Direct demodulation method for heavy-atom positions determination in protein crystallography

ZHOU Liang; LIU Zhong-Chuan; LIU Peng; DONG Yu-Hui

doi:10.1088/1674-1137/37/1/018002

Chinese Physics C> 2013, Vol. 37> Issue(1) : 018002 DOI: 10.1088/1674-1137/37/1/018002

Direct demodulation method for heavy-atom positions determination in protein crystallography

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Abstract：
The first step of phasing in any de novo protein structure determination using isomorphous replacement (IR) or anomalous scattering (AD) experiment is to find heavy-atom positions. Traditionally, heavy-atom positions can be solved by inspecting the difference Patterson maps. Due to the weak signals in isomorphous or anomalous difference and the noisy background in the Patterson map, the searching of heavy atoms may become difficult. Here, the direct demodulation (DD) method is applied to the difference Patterson maps to reduce the noisy backgrounds and sharpen the signal peaks. The real space Patterson search by using these optimized maps can locate the heavy-atom positions more correctly and accurately. It is anticipated that the direct demodulation method can play an assistant role in the heavy-atom positions determination and facilitate the de novo structure determination of proteins.

References

[1]

Perutz M F. Acta Cryst, 1956, 9: 867[2] Kendrew J C, Bodo G, Dintzis H M, Parrish R G, Wyckoff H, Phillips D C. Nature (London), 1958, 181: 662[3] Hendrickson W A, Smith J L, Phizackerley R P, Merritt E A. Proteins, 1988, 4: 77[4] Murthy H M, Hendrickson W A, Orme-Johnson W H, Merritt E A, Phizackerley R P. J. Biol. Chem, 1988, 263: 430[5] Stefan D. Knight. Acta Cryst. D, 2000, 56: 42[6] Collaborative Computational Project, Number 4. Acta Cryst. D, 1994, 50: 760[7] Terwilliger T C. Acta Cryst. D, 1999, 55: 1863[8] Terwilliger T C. Acta Cryst. D, 2000, 56: 965[9] LI T P, WU M. Astrophys. Space Sci., 1993, 206: 91[10] LI T P, WU M. Astrophys. Space Sci., 1994, 15: 213[11] ZHANG S, LI T P, WU M. Acta Astrophysica Sinica, 1997, 17(3): 263[12] CHENG Y, SONG L, LI T P et al. Acta Astronomica Sinica, 2000, 41(2): 214

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ZHOU Liang, LIU Zhong-Chuan, LIU Peng and DONG Yu-Hui. Direct demodulation method for heavy-atom positions determination in protein crystallography[J]. Chinese Physics C, 2013, 37(1): 018002. doi: 10.1088/1674-1137/37/1/018002

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Received: 2012-03-09
Revised: 2012-05-07

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通讯作者: 陈斌, bchen63@163.com

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沈阳化工大学材料科学与工程学院沈阳 110142

Direct demodulation method for heavy-atom positions determination in protein crystallography

Corresponding author: DONG Yu-Hui,

Received Date: 2012-03-09

Accepted Date: 2012-05-07

Available Online: 2013-01-05

Abstract: The first step of phasing in any de novo protein structure determination using isomorphous replacement (IR) or anomalous scattering (AD) experiment is to find heavy-atom positions. Traditionally, heavy-atom positions can be solved by inspecting the difference Patterson maps. Due to the weak signals in isomorphous or anomalous difference and the noisy background in the Patterson map, the searching of heavy atoms may become difficult. Here, the direct demodulation (DD) method is applied to the difference Patterson maps to reduce the noisy backgrounds and sharpen the signal peaks. The real space Patterson search by using these optimized maps can locate the heavy-atom positions more correctly and accurately. It is anticipated that the direct demodulation method can play an assistant role in the heavy-atom positions determination and facilitate the de novo structure determination of proteins.

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Direct demodulation method for heavy-atom positions determination in protein crystallography

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