MTMDAT-HADDOCK: High-throughput, protein complex structure modeling based on limited proteolysis and mass spectrometry

Abstract

Background: MTMDAT is a program designed to facilitate analysis of mass spectrometry data of proteins and biomolecularcomplexes that are probed structurally by limited proteolysis. This approach can provide information aboutstable fragments of multidomain proteins, yield tertiary and quaternary structure data, and help determine theorigin of stability changes at the amino acid residue level. Here, we introduce a pipeline between MTMDATand HADDOCK, that facilitates protein-protein complex structure probing in a high-throughput and highlyautomated fashion. Results: A new feature of MTMDAT allows for the direct identification of residues that are involved in complexformation by comparing the mass spectra of bound and unbound proteins after proteolysis. If 3D structures ofthe unbound components are available, this data can be used to define restraints for data-driven docking tocalculate a model of the complex. We describe here a new implementation of MTMDAT, which includes apipeline to the data-driven docking program HADDOCK, thus streamlining the entire procedure. Thisaddition, together with usability improvements in MTMDAT, enables high-throughput modeling of proteincomplexes from mass spectrometry data. The algorithm has been validated by using the protein-proteininteraction between the ubiquitin-binding domain of proteasome component Rpn13 and ubiquitin. Theresulting structural model, based on restraints extracted by MTMDAT from limited proteolysis and modeledby HADDOCK, was compared to the published NMR structure, which relied on twelve unambiguousintermolecular NOE interactions. The MTMDAT-HADDOCK structure was of similar quality to structuresgenerated using only chemical shift perturbation data derived by NMR titration experiments. Conclusions: The new MTMDAT-HADDOCK pipeline enables direct high-throughput modeling of protein complexes frommass spectrometry data. MTMDAT-HADDOCK can be downloaded fromhttp://www.ifm.liu.se/chemistry/molbiotech/maria_sunnerhagens_group/mtmdat/ together with the manualand example files. The program is free for academic/non-commercial purposes.