Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints.

Diego Del Alamo,Hassane S Mchaourab,Jens Meiler,Kevin L Jagessar

doi:10.1371/journal.pcbi.1009107

Diego Del Alamo, Hassane S Mchaourab + Show 2 more

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https://doi.org/10.1371/journal.pcbi.1009107

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Abstract

We describe an approach for integrating distance restraints from Double Electron-Electron Resonance (DEER) spectroscopy into Rosetta with the purpose of modeling alternative protein conformations from an initial experimental structure. Fundamental to this approach is a multilateration algorithm that harnesses sets of interconnected spin label pairs to identify optimal rotamer ensembles at each residue that fit the DEER decay in the time domain. Benchmarked relative to data analysis packages, the algorithm yields comparable distance distributions with the advantage that fitting the DEER decay and rotamer ensemble optimization are coupled. We demonstrate this approach by modeling the protonation-dependent transition of the multidrug transporter PfMATE to an inward facing conformation with a deviation to the experimental structure of less than 2Å Cα RMSD. By decreasing spin label rotamer entropy, this approach engenders more accurate Rosetta models that are also more closely clustered, thus setting the stage for more robust modeling of protein conformational changes.

Highlights

Distance measurements between pairs of spin labels by Double Electron-Electron Resonance (DEER) spectroscopy have been utilized extensively to investigate the structures and dynamics of proteins[1,2,3,4] and the assembly of protein-protein complexes[5,6,7,8]
Structural rearrangements that underlie conformational transitions are manifested by changes in the averages and widths of the distance distributions. To transform these distance distributions into restraints for modeling alternate protein conformations, we developed an algorithm in the modeling suite Rosetta for direct analysis of DEER primary data that yield the optimum ensemble of spin label positions in space, referred to as rotamers, that account for the data
The predicted distributions are broad relative to the experimental ones[18,20,28,29,30,31], which hinders DEER-based evaluation of protein structures or complexes as well as mapping of protein conformational changes. The latter can be obscured entirely if modeled distribution widths exceed distance changes observed between spin labels[1]. Another layer of complications in modeling of conformational changes arises if the ensemble of spin label rotamers is allowed to reconfigure, providing a low energy pathway to account for changes in distance distributions that originate from backbone movements

Summary

Introduction

Distance measurements between pairs of spin labels by Double Electron-Electron Resonance (DEER) spectroscopy have been utilized extensively to investigate the structures and dynamics of proteins[1,2,3,4] and the assembly of protein-protein complexes[5,6,7,8]. The echo-decay time traces are transformed into distributions consisting of distance components characterized by a mean and width[11,12,13,14,15] These distributions are compared to those predicted using one of several strategies, ranging from generic rotamer libraries[16,17,18], explicitly modeled pseudoatoms[1,19,20], or explicitly modeled spin label side chains[21,22,23,24,25,26,27]. These caveats limit the accuracy and precision of molecular models generated from DEER restraints

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