The determinant factors for map resolutions obtained using CryoEM single particle imaging method

doi:10.1088/1674-1056/27/12/128702

中国物理B ›› 2018, Vol. 27 ›› Issue (12): 128702-128702.doi: 10.1088/1674-1056/27/12/128702

• INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY • 上一篇下一篇

The determinant factors for map resolutions obtained using CryoEM single particle imaging method

Yihua Wang(王义华), Daqi Yu(余大启), Qi Ouyang(欧阳颀), Haiguang Liu(刘海广)

1 Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Institute of Condensed Matter Physics, School of Physics, Center for Quantitative Biology School of Physics, The Peking-Tsinghua Center for Life Sciences at School of Physics, Peking University, Beijing 100084, China;
2 Complex Systems Division, Beijing Computational Science Research Centre, Beijing 100193, China

收稿日期:2018-07-12 修回日期:2018-10-08 出版日期:2018-12-05 发布日期:2018-12-05
通讯作者: Haiguang Liu E-mail:hgliu@csrc.ac.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11774011, 11434001, U1530401, and U1430237).

The determinant factors for map resolutions obtained using CryoEM single particle imaging method

Yihua Wang(王义华)¹, Daqi Yu(余大启)¹, Qi Ouyang(欧阳颀)¹, Haiguang Liu(刘海广)²

1 Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Institute of Condensed Matter Physics, School of Physics, Center for Quantitative Biology School of Physics, The Peking-Tsinghua Center for Life Sciences at School of Physics, Peking University, Beijing 100084, China;
2 Complex Systems Division, Beijing Computational Science Research Centre, Beijing 100193, China

Received:2018-07-12 Revised:2018-10-08 Online:2018-12-05 Published:2018-12-05
Contact: Haiguang Liu E-mail:hgliu@csrc.ac.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11774011, 11434001, U1530401, and U1430237).

摘要/Abstract

摘要：

The CryoEM single particle structure determination method has recently received broad attention in the field of structural biology. The structures can be resolved to near-atomic resolutions after model reconstructions from a large number of CryoEM images measuring molecules in different orientations. However, the determining factors for reconstructed map resolution need to be further explored. Here, we provide a theoretical framework in conjunction with numerical simulations to gauge the influence of several key factors to CryoEM map resolutions. If the projection image quality allows orientation assignment, then the number of measured projection images and the quality of each measurement (quantified using average signal-to-noise ratio) can be combined to a single factor, which is dominant to the resolution of reconstructed maps. Furthermore, the intrinsic thermal motion of molecules has significant effects on the resolution. These effects can be quantitatively summarized with an analytical formula that provides a theoretical guideline on structure resolutions for given experimental measurements.

关键词: Cryo-EM, resolution, noise, conformation heterogeneity

Abstract:

Key words: Cryo-EM, resolution, noise, conformation heterogeneity

中图分类号: (Electron microscopy)

87.64.Ee

87.57.cf (Spatial resolution) 87.57.cm (Noise) 87.15.hp (Conformational changes)

王义华, 余大启, 欧阳颀, 刘海广. The determinant factors for map resolutions obtained using CryoEM single particle imaging method[J]. 中国物理B, 2018, 27(12): 128702-128702.

Yihua Wang(王义华), Daqi Yu(余大启), Qi Ouyang(欧阳颀), Haiguang Liu(刘海广). The determinant factors for map resolutions obtained using CryoEM single particle imaging method[J]. Chin. Phys. B, 2018, 27(12): 128702-128702.

参考文献 43

[1]	Bai X C, McMullan G and Scheres. S H W 2012 Nat. Methods 9 853 doi: 10.1038/nmeth.2115
[2]	Faruqi A R and McMullan G 2011 Quarterly Rev. Biophys. 44 357 doi: 10.1017/S0033583511000035
[3]	Tang G, Peng L, Baldwin P R, Mann D S, Jiang W, Rees I and Ludtke S J 2007 J. Struct. Biol. 157 38 doi: 10.1016/j.jsb.2006.05.009
[4]	Scheres S H 2012 J. Struct. Biol. 180 519 doi: 10.1016/j.jsb.2012.09.006
[5]	Grigorieff N 2016 Methods Enzymol. 579 191 doi: 10.1016/bs.mie.2016.04.013
[6]	da Fonseca P C A and Morris E P 2015 Nat. Commun. 6 7573 doi: 10.1038/ncomms8573
[7]	Passmore L A and Russo C J 2016 Methods in Enzymology 579 51 doi: 10.1016/bs.mie.2016.04.011
[8]	Bernecky C, Herzog F, Baumeister W, Plitzko J M and Cramer P 2016 Nature 529 551 doi: 10.1038/nature16482
[9]	Li X, Mooney P, Zheng S, Booth C R, Braunfeld M B, Gubbens S, Agard D A and Cheng Y 2013 Nat. Methods 10 584 doi: 10.1038/nmeth.2472
[10]	Zheng S Q, Palovcak E, Armache J P, Verba K A, Cheng Y and Agard D A 2017 Nat. Methods 14 331 doi: 10.1038/nmeth.4193
[11]	Yu X, Jin L and Zhou Z H 2008 Nature 453 415 doi: 10.1038/nature06893
[12]	Chen J Z, Settembre E C, Aoki S T, Zhang X, Bellamy A R, Dormitzer P R, Harrison S C and Grigorieff N 2009 Proc. Natl. Acad. Sci. USA 106 10644 doi: 10.1073/pnas.0904024106
[13]	Zhang X, Jin L, Fang Q, Hui W H and Zhou Z H 2010 Cell 141 472 doi: 10.1016/j.cell.2010.03.041
[14]	Cao E, Liao M, Cheng Y and Julius D 2013 Nature 504 113 doi: 10.1038/nature12823
[15]	Bernstein F C, Koetzle T F, Williams G J, Meyer E F Jr, Brice M D, Rodgers J R, Kennard O, Shimanouchi T and Tasumi M 1977 J. Mol. Biol. 112 535 doi: 10.1016/S0022-2836(77)80200-3
[16]	Berman H M, Westbrook J, Feng Z, Gillil, G, Bhat T N, Weissig H, Shindyalov I N and Bourne P E 2000 Nucleic Acids Res. 28 235 doi: 10.1093/nar/28.1.235
[17]	Newman R, Chagoyen M, Carazo J M and Henrick K 2002 Trends BioChem. Sci. 27 11 doi: 10.1016/S0968-0004(01)01999-5
[18]	Henrick K, Newman R, Tagari M and Chagoyen M 2003 J. Struct. Biol. 144 228 doi: 10.1016/j.jsb.2003.09.009
[19]	Rose P W, Prlic A, Bi C, Bluhm W F, Christie C H, Dutta S, Green R K, Goodsell D S, Westbrook J D, Woo J, Young J, Zardecki C, Berman
	H M, Bourne P E and Burley S K 2015 Nucleic Acids Res. 43 D345 [20] Nogales E 2016 Nat. Methods 13 24
[21]	Lawson C L, Patwardhan A, Baker M L, Hryc C, Garcia E S, Hudson B P, Lagerstedt I, Ludtke S J, Pintilie G, Sala R, Westbrook J D, Berman H M, Kleywegt G J and Chiu W 2016 Nucleic Acids Res. 44 D396
[22]	Morris A L, MacArthur M W, Hutchinson E G and Thornton J M 1992 Proteins: Structure, Function, and Genetics 12 345 doi: 10.1002/prot.340120407
[23]	Karplus P A and Diederichs K 2012 Science 336 1030 doi: 10.1126/science.1218231
[24]	Heel M v and Harauz G 1986 Optik 73 146
[25]	Bottcher B, Wynne S A and Crowther R A ¨ 1997 Nature 386 88 doi: 10.1038/386088a0
[26]	Rosenthal P B and Henderson R 2003 J. Mol. Biol. 333 721 doi: 10.1016/j.jmb.2003.07.013
[27]	Scheres S H and Chen S 2012 Nat. Methods 9 853 doi: 10.1038/nmeth.2115
[28]	Kucukelbir A, Sigworth F J and Tagare H D 2014 Nat. Methods 11 63 doi: 10.1038/nmeth.2727
[29]	Henderson R 1995 Quarterly Rev. BioPhys. 28 171 doi: 10.1017/S003358350000305X
[30]	Penczek P A 2010 Methods Enzymol. 482 73 doi: 10.1016/S0076-6879(10)82003-8
[31]	Liao H Y and Frank J 2010 Structure 18 768 doi: 10.1016/j.str.2010.05.008
[32]	Bartesaghi A, Merk A, Banerjee S, Matthies D, Wu X W, Milne J L S and Subramaniam S 2015 Science 348 1147 doi: 10.1126/science.aab1576
[33]	Merk A, Bartesaghi A, Banerjee S, Falconieri V, Rao P, Davis M I, Pragani R, Boxer M B, Earl L A, Milne J L and Subramaniam S 2016 Cell 165 1698 doi: 10.1016/j.cell.2016.05.040
[34]	Bartolucci C, Lamba D, Grazulis S, Manakova E and Heumann H 2005 J. Mol. Biol. 354 940 doi: 10.1016/j.jmb.2005.09.096
[35]	Shaikh T R, Gao H, Baxter W T, Asturias F J, Boisset N, Leith A and Frank J 2008 Nat. Protocols 3 1941 doi: 10.1038/nprot.2008.156
[36]	Yershova A, Jain S, Lavalle S M and Mitchell J C 2010 Int. J. Rob. Res. 29 801 doi: 10.1177/0278364909352700
[37]	Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon T R and Bahar I 2014 Bioinformatics 30 2681 doi: 10.1093/bioinformatics/btu336
[38]	Dashti A, Schwander P, Langlois R, Fung R, Li W, Hosseinizadeh A, Liao H Y, Pallesen J, Sharma G, Stupina V A, Simon A E, Dinman J D, Frank J and Ourmazd A 2014 Proc. Natl. Acad. Sci. USA 111 17492 doi: 10.1073/pnas.1419276111
[39]	Chen S, Wu J, Lu Y, Ma Y B, Lee B H, Yu Z, Ouyang Q, Finley D J, Kirschner M W and Mao Y 2016 Proc. Natl. Acad. Sci. USA 113 12991 doi: 10.1073/pnas.1614614113
[40]	Dashti A, Ben Hail D, Mashayekhi G, Schwander P, des Georges A, Frank J and Ourmazd A 2017 BioRxiv 167080
[41]	Trueblood K N, Bürgi H B, Burzlaff H, Dunitz J D, Gramaccioli C M, Schulz H H, Shmueli U and Abrahams S C 1996 Acta Crystallographica A52 770
[42]	Frank J and Ourmazd A 2016 Methods 100 61 doi: 10.1016/j.ymeth.2016.02.007
[43]	Hosseinizadeh A, Mashayekhi G, Copperman J, Schwander P, Dashti A, Sepehr R, Fung R, Schmidt M, Yoon C H, Hogue B G, Williams G J, Aquila A and Ourmazd A 2017 Nat. Methods 14 877 doi: 10.1038/nmeth.4395

The determinant factors for map resolutions obtained using CryoEM single particle imaging method

The determinant factors for map resolutions obtained using CryoEM single particle imaging method

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