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

Abstract

BackgroundMTMDAT is a program designed to facilitate analysis of mass spectrometry data of proteins and biomolecular complexes that are probed structurally by limited proteolysis. This approach can provide information about stable fragments of multidomain proteins, yield tertiary and quaternary structure data, and help determine the origin of stability changes at the amino acid residue level. Here, we introduce a pipeline between MTMDAT and HADDOCK, that facilitates protein-protein complex structure probing in a high-throughput and highly automated fashion.ResultsA new feature of MTMDAT allows for the direct identification of residues that are involved in complex formation by comparing the mass spectra of bound and unbound proteins after proteolysis. If 3D structures of the unbound components are available, this data can be used to define restraints for data-driven docking to calculate a model of the complex. We describe here a new implementation of MTMDAT, which includes a pipeline to the data-driven docking program HADDOCK, thus streamlining the entire procedure. This addition, together with usability improvements in MTMDAT, enables high-throughput modeling of protein complexes from mass spectrometry data. The algorithm has been validated by using the protein-protein interaction between the ubiquitin-binding domain of proteasome component Rpn13 and ubiquitin. The resulting structural model, based on restraints extracted by MTMDAT from limited proteolysis and modeled by HADDOCK, was compared to the published NMR structure, which relied on twelve unambiguous intermolecular NOE interactions. The MTMDAT-HADDOCK structure was of similar quality to structures generated using only chemical shift perturbation data derived by NMR titration experiments.ConclusionsThe new MTMDAT-HADDOCK pipeline enables direct high-throughput modeling of protein complexes from mass spectrometry data. MTMDAT-HADDOCK can be downloaded from http://www.ifm.liu.se/chemistry/molbiotech/maria_sunnerhagens_group/mtmdat/together with the manual and example files. The program is free for academic/non-commercial purposes.

The proteomics and interactomics of human erythrocytes

“…The fusion of proteomics with computational analysis and informatics has led to software which can couple interactome networks to the three-dimensional structure of the interacting proteins. [87][88][89][90][91][92][93] When this is coupled to software that can analyse the affinities and on/off rates of PPI, then we will have more valuable 3D interactome networks which will be able to accurately predict in silico the physiological effects of disease-related protein defects and the results of pharmaco-proteomic changes upon cellular homoeostasis. Five years from now, the combined software capabilities and MS hardware sophistication should be in place to link modified structure and function of proteins in SS erythrocytes and leukocytes to changes in their 3D interactome network that leads to the pathophysiology of SCD including the cellular interactions that lead to vasoocclusion.…”

Towards integrative structural mass spectrometry: Benefits from hybrid approaches

“…The emergence of different integrative platforms using more and more MS-based data is another sign of the increasing importance of these methods in structural biology. The HADDOCK (High-Ambiguity-Driven DOCKing) server can, for instance, incorporate data coming from IM-MS [159], cross-linking, limited proteolysis [160], and, more recently, HDX experiments [161]. Other molecular modeling suites that are available online include the Integrative Modeling Platform [162] and ROSETTA [163].…”

Resolution of protein structure by mass spectrometry

“…This high-resolution information can be achieved by a combination of the outcome of a limited proteolysis experiment with, for example, the static picture of the protein obtained with protein X-ray crystallography. The combination of partial digestion and other structuredetermination methods allowed one to monitor conformational transitions upon substrate, cofactor, or inhibitor binding (McCulloch & Fitzpatrick, 1999;Kang, Wilson, & Kermode, 2008;Crain & Broderick, 2013;Diestel et al, 2013;), and during protein-protein interactions (Dhungana et al, 2009;Grote et al, 2010;Hennig et al, 2012;O'Neill et al, 2012;Feng et al, 2014).…”