中国物理B ›› 2007, Vol. 16 ›› Issue (10): 3022-3028.doi: 10.1088/1009-1963/16/10/034

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SIR phasing by combination of SOLVE/RESOLVE and dual-space fragment extension involving OASIS

何 尧1, 古元新1, 郑朝德1, 范海福1, 林政炯2   

  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
  • 收稿日期:2007-07-16 修回日期:2007-07-17 出版日期:2007-10-08 发布日期:2007-10-08
  • 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.

SIR phasing by combination of SOLVE/RESOLVE and dual-space fragment extension involving OASIS

He Yao(何尧)a), Gu Yuan-Xin(古元新)a)† , Lin Zheng-Jiong(林政炯)a)b), Zheng Chao-De(郑朝德)a), and Fan Hai-Fu(范海福)a)   

  1. a Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China; b Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
  • Received:2007-07-16 Revised:2007-07-17 Online:2007-10-08 Published:2007-10-08
  • 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： A new phasing procedure has been proposed for dealing with single isomorphous replacement (SIR) x-ray diffraction data. The procedure combines {SOLVE/RESOLVE} with the dual-space fragment extension involving {OASIS}. Two sets of SIR data at 0.28~nm resolution taken from the protein (R)-phycoerythrin (PDB code: 1LIA) were used in the test. For one of the two SIR data sets, a default run of {SOLVE/RESOLVE} based on the heavy-atom substructure found by {SHLEXD} led automatically to an interpretable electron density map. {OASIS} could not effectively improve the result. For the other set of SIR data, {SOLVE/RESOLVE} resulted in a fragmented model consisting of 454 of the total 668 residues, in which only 29 residues were docked into the sequence. Based on this model, 7 iteration cycles of {OASIS-DM-RESOLVE} (build only) yielded automatically a model of 547 residues with 133 residues docked into the sequence. The overall-averaged phase error decreased considerably and the quality of electron density map was improved significantly. Two more cycles of iterative {OASIS}-{DM}-{RESOLVE} were carried out, in which the output phases and figures of merit from {DM} were merged with that from the original run of {SOLVE/RESOLVE} before they were passed onto {RESOLVE} (build only). This led automatically to a model containing 452 residues with 173 docked into the sequence. The resultant electron density map is manually traceable. It is concluded that when results of {SOLVE/RESOLVE} are not sufficiently satisfactory, the combination of {SOLVE/RESOLVE} and {OASIS}-{DM}-{RESOLVE} (build only) may significantly improve them.

关键词: SIR phasing, SOLVE/RESOLVE, OASIS, dual-space fragment extension for proteins

Abstract: A new phasing procedure has been proposed for dealing with single isomorphous replacement (SIR) x-ray diffraction data. The procedure combines SOLVE/RESOLVE with the dual-space fragment extension involving OASIS. Two sets of SIR data at 0.28 nm resolution taken from the protein (R)-phycoerythrin (PDB code: 1LIA) were used in the test. For one of the two SIR data sets, a default run of SOLVE/RESOLVE based on the heavy-atom substructure found by SHLEXD led automatically to an interpretable electron density map. OASIS could not effectively improve the result. For the other set of SIR data, SOLVE/RESOLVE resulted in a fragmented model consisting of 454 of the total 668 residues, in which only 29 residues were docked into the sequence. Based on this model, 7 iteration cycles of OASIS-DM-RESOLVE (build only) yielded automatically a model of 547 residues with 133 residues docked into the sequence. The overall-averaged phase error decreased considerably and the quality of electron density map was improved significantly. Two more cycles of iterative OASIS-DM-RESOLVE were carried out, in which the output phases and figures of merit from DM were merged with that from the original run of SOLVE/RESOLVE before they were passed onto RESOLVE (build only). This led automatically to a model containing 452 residues with 173 docked into the sequence. The resultant electron density map is manually traceable. It is concluded that when results of  SOLVE/RESOLVE are not sufficiently satisfactory, the combination of SOLVE/RESOLVE and OASIS-DM-RESOLVE (build only) may significantly improve them.

Key words: SIR phasing, SOLVE/RESOLVE, OASIS, dual-space fragment extension for proteins

中图分类号:  (Biophysical techniques (research methods))

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