Publications by Dongchun Ni | EPFL Graph Search

Structural basis of SIRT7 nucleosome engagement and substrate specificity

Henning Paul-Julius Stahlberg, Beat Fierz, Dongchun Ni, Babatunde Edukpe Ekundayo, Carlos Moreno Yruela

Chromatin-modifying enzymes target distinct residues within histones to finetune gene expression profiles. SIRT7 is an NAD+-dependent deacylase often deregulated in cancer, which deacetylates either H3 lysine 36 (H3K36) or H3K18 with high specificity withi ...

NATURE PORTFOLIO2025

Identification of a binding site for small molecule inhibitors targeting human TRPM4

Henning Paul-Julius Stahlberg, Dongchun Ni, Babatunde Edukpe Ekundayo

Transient receptor potential (TRP) melastatin 4 (TRPM4) protein is a calcium-activated monovalent cation channel associated with various genetic and cardiovascular disorders. The anthranilic acid derivative NBA is a potent and specific TRPM4 inhibitor, but ...

Nature Portfolio2025

Arrestin recognizes GPCRs independently of the receptor state

Henning Paul-Julius Stahlberg, Dongchun Ni, Meltem Tatli

Only two nonvisual arrestins recognize many hundreds of different, intracellularly phosphorylated G protein-coupled receptors (GPCRs). Due to the highly dynamic nature of GPCR•arrestin complexes, the critical determinants of GPCR–arrestin recognition have ...

Proceedings of the National Academy of Sciences2025

Structure-function analysis of the cyclic β-1,2-glucan synthase from Agrobacterium tumefaciens

Henning Paul-Julius Stahlberg, Dongchun Ni

The synthesis of complex sugars is a key aspect of microbial biology. Cyclic beta-1,2-glucan (C beta G) is a circular polysaccharide critical for host interactions of many bacteria, including major pathogens of humans (Brucella) and plants (Agrobacterium). ...

Nature Portfolio2024

Computational drug development for membrane protein targets

Henning Paul-Julius Stahlberg, Pierre Vogel, Shuguang Yuan, Dongchun Ni, Babatunde Edukpe Ekundayo

The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learni ...

2024

Modulation of ABCG2 Transporter Activity by Ko143 Derivatives

Henning Paul-Julius Stahlberg, Dongchun Ni

ABCG2 is a multidrug transporter that protects tissues from xenobiotics, affects drug pharmacokinetics, and contributes to multidrug resistance of cancer cells. Here, we present tetracyclic fumitremorgin C analog Ko143 derivatives, evaluate their in vitro ...

2024

Structural Basis of the Allosteric Inhibition of Human ABCG2 by Nanobodies

Henning Paul-Julius Stahlberg, Dongchun Ni

ABCG2 is an ATP-binding cassette transporter that exports a wide range of xenobiotic compounds and has been recognized as a contributing factor for multidrug resistance in cancer cells. Substrate and inhibitor interactions with ABCG2 have been extensively ...

Academic Press Ltd- Elsevier Science Ltd2023

Activation mechanism of a short argonaute-TIR prokaryotic immune system

Henning Paul-Julius Stahlberg, Dongchun Ni, Babatunde Edukpe Ekundayo

Short prokaryotic argonaute (pAgo) and toll/interleukin-1 receptor/resistance protein (TIR)-analog of PAZ (APAZ) form a heterodimeric SPARTA complex that provides immunity to its prokaryotic host through an abortive infection mechanism. Monomeric SPARTA se ...

AMER ASSOC ADVANCEMENT SCIENCE2023

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

Henning Paul-Julius Stahlberg, Didier Trono, Priscilla Turelli, Anthony Marchand, Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld, Pablo Gainza Cirauqui, Andreas Scheck, Sarah Wehrle, Alexandra Krina Van Hall-Beauvais, Casper Alexander Goverde, Dongchun Ni

WILEY2023

Structure of a membrane-bound menaquinol:organohalide oxidoreductase

Henning Paul-Julius Stahlberg, Christof Holliger, Julien Maillard, Lorenzo Cimmino, Dongchun Ni, Babatunde Edukpe Ekundayo

Organohalide-respiring bacteria are key organisms for the bioremediation of soils and aquifers contaminated with halogenated organic compounds. The major players in this process are respiratory reductive dehalogenases, corrinoid enzymes that use organohali ...

Nature Research2023

De novo design of protein interactions with learned surface fingerprints

Henning Paul-Julius Stahlberg, Didier Trono, Priscilla Turelli, Charlène Mireille Raymonde Raclot, Sandrine Madeleine Suzanne Georgeon, Beat Fierz, Aaron Simone Petruzzella, Anthony Marchand, Bruno Emanuel Ferreira De Sousa Correia, Elisa Oricchio, Zander Harteveld, Pablo Gainza Cirauqui, Freyr Sverrisson, Andreas Scheck, Sarah Wehrle, Stéphane Rosset, Alexandra Krina Van Hall-Beauvais, Alexandra Teslenko, Jane Marsden, Michael Bronstein, Casper Alexander Goverde, Stephen Michael Buckley, Dongchun Ni, Martin Pacesa

Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. This k ...

2023

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

Henning Paul-Julius Stahlberg, Didier Trono, Priscilla Turelli, Florence Pojer, Sergey Nazarov, Kelvin Ka Ching Lau, Dongchun Ni, Alexander Myasnikov, Emiko Uchikawa

nvestigation of potential hosts of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is crucial to understanding future risks of spillover and spillback. SARS-CoV-2 has been reported to be transmitted from humans to various animals after req ...

2023

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

Henning Paul-Julius Stahlberg, Dongchun Ni

BSEP (ABCB11) is an ATP-binding cassette transporter that is expressed in hepatocytes and extrudes bile salts into the canaliculi of the liver. BSEP dysfunction, caused by mutations or induced by drugs, is frequently associated with severe cholestatic live ...

Nature Portfolio2023

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

Kelvin Ka Ching Lau, Dongchun Ni

There has been limited characterisation of bat-borne coronaviruses in Europe. Here, we screened for coronaviruses in 48 faecal samples from 16 of the 17 bat species breeding in the UK, collected through a bat rehabilitation and conservationist network. We ...

Nature Portfolio2023

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

Henning Paul-Julius Stahlberg, Sergey Nazarov, Dongchun Ni, Alexander Myasnikov, Babatunde Edukpe Ekundayo

The CRISPR-guided caspase (Craspase) complex is an assembly of the target-specific RNA nuclease known as Cas7-11 bound to CRISPR RNA (crRNA) and an ancillary protein known as TPR-CHAT (tetratricopeptide repeats (TPR) fused with a CHAT domain). The Craspase ...

2023

It takes two times two to tango - cryoEM structure resolution of the membrane-bound tetrachloroethene reductive dehalogenase complex

Christof Holliger, Julien Maillard, Lorenzo Cimmino, Dongchun Ni, Babatunde Edukpe Ekundayo

ELSEVIER2022

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

Henning Paul-Julius Stahlberg, Dongchun Ni

Type I CRISPR-Cas systems typically rely on a two-step process to degrade DNA. First, an RNA-guided complex named Cascade identifies the complementary DNA target. The helicase-nuclease fusion enzyme Cas3 is then recruited in trans for processive DNA degrad ...

CELL PRESS2022

Mechanism ofcyclic beta-glucan export by ABC transporter Cgt of Brucella

Henning Paul-Julius Stahlberg, Na Wu, Dongchun Ni

Polysaccharides play critical roles in bacteria, including the formation of protective capsules and biofilms and establishing specific host cell interactions. Their transport across membranes is often mediated by ATP-binding cassette (ABC) transporters, wh ...

NATURE PORTFOLIO2022

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

Henning Paul-Julius Stahlberg, Didier Trono, Priscilla Turelli, Florence Pojer, Charlène Mireille Raymonde Raclot, Kelvin Ka Ching Lau, Dongchun Ni

The SARS-CoV-2 Omicron variant has very high levels of transmission, is resistant to neutralization by authorized therapeutic human monoclonal antibodies (mAb) and is less sensitive to vaccine-mediated immunity. To provide additional therapies against Omic ...

2022

Structural basis of drug recognition by the multidrug transporter ABCG2

Henning Paul-Julius Stahlberg, Dongchun Ni

ABCG2 is an ATP-binding cassette (ABC) transporter whose function affects the pharmacokinetics of drugs and contributes to multidrug resistance of cancer cells. While its interaction with the endogenous substrate estrone-3-sulfate (E1S) has been elucidated ...

Elsevier2021