEBS Congress
  • Place of Presentation: Berlin, Germany
  • Year and Date: 2015-07-04
  • Int'l Joint Research
• [Presentation] Functional analysis of GPI transamidase with molecular phylogenetic tree (2015)
  • Author(s): Daiki Takahashi, Tsubasa Ogawa, Kota Hamada, Kenji Etchuya, Yuri Mukai
  • Organizer: 40th FEBS Congress
  • Place of Presentation: Berlin, Germany
  • Year and Date: 2015-07-04
  • Int'l Joint Research
• [Presentation] O型糖鎖修飾を受ける哺乳類タンパク質の構造的解析 (2014)
  • Author(s): 越中谷賢治, 池田(向井) 有理
  • Organizer: 第37回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2014-11-25 – 2014-11-27
• [Presentation] Study of 3D Recognition by Glycosyltransferase in Protein Sugar Modification. (2014)
  • Author(s): Kenji Etchuya, Makoto Ohta, Yuri Mukai
  • Organizer: Eleventh International Conference on Flow Dynamics (ICFD2014)
  • Place of Presentation: Sendai, Japan
  • Year and Date: 2014-10-08 – 2014-10-10
• [Presentation] Structural Characteristics of Fuc Modification Sites in Mammalian Proteins (2014)
  • Author(s): Kenji Etchuya, Yuri Mukai
  • Organizer: 13th European Conference on Computational Biology
  • Place of Presentation: Strasbourg, France
  • Year and Date: 2014-09-07 – 2014-09-10
• [Book] バイオインフォマティクス入門 （分担執筆: 第1章 生命科学） (2015)
  • Author(s): 向井有理、越中谷賢治、濱田康太ほか
  • Total Pages: 49
  • Publisher: 慶應義塾大学出版会
• [Book] バイオインフォマティクス技術者入門 (2015)
  • Author(s): 日本バイオインフォマティクス学会編（分担執筆：向井有理・越中谷賢治・濱田康太）
  • Publisher: 慶應義塾大学出版会