中国物理B ›› 2008, Vol. 17 ›› Issue (1): 1-9.doi: 10.1088/1674-1056/17/1/001

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SAD phasing by OASIS at different resolutions down to 0.30nm and below

古元新1, 郑朝德1, 范海福1, 林政炯2, 姚德强3, 渡邉信久4, 沙炳东5, 李鹤6, 陈强7   

  1. (1)Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,\Chinese Academy of Sciences, Beijing 100080, China; (2)Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,\Chinese Academy of Sciences, Beijing 100080, China;Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; (3)Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,\Chinese Academy of Sciences, Beijing 100080, China;National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230026, China; (4)Department of Biotechnology and Biomaterial Chemistry, Nagoya University, Nagoya 4648603, Japan; (5)Department of Cell Biology, University of Alabama at Birmingham, USA; (6)Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; (7)National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871, China
  • 收稿日期:2007-07-20 出版日期:2008-01-20 发布日期:2008-01-20
  • 基金资助:
    Project supported by the Innovation Project of the Chinese Academy of Sciences and the 973 Project (Grant No 2002CB713801) of the Ministry of Science and Technology of China.

SAD phasing by OASIS at different resolutions down to 0.30nm and below

Yao De-Qiang(姚德强)a)b), Li He(李鹤)c), Chen Qiang(陈强)d), Gu Yuan-Xin(古元新)a), Zheng Chao-De(郑朝德)a), Lin Zheng-Jiong(林政炯)a)c), Fan Hai-Fu(范海福)a)†, Nobuhisa Watanabe(渡邉信久)e), and Sha Bing-Dong(沙炳东)f)   

  1. a Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China; b National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230026, China; c Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; d National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871, China; e Department of Biotechnology and Biomaterial Chemistry, Nagoya University, Nagoya 4648603, Japan; f Department of Cell Biology, University of Alabama at Birmingham, USA
  • Received:2007-07-20 Online:2008-01-20 Published:2008-01-20
  • Supported by:
    Project supported by the Innovation Project of the Chinese Academy of Sciences and the 973 Project (Grant No 2002CB713801) of the Ministry of Science and Technology of China.

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摘要： Single-wavelength anomalous diffraction (SAD) phasing is increasingly important in solving de novo protein structures. Direct methods have been proved very efficient in SAD phasing. This paper aims at probing the low-resolution limit of direct-method SAD phasing. Two known proteins TT0570 and Tom70p were used as test samples. Sulfur-SAD data of the protein TT0570 were collected with conventional Cu-K\alpha source at 0.18nm resolution. Its truncated subsets respectively at 0.21, 0.30, 0.35 and 0.40nm resolutions were used in the test. TT0570 Cu-K$\alpha$ sulfur-SAD data have an expected Bijvoet ratio <\vert\Delta F\vert>/\ \sim 0.55%. In the 0.21nm case, a single run of OASIS-DM-ARP/wARP led automatically to a model containing 1178 of the total 1206 residues all docked into the sequence. In 0.30 and 0.35nm cases, SAD phasing by OASIS-DM led to traceable electron density maps. In the 0.40nm case, SAD phasing by OASIS-DM resulted in a degraded electron density map, which may be difficult to trace but still contains useful secondary-structure information. Test on real 0.33nm selenium-SAD data of the protein Tom70p showed that even automatic model building was not successful, the combination of manual tracing and direct-method fragment extension was capable of significantly improving the electron-density map. This provides the possibility of effectively improving the manually built model before structure refinement is performed.

关键词: OASIS, SAD phasing, dual-space fragment extension, proteins

Abstract: Single-wavelength anomalous diffraction (SAD) phasing is increasingly important in solving de novo protein structures. Direct methods have been proved very efficient in SAD phasing. This paper aims at probing the low-resolution limit of direct-method SAD phasing. Two known proteins TT0570 and Tom70p were used as test samples. Sulfur-SAD data of the protein TT0570 were collected with conventional Cu-K$\alpha$ source at 0.18nm resolution. Its truncated subsets respectively at 0.21, 0.30, 0.35 and 0.40nm resolutions were used in the test. TT0570 Cu-K$\alpha$ sulfur-SAD data have an expected Bijvoet ratio $<\vert\Delta F\vert>\sim$ 0.55%. In the 0.21nm case, a single run of OASIS-DM-ARP/wARP led automatically to a model containing 1178 of the total 1206 residues all docked into the sequence. In 0.30 and 0.35nm cases, SAD phasing by OASIS-DM led to traceable electron density maps. In the 0.40nm case, SAD phasing by OASIS-DM resulted in a degraded electron density map, which may be difficult to trace but still contains useful secondary-structure information. Test on real 0.33nm selenium-SAD data of the protein Tom70p showed that even automatic model building was not successful, the combination of manual tracing and direct-method fragment extension was capable of significantly improving the electron-density map. This provides the possibility of effectively improving the manually built model before structure refinement is performed.

Key words: OASIS, SAD phasing, dual-space fragment extension, proteins

中图分类号:  (Proteins)

  • 87.14.E-
87.15.B- (Structure of biomolecules) 87.15.A- (Theory, modeling, and computer simulation) 87.15.Cc (Folding: thermodynamics, statistical mechanics, models, and pathways)