杨茵,陈家良,苏循成*?
收稿日期:
2013-05-02
修回日期:
2013-05-06
出版日期:
2014-06-05
发布日期:
2014-06-05
作者简介:
苏循成,1972年8月出生.2001年在南开大学获得理学博士学位.分别于2001~2004年和2004~2010年先后在意大利佛罗伦萨磁共振中心、澳大利亚国立大学做博士后研究.自 2010年10月起任南开大学元素有机化学国家重点实验室博士生导师.主要研究方向为顺磁效应下的生物核磁共振技术与方法,并利用此技术研究生物大分子结构、功能与动态学间的相互关系.杨茵(1985-),女,天津人,博士研究生,从事顺磁效应下的生物核磁共振研究.*通讯联系人:苏循成,电话:022-23500623, E-mail: xunchengsu@nankai.edu.cn.
基金资助:
国家重大科学研究计划资助项目(2013CB910200);国家自然科学基金资助项目(21073101, 21273121, 21121002).
YANG Yin,CHEN Jia-liang,SU Xun-cheng*
Received:
2013-05-02
Revised:
2013-05-06
Online:
2014-06-05
Published:
2014-06-05
About author:
*Corresponding author:SU Xun-cheng, Tel: 022-23500623; E-mail: xunchengsu@nankai.edu.cn.
Supported by:
国家重大科学研究计划资助项目(2013CB910200);国家自然科学基金资助项目(21073101, 21273121, 21121002).
摘要:
未配对电子与蛋白质分子自旋核的作用能提供丰富的长程结构信息,这些顺磁信息通常可用顺磁弛豫增强、赝接触位移和残余偶极耦合描述,其中赝接触位移包含生物大分子内重要的距离和角度信息.稀土离子具有相似的配位化学性质和不同的顺磁物理特性,而大多稀土离子具有磁各向异性,在与大分子作用过程中会产生赝接触位移.由于大多数蛋白质没有顺磁中心,获得这些顺磁信息需要通过定点选择标记蛋白质来实现.该文旨在对近年来蛋白质顺磁标记的方法和进展进行介绍,在顺磁标记基础上阐述赝接触位移在结构生物学中的应用.
中图分类号:
杨茵,陈家良,苏循成*. 蛋白质顺磁标记技术与生物核磁共振中的赝接触位移[J]. 波谱学杂志.
YANG Yin,CHEN Jia-liang,SU Xun-cheng*.
[1] Bertini I, Luchinat C, Parigi G. Paramagnetic constraints: an aid for quick solution structure determination of paramagnetic metalloproteins[J]. Concepts Magn Reson, 2002, 14(4): 259-286. [2] Bertini I, Luchinat C, Parigi G. Magnetic susceptibility in paramagnetic NMR[J]. Prog NMR Spectr, 2002, 40: 249-273. [3] Clore G M, Iwahara J. Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes[J]. Chem Rev, 2009, 109(9): 4 108- 4 139. [4] Otting G. Protein NMR using paramagnetic ions[J]. Annu Rev Biophys, 2010, 39: 387-405. [5] Liu Zhu(刘主), Tang Chun(唐淳). Paramagnetic relaxation enhancement-a tool for visualizing transient protein structures(顺磁弛豫增强技术与蛋白质瞬态结构)[J]. Chinese J Magn Reson(波谱学杂志), 2011, 28(3): 301-316. [6] Banci L, Bertini I, Bren K L, et al. The use of pseudocontact shifts to refine solution structures of paramagnetic metalloproteins: Met80Ala cyano-cytochrome c as an example[J]. J Biol Inorg Chem, 1996, 1(2): 117-126. [7] Banci L, Bertini I, Savellini G G, et al. Pseudocontact shifts as constraints for energy minimization and molecular dynamics calculations on solution structures of paramagnetic metalloproteins[J]. Proteins, 1997, 29(1): 68-76. [8] Schmitz C, Stanton-Cook M J, Su X C, et al. Numbat: an interactive software tool for fitting Δχ-tensors to molecular coordinates using pseudocontact shifts[J]. J Biomol NMR, 2008 41(3): 179-189. [9] Yang Y, Li Q F, Cao C, et al. Site-specific labeling of proteins with a chemically stable, high-affinity tag for protein study[J]. Eur J Chem, 2013, 19(3): 1 097-1 103. [10] Allegrozzi M, Bertini I, Janik M B L, et al. Lanthanide-induced pseudocontact shifts for solution structure refinements of macromolecules in shells up to 40 Å from the metal ion[J]. J Am Chem Soc, 2000, 122(17): 4 154-4 161. [11] Su X C, Otting G. Paramagnetic labelling of proteins and oligonucleotides for NMR[J]. J Biomol NMR, 2010, 46(1): 101-112. [12] Edwards T E, Sigurdsson S T. Site-specific incorporation of nitroxide spin-labels into 2'-positions of nucleic acids[J]. Nat Protoc, 2007, 2(8): 1 954-1 962. [13] Shelke S A, Sigurdsson S T. Effect of N3 modifications on the affinity of spin label ç for abasic sites in duplex DNA[J]. Chembiochem, 2012, 13(5): 684-690. [14] Jakobsen U, Shelke S A, Vogel S, et al. Site-directed spin-labeling of nucleic acids by click chemistry: detection of abasic sites in duplex DNA by EPR spectroscopy[J]. J Am Chem Soc, 2010, 132(30): 10 424-10 428. [15] Lee L, Sykes B D. Proton nuclear magnetic resonance determination of the sequential ytterbium replacement of calcium in carp parvalbumin[J]. Biochemistry, 1981, 20(5): 1 156-1 162. [16] Pintacuda G, Keniry M A, Huber T, et al. Fast structure-based assignment of 15N HSQC spectra of selectively 15N-labeled paramagnetic proteins[J]. J Am Chem Soc, 2004, 126(9): 2 963-2 970. [17] Keniry M A, Park A Y, Owen E A, et al. Structure of the theta subunit of Escherichia coli DNA polymerase III in complex with the epsilon subunit[J]. J Bacteriol, 2006, 188(12): 4 464-4 473. [18] Biekofsky R R, Muskett F W, Schmidt J M, et al. NMR approaches for monitoring domain orientations in calcium-binding proteins in solution using partial replacement of Ca2+ by Tb3+[J]. FEBS Lett, 1999, 460(3): 519-526. [19] Bertini I-8 021., Gelis I, Katsaros N, et al. Tuning the affinity for lanthanides of calcium binding proteins[J]. Biochemistry, 2003, 42(26): 8 011 [20] Li S, Yang W, Maniccia A W, et al. Rational design of a conformation-switchable Ca2+- and Tb3+-binding protein without the use of multiple coupled metal-binding sites[J]. FEBS J, 2008, 275(20): 5 048-5 061. [21] Ma C, Opella S J. Lanthanide ions bind specifically to an added “EF-hand” and orient a membrane protein in micelles for solution NMR spectroscopy[J]. J Magn Reson, 2000, 146(2): 381-384. [22] Nitz M, Franz K J, Maglathlin R L, et al. A powerful combinatorial screen to identify high-affinity terbium(III)-binding peptides[J]. Chembiochem, 2003, 4(4): 272-276. [23] Wöhnert J, Franz K J, Nitz M, et al. Protein alignment by a coexpressed lanthanide-binding tag for the measurement of residual dipolar couplings[J]. J Am Chem Soc, 2003, 125(44): 13 338-13 339. [24] Martin L J, Hähnke M J, Nitz M, et al. Double-lanthanide-binding tags: design, photophysical properties, and NMR applications[J]. J Am Chem Soc, 2007, 129(22): 7 106-7 113. [25] Barthelmes K, Reynolds A M, Peisach E, et al. Engineering encodable lanthanide-binding tags into loop regions of proteins[J]. J Am Chem Soc, 2011, 133(4): 808-819. [26] Su X C, Huber T, Dixon N E, et al. Site-specific labelling of proteins with a rigid lanthanide-binding tag[J]. Chembiochem, 2006, 7(10): 1 599-1 604. [27] Su X C, McAndrew K, Huber T, et al. Lanthanide-binding peptides for NMR measurements of residual dipolar couplings and paramagnetic effects from multiple angles[J]. J Am Chem Soc, 2008, 130(5): 1 681-1 687. [28] Saio T, Ogura K, Yokochi M, et al. Two-point anchoring of a lanthanide-binding peptide to a target protein enhances the paramagnetic anisotropic effect[J]. J Biomol NMR, 2009, 44(3): 157-166. [29] Pintacuda G, Moshref A, Leonchiks A, et al. Site-specific labelling with a metal chelator for protein-structure refinement[J]. J Biomol NMR, 2004, 29(3): 351-361. [30] Ikegami T, Verdier L, Sakhaii P, et al. Novel techniques for weak alignment of proteins in solution using chemical tags coordinating lanthanide ions[J]. J Biomol NMR, 2004, 29(3): 339-349. [31] Leonov A, Voigt B, Rodriguez-Castañeda F, et al. Convenient synthesis of multifunctional EDTA-based chiral metal chelates substituted with an S-mesylcysteine[J]. Eur J Chem, 2005, 11(11): 3 342-3 348. [32] Haberz P, Rodriguez-Castañeda F, Junker J, et al. Two new chiral EDTA-based metal chelates for weak alignment of proteins in solution-1 278.[J]. Org Lett, 2006, 8(7): 1 275 [33] Prudêncio M, Rohovec J, Peters J A, et al. A caged lanthanide complex as a paramagnetic shift agent for protein NMR[J]. Eur J Chem, 2004, 10(13): 3 252-3 260. [34] Peters F, Maestre-Martinez M, Leonov A, et al. Cys-Ph-TAHA: a lanthanide binding tag for RDC and PCS enhanced protein NMR[J]. J Biomol NMR, 2011, 51(3): 329-337. [35] Su X C, Man B, Beeren S, et al. A dipicolinic acid tag for rigid lanthanide tagging of proteins and paramagnetic NMR spectroscopy[J]. J Am Chem Soc, 2008, 130(32): 10 486-10 487. [36] Swarbrick J D, Ung P, Su X C, et al. Engineering of a bis-chelator motif into a protein α-helix for rigid lanthanide binding and paramagnetic NMR spectroscopy[J]. Chem Commun (Camb), 2011, 47(26): 7 368-7 370. [37] Swarbrick J D, Ung P, Chhabra S, et al. An iminodiacetic acid based lanthanide binding tag for paramagnetic exchange NMR spectroscopy[J]. Angew Chem Int Ed Engl, 2011, 50(19): 4 403-4 406. [38] Yagi H, Maleckis A, Otting G. A systematic study of labelling an α-helix in a protein with a lanthanide using IDA-SH or NTA-SH tags[J]. J Biomol NMR, 2013, 55(2): 157-166. [39] Man B, Su X C, Liang H, et al. 3-Mercapto-2,6-pyridinedicarboxylic acid: a small lanthanide-binding tag for protein studies by NMR spectroscopy[J]. Eur J Chem, 2010, 16(12): 3 827-3 832. [40] Jia X, Maleckis A, Huber T, et al. 4,4'-dithiobisdipicolinic acid: a small and convenient lanthanide binding tag for protein NMR spectroscopy[J]. Eur J Chem, 2011, 17(24): 6 830-6 836. [41] Keizers P H, Saragliadis A, Hiruma Y, et al. Design, synthesis, and evaluation of a lanthanide chelating protein probe: CLaNP-5 yields predictable paramagnetic effects independent of environment[J]. J Am Chem Soc, 2008, 130(44): 14 802-14 812. [42] Häussinger D, Huang J R, Grzesiek S. DOTA-M8: An extremely rigid, high-affinity lanthanide chelating tag for PCS NMR spectroscopy[J]. J Am Chem Soc, 2009, 131(41): 14 761-14 767. [43] Graham B, Loh C T, Swarbrick J D, et al. DOTA-amide lanthanide tag for reliable generation of pseudocontact shifts in protein NMR spectra[J]. Bioconjug Chem, 2011, 22(10): 2 118-2 125. [44] Li Q F, Yang Y, Maleckis A, et al. Thiol-ene reaction: a versatile tool in site-specific labelling of proteins with chemically inert tags for paramagnetic NMR[J]. Chem Commun (Camb), 2012, 48(21): 2 704-2 706. [45] Su X C, Liang H, Loscha K V, et al. [Ln(DPA)3]3– is a convenient paramagnetic shift reagent for protein NMR studies[J]. J Am Chem Soc, 2009, 131(30): 10 352-10 353. [46] Jia X, Yagi H, Su X C, et al. Engineering [Ln(DPA)3] 3– binding sites in proteins: a widely applicable method for tagging proteins with lanthanide ions[J].J Biomol NMR, 2011, 50(4): 411-420. [47] Wei Z, Yang Y, Li Q F, et al. Noncovalent tagging proteins with paramagnetic lanthanide complexes for protein study[J]. Eur J Chem, 2013, 19(18): 5 758-5 764. [48] Wang L, Xie J, Schultz P G. Expanding the genetic code[J]. Annu Rev Biophys Biomol Struct, 2006, 35: 225-249. [49] Nguyen T H, Ozawa K, Stanton-Cook M, et al. Generation of pseudocontact shifts in protein NMR spectra with a genetically encoded cobalt(II)-binding amino acid[J]. Angew Chem Int Ed Engl, 2011, 50(3): 692-694. [50] Loh C T, Ozawa K, Tuck K L, et al. Lanthanide tags for site-specific ligation to an unnatural amino acid and generation of pseudocontact shifts in proteins[J]. Bioconjug Chem, 2013, 24(2): 260-268. [51] Banci L, Bertini I, Gori Savellini G G, et al. Pseudocontact shifts as constraints for energy minimization and molecular dynamic calculations on solution structures of paramagnetic metalloproteins[J]. Proteins Struct Funct Genet, 1997, 29(1): 68-76. [52] Banci L, Bertini I, Cavallaro G, et al. Paramagnetism-based restraints for Xplor-NIH[J]. J Biomol NMR, 2004, 28(3): 249-261. [53] Yagi H, Pilla K B, Maleckis A, et al. Protein fold determination from backbone amide pseudocontact shifts generated by lanthanide tags at multiple sites[J]. Structure, 2013, 21(6): 883-890. [54] Bertini I, Del Bianco C, Gelis I, et al. Experimentally exploring the conformational space sampled by domain reorientation in calmodulin[J]. Proc Natl Acad Sci USA, 2004, 101(18): 6 841-6 846. [55] Bertini I, Giachetti A, Luchinat C, et al. Conformational space of flexible biological macromolecules from average data[J]. J Am Chem Soc, 2010, 132(38): 13 553-13 558. [56] Bertini I, Gupta Y K, Luchinat C, et al. Paramagnetism-based NMR restraints provide maximum allowed probabilities for the different conformations of partially independent protein domains[J]. J Am Chem Soc, 2007, 129(42): 12 786-12 794. [57] Pintacuda G, Park A Y, Keniry M A, et al. Lanthanide labeling offers fast NMR approach to 3D structure determinations of protein-protein complexes[J]. J Am Chem Soc, 2006, 128(11): 3 696-3 702. [58] Saio T, Yokochi M, Kumeta H, et al. PCS-based structure determination of protein-protein complexes[J]. J Biomol NMR, 2010, 46(4): 271-280. [59] Ruan Ke(阮科), Gao Jia(高佳), Ma Rong-sheng(马荣声). NMR in fragment based lead discovery(基于片断的先导化合物发现中的核磁共振).[J] Chinese J Magn Reson(波谱学杂志),2012, 29(2): 164-181. [60] John M, Pintacuda G, Park A Y, et al. Structure determination of protein-ligand complexes by transferred paramagnetic shifts[J]. J Am Chem Soc, 2006, 128(39): 12 910-12 916. [61] Balogh E, Wu D, Zhou G, et al. NMR second site screening for structure determination of ligands bound in the hydrophobic pocket of HIV-1 gp41[J]. J Am Chem Soc, 2009, 131(8): 2 821-2 823. [62] Saio T, Ogura K, Shimizu K, et al. An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe[J]. J Biomol NMR, 2011, 51(3): 395-408. [63] de la Cruz L, Nguyen TH, Ozawa K, et al. Binding of low molecular weight inhibitors promotes large conformational changes in the dengue virus NS2B-NS3 protease: fold analysis by pseudocontact shifts[J]. J Am Chem Soc, 2011, 133(47):19 205-19 215. [64] Guan J Y, Keizers P H, Liu W M, et al. Small-molecule binding sites on proteins established by paramagnetic NMR spectroscopy[J]. J Am Chem Soc. 2013, 135(15): 5 859-5 868. [65] Wang Ya-qiang(王亚强), Li Cong-gang(李从刚), Pielak G J. In-cell protein magnetic resonance spectroscopy(细胞内蛋白质核磁共振).[J] Chinese J Magn Reson(波谱学杂志), 2012, 29(4): 475-487. [66] Li J P, Pilla K B, L Q F, et al. Magnic angle spinning NMR structure determination of proteins from pseudocontact shifts[J]. J Am Chem Soc. 2013, 135(22): 8 294-8 303. |
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