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2007 Fiscal Year Final Research Report Summary

Development of the Free energy Calculation method and the Construction of Carbohydrate Structure Library

Research Project

Project/Area Number 17300093
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionYokohama National University

Principal Investigator

UEDA Kazuyoshi  Yokohama National University, Graduate School of Enginneering, Professor (40223458)

Project Period (FY) 2005 – 2007
KeywordsMolecular dynamics / Bioinformatics / Free energy / Carbohydrate
Research Abstract

We have been investigating the confirmation of the carbohydrates in solution by using molecular dynamics simulation. In order to obtain the fine energy of the conformational change in solution, we applied the umbrella sampling method to charmm program. We obtained the Ramachandran free energy map of the conformational potential mean force for neocarrabiose in water. The potential energy map showed the different behavior compared with that of calculated in a previous study for this molecule in vacuum. This method was tried to apply to other carbohydrates in solution, such as oligosaccharide in immunoglogrin G.
Carbohydrates in glycoprotein attract a great deal of attention because the glycan chains are suggested to play a variety of biological functions. However, the details of the role of glycan chains have not fully understood yet. Immunoglobulin G (IgG) is known to form antigen-antibody complex and it further bind to the receptors (FcR) for the Fc portion of IgG.. Nose and Wigzell com … More pared the IgG antibodies with or without carbohydrate chains and showed that the carbohydrate-deficient IgG will lead to an inability of the antibodies to interact with FcR on macrophages. Kato performed NMR experiment and suggested that the Fc portion takes different conformation between the conditions with or without glycan chains. In order to investigate the role of glycan chain more precisely, molecular dynamics simulation of the Fc portion of IgG was performed. The structure of the Fc portion of IgG was constructed from the crystal structure of Harris, et. Al. by removing the Fab fragments. Although the calculation with explicit water molecules is crucial in a proper treatment of biopolymers in aqueous solution, such calculation is too expensive in this case. Therefore, we first tried to perform the molecular dynamics simulation by using simple method, which mimic the solvent effect, such as high dielectric constant and generalized Born method. As a basic information for this work, we calculated the ramachandran potential surface map for disaccharides which constructs the IgG oligosaccharide.
We further studied the basic interaction exists in the carbohydrate-carbohydrate and carbohydrate-protein complexes, such as CH-p interaction. Ring interconversion of the glucopyranose ring was also investigated by using ab initio calculation. The results showed that the E_3 conformation was found to be a transition state of the ring interconversion. Intrinsic reaction coordinate (IRC) calculations indicated that the E_3 conformation is a transition state of the ring interconversion path from ^4C_1 to B_3,o via E_3 conformation. Less

  • Research Products

    (36 results)

All 2008 2007 2006

All Journal Article (14 results) (of which Peer Reviewed: 7 results) Presentation (22 results)

  • [Journal Article] Origin of the axial-alkyl preference of(R)-a-phellandrene and related compounds investigated by high-level ab initio MO calculatlons. Importance of the CH/π Hydrogen Bond2008

    • Author(s)
      Osamu Takahashi
    • Journal Title

      Tetrahedron. 64

      Pages: 5773-5778

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] Origin of the axial-alkyl preference of(R)-a-phellandrene and related compounds investigated by high-level ab initio MO calculations. Importance of the CH/π Hydrogen Bond2008

    • Author(s)
      Osamu, Takahashi, Katsuyoshi, Yamasaki, Yuji, Kohno, Kazuyoshi, Ueda, Hiroko, Suezawa, Motohiro, Nishio
    • Journal Title

      Tetrahedron 64

      Pages: 5773-5778

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] The anomeric effect revisited. A possible role of the CH/n hydrogen bond.2007

    • Author(s)
      Osamu Takahashi, 他
    • Journal Title

      Carbohydrate Research. 342

      Pages: 1202-1209

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] Origin of the gauche preference of n-propyl halides and related molecules investigated by ab initio MO calculations: Importance of the CH/n hydrogen bond2007

    • Author(s)
      Osamu Takahashi, 他
    • Journal Title

      Chem. Phys. Lett. 440

      Pages: 64-69

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] The Conformation of Alkyl Cyclohexanones and Terpenic Ketones. Interpretation for the"Alkylketone Effect"Based on the CH/π(C=O)Hydrogen Bond2007

    • Author(s)
      Osamu Takahashi, 他
    • Journal Title

      Tetrahedron. 64

      Pages: 2433-2440

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] AlKali-Cation Affinities of Polyoxyethylene Dodecylethers and Helical Conformations of Their Cationized Molecules Studied by Electrospray Mass Spectrometry2007

    • Author(s)
      Yukio Yokoyama, 他
    • Journal Title

      J. Am. Soc. Mass Spectrom. 18

      Pages: 1914-1920

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] The anomeric effect revisited. A possible role of the CH/n hydrogen bond2007

    • Author(s)
      Osamu, Takahashi, Katsuyoshi, Yamazaki, Yuji, Kohno, Ryuta, Otaki, Kazuyoshi, Ueda, Hiroko, Suezawa, Yoji, Umezawa, Motohiro, Nishio
    • Journal Title

      Carbohydr. Res 342

      Pages: 1202-1209

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Origin of the gauche preference of n-propyl halides and related molecules investigated by ab initio MO calculations: Importance of the CH/n hydrogen bond2007

    • Author(s)
      Osamu, Takahashi, Katsuyoshi, Yamasaki, Yuji, Kohno, Kazuyoshi, Ueda, Hiroko, Suezawa, Motohiro, Nishio
    • Journal Title

      Chem. Phys. Lett 440

      Pages: 64-69

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] The Conformation of Alkyl Cyclohexanones and Terpenic Ketones. Interpretation for the "Alkylketone Effect" Based on the CH/π(C=O) Hydrogen Bond2007

    • Author(s)
      Osamu, Takahashi, Katsuyoshi, Yamasaki, Yuji, Kohno, Youji, Kurihara, Kazuyoshi, Ueda, Yoji, Umezawa, Hiroko, Suezawa, Motohiro, Nishio
    • Journal Title

      Tetrahedron 64

      Pages: 2433-2440

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] AlKali-Cation Affmities of Polyoxyethylene Dodecylethers and Helical Conformations of Their Cationized Molecules Studied by Electrospray Mass Spectrometry2007

    • Author(s)
      Yukio, Yokoyama, Rui, Hirajima, Ken, Morigaki, Yoshitaka, Yamaguchi, Kazuyoshi Ueda
    • Journal Title

      J. Am. Soc. Mass Spectrom 18

      Pages: 1914-1920

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] An investigation of the pyranose ring inter-conversion path of α-L-Idose calculated using Density Functional Theory.2006

    • Author(s)
      Youji Kurihara, 他
    • Journal Title

      Carbohydrate Research. 341

      Pages: 2565-2574

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] Origin of the π-facial stereoselectivity in the addition of nucleophilic reagents to chiral aliphatic ketones as evidenced by high-level ab initio Molecular-Orbital calculations.2006

    • Author(s)
      Osamu Takahashi, 他
    • Journal Title

      Chem Asian J. 1

      Pages: 852-859

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] An investigation of the pyranose ring inter-conversion path of a-L-Idose calculated using Density Functional Theory2006

    • Author(s)
      Youji, Kurihara, Kazuyoshi, Ueda
    • Journal Title

      Carbohydrate Research 341

      Pages: 2565-2574

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Origin of the π-facial stereoselectivity in the addition of nucleophilic reagents to chiral aliphatic ketones as evidenced by high-level ab initio Molecular-Orbital calculations2006

    • Author(s)
      Osamu, Takahashi, Katsuyoshi, Yamazaki, Yuji, Kohno, Kazuyoshi, Ueda, Hiroko, Suezawa, Motohiro, Nishio
    • Journal Title

      Chem Asian J 1

      Pages: 852-859

    • Description
      「研究成果報告書概要(欧文)」より
  • [Presentation] セルロース誘導体を用いた不斉認識機構及び構造のシミュレーションによる解析2007

    • Author(s)
      大滝竜太
    • Organizer
      日本化学会第1回関東支部大会
    • Place of Presentation
      首都大学東京南大沢キャンパス
    • Year and Date
      20070927-28
    • Description
      「研究成果報告書概要(和文)」より
  • [Presentation] 分子動力学シミュレーションによる脂質二重膜中でのボンボリチンの構造解析2007

    • Author(s)
      出川嘉朗
    • Organizer
      日本化学会第1回関東支部大会
    • Place of Presentation
      首都大学東京南大沢キャンパス
    • Year and Date
      20070927-28
    • Description
      「研究成果報告書概要(和文)」より
  • [Presentation] N-アセチルグルコサミンの分子動力学シミュレーション用分子パラメターの作成と構造解析2007

    • Author(s)
      北田和久
    • Organizer
      日本化学会第1回関東支部大会
    • Place of Presentation
      首都大学東京南大沢キャンパス
    • Year and Date
      20070927-28
    • Description
      「研究成果報告書概要(和文)」より
  • [Presentation] Immunoglobulin G の糖鎖を構成する3糖のコンフォメーション解析2007

    • Author(s)
      野村 隆
    • Organizer
      日本化学会第1回関東支部大会
    • Place of Presentation
      首都大学東京南大沢キャンパス
    • Year and Date
      20070927-28
    • Description
      「研究成果報告書概要(和文)」より
  • [Presentation] 計算化学を用いたセルロース誘導体のコンフォメーションに関する研究2007

    • Author(s)
      上田 一義
    • Organizer
      セルロース学会第14回年次大会
    • Place of Presentation
      静岡大学大学会館
    • Year and Date
      20070719-20
    • Description
      「研究成果報告書概要(和文)」より
  • [Presentation] 密度汎関数法によるグルコースの環配座変換2007

    • Author(s)
      栗原庸次
    • Organizer
      セルロース学会第14回年次大会
    • Place of Presentation
      静岡大学大学会館
    • Year and Date
      20070719-20
    • Description
      「研究成果報告書概要(和文)」より
  • [Presentation] 計算機化学的方法を用いたセルロース誘導体のコンフォメーションに関する研究2007

    • Author(s)
      上田 一義
    • Organizer
      第56回高分子学会年次大会
    • Place of Presentation
      京都国際会議場
    • Year and Date
      20070529-31
    • Description
      「研究成果報告書概要(和文)」より
  • [Presentation] 密度汎関数法によるグルコースの環配座変換2007

    • Author(s)
      栗原庸次
    • Organizer
      日本コンピューター化学会2006春季年会
    • Place of Presentation
      東京工業大学
    • Year and Date
      20070524-25
    • Description
      「研究成果報告書概要(和文)」より
  • [Presentation] Ring inter-conversion path of glucose calculated using Density Functional Theory2007

    • Author(s)
      Youji, Kurihara, Kazuyoshi, Ueda
    • Organizer
      Annual meeting, 2007, Spring, Society of Computer Chemistry, Japan preprint
    • Year and Date
      20070000
    • Description
      「研究成果報告書概要(欧文)」より
  • [Presentation] Conformational properties of cellulose derivatives studied by computational chemistry2007

    • Author(s)
      Kazuyoshi, Ueda, Tohei, Takarada
    • Organizer
      Polymer Preprints, Japan
    • Year and Date
      20070000
    • Description
      「研究成果報告書概要(欧文)」より
  • [Presentation] Conformational properties of cellulose derivatives studied by computational chemistry2007

    • Author(s)
      Kazuyoshi, Ueda, Tohei, Takarada
    • Organizer
      Preprints of 2006 Cellulose R&D 146 Annual Meeting of The Cellulose Society of Japan
    • Year and Date
      20070000
    • Description
      「研究成果報告書概要(欧文)」より
  • [Presentation] Ring inter-conversion path of glucose calculated using Density Functional Theory2007

    • Author(s)
      Youji, Kurihara, Kazuyoshi, Ueda
    • Organizer
      Preprints of 2006 Cellulose R&D 14th Annual Meeting of The Cellulose Society of Japan
    • Year and Date
      20070000
    • Description
      「研究成果報告書概要(欧文)」より
  • [Presentation] Molecular dynamics simulation of the Chiral separation mechanism by the cellulose derivatives2007

    • Author(s)
      Ryuta Otaki, Kazuyoshi, Ueda
    • Organizer
      Annual meeting of Kanto Branch, 2007, Chemical Society of Japan preprint
    • Year and Date
      20070000
    • Description
      「研究成果報告書概要(欧文)」より
  • [Presentation] Molecular dynamics simulation of Bombolitin in lipid bilayers2007

    • Author(s)
      Yoshiaki, Degawa, Kazuyoshi, Ueda
    • Organizer
      Annual meeting of Kanto Branch, 2007, Chemical Society of Japan preprint
    • Year and Date
      20070000
    • Description
      「研究成果報告書概要(欧文)」より
  • [Presentation] Parameterization of the N-acetyl glucosamine for Molecular dynamics simulation2007

    • Author(s)
      Kazuhisa, Kitada, Kazuyoshi, Ueda
    • Organizer
      Annual meeting of Kanto Branch, 2007, Chemical Society of Japan preprint
    • Year and Date
      20070000
    • Description
      「研究成果報告書概要(欧文)」より
  • [Presentation] Molecular dynamics simulation of the trimer oligosaccharides in immunoglibrin G2007

    • Author(s)
      Takashi, Nomura, Kazuyoshi, Ueda
    • Organizer
      Annual meeting of Kanto Branch, 2007, Chemical Society of Japan preprint
    • Year and Date
      20070000
    • Description
      「研究成果報告書概要(欧文)」より
  • [Presentation] セルロースプロピオネートのコンフォメーションに関する研究2006

    • Author(s)
      宝田庸平
    • Organizer
      セルロース学会第13回年次大会
    • Place of Presentation
      東京大学弥生講堂
    • Year and Date
      20060713-14
    • Description
      「研究成果報告書概要(和文)」より
  • [Presentation] 密度汎関数法によるイドースの環配座の変換経路II2006

    • Author(s)
      栗原庸次
    • Organizer
      日本コンピューター化学会2006春季年会
    • Place of Presentation
      東京工業大学
    • Year and Date
      20060601-02
    • Description
      「研究成果報告書概要(和文)」より
  • [Presentation] Leptothrix cholodniiが構築する鞘多糖の分子シミュレーションによる高次構造解析2006

    • Author(s)
      大滝 敦史
    • Organizer
      第55回高分子学会年次大会
    • Place of Presentation
      名古屋国際会議場
    • Year and Date
      20060525-27
    • Description
      「研究成果報告書概要(和文)」より
  • [Presentation] Molecular Simulation of a Polysaccharide isolated from Leptothrix cholodnii2006

    • Author(s)
      Atsusi, Otaki, Kazuyoshi, Ueda
    • Organizer
      Polymer Preprints
    • Place of Presentation
      Japan
    • Year and Date
      20060000
    • Description
      「研究成果報告書概要(欧文)」より
  • [Presentation] Conformational analysis of the Cellulose Propionate2006

    • Author(s)
      Yohei, Takarada, Kazuyoshi, Ueda
    • Organizer
      Preprints of 2006 Cellulose R&D 13th Annual Meeting of The Cellulose Society of Japan
    • Year and Date
      20060000
    • Description
      「研究成果報告書概要(欧文)」より
  • [Presentation] pyranose ring inter-conversion path of a-L-Idose calculated using Density Functional Theory II2006

    • Author(s)
      Youji, Kurihara, Kazuyoshi, Ueda
    • Organizer
      Annual meeting, 2006, Spring, Society of Computer Chemistry, Japan preprint
    • Year and Date
      20060000
    • Description
      「研究成果報告書概要(欧文)」より

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Published: 2010-02-04  

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