Summary The Artificial Intelligence-based structure prediction program AlphaFold-Multimer enabled structural modelling of protein complexes with unprecedented accuracy. Increasingly, AlphaFold-Multimer is also used to discover new protein-protein interactions. Here, we present AlphaPulldown, a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer. It provides a convenient command line interface, a variety of confidence scores, and a graphical analysis tool. Availability AlphaPulldown is freely available at https://www.embl-hamburg.de/AlphaPulldown Supplementary information Supplementary note is available at Bioinformatics online.

The Artificial Intelligence-based structure prediction program AlphaFold-Multimer enabled structural modelling of protein complexes with unprecedented accuracy. Increasingly, AlphaFold-Multimer is also used to discover new protein-protein interactions. Here, we present AlphaPulldown, a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer. It provides a convenient command line interface, a variety of confidence scores, and a graphical analysis tool.

Lassa virus is a negative-strand RNA virus with only four structural proteins that causes periodic outbreaks in West Africa. The nucleoprotein (NP) encapsidates the viral genome, forming the ribonucleoparticles together with the viral RNA and the L protein, which have to be continuously restructured during viral genome replication and transcription. Z protein is important for ribonucleoparticle recruitment, viral particle assembly and budding, and has also been shown to interact with the L protein. However, the interaction of NP, viral RNA and Z is poorly understood. Here, we characterize the interactions between Lassa virus NP, Z and RNA using structural mass spectrometry. We identify the presence of RNA as the driver for disassembly of ring-like NP trimers into monomers to subsequently form higher order assemblies. We locate the interaction site of Z and NP and demonstrate that while NP binds Z independently of the presence of RNA, this interaction is pH-dependent. These data improve our understanding of ribonucleoparticle assembly and recruitment.