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元素有机化学国家重点实验室(南开大学)

Tenure制研究员

研究队伍

苏循成  特聘研究员 博士生导师

Prof. Xun-Cheng Su ( X. C. Su)

Tel: 86-22-23503461

E-mail: xunchengsu@nankai.edu.cn


EDUCATION

1995-2001

Department of Chemistry, Nankai University,Tianjin, China.
Received Ph.D. degree in June, 2001 (with Prof. Yun-Ti Chen).

1991-1995

Department of Chemistry, Qufu Normal University, Qufu,
China.
Received B. Sc. Degree in June, 1995.



 ACADEMIC CAREER

l PhD (with Professor Chen Yun-Ti), Nankai University (2001)

l Postdoctoral (with Professor Ivano Bertini), Center of Magnetic Resonance, University of Florence, Florence, Italy (2001-2004)

l Research fellow (with Professor Gottfried Otting), Australian National University, Canberra, Australia (2004-2010)

l Professor, State Key Laboratory of Elemento-organic Chemistry (2010-)


长期从事生物核磁共振方法学和化学生物学研究,已在国外核心期刊上发表研究论文50篇,H-index 26. 目前课题组主要研究方向是生物大分子的定点修饰化学和高分辨生物核磁共振方法学,发展研究离体和在体环境下大分子动态结构与作用机制的高分辨磁共振方法,并利用该技术阐明大分子的作用机制、聚集行为与功能的关系顺磁核磁共振研究相互作用下主客体分子识别机制与小分子化合物结构测定。


研究方向:化学生物学、镧系离子与结构生物学、生命有机分析化学

Research Interests: Chemical biology, Bioanalytical chemistry, NMR spectroscopy

We are interested in site-specific modifications of proteins both in vitro and in vivo and apply these methods to dissect the protein dynamics and interactions in vitro and in cells using NMR, EPR and fluorescence spectroscopy.

 

研究内容

  • 有机合成化学:功能有机小分子探针的设计与合成;非天然氨基酸的设计与合成
  • 生物大分子标记化学与应用:生物大分子标记策略与标记中的化学反应性
  • 小分子/大分子-大分子作用的高分辨分析方法:小分子与大分子作用的高分辨结构;有效药物先导分子的筛选与优化
  • 蛋白质动态学研究的新方法与新技术


 

基金资助

1. 国家自然科学基金面上项目(21073101 )用于结构生物学和药物研发的蛋白质顺磁标记 2011. 1-2013. 12 主持

2. 国家自然科学基金面上项目(21273121 )位点特异标记稀土金属离子在蛋白质构象分析中的应用 2013.1 – 2016.12,主持

3. 国家重大研究计划973项目(2013CB910200)蛋白质动态学研究的新技术、新方法 2013. 1 - 2017. 8,参与

4. 国家自然科学基金面上项目(21473095)利用顺磁核磁共振研究固有无归结构蛋白质的探索”, 2015.1-2018.12 主持

5. 国家自然科学基金面上项目(21673122)利用赝接触位移研究蛋白质瞬态复合物三维结构的测定方法”, 2017.1-2020.12,主持

6. 国家重点研发计划(2016YFA0501202):”蛋白质机器的动态结构的核磁共振研究方法及应用 2016.7-2021.6,参与

 

在读研究生

陈家良,曹婵,王晓,杨峰,陈甚娜,张凌阳,李骘,公言军,潘彬彬,李尚,赵丽娜,翟程梁,肖宇昊

本科生

金科,吉佳,方恬,夏君,王文举,于正鑫,赵阳

已毕业研究生

李庆峰,魏珍,黄凤,杨茵,王金涛,左会会,裴莹莹,马飞贺,刘洪开,张琳琳,赵宇,侯萌萌

 

 

We have been focusing on chemical modifications of proteins with functional groups especially for NMR and EPR analysis both in vitro and in living cells. Using this technique, we attempt to delineate the dynamics, structures and interactions of protein and protein and protein-ligand interactions. With developed tagging methods, molecular recognition and dynamics at atomic resolution in cells will be ultimately discovered.

Research Highlights

  1. Site-specific labeling of proteins with lanthanide ions for high-resolution NMR in structural biology and chemical biology

Strategy in site-specific labeling of proteins with paramagnetic species for NMR and EPR study.

 

1) Labeling of proteins with dual functional tags for protein assay: 4MTDA and 4MMTDA are rigid fluorescent and paramagnetic tags, which can be attached to protein with the formation of a disulfide bonds

(Chem Eur J 2013, 17141 and J Biomol NMR 2014, 59, 251).

UV and fluorescence spectra of Tb(III) complexed with 4MTDA tagged ubiquitin at different sites.

1ubi_strucuture_HF1              A28C_HF1Red_TmBlack

 

2) Site specific labeling of proteins with Michael addition like thio-ene reaction: mild condition in aqueous solution (pH about 7.6-9), no generation of new chiral center, and no radical initiation

(Chem Comm 2012, 2704, Eur J Chem 2013, 1097 and J Biomol NMR 2014, 251).

4-VinylPyMTA forms stable complex with lanthanide ions and has shown to be suitable for in situ NMR analysis (Chem Eur J 2013, 1097) and then was further applied for in-cell EPR by Drescher et al in JACS 2014, 136, 15366.

 

15N-HSQC indicated lanthanide complex with 4-Vinyl PyMTA conjugated protein is stable in high concentrations of HEWL (300 mg) (A) and BSA (100 mg) (B).

 

The protein-2V-8HQ forms a stable complex with transition metal ions, Co(II), Cu(II), Mn(II) and Ni(II), and the paramagnetic effects generated by these paramagnetic ions were evaluated by NMR spectroscopy. We show that 2V-8HQ is a rigid and stable transition metal binding tag, of which the coordination to metal ion is assisted by protein sidechain. Tunable paramagnetic tensors can be simply achieved in an α helix that possesses a i and i+4 segment, where i depicts residue Glu(or His) and i+4 the residue to be mutated to cysteine, respectively. Extensive PRE effects have been evaluated. Reliable PREs can be achieve by the high-binding affinity of paramagnetic tag.

 

A28C_2V8HQ_Zn.ps E24HA28C_2V8HQ_Zn.PS

 

 

tocsPRE_E24HA28C8HQ_sep20150911.ps

 

 

The paramagnetic anisotropy and fluorescence of protein-2V-8HQ conjugate with metal complex can be tuned by the coordination of amino acid sidechains in the helix.

 

3) Phenylsulfonated pyridine derivatives are rigid and stable lanthanide binding tags.

High stability of phenylsulfonated pyridine derivatives permits the in-cell NMR and EPR measurements.

 

4) Selective 15N-labeling of Gln and Asn sidechains and combination with paramagnetic tagging

We developed an efficient way of selectively labeling the side chains of asparagine, or asparagine and glutamine residues with 15NH2.

Fig 4_2

15NH2-Asn labeled ubiquitin             

Fig 5_2

15NH2-Asn + Gln labeled ubiquitin

 

Fig 5_2

 

 

 

We developed an efficient way of selectively labeling the side chains of asparagine, or asparagine and glutamine residues with 15NH2. Those side-chains lend themselves particularly

well to determinations of Dc tensors, offering a promising approach to study protein–ligand complexes of high-molecular weight systems where the signals of side-chain amides are more easily

detected than the resonances of backbone amides.

 

  1. Application of paramagnetic tagging proteins in structural biology.

1) Protein dynamics delineated by paramagnetic NMR spectroscopy: multi-domain replacement (in collaboration with Professor Gottfried Otting and Professor Thomas Huber)

fig3_new

Figure1_HSQC

fig5_new

The data indicate that, in solution and in the absence of substrate, the structure of T4 lysozyme is on average more open than suggested by the closed conformation of the crystal structure of wild-type protein.

In collaboration with Professors Gottfried Otting and Thomas Huber at Australian National University.


F:\T4L-final\ms\Figure\DPCS-G12R-WT-Tm-Tb-4MMDPA.jpg

 

2) Rigid lanthanide binding tag produces narrow distance distributions measured by DEER experiments: NMR and EPR are complementary tools in structure biology (in collaboration with Professor Daniella Goldfarb)

 

We used NMR spectroscopy optimized paramagnetic tags and conjugated proteins with these rigid tags for DEER measurements (Dalton 2015, 20812).

In collaboration with Professor Daniella Goldfarb at Weizmann Institute of Science, Israel.

 

Rigid, stable and efficient Gd(III) spin label for in-cell DEER measurements:

In collaboration with Professor Daniella Goldfarb, we reported a new Gd(III) spin label, DO3MA-3BrPy-Gd(III) for in-cell DEER measurements.

The new Ln(III) spin label has first been optimized by NMR and then applied for PD-EPR. The high performance of DO3MA-3BrPy-Gd(III) is demonstrated on doubly labelled ubiquitin D39C/E64C, both in vitro and in HeLa cells. High-quality DEER data could be obtained in HeLa cells up to 12 h after protein delivery at in-cell protein concentrations as low as 5-10 mM (Angew. Chem. DOI: 10.1002/anie.201611051R1).

 

3) In-cell NMR analysis using stable paramagnetic tags: structures and dynamics of proteins delineated by paramagnetic NMR spectroscopy

3D structure determination of a protein in living cells using paramagnetic NMR spectroscopy (in collaboration with Professors Thomas Huber and Conggang Li).

Determining the three-dimensional structure of a protein in living cells remains particularly challenging. We demonstrated that the integration of site-specific tagging proteins and GPS-Rosetta calculations provides a fast and effective way of determining the structures of proteins in living cells, and in principle the interactions and dynamics of protein-ligand complexes (Chem. Commun. 2016, 10237).

 

toc

 

15N-HSQC spectra recorded for GB1 V21C-PyMTA complexed lanthanide ion in living Xenopus laevis oocytes (total acquisition time within 2 hours).

 

figure2_structure

High-resolution structure calculation from in-cell PCS data using GPS-Rosetta. We have presented an efficient way to determine the structure of a protein in living cells by employing paramagnetic restraints from PCSs. PCSs are readily measured by the chemical shift differences observed in 15N-HSQC spectra. The high sensitivity of the experiment allows accurate PCS data to be recorded in living cells where the limited lifetime of the cells under the condition of the NMR measurement prohibits long measurement times and/or protein concentration can be a limiting factor. Moreover, low protein concentration (~0.05 mM) was sufficient for recording 15N-HSQC spectra within 2 hours. This work was highlighted in ChemistryWorld,

https://www.chemistryworld.com/news/molecular-beacon-homes-in-on-protein-structures/1017298.article.

 

4) 3D structure of transient and unstable enzyme intermediate determined by paramagnetic NMR spectroscopy

Enzyme catalysis of chemical reactions relies on conformational plasticity but structural information on transient intermediates is difficult to obtain. Here we show that the three-dimensional (3D) structure of an unstable, low abundance enzymatic intermediate can be determined by nuclear magnetic resonance (NMR) spectroscopy. The approach is demonstrated for Staphylococcus aureus sortase A (SrtA), which is an established drug target and biotechnological reagent. SrtA is a transpeptidase that converts an amide bond of substrate peptide to a thioester. By measuring pseudocontact shifts (PCS) generated by a site-specific cysteine-reactive paramagnetic tag that does not react with the active site residue Cys184, a sufficient number of restraints could be collected to determine the 3D structure of the unstable thioacyl intermediate of SrtA that is present only as a minor species under non-equilibrium conditions (Angew. Chem. 2016, 55, 13744).

Low abundance of thioester intermediate formed by SrtA and QALPETG peptide determined by NMR.

To the best of our knowledge, the structure of the short-lived thioester intermediate of SrtA determined here with the help of PCSs presents the first 3D structural view, in solution, of an enzymatic intermediate present only as a minor species under non-equilibrium conditions. The structure determination relied on lanthanide tags of carefully tuned reactivity to avoid modifying Cys184 at the active site.

 

Publications:

  1. Cao C, Wang S, Cui T, Su X. C.*, Chou J*. Ion and inhibitor binding of the double-ring ion selectivity filter of the Mitochondrial calcium uniporter. Proc. Natl. Acad. Sci. USA 2017, doi/10.1073/pnas.16203166114
  2. A reactive, rigid Gd(III) labelling tag for in-cell EPR distance measurements in proteins. Y. Yang, F. Yang, Y. J. Gong, J. L. Chen, D. Goldfarb, X. C. Su, Angew. Chem. Int. Ed. Engl. 2017, 56, 2914-2918.
  3. Deciphering the Multisite Interactions of a Protein and Its Ligand at Atomic Resolution by Using Sensitive Paramagnetic Effects. F. H. Ma, X. Wang, J. L. Chen, X. Wen, H. Sun, X. C. Su, Chem. Eur. J. 2017, 23, 926-934.
  4. 3D Structure determination of an unstable transient enzyme intermediate by paramagnetic NMR spectroscopy. J. L.  Chen, X. Wang, F. Yang, C. Cao, G. Otting, X. C. Su, Angew. Chem. Int. Ed. Engl. 2016, 55, 13744-13748.
  5. Single-armed phenylsulfonated pyridine derivative of DOTA is rigid and stable paramagnetic tag in protein analysis. F. Yang, X. Wang, B. B. Pan, X. C. Su, Chem. Commun. 2016, 52, 11535-11538.
  6. 3D structure determination of a protein in living cells using paramagnetic NMR spectroscopy. B. B. Pan, F. Huang, Y. S. Ye, Q. Wu, C. G. Li, T. Huber, X. C. Su, Chem. Commun. 2016, 52, 10237.
  7. Determination of pseudocontact shifts of low-populated excited states by NMR chemical exchange saturation transfer. R. S. Ma, Q. F. Li, A. D. Wang, J. H. Zhang, Z. J. Liu, J. H. Wu, X. C. Su, Phys. Chem. Chem. Phys. 2016, 18, 13794.
  8. Site-specific tagging proteins with a rigid, small and stable transition metal chelator, 8-hydroxyquinoline, for paramagnetic NMR analysis. Y. Yang, F. Huang, T. Huber, X. C. Su, J. Biomol. NMR 2016, 64, 103-113.
  9. Analysis of the solution conformations of T4 lysozyme by paramagnetic NMR spectroscopy. J. L. Chen, Y. Yang, L. L. Zhang, H. B. Liang, T, Huber, X. C. Su, G. Otting, Phys. Chem. Chem. Phys. 2016, 18, 5850-5859.
  10. Mn(II) tags for DEER distance measurements in proteins via C-S attachment. A. Martonrana, Y. Yang, Y. Zhao, Q. F. Li, X. C. Su, D. Goldfarb, Dalton Trans. 2015, 44, 20812-20816.
  11. Site-specific tagging proteins via a rigid, stable and short thiolether tether for paramagnetic spectroscopic analysis. Y. Yang, J. T. Wang, Y. Y. Pei, X. C. Su, Chem. Commun. 2015, 51, 2824-2827.
  12. Selective 15N-labeling of the side-chain amide groups of asparagine and glutamine for applications in paramagnetic NMR spectroscopy. C. Cao, J. L. Chen, Y. Yang, F. Huang, G. Otting, X. C. Su, J. Biomol. NMR 2014, 59, 251-261.
  13. Kinetic Assay of the Michael Addition-Like Thiol-Ene Reaction and Insight into Protein Bioconjugation. F. H. Ma, J. L. Chen, Q. F. Li, H. H. Zuo, F. Huang, X. C. Su, Chem. Asian J. 2014, 9, 1808-1816.
  14. Bound or Free: Interaction of the C-Terminal Domain of Escherichia coli Single-Stranded DNA-Binding Protein (SSB) with the Tetrameric Core of SSB. X. C. Su, Y. Wang, H. Yagi, D. Shishimarev, C.E.Mason, P. J. Smith, M. Vandevenne, N. E. Dixon, G. Otting, Biochemistry. 2014, 53, 1925-1934.
  15. Intramolecular binding mode of the C-terminus of Escherichia coli single-stranded DNA binding protein determined by nuclear magnetic resonance spectroscopy. D. Shishmarev, Y. Wang, C.E. Mason, X.C. Su, A. J. Oakley, B. Graham, T. Huber, N. E. Dixon, G. Otting, Nucleic Acids Research 2014, 42, 2750-2757.
  16. Bioconjugation of proteins with a paramagnetic NMR and fluorescent tag. F. Huang, Y. Y. Pei, H. H. Zuo, J.L. Chen, X. C. Su, Chem. Eur. J. 2013, 19, 17141-17149.
  17. Noncovalent tagging proteins with paramagnetic lanthanide complexes for protein study. Z. Wei, Y. Yang, Q. F. Li, F. Huang, H. H. Zuo, X. C. Su, Chem. Eur. J. 2013, 19, 1097-1013.
  18. Magic angle spinning NMR structure determination of proteins from pseudocontact shifts. Li J, Pilla KB, Li QF, Zhang Z, Su XC, Huber T, Yang J, J. Am. Chem. Soc. 2013, 135, 8294-8303.
  19. Site-specific labeling of proteins with a chemically stable, high-affinity tag for protein study. Y. Yang, Q. F. Li, C. Cao, F. Huang, X. C. Su, Chem. Eur. J. 2013, 19, 1097-1013.
  20. Thiol-ene reaction: a versatile tool in site-specific labelling of proteins with chemically inert tags for paramagnetic NMR. Q. F. Li, Y. Yang, A. Maleckis, G. Otting, X. C. Su, Chem. Commun. 2012, 48, 2704-2706.
  21. Suppression of isotope scrambling in cell-free protein synthesis by broadband inhibition of PLP enzymes for selective 15N-labelling and production of perduterated proteins in H2O, X. C. Su, C.-T. Loh, Q. Ru, G. Otting, J. Biomol. NMR 2011, 50, 35-42.
  22. Paramagnetic labelling of proteins and oligonucleotides for NMR, X. C. Su, G. Otting, J. Biomol. NMR 2010, 46, 101-112.
  23. NMR Analysis of the Dynamic Exchange of the NS2B Cofactor between Open and Closed Conformations of the West Nile Virus NS2B-NS3 Protease, X. C. Su, K. Ozawa, R. Qi, S.G. Vasudevan, P.L. Lim, G. Otting,PLoS Negl. Trop. Dis. 2009, 3, e561.
  24. [Ln(DPA)3]3- is a convenient paramagnetic shift reagent for protein NMR studies, X. C. Su, H. Liang, K.V. Loscha, G. Otting, J. Am. Chem. Soc. 2009, 131, 10352-10353.
  25. A dipicolinic acid tag for rigid lanthanide tagging of proteins and paramagnetic NMR spectroscopy. X. C. Su, B. Man, S. Beeren, H. Liang, S. Simonsen, C. Schmitz, T. Huber, B. A. Messerle, G. Otting G. J. Am. Chem. Soc. 2008, 130, 10486-10487.
  26. Lanthanide-binding peptides for NMR measurements of residual dipolar couplings and paramagnetic effects from multiple angles. X. C. Su, K. McAndrew, T. Huber, G. Otting. J. Am. Chem. Soc. 2008, 130, 1681-1687.


 

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2010 年第一届研究生合影

 

20136月第一届研究生答辩

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2016年研究生毕业照