Su Xiaodong

Professor, School of Life Sciences, Peking University

Email: xdsu@pku.edu.cn

Education

1994, Ph. D., Karolinska Institutet

1985, B. S., Peking University, Physics

Research Areas

1.Structural and functional studies of biological macromolecules by X-ray crystallography, including novel approaches in protein crystallization

2.Rational design of drugs and vaccines by structure/function-based methods, particularly for cancer immune-therapy related molecules

3.Currently, my group also started to do single molecule biophysics and NGS (next generation sequencing) related technique developments, for understanding kinetic properties of above bio-macromolecules, particularly protein- DNA interactions

Research Progress

Su laboratory has been working in the fields of structural biology and molecular biophysics for the last 20 years, the main activities have been: Structural, functional and evolutionary studies of bio-macromolecules by X-ray crystallographic, biochemical and biophysical methods, particularly working on macromolecules related to innate immunity and cancer; Rational design of drugs by structure/function based methods; Utilizing and developing anomalous dispersion (SAD) methods for X-ray crystallography; Novel approaches in protein crystallization. Currently, Su group has also started to work on single molecule biophysics and NGS (next-generation sequencing) related technique developments, particularly cancer genomics.

Selected Publications

Xu H, Wang B, Zhao TN, Liang ZT, Peng TB, Song XH, Wu JJ, Wang YC,Su XD. (2021) Structure-based analyses of neutralization antibodies interacting with naturally occurring SARS-CoV-2 RBD variants. Cell Res., 31: 1126–1129.

Liu WZ, Li J, Xu YP, Yin DB, Zhu X, Fu HY,Su XD, Guo XF. (2021) Complete Mapping of DNA-Protein Interactions at the Single-Molecule Level.Adv. Sci., 8: e2101383.

Dai LQ, Xu YP, Du ZW,Su XD, Yu J. (2021) Revealing atomic-scale molecular diffusion of a plant-transcription factor WRKY domain protein along DNA.Proc. Natl. Acad. Sci. U. S. A., 118: e2102621118.

Lupala CS, Li XX, Lei J, Chen H, Qi JX, Liu HG,Su XD. (2021) Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein.Quant. Biol., 9: 61-72.

Zhang L, Cui ZM, Li QQ, Wang B, Yu YL, Wu JJ, Nie JH, Ding RX, Wang HX, Zhang Y, Liu S, Chen ZH, He YQ,Su XD, Xu WB, Huang WJ , Wang YC. (2021) Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization.Commu. Biol., 4: 1196.

Garofano L, Migliozzi S, Oh YT, D’Angelo F, Najac RD, Ko A, Frangaj B, Caruso FP, Yu K, Yuan J, Zhao W, Di Stefano AL, Bielle F, Jiang T, Sims P, Suvà ML, Tang F,Su XD, Ceccarelli M, Sanson M, Lasorella A, Lavarone A. (2021) Pathway-based classification of glioblastoma uncovers a mitochondrial subtype with therapeutic vulnerabilities.Nat. Cancer., 2: 141-156.

Lupala CS, Kumar V,Su XD, Wu C, Liu HG. (2021) Computational insights into differential interaction of mammalian angiotensin-converting enzyme 2 with the SARS-CoV-2 spike receptor binding domain.Comput. Biol. Med., 105017.

Du S, Cao YL, Zhu QY, Yu P, Qi FF, Wang GP, Du XX, Bao LL, Deng W, Zhu H, Liu JN, Nie JH, Zheng YH, Liang HY, Liu RX, Gong SR, Xu H, Yisimayi AJ, Lv Q, Wang B, He RS, Han YL, Zhao WJ, Bai YL, Qu YJ, Gao X, Ji CG, Wang QS, Gao N, Huang WJ, Wang YC, Xie XS,Su XD, Xiao JY, Qin C. (2020) Structurally resolved SARS-CoV-2 antibody shows high efficacy in severely infected hamsters and provides a potent cocktail pairing strategy.Cell, 183: 1013-1023.

Li YX, Wang GP, Li NN, Wang YX, Zhu QY, Chu HR, Wu WJ, Tan Y, Yu F,Su XD, Gao N, Xiao JY. (2020) Structural insights into immunoglobulin M.Science, 367: 1014-1017.

Xu YP, Xu H, Wang B,Su XD. (2020) Crystal structures of N-terminal WRKY transcription factors and DNA complexes.Protein Cell., 11: 208-213.

Yu K, Hu YQ, Wu F, Guo QF, Qian ZH, Hu WE, Chen J, Wang KY, Fan XY, Wu XL, Rasko JEJ, Fan XL, Iavarone A, Jiang T, Tang FC,Su XD. (2020) Surveying brain tumor heterogeneity by single-cell RNA-sequencing of multi-sector biopsies.Natl. Sci. Rev., 7: 1306-1318.

Ye ZY, Brostromer E, Nan J, Cao XF, Liu X, Qiao L, Liu ZJ,Su XD. (2020) Protein crystallization benefits from the rough well surface of a 48-well polystyrene microplate.J. Cryst. Growth, 532: 125425.

Zhao Z, Ma ZX, Wang B, Guan YK,Su XD, Jiang ZF. (2020) Mn2+directly activates cGAS and structural analysis suggests Mn2+induces a noncanonical catalytic synthesis of 2'3'-cGAMP.Cell Rep., 32: 108053.

Cao YL, Su B, Guo XH, Sun WJ, Deng YQ, Bao LL, Zhu QY, Zhang X, Zheng YH, Geng CY, Chai XR, He RS, Li XF, Lv Q, Zhu H, Deng W, Xu YF, Wang YJ, Qiao LX, Tan YF, Song LY, Wang GP, Du XX, Gao N, Liu JN, Xiao JY,Su XD, Du ZM, Feng YM, Qin C, Qin CF, Jin RH, Xie XS. (2020) Potent neutralizing antibodies against SARS-CoV-2 Identified by high-throughput single-cell sequencing of convalescent patients' B cells.Cell, 182: 73-84.

Zhao K, Li YW, Liu ZY, Long HF, Zhao CY, Luo F, Sun YP, Tao YQ,Su XD, Li D, Li XM, Liu C. (2020) Parkinson’s disease associated mutation E46K of α-synuclein triggers the formation of a distinct fibril structure.Nat. Commun., 11: 2643.

Sun YP, Hou SQ, Zhao K, Long HF, Liu ZY, Gao J, Zhang YY,Su XD, Li D, Liu C. (2020) Cryo-EM structure of full-length α-synuclein amyloid fibril with Parkinson’s disease familial A53T mutation.Cell Res., 30: 360-362.

Caruso FP, Garofano L, D'Angelo F, Yu K, Tang FC, Yuan JZ, Zhang J, Cerulo LG, Pagnotta SM, Bedognetti D, Sims PA, SuvàM,Su XD, Lasorella A, Lavarone A, Ceccarelli M. (2020) A map of tumor–host interactions in glioma at single-cell resolution.GigaScience, 9: 1-14.

Hu WE, Zhang X, Guo QF, Yang JW, Yang Y, Wei SC,Su XD. (2019) HeLa-CCL2 cell heterogeneity studied by single-cell DNA and RNA sequencing.PLoS One, 14: e0225466.

Deng MJ, Tao J, E C, Ye ZY, Jiang Z, Yu J,Su XD. (2018) Novel Mechanism for Cyclic Dinucleotide Degradation Revealed by Structural Studies of Vibrio Phosphodiesterase V-cGAP3.J Mol Biol.,430: 5080-5093.

Wang S, Shuai Y, Sun CY, Xue BX, Hou YP,Su XD, Sun YJ. (2018) Lighting up Live Cells with Smart Genetically Encoded Fluorescence Probes from GMars Family.ACS Sens., 3: 2269−2277.

Wang CG, Guan YK, Lv MZ, Zhang R, Guo ZY, Wei XM, Du XX, Yang J, Li T, Wan Y,Su XD, Huang XJ, Jiang ZF. (2018) Manganese Increases the Sensitivity of the cGAS-STING Pathway for Double-Stranded DNA and Is Required for the Host Defense against DNA Viruses.Immunity., 48: 675–687.

Li H, Zhu L, Chen H, Li T, Han Q1, Wang S, Yao X, Feng H, Fan L, Gao S, Boyd R, Cao X, Zhu P, Li J, Keating A,Su XD, Zhao RC. (2018) Generation of Functional Hepatocytes from Human Adipose-Derived MYC+KLF4+GMNN+Stem Cells Analyzed by Single-Cell RNA-Seq Profiling.Stem CellsTransl Med., 7: 792-805.

Li Y, Shao S, Xu X,Su XD, Sun YJ, Wei SC.(2018). MapZ Forms a Stable Ring Structure That Acts As a Nanotrack for FtsZ Treadmilling in Streptococcus mutans.ACS Nano., 12: 6137-6146.

Huang S, Li Y, Yuan X, Zhao M, Wang J, Li Y, Li Y, Lin H, Zhang Q, Wang W, Li D, Dong X, Li L, Liu M, Huang W, Huang C. (2018) The UbL-UBA Ubiquilin4 protein functions as a tumor suppressor in gastric cancer by p53-dependent and p53-independent regulation of p21.Cell Death Differ., 10.1038.

Wang YT, Ning XH, Gao PF, Wu SX, Sha MY, Lv MZ, Zhou X, Gao JY, Fang R, Meng GX, Su XD, Jiang ZF. (2017) Inflammasome Activation Triggers Caspase-1-Mediated Cleavage of cGAS to Regulate Responses to DNA Virus Infection. Immunity, 46: 393-404.

Che X, Du XX, Cai XX, Zhang J, Xie WJ, Long ZR, Ye ZY, Zhang H, Yang LJ, Su XD, Gao YQ. (2017) Single Mutations Reshape the Structural Correlation Network of the DMXAA-Human STING Complex. J Phys Chem B., 121: 2073-2082.

Lian TF, Xu YP, Li LF, Su XD. (2017) Crystal Structure of Tetrameric Arabidopsis MYC2 Reveals the Mechanism of Enhanced Interaction with DNA. Cell Rep., 19: 1334-1342.

Tao JL, Zhang XW, Jin JS, Du XX, Lian TF, Yang J, Zhou X, Jiang ZF, Su XD. (2017) Nonspecific DNA Binding of cGAS N Terminus Promotes cGAS Activation. J Immunol., 198: 3627-3636.

Da LT, Chao E, Shuai Y, Wu SG, Su XD, Yu J (2017) T7 RNA polymerase translocation is facilitated by a helix opening on the fingers domain that may also prevent backtracking. Nucleic Acids Res., 45: 7909-9721.

Li XY, Nai SS, Ding YH, Geng QZ, Zhu BT, Yu K, Zhu WG, Dong MQ, Su XD, Xu XZ, Li J (2017) Polo-like kinase 1 (PLK1)-dependent phosphorylation of methylenetetrahydrofolate reductase (MTHFR) regulates replication via histone methylation. Cell Cycle.,16: 1933-1942.