Please wait a minute...
Chin. Phys. B, 2008, Vol. 17(1): 1-9    DOI: 10.1088/1674-1056/17/1/001
RAPID COMMUNICATION   Next  

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)
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, ChinaDepartment of Biotechnology and Biomaterial Chemistry, Nagoya University, Nagoya 4648603, JapanDepartment of Cell Biology, University of Alabama at Birmingham, USA
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.
Keywords:  OASIS      SAD phasing      dual-space fragment extension      proteins  
Received:  20 July 2007      Accepted manuscript online: 
PACS:  87.14.E- (Proteins)  
  87.15.B- (Structure of biomolecules)  
  87.15.A- (Theory, modeling, and computer simulation)  
  87.15.Cc (Folding: thermodynamics, statistical mechanics, models, and pathways)  
Fund: 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.

Cite this article: 

Yao De-Qiang(姚德强), Li He(李鹤), Chen Qiang(陈强), Gu Yuan-Xin(古元新), Zheng Chao-De(郑朝德), Lin Zheng-Jiong(林政炯), Fan Hai-Fu(范海福), Nobuhisa Watanabe(渡邉信久), and Sha Bing-Dong(沙炳东) SAD phasing by OASIS at different resolutions down to 0.30nm and below 2008 Chin. Phys. B 17 1

[1] Biased random walk with restart for essential proteins prediction
Pengli Lu(卢鹏丽), Yuntian Chen(陈云天), Teng Zhang(张腾), and Yonggang Liao(廖永刚). Chin. Phys. B, 2022, 31(11): 118901.
[2] Modeling hydrogen exchange of proteins by a multiscale method
Wentao Zhu(祝文涛), Wenfei Li(李文飞), and Wei Wang(王炜). Chin. Phys. B, 2021, 30(7): 078701.
[3] Knowledge-based potentials in bioinformatics: From a physicist's viewpoint
Zheng Wei-Mou (郑伟谋). Chin. Phys. B, 2015, 24(12): 128701.
[4] Proteins:From sequence to structure
Zheng Wei-Mou (郑伟谋). Chin. Phys. B, 2014, 23(7): 078705.
[5] Predicting the subcellular location of apoptosis proteins based on recurrence quantification analysis and the Hilbert–Huang transform
Han Guo-Sheng(韩国胜), Yu Zu-Guo(喻祖国), and Anh Vo . Chin. Phys. B, 2011, 20(10): 100504.
[6] Combining SAD/SIR iteration and MR iteration in partial-model extension of proteins
Zhang Tao(张涛), Wu Li-Jie(武丽杰), Gu Yuan-Xin(古元新), Zheng Chao-De(郑朝德), and Fan Hai-Fu(范海福). Chin. Phys. B, 2010, 19(9): 096101.
[7] New expression of bimodal phase distributions in direct-method phasing of protein single-wavelength anomalous diffraction data
Zhang Tao (张涛), Gu Yuan-Xin (古元新), Zheng Chao-De (郑朝德), Fan Hai-Fu (范海福). Chin. Phys. B, 2010, 19(8): 086102.
[8] OASIS4.0—a new version of the program OASIS for phasing protein diffraction data
Zhang Tao(张涛), Gu Yuan-Xin(古元新), Zheng Chao-De(郑朝德), and Fan Hai-Fu(范海福). Chin. Phys. B, 2010, 19(8): 086103.
[9] Chaos game representation of functional protein sequences, and simulation and multifractal analysis of induced measures
Yu Zu-Guo(喻祖国), Xiao Qian-Jun(肖前军), Shi Long(石龙), Yu Jun-Wu(余君武), and Vo Anh. Chin. Phys. B, 2010, 19(6): 068701.
[10] Structural statistical properties of knotted proteins
Wang Xiang-Hong(王向红), Shen Yu(沈瑜), and Zhang Lin-Xi(章林溪). Chin. Phys. B, 2009, 18(4): 1684-1690.
[11] Statistical interior properties of globular proteins
Jiang Zhou-Ting(姜舟婷), Zhang Lin-Xi(章林溪), Sun Ting-Ting(孙婷婷), and Wu Tai-Quan(吴太权). Chin. Phys. B, 2009, 18(10): 4580-4590.
[12] SIR phasing by combination of SOLVE/RESOLVE and dual-space fragment extension involving OASIS
He Yao(何尧), Gu Yuan-Xin(古元新), Lin Zheng-Jiong(林政炯), Zheng Chao-De(郑朝德), and Fan Hai-Fu(范海福). Chin. Phys. B, 2007, 16(10): 3022-3028.
No Suggested Reading articles found!