RosettaEPR: Rotamer Library for Spin Label Structure and Dynamics

Abstract

An increasingly used parameter in structural biology is the measurement of distances between spin labels bound to a protein. One limitation to these measurements is the unknown position of the spin label relative to the protein backbone. To overcome this drawback, we introduce a rotamer library of the methanethiosulfonate spin label (MTSSL) into the protein modeling program Rosetta. Spin label rotamers were derived from conformations observed in crystal structures of spin labeled T4 lysozyme and previously published molecular dynamics simulations. Rosetta’s ability to accurately recover spin label conformations and EPR measured distance distributions was evaluated against 19 experimentally determined MTSSL labeled structures of T4 lysozyme and the membrane protein LeuT and 73 distance distributions from T4 lysozyme and the membrane protein MsbA. For a site in the core of T4 lysozyme, the correct spin label conformation (Χ1 and Χ2) is recovered in 99.8% of trials. In surface positions 53% of the trajectories agree with crystallized conformations in Χ1 and Χ2. This level of recovery is on par with Rosetta performance for the 20 natural amino acids. In addition, Rosetta predicts the distance between two spin labels with a mean error of 4.4 Å. The width of the experimental distance distribution, which reflects the flexibility of the two spin labels, is predicted with a mean error of 1.3 Å. RosettaEPR makes full-atom spin label modeling available to a wide scientific community in conjunction with the powerful suite of modeling methods within Rosetta.

Studies on the X-Ray and Solution Structure of FeoB from Escherichia coli BL21

“…3 B) for the open and closed states of the N32R1-K127R1 mutant, respectively. Considering the error of in silico spin labeling programs of 5 3 Å (22,30,31), the prediction made by mtsslWizard for the open state provides a good fit to the experimental distance distribution. Therefore, it seems safe to assume that apo-NFeoB adopts the open conformation in solution.…”

Chapter 2. Computational approaches for simulating motional EPR spectra

“…Such an approach will provide additional information and complement current approaches for rotamer search techniques and building rotamer libraries of spin labelled cysteines for EPR distance measurements such as developed by Jeschke and coworkers and other groups. [125][126][127][128] A strong impact of MD simulations on the calculation of EPR relaxation times (e.g. T 1 and T 2 ) is also anticipated which can be compared to those obtained from various pulsed EPR techniques.…”

The RosettaCon 2012 Special Collection: Code Writ on Water, Documentation Writ in Stone

“…Notably, peptidomimetic design has already been incorporated into a ROSIE server. Alexander et al [25] also explore the addition of new chemistries to Rosetta via improvements to RosettaEPR, a framework for using Electron Paramagnetic Resonance data to improve structure prediction. The new version of RosettaEPR includes a new rotamer library for a common spin label and more accurate reproduction of experimentally determined distance distributions.…”