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Characteristics of dislocations in protein crystals

Research Project

Project/Area Number 18560648
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Physical properties of metals
Research InstitutionYokohama City University

Principal Investigator

KOJIMA Kenichi  Yokohama City University, Graduate school of Arts and Sience, Professor (90046095)

Co-Investigator(Kenkyū-buntansha) TACHIBANA Maseru  Yokohama City University, Graduate school of Arts and Science, Professor (80236546)
Project Period (FY) 2006 – 2007
Project Status Completed (Fiscal Year 2007)
Budget Amount *help
¥3,750,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥150,000)
Fiscal Year 2007: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2006: ¥3,100,000 (Direct Cost: ¥3,100,000)
KeywordsCrystal defect / Dislocation / X-ray topogranhy / Protein crystal / Structure biology / X-rav rocking curve / Mosaic structure / Synchrotron X-ray / X-線トポグラフ / 放射光トポグラフ / ロッキングカーブ / 結晶成長 / フラットパネルセンサー / X線回析強度曲線
Research Abstract

The object of this research is to understand characteristics of dislocations in protein crystals. We have attacked the problems by means of two ways. One is to observe clear images of dislocations and to determine the Burgers vectors by synchrotron X-ray topography. The other is to estimate the elastic energy of dislocations and the mechanical strength by an ultrasonic pulse echo method and an indentation method.
Crystal defects, especially dislocations, in hen egg-white lysozyme crystals that are a typical protein crystal that have - multiple polymorphisms, for example tetragonal, orthorhombic and monoclinic forms were investigated by means of synchrotron white and monoclinic-beam X-ray topography. The observed topographic images of dislocations were much clearer compared to those of any protein crystals that have been reported so far. It was demonstrated that millimeter-size crystals larger than extinction length for X-ray topographic reflections are required to obtain clear images, t … More hat is, direct images for protein crystals. In addition the weak beam technique was found to be useful for obtaining clear images. Straight, curved and loop-type dislocations were clearly resolved on the topographs. This shows that dislocations observed in common inorganic and organic with small molecules can also be introduced even in protein crystals. The shapes and distributions of dislocations strongly depended on the crystal polymorphisms. This suggests that the growth mechanisms in the different crystal forms studied could differ. Therefore, X -ray topography provides a useful tool for the characterization of protein crystal dislocations.
We have succeeded the measurement of all components of elastic constants in hen egg-white lysozyme crystals using an ultrasonic pulse echo method. The measurements of the sound velocity were performed using (110) , (101) and (001) crystal surfaces. Consequently, all the six elastic constants of the dehydrated tetragonal HEW lysozyme crystals were determined to be C_<11>= C_<22>= 12.44 GPa, C_<12> =7.03 GPa, C_<13>= C_<28> =8.36 GPa, C_<88> =12.79 GPa, C_<44>=C_<55> =2.97 Gpa and C_<66>=2.63 Gpa, respectively.
In addition, Mechanical properties of high quality tetragonal hen egg-white lysozyme single crystals, which are one of protein crystals were investigated by the indentation method. The indentation marks were clearly observed on the crystal surface and no elastic recovery of them occurred. The value of the micro-Vickers hardness in wet condition was estimated to be about 20 MPa at room temperature. The hardness greatly depended on the amount of water (intra-crystalline water) contained in the crystals. The hardness increased with increasing evaporation time to air at room temperature. It reached the maximum at about 260 MPa, which is 20 times as much as that in the wet condition. The origin of such a change in hardness was explained in terms of the dislocation mechanisms in lysozyme single crystals. Less

Report

(3 results)
  • 2007 Annual Research Report   Final Research Report Summary
  • 2006 Annual Research Report
  • Research Products

    (47 results)

All 2008 2007 2006 2005 Other

All Journal Article (26 results) (of which Peer Reviewed: 13 results) Presentation (19 results) Remarks (2 results)

  • [Journal Article] Effect of intra-crystalline water on micro-hardness in hen egg- whitelysozyme crystals2008

    • Author(s)
      H. Koizumi
    • Journal Title

      J. Phys. D: Appl. Phys. 41

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Dislocation motions in C60 crystals by an indentation test2008

    • Author(s)
      N. Aota
    • Journal Title

      J. Phys. D: Appl. Phys. 41

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Effect of intra-crystalline water on micro-hardness in hen-egg- white lysozyme crystals2008

    • Author(s)
      H. Koizumi M. Tachibana, H. Kawamoto, K. Kojima
    • Journal Title

      J. Phys. D: Appl. Phys 41

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Dislocation motions in C60 crystals by an indentation test2008

    • Author(s)
      N. Aota, M. Tachibana, K. Kojima
    • Journal Title

      J. Phys. D: Appl. Phys 41

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Effects of intra-crystalline water on micro-Vickers hardness in tetragonal hen-egg white lysozyme crystals.2008

    • Author(s)
      H. Koizumi, H. Kawamoto, M. Tachibana and K. Kojima
    • Journal Title

      J. of Physics D; Applied Physics 41

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Observation of clear images of dislocations in proteincrystals by synchrotron monochromatic beam X-raytopography2007

    • Author(s)
      M. Koishi
    • Journal Title

      J. Crystal Growth and Design 7

      Pages: 2182-2186

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Dislocation structures in tetragonal hen egg-white lysozyme crystalsusing synchrotron white beam topography2007

    • Author(s)
      H. Koizumi
    • Journal Title

      Physica B 401-402

      Pages: 691-694

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Charactrerization of dislocations in orthorhombic hen egg-whitelysozyme crystals by synchrotron X-ray topography2007

    • Author(s)
      H. Koizumi
    • Journal Title

      Phys. Status Solidi (a) 204

      Pages: 2688-2693

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Observation of clear images of dislocations in protein crystals by synchrotron monochromatic beam X-ray topography2007

    • Author(s)
      M. Koishi, N. Ohya, Y., Mukoubayashi, H. Kitajima, H.Koizumi, K. Kojima, M. Tachibana
    • Journal Title

      J. Crystal Growth and Design 7

      Pages: 2182-2186

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Dislocation structures in tetragonal hen egg-white lysozyme crystals using synchrotron white beam topography2007

    • Author(s)
      H. Koizumi M. Tachibana, K. Kojima, I. Yonenaga
    • Journal Title

      Physica B 401-402

      Pages: 691-694

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Charactrerization of dislocations in orthorhombic hen egg-white lysozyme crystals by synchrotron X-ray topography2007

    • Author(s)
      H. Koizumi, M. Shimizu, M. Tachibana, K. Kojima
    • Journal Title

      Phys. Status Solidi (a) 204

      Pages: 2688-2693

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Observation of clear images of dislocations in protein crystals by synchrotron monochromatic beam X-ray topography.2007

    • Author(s)
      M. Koishi, K. Kojima, M. Tachibana, et. al.
    • Journal Title

      J. Crystal Growth and Design 7

      Pages: 2182-2186

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dislocation structures in tetragonal hen egg-white lysozyme crystals using synchrotron white beam topography2007

    • Author(s)
      H. Koizumi M. Tachibana, K. Kojima and I. Yonenaga
    • Journal Title

      Physica B 401-402

      Pages: 691-694

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Characterization of dislocations in orthorhombic hen egg-white lysozyme crystals by synchrotron X-ray topography2007

    • Author(s)
      H. Koizumi M. Shimizu, M. Tachibana and K. Kojima
    • Journal Title

      Physica Status Solidi(a), 204

      Pages: 2688-2693

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Charactrerization of dislocations in orthorhombic hen egg-white lysozyme crystals by synchrotron X-ray topography;2007

    • Author(s)
      H.Koizumi, M.Tachibana, K.Kojima
    • Journal Title

      Phys. Status Solidi (印刷中)

    • Related Report
      2006 Annual Research Report
  • [Journal Article] タンパク質結晶品質に及ぼす不純物の影響2006

    • Author(s)
      吉崎 泉
    • Journal Title

      結晶成長学会誌 33

      Pages: 359-365

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Observation of all components of elastic constants of tetragonal henegg-white lysozyme crystals dehydrated at 42% relative humidity2006

    • Author(s)
      H. Koizumi
    • Journal Title

      Phys.Rev.E 73

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Impurity-induced defect and its effect on protein crystal perfection2006

    • Author(s)
      I. Yoshizaki
    • Journal Title

      J.Crystal Growth 290

      Pages: 185-191

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Effects of crystal quality of impurity effects in protein crystals2006

    • Author(s)
      I. Yoshizaki, S. Fukuyama, H. Koizumi, M. Tachibana, K. Kojima, et. al.
    • Journal Title

      Bulletin of Japanese Association for Crystal Growth 33

      Pages: 359-365

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Observation of all components of elastic constants of tetragonal hen egg-white lysozyme crystals dehydrated at 42% relative humidity2006

    • Author(s)
      H. Koizumi, M. Tachibana, K. Kojima
    • Journal Title

      Phys. Rev. E73

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Impurity-induced defect and its effect on protein crystal perfection2006

    • Author(s)
      I. Yoshizaki, S. Fukuyama, H. Koizumi, M. Tachibana, K. Kojima, et. al.
    • Journal Title

      J. Crystal Growth 290

      Pages: 185-191

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] タンパク質結晶品質に及ぼす不純物の影響2006

    • Author(s)
      吉崎泉, 飯村好和, 福山誠二郎, 門脇昭夫, 小泉晴比古, 橘勝, 小島謙一, 栄龍, 足立聡, 依田真一
    • Journal Title

      結晶成長学会誌 33

      Pages: 359-365

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Observation of all components of elastic constants of tetragonal hen egg-white lysozyme crystals dehydrated at 42% relative humidity2006

    • Author(s)
      H.Koizumi, M.Tachibana, K.Kojima
    • Journal Title

      Phys. Rev. E 73

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Impurity-induced defect and its effect on protein crystal perfection2006

    • Author(s)
      I.Yoshizaki, S.Fukuyama, H.Koizumi, M.Tachibana, K.Kojima, et al.
    • Journal Title

      J. Crystal Glowth 290

      Pages: 185-191

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Analysis of dislocation images in X-ray topography of protein crystals:tetragonal hen egg-white lysozyme crystals2005

    • Author(s)
      H. Koizumi
    • Journal Title

      Phil.Mag. 85

      Pages: 3709-3717

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Analysis of dislocation images in X-ray topography of protein crystals: tetragonal hen egg-white lysozyme crystals2005

    • Author(s)
      H. Koizumi, M. Tachibana, K. Kojima
    • Journal Title

      Phil. Mag. 85

      Pages: 3709-3717

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Crystal growth and dislocations in hen egg-white lysozyme crystals using synchrotron x-ray topography.(invitedtalk)2008

    • Author(s)
      Kenichi Kojima
    • Organizer
      The 4-th Asian Conferenceon Crystal Growth and Crystal Technology
    • Place of Presentation
      東北大学
    • Year and Date
      2008-05-23
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Crystal Growth and dislocations in lysozyme crystals using synchrotron-ray.2008

    • Author(s)
      Kenichi Kojima
    • Organizer
      Asian Conference on Crystal Growth and Crystal Technology
    • Place of Presentation
      Tohoku University
    • Year and Date
      2008-05-23
    • Related Report
      2007 Annual Research Report
  • [Presentation] タンパク質結晶の放射光トポグラフによる結晶の評価2008

    • Author(s)
      小島 謙一
    • Organizer
      タンパク質結晶育成研究会
    • Place of Presentation
      日立シビックセンター
    • Year and Date
      2008-03-18
    • Related Report
      2007 Annual Research Report
  • [Presentation] Crystal growth and dislocations in hen egg-white lysozyme crystals using synchrotron x-ray topography2008

    • Author(s)
      K. Kojima
    • Organizer
      The 4-th Asian Conference on Crystal Growth and Crystal Technology, invited talk, Sendai
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] X-ray topographic work on lysozyme crystals grown in ground and space2007

    • Author(s)
      Kenichi Kojima
    • Organizer
      ITT2
    • Place of Presentation
      Nara
    • Year and Date
      2007-10-21
    • Related Report
      2007 Annual Research Report
  • [Presentation] タンパク質結晶の欠陥の放射光トポグラフによる評価2007

    • Author(s)
      小島 謙一
    • Organizer
      平成19年度日本結晶成長学会
    • Place of Presentation
      北海道大学
    • Year and Date
      2007-10-04
    • Related Report
      2007 Annual Research Report
  • [Presentation] タンパク質結晶の転位と力学的性質2007

    • Author(s)
      小島 謙一
    • Organizer
      平成19年度秋日本物理学会
    • Place of Presentation
      北海道大学
    • Year and Date
      2007-09-24
    • Related Report
      2007 Annual Research Report
  • [Presentation] Crystal growth and synchrotron x-ray topography of orthorhombic hen egg-white lysozyme crystals2007

    • Author(s)
      Kenichi Kojima
    • Organizer
      The 15th International Conference on Crystal Growth
    • Place of Presentation
      Salt Lake City
    • Year and Date
      2007-08-14
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Indentation and dislocations in protein crystals2007

    • Author(s)
      Kenichi Kojima
    • Organizer
      International Indentation Workshop 3
    • Place of Presentation
      Cambridge University
    • Year and Date
      2007-07-19
    • Related Report
      2007 Annual Research Report
  • [Presentation] Indentations and Dislocations in Protein Crystals.(invited talk)2007

    • Author(s)
      Kenichi Kojima
    • Organizer
      The third International Work Shop on Indentation
    • Place of Presentation
      Cambridge(UK)
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] X-ray topographic work on lysozyme crystals grown in space.(invited talk)2007

    • Author(s)
      Kenichi Kojima
    • Organizer
      The second International Topic Team Meeting on Crystal Growth
    • Place of Presentation
      Nara(Japan)
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] タンパク質結晶の転位と力学的性質2007

    • Author(s)
      小島 謙一
    • Organizer
      日本物理学会第62回年次大会特別講演
    • Place of Presentation
      札幌(北海道大学
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Crystal perfection and intra-crystalline water on mechanical property of protein Crystal2007

    • Author(s)
      K. Kojima
    • Organizer
      The 15th International Conference on Growth
    • Place of Presentation
      Salt Lake City
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Mechanical properties and dislocations in protein crystals2007

    • Author(s)
      K. Kojima
    • Organizer
      Annual meeting of Physical society of Japan (Invited lecture) Sapporo
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] X-ray topographic work on lysozyme crystals grown in space2007

    • Author(s)
      K. Kojima
    • Organizer
      The 2nd International Topic Team Meeting on Crystal Growth, Nara (Japan), invited talk
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Indentations and Dislocations in Protein Crystals2007

    • Author(s)
      K. Kojima
    • Organizer
      The third International Work Shop on Indentation, Cambridge (UK), invited talk
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Relationship between elastic constants and intracrystallin water in rotein crystals2006

    • Author(s)
      Kenichi Kojima
    • Organizer
      The 11th International Conferenceon Crystallization of BioMacromolecules(ICCBM11)
    • Place of Presentation
      Quebec(Canada)
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Relationship between elastic constants and intracrystallin water in protein crystals2006

    • Author(s)
      K. Kojima
    • Organizer
      The 11th International Conference on Crystallization of Bio-Macromolecules(ICCBM11)
    • Place of Presentation
      Quebec, Canada
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Double images in X-ray topography of protein crystals2006

    • Author(s)
      H. Koizumi, M. Tachibana, K. Kojima
    • Organizer
      8th Biennial Conference on High Resolution X-Ray Diffraction and Imaging (XTOP2006), Baden-Baden
    • Place of Presentation
      Germany
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Remarks] 「研究成果報告書概要(和文)」より

    • URL

      http://nanomate.sci.yokohama-cu.ac.jp/

    • Related Report
      2007 Final Research Report Summary
  • [Remarks]

    • URL

      http://nanomate.sci.yokohama-cu.ac.jp/

    • Related Report
      2007 Annual Research Report

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Published: 2006-04-01   Modified: 2016-04-21  

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