OALib Journal期刊
IPET:测定独个生物大分子三维空间结构的实验方法
DOI: 10.7536/PC121105
Keywords: 蛋白质动态结构 ,独个蛋白质结构 ,单分子电子断层成像方法 ,FETR算法
Abstract:
蛋白质的动态特性和结构活性对于蛋白质功能的调控具有根本意义。传统的结构确定方法(包括X射线和电子显微镜单颗粒分析技术等)往往需要成千上万不同蛋白质分子的平均信号,因此难以确定蛋白质分子的动态结构。而电子显微断层成像技术是一种对独个生物个体结构从不同的观测角度照相、并计算来恢复该个体的三维结构密度图的方法。传统的冷冻电子断层成像重构方法采用整个大尺寸电镜图像进行重构计算,通常用来研究细菌、细胞切片等大尺寸生物个体在较低分辨率下的结构;由于分辨率的限制,不足以获得小尺寸的蛋白质分子的结构细节。最近,任罡研究小组提出一种独个生物颗粒的电子显微断层成像方法(individual-particleelectrontomography,IPET)。该方法通过减小图像尺寸(直至所选区域只包含单个蛋白质分子)的策略,运用提出的FETR(focusedelectrontomographyreconstruction)算法来提高独个大分子重构的分辨率。此方法不需要初始模型和大量分子的平均信号,同时能够容忍一定的测角误差。本文综述了IPET/FETR方法在确定独个分子结构过程中的具体步骤以及如何应用该方法来研究蛋白动态特性和结构变化特征。期望通过该综述和国内同行交流,分享最新的前沿研究,为赶超世界科技前沿的建设添砖加瓦。
References
[1] Ren G, Rudenko G, Ludtke S J, Deisenhofer J, Chiu W, Pownall H J. Proc. Natl. Acad. Sci. U. S. A., 2010, 107: 1059-1064 [2] Ludtke S J, Baldwin P R, Chiu W. J. Struct. Biol., 1999, 128: 82-97 [3] Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, Leith A. J. Struct. Biol., 1996, 116: 190-199 [4] Liu J, Bartesaghi A, Borgnia M J, Sapiro G, Subramaniam S. Nature, 2008, 455: 109-113 [5] Fernando K V. J. Struct. Biol., 2008, 164: 49-59 [6] Schaffer B, Kothleitner G, Grogger W. Ultramicroscopy, 2006, 106: 1129-1138 [7] Ren G, Zuo J M, Peng L M. Micron, 1997, 28: 459-467 [8] Zhang L, Ren G. Biophys. J., 2010, 98: 441a, 2278-Pos [9] Zhang L, Ren G. Biophy. J., 2010, 98: 441a, 2277-Pos [10] Ren G, Zhang L. Biophys. J., 2012, 102: 394a, 2003-Pos [11] Zhang L, Ren G. PLoS ONE, 2012, 7: art. no. e30249 [12] Leschziner A E, Nogales E. J. Struct. Biol., 2006, 153: 284-299 [13] Van Heel M, Stoffler-Meilicke M. EMBO J., 1985, 4: 2389-2395 [14] Unser M, Trus B L, Steven A C. Ultramicroscopy, 1987, 23: 39-51 [15] Saxton W O, Baumeister W. J. Microsc., 1982, 127: 127-138 [16] Jiang W, Li Z, Zhang Z, Baker M L, Prevelige P E Jr, Chiu W. Nat. Struct. Biol., 2003, 10: 131-135 [17] Jiang W, Baker M L, Jakana J, Weigele P R, King J, Chiu W. Nature, 2008, 451: 1130-1134 [18] Cantele F, Zampighi L, Radermacher M, Zampighi G, Lanzavecchia S. J. Struct. Biol., 2007, 158: 59-70 [19] Frank J, Wagenknecht T, McEwen B F, Marko M, Hsieh C E, Mannella C A. J. Struct. Biol., 2002, 138: 85-91 [20] Grigorieff N. J. Struct. Biol., 2007, 157: 117-125 [21] Ren G, Cheng A, Reddy V, Melnyk P, Mitra A K. J. Mol. Biol., 2000, 301: 369-387 [22] Rosenthal P B, Henderson R. J. Mol. Biol., 2003, 333: 721-745 [23] Frauenfelder H, Chen G, Berendzen J, Fenimore P W, Jansson H, McMahon B H, Stroe I R, Swenson J, Young R D. Proc. Natl. Acad. Sci. U. S. A., 2009, 106: 5129-5134 [24] Karplus M, Kuriyan J. Proc. Natl. Acad. Sci. U. S. A., 2005, 102: 6679-6685 [25] Milne J L, Subramaniam S. Nat. Rev. Microbiol., 2009, 7: 666-675 [26] Koning R I, Koster A J. Ann. Anat., 2009, 191: 427-445 [27] Frank J. Electron Tomography: Methods for Three-Dimensional Visualization of Structures in the Cell. 2nd ed. NY: Springer, 2006. 17-216 [28] Frey T G, Perkins G A, Ellisman M H. Annu. Rev. Biophys. Biomol. Struct., 2006, 35: 199-224 [29] Jones M K, Zhang L, Catte A, Li L, Oda M N, Ren G, Segrest J P. J. Biol. Chem., 2010, 285: 41161-41171 [30] Zhang L, Kaspar A, Woodnutt G, Ren G. Biophys. J., 2010, 98: 440a-441a, 2276-Pos [31] Zhang L, Cavigiolio G, Wang J, Rye K A, Oda M, Ren G. Biophys. J., 2010, 98: art. no. 440a [32] Hollenstein K, Frei D C, Locher K P. Nature, 2007, 446: 213-216 [33] Van Heel M, Harauz G, Orlova E V, Schmidt R, Schatz M. J. Struct. Biol., 1996, 116: 17-24 [34] Bottcher B, Wynne S A, Crowther R A. Nature, 1997, 386: 88-91 [35] Xiang S, Carter C W Jr, Bricogne G, Gilmore C J. Acta. Crystallogr. D. Biol. Crystallogr., 1993, 49: 193-212 [36] Hue F, Johnson C L, Lartigue-Korinek S, Wang G, Buseck P R, Hytch M J. J. Electron. Microsc. (Tokyo), 2005, 54: 181-190 [37] Stokroos I, Oosterbaan J A, Arends J. J. Biol. Buccale, 1983, 11: 339-345 [38] Henderson R, Baldwin J M, Ceska T A, Zemlin F, Beckmann E, Downing K H. J. Mol. Biol., 1990, 213: 899-929 [39] Hohn M, Tang G, Goodyear G, Baldwin P R, Huang Z, Penczek P A, Yang C, Glaeser R M, Adams P D, Ludtke S J. J. Struct. Biol., 2007, 157: 47-55 [40] Zhang L, Song J, Cavigiolio G, Ishida B Y, Zhang S, Kane J P, Weisgraber K H, Oda M N, Rye K A, Pownall H J, Ren G. J. Lipid Res., 2011, 52: 175-184 [41] Zhang L, Song J, Newhouse Y, Zhang S, Weisgraber K H, Ren G. J. Lipid Res., 2010, 51: 1228-1236 [42] Zhang L, Tong H, Garewal M, Ren G. Biochim. Biophys. Acta, 2012, 1830: 2150-2159 [43] Cavigiolio G, Shao B, Geier E G, Ren G, Heinecke J W, Oda M N. Biochemistry, 2008, 47: 4770-4779 [44] Chen B, Ren X, Neville T, Jerome W G, Hoyt D W, Sparks D, Ren G, Wang J. Protein Sci., 2009, 18: 921-935 [45] Ren G, Reddy V S, Cheng A, Melnyk P, Mitra A K. Proc. Natl. Acad. Sci. U. S. A., 2001, 98: 1398-1403
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