RotamerConvolveMD 1.3.2

Analysis of spin label distances over structural ensembles

Author:

Philip W Fowler, Oliver Beckstein, Katrin Reichel, and AUTHORS

Year:

2013

Licence:

GNU Public Licence, version 2 (or higher)

Copyright:

© 2013 Philip W Fowler, Oliver Beckstein, © 2014–2017 AUTHORS

Citation:

LS Stelzl, PW Fowler, MSP Sansom, O Beckstein. J Mol Biol 426 (2014), 735-751. doi: 10.1016/j.jmb.2013.10.024

Documentation:

This package contains the MTSL rotamer library R1A_298K (2011) and an updated MTSL rotamer library R1A_298K (2015) provided by Gunnar Jeschke, which is also published under the GPL with his permission. The updated rotamer library was sent by Gunnar Jeschke after personal discussion.

Summary

This package analyses molecular dynamics trajectories or conformational ensembles in terms of spin-label distances as probed in double electron-electron resonance (DEER) experiments and spin-label to amide protin distances as probed in paramagnetic relaxation enhancement (PRE) experiments. The spin labels are fitted on trajectories and the spin label mobility is taken into account using a rotamer library.

For further details see the RotamerConvolveMD documentation.

Background

Site-directed spin labeling (SDSL) is a common technique to investigate structure and dynamics of macromolecular systems. Covalentry attached spin labels are introduced to the system and induce electron spin resonance. Double electron electron spin resonance (DEER) is an EPR technique for measuring distances between two spin labels that have been covalently attached to a protein. Two cysteine residues are introduced into the protein and subsequently labelled. Paramagnetic relaxation enhancement (PRE) is an NMR technique for measuring distances between a spin label and the amide protons of the protein backbone. One cysteine residue is introduced at the position of the label The positions are chosen to report on the expected conformational change. A commonly used spin label is (1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl)-methanethiosulfonate (MTSL). MTSL has a linker with five rotatable bonds and is therefore very flexible. The distance distributions between the two spin labels (DEER) or one spin label and the amide protons are measured by experiments are typically broad and often multi-modal. The distributions are therefore a convolution of the flexibility of the MTSL spin label and the conformational spread of the proteins in the sample. To ensure that we compared like with like we developed a method that

1. maps rotamer libraries of the MTSL spin label onto each position,

2. discards those rotamers that sterically clash with the protein (typically distances <2 Å) and

3. calculates all (weighted) distance pairs between the remaining rotamers and

4. thereby estimates a distance distribution for that structure.

The code was written in Python using the MDAnalysis library [Michaud-Agrawal2011] and a published rotamer library for MTSL [Polyhach2011]. It is available for download from the MDAnalysis website, https://github.com/MDAnalysis/RotamerConvolveMD .

Our approach improves upon the existing method [Polyhach2011] by increasing computational efficiency and implementing, via the MDAnalysis library, analysis of ensembles of hundreds of structures, which allowed us to estimate distance distributions for entire simulation trajectories. In the case of PRE measurements, it enables the user to calculate back the transverse relaxation enhancement to compare raw data without calculating the distances based on the experiment.

In the case of MTSL, the distances are determined by considering the position of the free electron located between nitrogen (N1) and (O1).

Examples of the application of this approach can be found in [Stelzl2014].

Installation

Typically, install the package with pip

pip install RotamerConvolveMD

(see also the file INSTALL.rst)

This will automatically install MDAnalysis and other dependencies. If problems arise, try installing MDAnalysis first (see http://www.mdanalysis.org for help).

Analysis is performed with the script convolve-mtss-rotamers.py (DEER) or convolve-mtss-rotamers_pre.py (PRE), which will have been installed in your bin directory. You might have to add the bin directory to your PATH. Consult your Python documentation for the details although often this will be ~/.local/bin (for a --user installation or /usr/local/bin for site-wide installation).

Usage

DEER

Analysis for standard DEER experiments with MTSL spin labels is performed with the script convolve-mtss-rotamers.py. It takes as input

• a topology or structure file (psf, gro, pdb, … any topology format recognized by mdanalysis)

• a trajectory (dcd, xtc, trr, … any trajectory format that mdanalysis can read)

a typical invocation:

convolve-mtss-rotamers.py \
    --resid 47 330  \
    --histogramBins 0 80 1  \
    --clashDistance 2.2  \
    --output "dat/peptso-xrd" \
    --plotname "dat/peptso-xrd.pdf" \
    --outputRawDistances "dat/peptso-xrd" \
    --dcdfilename "dcd/peptso-xrd" \
    --dcdfilenameNoClashes "dcd/peptso-xrd" \
    --useNOelectron \
    --libname "MTSSL 298K 2015" \
    peptso.gro peptso.xtc

It loads the MD trajectory from the topology peptso.gro and the trajectory peptso.xtc. The --resid pair is required and denotes the residue numbers (in the topology) to which the MTSSL spin labels would be attached. Rotamers that overlap with protein atoms as measured by an atom-atom distance smaller than the --clashDistance will be discarded and not counted in the distance calculations. The user can decide to use either N1 --no-useNOelectron or the geometric midpointis N1 and O1 --useNOelectron to calculate the distances. Two libraries are offered: MTSSL 298K 2011 or MTSSL 298K 2015 (default) by defining the option --libname. For further explanations see the --help option.

For an example, see doc/example in the source distribution. The example can also be run to test the installation as reference output is provided.

PRE

Analysis for standard PRE experiments with MTSL spin label is performed with the script convolve-mtss-rotamers_pre.py. Similar to the analysis of DEER experiments, it takes as inputs:

• a topology or structure file (psf, gro, pdb, … any topology format recognized by mdanalysis)

• a trajectory (dcd, xtc, trr, … any trajectory format that mdanalysis can read)

a typical invocation:

convolve-mtss-rotamers_pre.py \
    --resid 47  \
    --clashDistance 2.2  \
    --plotname "dat/peptso-xrd-47.pdf" \
    --outputRawDistances "dat/peptso-xrd" \
    --dcdfilenameAll "dcd/peptso-xrd" \
    --dcdfilenameNoClashes "dcd/peptso-xrd" \
    --useNOelectron \
    --libname "MTSSL 298K 2015" \
    peptso.gro peptso.xtc

The --resid is required and denotes the residue number (in the topology) to which the MTSSL spin label would be attached. Rotamers that overlap with protein atoms as measured by an atom-atom distance smaller than the --clashDistance will be discarded and not counted in the distance calculations. The user can decide to use either N1 --no-useNOelectron or the geometric midpointis N1 and O1 --useNOelectron to calculate the distances. Two libraries are offered: MTSSL 298K 2011 or MTSSL 298K 2015 (default) by defining the option --libname. For further explanations see the --help option.

Help

If you have questions or problems installing the package then ask on the MDAnalysis user mailing list: http://groups.google.com/group/mdnalysis-discussion

References

[Michaud-Agrawal2011]

N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. J Comp Chem, 32:2319-2327, 2011. doi:10.1002/jcc.21787. http://www.mdanalysis.org

[Polyhach2011] (1,2)

Y. Polyhach, E. Bordignon, and G. Jeschke. Rotamer libraries of spin labelled cysteines for protein studies. Phys. Chem. Chem. Phys., 13:2356-2366, 2011. doi: 10.1039/C0CP01865A.

[Stelzl2014]

L. S. Stelzl, P. W. Fowler, M. S. P. Sansom, and O. Beckstein. Flexible gates generate occluded intermediates in the transport cycle of LacY. J Mol Biol, 426:735-751, 2013. doi: 10.1016/j.jmb.2013.10.024