Cross-Link Guided Molecular Modeling with ROSETTA

Abdullah Kahraman,Alexander Leitner,Ruedi Aebersold,Franz Herzog,Lars Malmström,George Rosenberger,Narcis Fernandez-Fuentes

doi:10.1371/journal.pone.0073411

Abdullah Kahraman, Alexander Leitner + Show 5 more

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https://doi.org/10.1371/journal.pone.0073411

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Abstract

Chemical cross-links identified by mass spectrometry generate distance restraints that reveal low-resolution structural information on proteins and protein complexes. The technology to reliably generate such data has become mature and robust enough to shift the focus to the question of how these distance restraints can be best integrated into molecular modeling calculations. Here, we introduce three workflows for incorporating distance restraints generated by chemical cross-linking and mass spectrometry into ROSETTA protocols for comparative and de novo modeling and protein-protein docking. We demonstrate that the cross-link validation and visualization software Xwalk facilitates successful cross-link data integration. Besides the protocols we introduce XLdb, a database of chemical cross-links from 14 different publications with 506 intra-protein and 62 inter-protein cross-links, where each cross-link can be mapped on an experimental structure from the Protein Data Bank. Finally, we demonstrate on a protein-protein docking reference data set the impact of virtual cross-links on protein docking calculations and show that an inter-protein cross-link can reduce on average the RMSD of a docking prediction by 5.0 Å. The methods and results presented here provide guidelines for the effective integration of chemical cross-link data in molecular modeling calculations and should advance the structural analysis of particularly large and transient protein complexes via hybrid structural biology methods.

Highlights

Conventional structural biology techniques like X-ray crystallography or Nuclear Magnetic Resonance (NMR) spectroscopy solved the structure of a large number of macromolecular complexes [1]
Distance restraints derived from XL-MS experiments are useful for driving modeling calculations towards native-like conformations
We have described three different computational protocols for comparative and de novo structure prediction and protein-protein docking and demonstrated the added value of the distance restraints on the computational predictions

Summary

Introduction

Conventional structural biology techniques like X-ray crystallography or Nuclear Magnetic Resonance (NMR) spectroscopy solved the structure of a large number of macromolecular complexes [1]. The requirement of these techniques for relatively large amounts of pure and highly concentrated protein samples has caused a bias in the structural elucidation of monomeric proteins and homomeric protein complexes. Homobifunctional cross-linking reagents, for example amine-reactive succinimide esters are used in XL-MS studies They react predominantly with primary amine groups on lysine side chains and N-termini [15]. Recent advances in the protocols to generate and process cross-linked samples [18,19], the mass spectrometric methods to generate fragment ion spectra of cross linked peptides [20] and the development of software tools for the identification of the cross-linked peptides [21,22] have contributed to the increasing maturity and robustness of the XL-MS technology

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