Functional annotation of innate immunity proteins

• Project/Area Number: 21570169
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Biophysics
• Research Institution: Osaka University
• Principal Investigator: STANDLEY Daron 大阪大学, 免疫学フロンティア研究センター, 特任准教授 (00448028)
• Project Period (FY): 2009 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2011: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000); Fiscal Year 2010: ¥390,000 (Direct Cost: ¥300,000、Indirect Cost: ¥90,000); Fiscal Year 2009: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
• Keywords: Protein structure / protein function / threading / alignment / 多重配列アライメント / スレッディング / 構造モデリング / タンパク質の構造予想 / タンパク質の機能予想 / ウェブサーバー / 位置特異的スコアリングマトリクス / ホモロジー / タンパク質の構造予測 / タンパク質の機能予測 / ウェブサーバ / アライメント / アルゴリズム / タンパク質構造モデリング / 免疫反応 / RNase / 二重特異性キナーゼ / STAT3

Research Abstract

A pipeline(SFAS) was constructed that predicts the location of functional domains based on several tools. Intrinsically disordered domains can be analyzed IDD Navigator. Structual domains can be analyzed using several novel methods have been developed by our group and integrated. In particular, sequence alignment(SEEKQUENCER, MAFFTash) and structure refinement(Spanner, OSCAR) show significant improvement over existing methods. The pipeline has been validated using large-scale benchmarks as well as case studies.

Research Products

• [Journal Article] Modeling the alternative oxidase from the human pathogen Blastocystis using automated hybrid structural template assembly (2012)
  • Author(s): Standley DM, van der Giezen M
  • Journal Title: Research and Reports in Biochemistry Volume: 2 Pages: 1-8
• [Journal Article] Protein loop modeling with optimized backbone potential functions (2012)
  • Author(s): Liang S, Zhang C, Sarmiento J, Standley DM
  • Journal Title: J Chem Theory Comput Volume: (in press)
• [Journal Article] Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using Idd Navigator (2011)
  • Author(s): Patil A, Teraguchi S, Dinh H, Nakai K, Standley DM
  • Journal Title: Pac Symp Biocomput Volume: 17 Pages: 164-175
• [Journal Article] Bridging the gap between single-template and fragment based protein structure modeling using Spanner (2011)
  • Author(s): Lis M, Kim T, Sarmiento J, Kuroda D, Dinh H, Kinjo AR, Devadas S, Nakamura H, Standley DM
  • Journal Title: Immunome Research Volume: 7
• [Journal Article] Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions (2011)
  • Author(s): Liang S, Zhou Y, Grishin N, Standley DM
  • Journal Title: J COMPUT CHEM Volume: 32 Pages: 1680-1686
• [Journal Article] Fast and accurate prediction of protein side-chain conformations (2011)
  • Author(s): Liang S, Zheng D, Zhang C, Standley DM
  • Journal Title: Bioinformatics Volume: 27 Pages: 2913-2914
• [Journal Article] Protein loop selection using orientation-dependent force fields derived by parameter optimization (2011)
  • Author(s): Liang S, Zhang C, Standley DM
  • Journal Title: Proteins Volume: 79 Pages: 2260-2267
• [Journal Article] Binding Energetics of Ferredoxin-NADP(+) Reductase with Ferredoxin and Its Relation to Function (2011)
  • Author(s): Lee YH, Ikegami T, Standley DM, Sakurai K, Hase T, Goto Y
  • Journal Title: ChemBioChem
• [Journal Article] A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans (2011)
  • Author(s): Kitamura A, Maekawa Y, Uehara H, Izumi K, Kawachi I, Nishizawa M, Toyoshima Y, Takahashi H, Standley DM, Tanaka K, et al
  • Journal Title: J Clin Invest Volume: 121 Pages: 4150-4160
• [Journal Article] Protein Data Bank Japan(PDBj): maintaining a structural data archive and resource description framework format (2011)
  • Author(s): Kinjo AR, Suzuki H, Yamashita R, Ikegawa Y, Kudou T, Igarashi R, Kengaku Y, Cho H, Standley DM, Nakagawa A, Nakamura H
  • Journal Title: Nucleic Acids Res Volume: 40 Pages: 453-460
• [Journal Article] Prediction of dinucleotide-specific RNA-binding sites in proteins (2011)
  • Author(s): Fernandez M, Kumagai Y, Standley DM, Sarai A, Mizuguchi K, Ahmad S
  • Journal Title: BMC Bioinformatics Volume: 12 Suppl 13:S5
  • Peer Reviewed
• [Journal Article] Functional characterization of protein domains common to animal viruses and mouse (2011)
  • Author(s): Kinjo AR, Kumagai Y, Dinh H, Takeuchi O, Standley DM
  • Journal Title: BMC Genomics Volume: 12 Suppl 3:S21
  • Peer Reviewed
• [Journal Article] Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations (2011)
  • Author(s): Teraguchi S, Kumagai Y, Vandenbon A, Akira S, Standley DM
  • Journal Title: Phys Rev E Stat Nonlin Soft Matter Phys Volume: 84(6-1):062903
  • Peer Reviewed
• [Journal Article] FUNCTIONAL ANNOTATION OF INTRINSICALLY DISORDERED DOMAINS BY THEIR AMINO ACID CONTENT USING IDD NAVIGATOR (2011)
  • Author(s): Patil A, Teraguchi S, Dinh H, Nakai K, Standley DM
  • Journal Title: Pac Symp Biocomput Volume: 17 Pages: 164-175
  • Peer Reviewed
• [Journal Article] The IκB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR-IL-1R by controlling degradation of regnase-1. (2011)
  • Author(s): Iwasaki H, Takeuchi O, Teraguchi S, Matsushita K, Uehata T, Kuniyoshi K, Satoh T, Saitoh T, Matsushita M, Standley DM, Akira S.
  • Journal Title: Nat Immunol. Volume: 12 Issue: 12 Pages: 1167-1175
  • DOI: 10.1038/ni.2137
  • Peer Reviewed
• [Journal Article] Community-wide assessment of protein-interface modeling suggests improvements to design methodology (2011)
  • Author(s): Fleishman SJ, Standley DM, et al
  • Journal Title: J Mol Biol Volume: 414(2) Pages: 289-302
  • Peer Reviewed
• [Journal Article] Protein Data Bank Japan (PDBj) : maintaining a structural data archive and resource description framework format (2011)
  • Author(s): Kinjo AR, Suzuki H, Yamashita R, Ikegawa Y, Kudou T, Igarashi R, Kengaku Y, Cho H, Standley DM, Nakagawa A, Nakamura H
  • Journal Title: Nucleic Acids Res Volume: 40(Database issue)
  • Peer Reviewed
• [Journal Article] Bridging the gap between single-template and fragment based protein structure modeling using Spanner (2011)
  • Author(s): Lis M, Kim T, Sarmiento JJ, Kuroda D, Dinh HV, Kinjo AR, Amada K, Devadas S, Nakamura H, Standley DM
  • Journal Title: Immunome Res Volume: 7(1) Pages: 1-8
  • Peer Reviewed
• [Journal Article] A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans (2011)
  • Author(s): Kitamura A, Maekawa Y, Uehara H, Izumi K, Kawachi I, Nishizawa M, Toyoshima Y, Takahashi H, Standley DM, Tanaka K, Hamazaki J, Murata S, Obara K, Toyoshima I, Yasutomo K.
  • Journal Title: J Clin Invest Volume: 121 Issue: 10 Pages: 4150-4160
  • DOI: 10.1172/jci58414
  • Peer Reviewed
• [Journal Article] Binding energetics of ferredoxin-NADP+ reductase with ferredoxin and its relation to function (2011)
  • Author(s): Lee YH, Ikegami T, Standley DM, Sakurai K, Hase T, Goto Y
  • Journal Title: Chembiochem Volume: 12(13) Issue: 13 Pages: 2062-70
  • DOI: 10.1002/cbic.201100189
  • Peer Reviewed
• [Journal Article] Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions (2011)
  • Author(s): Liang S, Zhou Y, Grishin N, Standley DM
  • Journal Title: J Comput Chem Volume: 32(8) Issue: 8 Pages: 1680-6
  • DOI: 10.1002/jcc.21747
  • Peer Reviewed
• [Journal Article] Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins (2010)
  • Author(s): Teraguchi S, Patil A, Standley DM
  • Journal Title: BMC Bioinformatics Volume: S7 Pages: 11-11
• [Journal Article] SeSAW balancing sequence and structural information in protein functional mapping (2010)
  • Author(s): Standley DM, Yamashita R, Kinjo AR, Toh H, Nakamura H
  • Journal Title: Bioinformatics Volume: 26 Pages: 1258-1259
• [Journal Article] The DBCLS BioHackathon : standardization and interoperability for bioinformatics web services and workflows (2010)
  • Author(s): Katayama T, Arakawa K, Nakao M, Ono K, K. F A-K, Yamamoto Y, Aerts J, Aranda B, Barboza LH, Bonnal R, (+ 36 authors), Standley DM, (+ 10 authors)
  • Journal Title: Journal of Biomedical Semantics Volume: 1
• [Journal Article] Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster (2010)
  • Author(s): Ikebe J, Standley DM, Nakamura H, Higo J
  • Journal Title: Protein Science Volume: 20 Pages: 187-196
• [Journal Article] The DBCLS BioHackathon : standardization and interoperability for bioinformatics web services and workflows (2010)
  • Author(s): Katayama T, Standley D
  • Journal Title: Journal of Biomedical Semantics Volume: 21 Pages: 8-27
  • Peer Reviewed
• [Journal Article] SeSAW : balancing sequence and structural information in protein functional mapping (2010)
  • Author(s): Standley DM
  • Journal Title: Bioinformatics Volume: 26 Pages: 1258-1259
  • Peer Reviewed
• [Journal Article] Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins (2010)
  • Author(s): Teraguchi S, Standley D
  • Journal Title: BMC Bioinformatics Volume: 11 Pages: 2-12
  • Peer Reviewed
• [Journal Article] SeSAW : balancing sequence and structural information in protein functional mapping (2010)
  • Author(s): Standley DM, Yamashita R, Kinjo AR, Toh H, Nakamura H
  • Journal Title: Bioinformatics (印刷中)
  • Peer Reviewed
• [Journal Article] A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat3 (2009)
  • Author(s): Yamamoto M, Standley DM, Takashima S, Saiga H, Okuyama M, Kayama H, Kubo E, Ito H, Takaura M, Matsuda T, et al
  • Journal Title: J Exp Med Volume: 206 Pages: 2747-2760
• [Journal Article] Outcome of a workshop on applications of protein models in biomedical research (2009)
  • Author(s): Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV(+ 16 authors), Standley DM, (+ 5 authors)
  • Journal Title: Structure Volume: 17 Pages: 151-159
• [Journal Article] Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay (2009)
  • Author(s): Matsushita K, Takeuchi O, Standley DM, Kumagai Y, Kawagoe T, Miyake T, Satoh T, Kato H, Tsujimura T, Nakamura H, Akira S
  • Journal Title: Nature Volume: 458 Pages: 1185-1190
• [Journal Article] Membrane attachment facilitates ligand access to the active site in monoamine oxidase A (2009)
  • Author(s): Apostolov R, Yonezawa Y, Standley DM, Kikugawa G, Takano Y, Nakamura H
  • Journal Title: Biochemistry Volume: 48 Pages: 5864-5873
• [Journal Article] A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat3 (2009)
  • Author(s): Yamamoto M, Standley DM, Takashima S, Saiga H, Okuyama M, Kayama H, Kubo E, Ito H, Takaura M, Matsuda T, Soldati-Favre D, Takeda K
  • Journal Title: J Exp Med 206 Pages: 2747-2760
  • Peer Reviewed
• [Journal Article] Outcome of a workshop on applications of protein models in biomedical research (2009)
  • Author(s): Schwede T, et al. (23 authors), Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA
  • Journal Title: Structure 17 Pages: 151-159
  • Peer Reviewed
• [Journal Article] Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay (2009)
  • Author(s): Matsushita K, Takeuchi O, Standley DM, Kumagai Y, Kawagoe T, Miyake T, Satoh T, Kato H, Tsujimura T, Nakamura H, Akira S
  • Journal Title: Nature 458 Pages: 1185-1190
  • Peer Reviewed
• [Journal Article] Membrane attachment facilitates ligand access to the active site in monoamine oxidase A (2009)
  • Author(s): Apostolov R, Yonezawa Y, Standley DM, Kikugawa G, Takano Y, Nakamura H
  • Journal Title: Biochemistry 48 Pages: 5864-5873
  • Peer Reviewed
• [Presentation] Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator (2012)
  • Author(s): Standley DM
  • Organizer: Pacific Symposium on Biocomputing
  • Place of Presentation: Hawaii, USA
  • Year and Date: 2012-01-06
• [Presentation] Prediction of dinucleotide-specific RNA-binding sites in proteins (2011)
  • Author(s): Standley DM
  • Organizer: Malaysia
  • Place of Presentation: Kuala Lumpur
  • Year and Date: 2011-11-14
• [Presentation] Function prediction of structured and unstructured proteins (2011)
  • Author(s): Standley DM
  • Organizer: China 5th China Medical Biotech Forum(CMBF-2011)
  • Place of Presentation: Beiing
  • Year and Date: 2011-11-08
• [Presentation] A structural view of Innate immunity (2011)
  • Author(s): Standley DM
  • Organizer: Dana-Farber Cancer Institute
  • Place of Presentation: Cancer Vaccine Center, USA
• [Presentation] Restrained docking of protein molecular surfaces (2010)
  • Author(s): Daron M.Standley
  • Organizer: Department of Chemistry Colloquium
  • Place of Presentation: Columbia Univ.
  • Year and Date: 2010-11-08
• [Presentation] Restrained docking of protein molecular surfaces (2010)
  • Author(s): Standley DM
  • Organizer: Department of Chemistry
  • Place of Presentation: New York, USA : Columbia Univ
• [Presentation] An introduction to protein-protein docking II (2009)
  • Author(s): Daron M.Standley
  • Organizer: Ochanomizu Univ. Predictive Biology lecture series
  • Place of Presentation: お茶の水大学
  • Year and Date: 2009-11-11
• [Presentation] Functional Annotation using SeSAW (2009)
  • Author(s): Daron M.Standley
  • Organizer: MEI Center lecture series
  • Place of Presentation: 大阪大学中の島センター
  • Year and Date: 2009-11-07
• [Presentation] An introduction to protein-protein docking II (2009)
  • Author(s): Standley DM
  • Organizer: Predictive Biology lecture series
  • Place of Presentation: Tokyo, Japan : Ochanomizu Univ
• [Presentation] Functional Annotation using SeSAW (2009)
  • Author(s): Standley DM
  • Organizer: MEI Center lecture series
  • Place of Presentation: Osaka, Japan
• [Remarks]
  • URL: http://sysimm.ifrec.osaka-u.ac.jp/
• [Remarks]
  • URL: http://sysimm.ifrec.osaka-u.ac.jp/pipeline5/
• [Remarks]
  • URL: http://www.ifrec.osaka-u.ac.jp/jpn/laboratory/systemsimmunology/index.php
• [Remarks]
  • URL: http://sysimm.ifrec.osaka-u.ac.jp/sfas/
• [Remarks]
  • URL: http://sysimm.ifrec.osaka-u.ac.jp/SeSAW/
• [Remarks]
  • URL: http://sysimm.ifrec.osaka-u.ac.jp/MSThread/
• [Remarks]
  • URL: http://sysimm.ifrec.osaka-u.ac.jp/cgi-bin/spanner