Xiaodong Su Ph.D.
Structural biology laboratory
Professor, College of Life Sciences, Peking University
tel：
E-mail：xdsu@pku.edu.cn
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
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.
Zhang TZ, Shi C, Ye ZY, Deng J, Gu MY, Chen ZX, Huang LX, Su XD, Chang ZZ. (2024) Crystal structure combined with metabolomics and biochemical studies indicates that FAM3A participates in fatty acid beta-oxidation upon binding of acyl-L-carnitine. Biochem. Biophys. Res. Commun., 735: 150481.
Fan AL, Zhong BY, Liu D, Lu YB, Wu MY, Jin HW, Shi XM, Ren JW , Zhang B, Su XD, Ma M, Li SM , Lin WH. (2024) Biosynthesis of epipyrone a reveals a highly speciffc membrane bound fungal C‑glycosyltransferase for pyrone galactosylation. Org. Lett., 26: 1160-1165.
Zhang Y, Xu YP, Nie JK, Chen H, Qin G, Wang B, Su XD. (2023) DNA–TCP complex structures reveal a unique recognition mechanism for TCP transcription factor families. Nucl. Acids Res., 51: 434-448.
Wang B, Xu H, Liang ZT, Zhao TN, Zhang X, Peng TB, Wang YC, Su XD. (2023) Human antibody BD-218 has broad neutralizing activity against concerning variants of SARS-CoV-2. Int. J Biol. Macromol., 227: 896-902.
Chen CT, Song XH, Yu YL, Wang XW, Xu H, Ji WW, Ma JC, Zhao CY, Feng SL, Wang YC, Su XD, Wang W. (2023) Aptamer-based nanointerferometer enables amplification-free ultrasensitive detection and differentiation of SARS-CoV-2 variants. Anal. Chim. Acta, 1260: 341207.
Feng SL, Yu YL, Ma JC, Wang XW, Song XH, Xu H, Li YB, Mo KJ, Liu P, Song X, Xie ZL, Wang YC, Su XD, Wang W, Chen CT. (2023) High-affinity aptamers enable the rapid optical detection and differentiation of three SARS-CoV-2 VOCs. Microchem. J., 195: 109508.
Zhang LG, Ma J, Shen ZR, Wang B, Jiang QL, Ma F, Ju Y, Duan GX, Zhang Q, Su XD, Sodmergen.(2023) Low copy numbers for mitochondrial DNA moderates the strength of nuclear-cytoplasmic incompatibility in plants. J. Integr. Plant Biol., 65: 739-754.
Chen H, Xu YP, Jin JS, Su XD. (2023) KaScape: a sequencing-based method for global characterization of protein‒DNA binding affinity. Sci. Rep., 13: 16595.
Cheng Y, Wang HB, Xu H, Liu Y, Ma B, Chen XM, Zeng X, Wang XG, Wang B, Shiau C, Ovchinnikov S, Su XD, Wang C. (2023) Co-evolution-based prediction of metal-binding sites in proteomes by machine learning. Nat. Chem. Biol., 19: 548-555.
Falco AD, Caruso F, Su XD, Iavarone A, Ceccarelli M. (2023) A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data. Nat. Commun., 14: 1074.
Feng J , Zhao Z, Wei YF, Bao ZS , Zhang W, Wu F, Li GZ , Sun ZY , Tan YL , Li JY , Zhang YQ ,Duan ZJ , Qi XL , Yu K , Cong ZM , Yang JJ , Wang YX , Sun YY , Tang FC ,Su XD, Fang C, Jiang T, Fan XL. (2023) Temporal and spatial stability of the EM/PM molecular subtypes in adult diffuse glioma. Front. Med., 17: 240-262.
Wei YF, Li GZ, Feng J, Wu F, Zhao Z, Bao ZS, Zhang W, Su XD, Li JY, Qi XL, Duan ZJ, Zhang YQ, Vega SF, Jakola AS, Sun YY, Carén H, Jiang T, Fan XL. (2023) Stalled oligodendrocyte differentiation in IDH-mutant gliomas. Genome Biol.,15: 24.
Li F, Yang JJ, Sun ZY, Wang L, Qi LY, A S, Liu YQ, Zhang HM, Dang LF, Wang SJ, Luo CX , Nian WF, O’Connerg S, Ju LZ, Quan WP, Li XK, Wang C, Wang DP, You HL, Cheng ZK, Yan J, Tang FC, Yang DC, Xia CW, Gao G, Wang Y, Zhang BC, Zhou YH, Guo X, Xiang SH, Liu H, Peng TB, Su XD, Chen Y, Ouyang Q, Wang DH , Zhang DM, Xu ZH, Hou HW, Bai SN , Li L. (2023) Plant-on-chip: Core morphogenesis processes in the tiny plant Wolffia australiana. PNAS Nexus, 2: 1-18.
Zhang JW, Wang JL, Li MX, Su XD, Tian YF, Wang PW, Zhou XZ, Jin GS, Liu FS. (2023) Oncolytic HSV-1 suppresses cell invasion through downregulating Sp1 in experimental glioblastoma. Cell Signal., 103: 110581.
Lupala CS, Ye YJ, Chen H, Su XD, Liu HG. (2022) Mutations on RBD of SARS-CoV-2 Omicron variant result in stronger binding to human ACE2 receptor. Biochem. Biophys. Res. Commun., 590: 34-41.
Hei Y, Chen Y, Li Q, Mei Z, Pan JJ, Zhang SQ, Xiong CY, Su XD, Wei SC. (2022) Multifunctional immunoliposomes enhance the immunotherapeutic effects of PD-L1 antibodies against melanoma by reprogramming immunosuppressive tumor microenvironment. Small, 18: e2105118.
Zhang SQ, Sui Y, Yan S, Zhang YF, Ding C, Su XD, Xiong JW, Wei SC. (2022) Retinoic acid and FGF10 promote the differentiation of pluripotent stem cells into salivary gland placodes. Stem Cell Res. Ther., 13: 368.
Zheng XB, Song JN, Yu CN, Zhou ZG, Liu XW, Yu J, Xu GC, Yang JQ, He XJ, Bai X, Luo Y, Bao Y, Li HF, Yang L, Xu MQ, Song N, Su XD, Xu J, Ma XL Shi HB. (2022) Single-cell transcriptomic profiling unravels the adenoma-initiation role of protein tyrosine kinases during colorectal tumorigenesis. Signal Transduct. Target. Ther., 7: 60.
Lupala CS, Kumar V, Su XD, Wu C, Liu HG. (2022) Computational insights into differential interaction of mammalian angiotensin-converting enzyme 2 with the SARS-CoV-2 spike receptor binding domain. Comput. Biol. Med., 141: 105017.
Wang MY, Zhang L, Li QQ, Wang B, Liang ZY, Sun YQ, Nie JH, Wu JJ, Su XD, Qu XW, Li YH, Wang YC, Huang WJ. (2022) Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Emerg.Microbes Infect., 11: 18-29.
Tabar MS, Parsania C, Chen H, Su XD, Bailey CG, Rasko JEJ. (2022) Illuminating the dark protein-protein interactome. Cell Rep. Methods., 2: 100275.
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,S u 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.
Jiahui Yu, Hua Xu, Hong Chen, Tianning Zhao, Tianbo Peng, Xiaohui Song, Chuxin Chen, Binyao Huang, Tianyi Yang, Xingyu Chen, Ying Lin, Shuohan Dong, Chuang Yuan, Ruiqi Chen
