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Drug design based on the complex structure of HIV-Tat and its RNA aptamer

Research Project

Project/Area Number 12470487
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Physical pharmacy
Research InstitutionYokohama National University

Principal Investigator

KATAHIRA Masato  Yokohama National University, Faculty of Environment and Information Sciences, Associate Professor, 大学院・環境情報研究院, 助教授 (70211844)

Co-Investigator(Kenkyū-buntansha) UESUGI Seiichi  Yokohama National University, Faculty of Environment and Information Sciences, Professor, 大学院・環境情報研究院, 教授 (70028851)
Project Period (FY) 2000 – 2002
Project Status Completed (Fiscal Year 2002)
Budget Amount *help
¥8,400,000 (Direct Cost: ¥8,400,000)
Fiscal Year 2002: ¥2,000,000 (Direct Cost: ¥2,000,000)
Fiscal Year 2001: ¥3,000,000 (Direct Cost: ¥3,000,000)
Fiscal Year 2000: ¥3,400,000 (Direct Cost: ¥3,400,000)
KeywordsHIV / aptamer / Tat protein / NMR / three-dimensional structure / RNA-binding protein / RNA / drug design / トリプレットリピート / リボザイム / ダナミクス / テロメア / 4重鎖 / 安定同位体標識 / 水素結合 / Tat蛋白質 / 蛋白質-RNA相互作用
Research Abstract

An RNA aptamer containing two binding sites exhibits extremely high affinity to the HIV Tat protein. We have now determined the structure of the aptamer complexed with argininamide, the simplest analogue of the Tat protein, by NMR. We found that two argininamide molecules bind per aptamer. Two adjacent U : A : U base triples were formed, which widens the major groove to make space for the two argininamide molecules. The argininamide molecules bound to the G bases through hydrogen bonds. The binding is stabilized through stacking interactions.
The structure of the aptamer complexed with a Tat-derived argmine-rich peptide was also characterized. The Tat-derived peptide bound to the aptamer in a 1: 1 molar ratio. In spite of the difference in stoichiometry, similarity was noted between the argininamide- and peptide-bound forms of the aptamer in chemical shift perturbations of the aptamer upon complex formation and intermolecular contacts. These results suggest that two different arginine residues of the peptide interact with the two binding sites of the aptamer in the same way as two argininamide molecules do. Simultaneous interactions of the aptamer with two arginine residues of Tat could explain its high affinity compared to the authentic TAR RNA. The formation of the two adjacent base triples makes the simultaneous interactions possible by creating space for the accommodation of two arginine residues and linking residues of Tat, and also contributes to the stabilization of the binding through stacking interactions.
The elucidated structure of the aptamer gives clues to rationally design a new aptamer that exhibits even higher affinity to Tat. The way to design a new aptamer with a less side effect is also provided by the elucidated structure.

Report

(4 results)
  • 2002 Annual Research Report   Final Research Report Summary
  • 2001 Annual Research Report
  • 2000 Annual Research Report
  • Research Products

    (68 results)

All Other

All Publications (68 results)

  • [Publications] Yamamoto, R.: "A novel RNA motif that binds efficiently and specifically to the Tat protein of HIV and inhibits the Trans-activation by Tat of transcription in vivo and in vitro"Genes to Cells. 5. 371-388 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Tanaka, Y.: "NMR analysis of tertiary interactions in HDV ribozymes"Nucleic Acids Symp. Ser.. 44. 285-286 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Liu, H.: "NMR Study of a novel RNA quadruplex structure"Nucleic Acids Symp. Ser.. 44. 65-66 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] 片平正人: "テロメア配列DNA/RNA結合タンパク質hnRNP D0の立体構造と核酸構造遷移能"生物物理. 40(5). 326-330 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Matsugami, A.: "An intramolecular quadruplex of (GGA)4 triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction"J. Mol. Biol.. 313. 255-269 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Katahira, M.: "Structure of the C-terminal RNA-binding domain of hnRNP D0 (AUF1), its interactions with RNA and DNA, and change in backbone dynamics upon complex formation with DNA"J. Mol. Biol.. 311. 973-988 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Yasuno, K.: "Interaction of the C-terminal domain of the E. coli RNA polymerase alpha subunit with the UP element : recognizing the backbone structure in the minor groove surface"J. Mol. Biol.. 306. 213-225 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Matsugami, A.: "New quadruplex structure of GGA triplet repeat DNA -An intramolecular quadruplex composed of a G:G:G:G Tetrad and a G(:A): G(:A): G(:A):G neptad, and its dimerization"Nucleic Acids Res. Suppl.. 1. 271-272 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Tanaka, Y.: "Imino proton NMR analysis of HDV ribozymes : nested double pseudoknot structure and Mg^<2+> ion-binding site close to the catalytic core in solution"Nucleic Acids Res.. 30. 766-774 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Tanaka, Y.: "Cleavage reaction of HDV ribozymes in the presence of Mg^<2+> is accompanied by a conformational change"Genes to Cells. 7. 567-579 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Fukuda, H.: "Unfolding of quadruplex structure in the G-rich strand of the minisatellite Pc-1 and telomeric repeat by its binding protein MNBP-B/UP1"Proc. Natl. Acad. Sci. USA. 99. 12685-12690 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Liu, H.: "A dimeric RNA quadruplex architecture comprised of two G:G(:A):G:G(:A) hexads, G:G:G:G Tetrads and UUU loops"J. Mol. Biol.. 322. 955-970 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Liu, H.: "A comparison of the properties and the Solution Structure for RNA and DNA quadruplexes which contain two GGAGG Sequences joined with a tetranucleotide linker"Nucleoside, Nucleotide and Nucleic Acid. 21. 785-801 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Matsugami, A.: "Unique quadruplex structures of d(GGA)4 (12-mer) and d(GGA)8 (24-mer)-direct evidence of the formation of non-canonical base pairs and structural comparison"Nucleic Acids Res. Suppl.. 2. 49-50 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Liu, H.: "Quadruplex structures of RNA 14-mer, r(GGAGGUUUUGGAGG) and DNA 14-mer, d(GGAGGTTTTGGAGG)"Nucleic Acids Res Suppl.. 2. 177-178 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] 片平正人: "GGAトリプレットDNAが形成する特異な高次構造とその生物学的な意義"蛋白質核酸酵素. 47. 139-144 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] 片平正人: "RNA結合タンパク質及び機能性RNAの機能発現メカニズムに立体構造から迫る -hn RNP D(AUF1), Musashi, Tatアプタマー-"生体の科学. 53. 117-123 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Matsugami, A.: "Structural basis of the highly efficient trap of an HIV Tat protein by a new RNA aptamer"Structure. (in press). (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Katahira, M.: "Novel DNA and RNA quadruplex structures and their biological significance"J. Mol. Biol.. (in press). (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] 片平正人(分担): "有機薬科学実験講座:創薬指向の分子設計"廣川書店. 255 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] 片平正人(分担): "日本分光学会測定法シリーズ NMR分光法"学会出版センター. 269 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Yamamato, R.: "A novel RNA motif that binds efficiently and specifically to the Tat protein of HIV and inhibits the trans-activation by Tat of transcription in vivo and in vitro"Genes to Cells. 5. 371-388 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Tanaka, Y.: "NMR analysis of tertiary interactions in HDV ribozymes"Nucleic Acids Symp. Ser.. 44. 285-286 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Liu, H.: "NMR study of a novel RNA quadruples structure"Nucleic Acids Symp. Sen. 44. 65-66 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Katahira, M.: "Structure and ability to transform DNA conformation of telomere DNA binding protein, hnRNP D0"Biophysics. 40. 326-330 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Matsugami, A.: "An intramolecular quadruplex of (GGA)_4 triplet repeat DNA with a G : G : G : G tetrad and a G( : A) : G( : A) : G( : A) : G heptad, and its dimeric interaction"J. Mol. Biol.. 313. 255-269 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Katahira, M.: "Structure of the C-terminal RNA-binding Domain of hnRNP D0 (AUF1), its Interactions with RNA and DNA, and Change in Backbone Dynamics upon Complex Formation with DNA"J. Mol. Biol.. 311. 973-988 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Yasuno, K.: "Interaction of the C-terminal domain of the E. coli. RNA polymerase a subunit with the UP element : recognizing the backbone structure in me minor groove surface"J. Mol. Biol.. 306. 213-225 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Matsugami, A.: "New quadruplex structure of GGA triple repeat DNA -An intramolecular quadruplex composed of a G : G : G : G tetrad and a G( : A) : G( : A) : G : A) : G heptad, and its dimerization-"Nucleic Acids Res. Suppl.. No. 1. 271-272 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Tanaka, Y.: "Inmno proton NMR analysis of HDV ribozymes : nested double pseudoknot structure and Mg^2+ ion binding site close to the catalytic core in solution"Nucleic Acids Res.. 30. 766-774 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Tanaka, Y.: "Cleavage reaction of HDV ribozymes in the presence of Mg^2+ is accompanied by a conformational change"Genes to Cells. 7. 567-579 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Fukuda, H.: "Unfolding of quadruplex structure in the G-rich strand of the minisatellite Pc-1 and telomeric repeat by its binding protein MNBP-B/UP1"Proc. Natt. Acad. Sci. USA. 99. 12685-12690 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Liu, H.: "A dimeric RNA quadruplex architecture comprised of two G : G( : A) : G : G( : A) hexads, G : G : G : G tetrads and UUUU loops"J. Mol. Biol.. 322. 955-970 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Liu, H.: "A comparison of the properties and the solution structure for RNA and DNA quadruplexes which contain two GGAGG sequences joined with a tetranucleotide linker"Nucleoside, Nucleotide and Nucleic Acid. 21. 785-801 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Matsugami, A.: "Unique quadruplex structures of d(GGA)_4 (12-mer) and d(GGA)_8 (24-mer) -direct evidence of the formation of non-canonical base pairs and structural comparison-"Nucleic Acids Res. Suppl.. No. 2. 49-50 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Liu, H.: "Quadruplex structures of RNA 14-mer, r(GGAGGUUUUGGAGG) and DNA 14-mer, d(GGAGGTTTTGGAGG)"Nucleic Acids Res. Suppl.. No. 2. 177-178 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Katahira, M.: "Unique structure and its biological relevance of GGA triplet repeat DNA"Protein, Nucleic Acids and Enzyme. 47. 139-144 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Katahira, M.: "Structure and function of RNA-binding proteins and functional RNA-hnRNP D (AUF1), Musashi and Tat aptamer―"Seitai no Kagaku. 53. 117-123 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Matsugami, A.: "Structural basis of the highly efficient trap of an HIV Tat protein by a new RNA aptamer"Structure. in press. (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Katahira, M: "Novel DNA and RNA quadruplex structures and their biological significance"J. Mol. Biol.. in press. (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Katahira, M.: "Experimental Course on Organic Pharmaceutical Science"Hirokawa Shoten. 254 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Katahira, M.: "NMR spectroscopy"Gakkai Shuppan Center. 269 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Tanaka, Y.: "Imino proton NMR analysis of HDV ribozymes : nested double pseudoknot structure and Mg^<2+>ion binding site close to the catalytic core in Solution"Nucleic Acids Res.. 30. 766-774 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Tanaka, Y.: "Cleavage reaction of HDV ribozymes in the presence of Mg^<2+> is accompanied by a conformational change"Genes to Cells. 7. 567-579 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Fukuda, H.: "Unfolding of quadruplex structure the G-rich strand of the minisatellite Pc-1 and telomeric repeat by its binding protein MNBP-B/UP1"Proc.Natl.Acad.Sci.USA. 99. 12685-12690 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Liu, H.: "A dimeric RNA quadruplex architecture comprised of two G : G (:A) : G : G (:A) hexads, G : G : G : G tetrads and UUUU loops"J.Mol.Biol.. 322. 955-970 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Liu, H.: "A comparison of the properties and the solution structure for RNA and DNA quadruplexes which contain two GGAGG sequences joined with a tetranucleotide linker"Nucleoside, Nucleotide and Nucleic Acid. 21. 785-801 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Matsugami, A.: "Unique quadruplex structures of d(GGA)_4(12-mer) and d(GGA)_8(24-mer)-direct evidence of the formation of non-canonical base pairs and structural comparison-"Nucleic Acids Res.Suppi.. 2. 49-50 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Liu, H.: "Quadruplex structures of RNA 14-mer, r(GGAGGUUUUGGAGG) and DNA 14-mer, d(GGAGGTTTTGGAGG)"Nucleic Acids Res.Suppi.. 2. 177-178 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] 片平正人: "GGAトリプレットDNAが形成する特異な高次構造とその生物学的な意義"蛋白質核酸酵素. 47. 139-144 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] 片平正人: "RNA結合タンパク質及び機能性RNAの機能発現メカニズムに立体構造から迫る-hnRNP D(AUF1)、Musashi、Tatアプタマー-"生体の科学. 53. 117-123 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Matsugami, A.: "Structural basis of the highly efficient trap of an HIV Tat protein by a new RNA aptamer"Structure. (in press). (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] Katahira, M.: "Novel DNA and RNA quadruplex structures and their biological significance"J.Mol.Biol.. (in press). (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] 片平正人(分担): "NMR分光法"学会出版センター. 269 (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] K.Yasuno, T.Yamazaki, Y.Tanaka, T.Kodama, A.Matsugami, M.Katahira, A.Ishihama, Y.Kyogoku: "Interaction of C-terminal domain of the E. coli. RNA polymerase ♯alpha♯ subunit with the UP element : recognizing the backbone structure in minor groove surface"J. Mol. Biol.. 306. 213-215 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] M.katahira, Y.Miyanoiri, Y.Enokizono, G.Matsuda, T.Nagata, F.Ishikawa, S.Uesugi: "Structure of the c-terminal RNA-binding domain of hnRNP D0 (AUF1), its interactions with RNA and DNA, and change in backbone dynamics upon complex formation with DNA"J. Mol. Biol.. 311. 973-988 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] A.Matsugami, K. Ouhashi, M.Kanagawa, H.Liu, M.Kanagawa, S.Uesugi, M.Katahira: "An intramolecular quadruples of (GGA) $4$ triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction"J. Mol. Biol.. 313. 255-269 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] A.Matsugami, K.Ouhashi, M.Kanagawa, H.Liu, M.Kanagawa, S.Uesugi, M.Katahira: "New quadruplex structure of GGA triplet repeat DNA -an intramolecular quadruplex composed of a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimerization"Nucleic Acids Res. Suppl.. 1. 271-272 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Y.Tanaka, T.Hori, H.Tagaya, T.Sakamoto, Y.Kurihara, M.Katahira, S.Uesugi: "Imino proton NMR analysis of HDV ribozymes : nested double pseudoknot structure and Mg!2+! ion binding site close to the cataltic core in solution"Nucleic Acids Res.. 30. 766-774 (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] 片平正人: "GGAトリプレットDNAが形成する特異な高次構造とその生物学的な意義"蛋白質・核酸・酵素. 47. 139-144 (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] 片平正人: "RNA結合タンパク質及び機能性RNAの機能発現メカニズムに立体構造から迫る-hnRNP D (AUF1), Musashi, Tatアプタマー-"生体の科学. 53. 117-123 (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] Y.Tanaka, M. Tagaya, T.Hori, T.Sakamoto, Y.Kurihara, M.Katahira, S.Uesugi: "Cleavage reaction of HDV ribozymes in the presence of Mg!2+! is accompanied by a conformational change"Genes to Cells. (in press). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] Yamamoto,R.: "A novel RNA motif that binds efficiently and specifically to Taf protein of HIV"Genes to Cells. 5. 371-388 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Tanaka,Y.: "NMR analysis of tertiary interactions in HDV ribozymes"Nucleic Acids Symp.Ser.. 44. 285-286 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Liu,H.: "NMR study of a novel RNA quadrupley structure"Nucleis Acids Symp.Ser.. 44. 65-66 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] 片平正人: "テロメア配列DNA/RNA結合タンパク質hrRNP DOの立体構造と核酸構造遷移能"生物物理. 40. 326-330 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Yasuno,K.: "Interaction of the C-terminal domain of the E.coli RNA polymerase α subunit with the VP element"J.Mal.Biol.. (印刷中). (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] 片平正人(分担): "有機薬科学実験講座:創薬指向の分子設計"廣川書店. 253 (2000)

    • Related Report
      2000 Annual Research Report

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Published: 2000-04-01   Modified: 2016-04-21  

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