Please wait a minute...
Chin. Phys. B, 2010, Vol. 19(8): 086102    DOI: 10.1088/1674-1056/19/8/086102
RAPID COMMUNICATION Prev   Next  

New expression of bimodal phase distributions in direct-method phasing of protein single-wavelength anomalous diffraction data

Zhang Tao (张涛)ab, Gu Yuan-Xin (古元新)b, Zheng Chao-De (郑朝德)b, Fan Hai-Fu (范海福)b
a Research Institute of Magnetic Materials, School of Physical Sciences and Technology, Lanzhou University, Lanzhou 730000, China; b Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
Abstract  One of the essential points of the direct-method single-wavelength anomalous diffraction (SAD) phasing for proteins is to express the bimodal SAD phase distribution by the sum of two Gaussian functions peaked respectively at $\varphi''_h+|\Delta\varphi_h|$ and $\varphi''_h-|\Delta\varphi_h|$. The probability for $\Delta\varphi$ being positive (P+) can be derived based on the Cochran distribution in direct methods. Hence the SAD phase ambiguity can be resolved by multiplying the Gaussian function peaked at $\varphi''_h+|\Delta\varphi_h|$  with P+ and multiplying the Gaussian function peaked at $\varphi''_h-|\Delta\varphi_h|$  with P- (=1-P+).The direct-method SAD phasing has been proved powerful in breaking SAD phase ambiguities, in particular when anomalous-scattering signals are weak.However, the approximation of bimodal phase distributions by the sum of two Gaussian functions introduces considerable errors. In this paper we show that a much better approximation can be achieved by replacing the two Gaussian functions with two von Mises distributions. Test results showed that this leads to significant improvement on the efficiency of direct-method SAD-phasing.
Keywords:  direct methods      single-wavelength anomalous diffraction      OASIS program      proteins  
Received:  21 April 2010      Revised:  29 April 2010      Accepted manuscript online: 
PACS:  87.64.Cc (Scattering of visible, uv, and infrared radiation)  
  02.50.Ng (Distribution theory and Monte Carlo studies)  
  87.14.E- (Proteins)  
  87.15.B- (Structure of biomolecules)  
Fund: Project supported by the Innovation Foundation of the Chinese Academy of Sciences and by the National Basic Research Program of China (Grant No. 2002CB713801).

Cite this article: 

Zhang Tao (张涛), Gu Yuan-Xin (古元新), Zheng Chao-De (郑朝德), Fan Hai-Fu (范海福) New expression of bimodal phase distributions in direct-method phasing of protein single-wavelength anomalous diffraction data 2010 Chin. Phys. B 19 086102

[1] Ramachandran J N and Raman S 1956 Curr. Sci. 25 346
[2] Hendrickson W A and Teeter M M 1981 Nature 290 107
[3] Sim G A 1959 Acta Cryst. 12 813
[4] Ten Eyck L F and Arnone A 1976 J. Mol. Biol. 100 3
[5] Blundell T L and Johnson L N 1976 Protein Crystallography (London: Academic Press Inc.) p. 177
[6] Wang B C 1985 Methods in Enzymology 115 90
[7] Fan H F and Gu Y X 1985 Acta Cryst. A 41 280
[8] Cochran W 1955 Acta Cryst. 8 473
[9] Watanabe N, Kitago Y, Tanaka I, Wang J W, Gu Y X, Zheng C D and Fan H F 2005 Acta Cryst. D 61 1533
[10] Yao D Q, Li H, Chen Q, Gu Y X, Zheng C D, Lin Z J, Fan H F, Watanabe N and Sha B D 2008 Chin. Phys. B 17 1
[11] Zhang T, Wu L J, He Y, Wang J W, Zheng C D, Hao Q, Gu Y X and Fan H F 2009 OASIS4.0 – a direct-methods program for SAD/SIR phasing and reciprocal-space fragment extension Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China (Program available at http://cryst.iphy.ac.cn)
[12] Blow D M and Crick F H C 1959 Acta Cryst. 12 794
[13] Mor'e J J, Sorensen D C, Hillstrom K E and Garbow B S 1984 The MINPACK Project in Sources and Development of Mathematical Software ed. Cowell W J (Upper Saddle River: Prentice-Hall) pp. 88–111.
[14] Dodd F, Hasnain S S, Abraham Z H, Eady R R and Smith B E 1995 Acta Cryst. D 51 1052
[15] Ramagopal U A, Dauter M and Dauter Z 2003 Acta Cryst. D 59 1020
[16] Cowtan K D and Main P 1993 Acta Cryst. D 49 148
[17] Terwilliger T C 2003 Acta Cryst. D 59 38
[18] Terwilliger T C 2003 Acta Cryst. D 59 45
[19] Perrakis A, Morris R and Lamzin V S 1999 Nature Struct. Biol. 6 458
[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] Enhancement of MAD/MIR phasing at low resolution and a new procedure for automatic phase extension
Pu Han(韩普), Yuan-Xin Gu(古元新), Wei Ding(丁玮), Hai-Fu Fan(范海福). Chin. Phys. B, 2019, 28(7): 076108.
[4] Development of “Parameter space screening”-based single-wavelength anomalous diffraction phasing and structure determination pipeline
Wei Ding(丁玮), Xiao-Ting Wang(王小婷), Yang-Yang Yi(易阳旸). Chin. Phys. B, 2019, 28(11): 116101.
[5] Knowledge-based potentials in bioinformatics: From a physicist's viewpoint
Zheng Wei-Mou (郑伟谋). Chin. Phys. B, 2015, 24(12): 128701.
[6] Proteins:From sequence to structure
Zheng Wei-Mou (郑伟谋). Chin. Phys. B, 2014, 23(7): 078705.
[7] 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.
[8] 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.
[9] 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.
[10] 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.
[11] 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.
[12] 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.
[13] SAD phasing by OASIS at different resolutions down to 0.30nm and below
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) . Chin. Phys. B, 2008, 17(1): 1-9.
[14] 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.
[15] Phasing of lysozyme using one-wavelength anomalous scattering of sulphur atoms through the combination of direct methods and density modification
Jiang Fan (江凡), Gu Yuan-Xin (古元新), Zheng Chao-De (郑朝德), Fan Hai-Fu (范海福). Chin. Phys. B, 2003, 12(8): 890-894.
No Suggested Reading articles found!