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

Abstract
HTML
Reference
Related

PDF

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

[1]	M. Ablikim , et al . Determination of the number of ψ (3686) events at BESⅢ. Chinese Physics C, 2018, 42(2): 023001. doi: 10.1088/1674-1137/42/2/023001
[2]	Liuyuan Shen , Yicen Mou , Yunlong Zheng , Mingzhe Li . Direct couplings of mimetic dark matter and their cosmological effects. Chinese Physics C, 2018, 42(1): 015101. doi: 10.1088/1674-1137/42/1/015101
[3]	Chang-Lin Lan , Yi Zhang , Tao Lv , Bao-Lin Xie , Meng Peng , Ze-En Yao , Jin-Gen Chen , Xiang-Zhong Kong . Determination of neutron capture cross sections of ²³²Th at 14.1 MeV and 14.8 MeV using the neutron activation method. Chinese Physics C, 2017, 41(4): 044002. doi: 10.1088/1674-1137/41/4/044002
[4]	YANG Jie-Cheng , ZHANG Gao-Long , PANG Dan-Yang . Systematic analysis of fusion barrier heights and positions for proton projectiles using the single folding model. Chinese Physics C, 2014, 38(3): 034101. doi: 10.1088/1674-1137/38/3/034101
[5]	LIU Zun-Nian , SUN Jian-Meng , WANG Jin-Liang , REN Ai-Ge . Implementation of the direct demodulation method for natural gamma ray spectral logging. Chinese Physics C, 2014, 38(4): 046203. doi: 10.1088/1674-1137/38/4/046203
[6]	ZHOU Liang , LIU Peng , DONG Yu-Hui . Solution of the effects of twinning in femtosecond X-ray protein nanocrystallography. Chinese Physics C, 2013, 37(2): 028101. doi: 10.1088/1674-1137/37/2/028101
[7]	LI Lin , WANG Mei-Juan , WU Yuan-Fang . Neighboring azimuthal bin-bin multiplicity correlation as a direct measure for the shear viscosity in relativistic heavy ion collisions. Chinese Physics C, 2013, 37(9): 094102. doi: 10.1088/1674-1137/37/9/094102
[8]	CUI Xiang-Li , LV Yan , WANG Xiao-Lian , PENG Ru . Spatial anisotropy: a method to study anisotropic flow in heavy ion collisions. Chinese Physics C, 2011, 35(5): 471-474. doi: 10.1088/1674-1137/35/5/013
[9]	LI De-Sheng , TIAN Feng-Ge , CHEN Gang . Study on the method of mini-jet identification in relativistic heavy ion collisions. Chinese Physics C, 2011, 35(9): 833-837. doi: 10.1088/1674-1137/35/9/009
[10]	WANG Fan , CHEN Xiang-Song , LU Xiao-Fu , SUN Wei-Min . Gauge invariance and quantization applied to atom and nucleon internal structure. Chinese Physics C, 2010, 34(9): 1312-1319. doi: 10.1088/1674-1137/34/9/031
[11]	LIU Gui-Hua , MA Yu-Gang , CAI Xiang-Zhou , FANG De-Qing , SHEN Wen-Qing , TIAN Wen-Dong , WANG Kun . Impact parameter and beam energy dependence for azimuthal asymmetry of direct photons and free protons in intermediate energy heavy-ion collisions. Chinese Physics C, 2009, 33(S1): 89-91. doi: 10.1088/1674-1137/33/S1/029
[12]	MA Xiang . Determination of event start time at BESⅢ. Chinese Physics C, 2008, 32(9): 744-749. doi: 10.1088/1674-1137/32/9/012
[13]	WU Ling-Hui , WANG Yi-Fang , CHEN Yuan-Bo , LIU Jian-Bei , LIU Rong-Guang , MA Xiao-Yan . A study of the calibration of wire positions for the BESⅢ drift chamber using physics data without magnetic field. Chinese Physics C, 2008, 32(4): 264-268. doi: 10.1088/1674-1137/32/4/005
[14]	SHEN Zong-Jun , ZHOU Jian-Feng . Accelerated Direct Demodulation Imaging Method. Chinese Physics C, 2007, 31(11): 1016-1021.
[15]	Cheng Zitao , Qian Qing , Fu Yunchang , Chen Xuejun . Study of Antihydrogen-Atom Formation in Antiproton-Positronium Collisions. Chinese Physics C, 1993, 17(S2): 171-178.
[16]	Rong Gang , Ma Jimao , Mao Huishun , Wang Tajie , Bai Jingzhi , Li Weiguo . Application of dE/dr Method for e/π Identification of the Measurement of the Mass of τ Heavy Lepton by BES. Chinese Physics C, 1993, 17(S3): 215-224.
[17]	Feng Jun , Shen Wenqing , Ma Yugang , Zhan Wenlong , Zhu Yongtai , Guo Zhongyan . A Method for Identifying Medium-Heavy Products of Heavy Ion Reaction at SPEG Spectrometer. Chinese Physics C, 1993, 17(S2): 95-100.
[18]	Li Fubin . Construction of Creation-Annihilation Operators for Hydrogen Atom and Related Potentials with the Concepts of Supersymmetric Quantum Mechanics. Chinese Physics C, 1992, 16(S2): 173-177.
[19]	Yu Hong . A Direct Check for G(1590) as 0⁺⁺ Glueball Candidate. Chinese Physics C, 1990, 14(S2): 169-171.
[20]	Yu Hong . A New Method for the Determination of the Spin of ξ(2230). Chinese Physics C, 1989, 13(S1): 37-42.

Access

Get Citation

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

RIS(for EndNote,Reference Manager,ProCite)

BibTex

Txt

Milestone

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

Article Metric

Article Views(1893)
PDF Downloads(236)
Cited by(0)

Policy on re-use

To reuse of subscription content published by CPC, the users need to request permission from CPC, unless the content was published under an Open Access license which automatically permits that type of reuse.

通讯作者: 陈斌, bchen63@163.com

1.
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.

HTML

Reference (1)

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

Abstract：

References

Access

Article Metrics

Metrics

通讯作者: 陈斌, bchen63@163.com

Email This Article