Dongchun Ni

About

Dongchun joined Prof. Henning Stahlberg’s lab at the University of Basel as a PhD student in December 2017. Since then, he has had the great opportunity to contribute to one of the projects of the NCCR TransCure. He is applying high-resolution cryo-electron microscopy to unravel the 3D structure of proteins and understand their biological function and involvement in diseases.

Current Project

Cryo-EM on various proteins from everyday life

Biography

Education

11/2017 - 11/2020PhD in Structural Biology & Biophysics (Henning Stahlberg), Universität Basel, Biozentrum, Basel, Switzerland
09/2011 - 07/2014Master`s student, in Public Health Toxicology, Tianjin Medical University, Tianjin, China
01/2012 - 04/2014 Graduate student, in Structural Biology, protein crystallography (Yihua Huang), Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
09/2007 - 06/2011Undergraduate student in Pharmaceutical Science, South-Central University for Nationalities, Wuhan, China

Positions

02/2021 – pres. Scientist, Laboratory of Biological Electron Microscopy (LBEM), Institute of Physics, EPFL, Switzerland
12/2020 - 02/2021PostDoc, Universität Basel, Biozentrum, Basel, Switzerland
12/2015 - 12/2016Research scholar, Harvard Medical School & Boston Children's Hospital, Boston, USA
07/2014 - 12/2015Research assistant, Department of Cardiovascular Diseases, Tianjin Xiqing hospital, Tianjin, China
07/2010 - 04/2011 Internship, Department of Neurobiology, Peking University, Beijing, China

Publications

-+

Modulation of ABC...

Yu, Q., ..., Ni, D., Stahlberg, H., ...

(submitted), (2024)

22

Structural basis of TRPM4 inhibition by ...

Ekundayo, B., Aruliampalam, P., Hämmerli, A.-F., Guichard, S., Boukenna, M., Rougier, J.-S., Abriel, H., Stahlberg, H., Ni, D.

(submitted), (2024)

20

Computational drug development for membrane protein targets

Li, H., Sun, X., Cui, W., Xu, M., Dong, J., Ekundayo, B., Ni, D., Rao, Z., Stahlberg, H., Yuan, S., Vogel, H.

Nature Biotechnology 42, 229-242 (2024)

DOI: DOI

19

Structural basis of bile salt extrusion and small-molecule inhibition in human BSEP

Liu, H., Irobalieva, R., Kowal, J., Ni, D., Nosol, K., Bang-Sorensen, R., Lancien, L., Stahlberg, H., Stieger, B., Locher, K.

Nature Communications 14(7296), 1-12 (2023)

DOI: DOI

18

Structure of a membrane-bound menaquinol:organohalide oxidoreductase

Cimmino, L., Duarte, A., Ni, D., Ekundayo, B., Pereira, I.A.C., Stahlberg, H., Holliger, C., Maillard, J.

Nature Communications 14(7038), (2023)

DOI: DOI

17

Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential

Tan, C.C.S., Trew, J., Peacock, T.P., Mok, K.Y., Hart, C., Lau, K., Ni, D., ..., Balloux, F., Savolainen, V.

Nature Communications 14(3322), (2023)

PubMed

DOI: DOI

16

Structural basis of the allosteric inhibition of human ABCG2 by nanobodies

Irobalieva, R.N., Manolaridis, I., Jackson, S.M., Ni, D., Pardon, E., Stahlberg, H., Steyaert, J., Locher, K.P.

J. Mol. Biol. 435(19), 168234 (2023)

PubMed

DOI: DOI

15

Machine Learning in Protein Science De Novo Design of Site-Specific Protein Binders Using Surface Fingerprints

Van Hall-Beauvais, A., Gainza, P., Wehrle, S., Scheck, A., Marchand, A., Harteveld, Z., Goverde, C., Ni, D., Shuguang, T., Turelli, P., Trono, D., Stahlberg, H., Gao, G., Bronstein, M., Correia, B.

Protein Science 32(1), S106 (2023)

DOI: DOI

14

De novo design of protein interactions with learned surface fingerprints

Gainza, P., Wehrle, S., ..., Ni, D., ..., Fierz, B., Trono, D., Stahlberg, H., Bronstein, M., Correia, B.E.

Nature 617(5759), 176-184 (2023)

PubMed

DOI: DOI

12

Cryo-EM structures and binding of mouse and human ACE2 to SARS-CoV-2 variants of concern indicate that mutations enabling immune escape could expand host range

Ni, D., Turelli, P., Beckert, B., Nazarov, S., Uchikawa, E., Myasnikov, A., Pojer, F., Trono, D., Stahlberg, H., Lau, K.

PLoS Pathogens 19(4), e1011206 (2023)

PubMed

DOI: DOI

11

Structural insights into the regulation of Cas7-11 by TPR-CHAT

Ekundayo, B., Torre, D., Beckert, B., Nazarov, S., Myasnikov, A., Stahlberg, H., Ni, D.

Nature Struct. Mol. Biol. 30(2), 135-139 (2023)

PubMed

DOI: DOI

10

Allosteric control of type I-A CRISPR-Cas3 complexes and establishment as effective nucleic acid detection and human genome editing tools

Hu, C., Ni, D., Nam, K.H., Majumdar, S., McLean, J., Stahlberg, H., Terns, M.P., Ke, A.

Molecular Cell 82(15), 2754-2768 (2022)

PubMed

DOI: DOI

9

Mechanism of cyclic Beta-glucan export by ABC transporter Cgt of Brucella

Sedzicki, J., Ni, D., Lehmann, F., Wu, N., Zenobi, R., Jung, S., Stahlberg, H., Dehio, C.

Nature Struct. Mol. Biol. 29(12), 1170-1177 (2022)

PubMed

DOI: DOI

8

Patient-derived monoclonal antibody neutralizes SARS-CoV-2 Omicron variants and confers full protection in monkeys

Fenwick, C., Turelli, P., Ni, D., Perez, L., Lau, K., ..., Leyssen, P., Lévy, Y., Pojer, F., Stahlberg, H., LeGrand, R., Trono, D., Pantaleo, G.

Nature Microbiology 7(9), 1376-1389 (2022)

PubMed

DOI: DOI

7

Structural analysis of the Spike of the Omicron SARS-COV-2 variant by cryo-EM and implications for immune evasion

Ni, D., Lau, K., Turelli, P., Raclot, C., Beckert, B., Nazarov, S., Pojer, F., Myasnikov, A., Stahlberg, H., Trono, D.

bioRxiv 2021.12.27.474250, (2022)

DOI: DOI

6

Structural basis of drug recognition by the multidrug transporter ABCG2

Kowal, J., Ni, D., Jackson, S.M., Manolaridis, I., Stahlberg, H., Locher, K.P.

J. Mol. Biol. 433(13), 166980 (2021)

PubMed

DOI: bioRxiv

5

Structures of ABCG2 under turnover conditions reveal a key step in drug transport mechanism

Yu, Q., Ni, D., Kowal, J., Manolaridis, I., Jackson, S.M., Stahlberg, H., Locher, K.P.

Nature Comm. 12(4376), (2021)

PubMed

DOI: bioRxiv

4

Cryo-EM structures of a LptDE transporter in complex with Pro-macrobodies offer insight into lipopolysaccharide translocation

Botte, M., Ni, D., Schenck, S., Zimmermann, I., Chami, M., Bocquet, N., Egloff, P., Bucher, D., Trabuco, M., Cheng, R.K.Y., Brunner, J.D., Seeger, M.A., Stahlberg, H., Hennig, M.

Nature Communications 13(1), 1826 (2022)

DOI: DOI

3

Structural investigation of ACE2 dependent disassembly of the trimeric SARS-CoV-2 Spike glycoprotein

Ni, D., Lau, K., Lehmann, F., Fränkl, A., Hacker, D., Pojer, F., Stahlberg, H.

bioRxiv 2020.10.12.336016, (2020)

2