SS-map: Visualizing cooperative secondary structure elements in protein ensembles

Intrinsically Disordered Proteins
Jelisa IglesiasR Crehuet

Abstract

We present SS-map, a tool to visualize the secondary structure content of ensembles of proteins. When generating ensembles of intrinsically disordered proteins, we lose the understanding a single native structure gives for folded proteins. It then becomes difficult to visualize the composition of the ensembles or to detect transient helices such as MoRFs. Conformational propensities for single residues also hide the nature of cooperative structures. Here we show how SS-map describes folded and unfolded ensembles of some peptides and gives a new view of the ensembles used to describe intrinsically disordered proteins with residual structure in computational and NMR experiments. This tool is implemented in an open-source python code located at code.google.com/p/ss-map.

References

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Citations

Mar 7, 2020·Proceedings of the National Academy of Sciences of the United States of America·Alexander E ConicellaNicolas L Fawzi
May 26, 2018·The Journal of Physical Chemistry. B·Gül H ZerzePablo G Debenedetti
Aug 23, 2017·The Journal of Physical Chemistry. B·Gregory L DignonJeetain Mittal

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Methods Mentioned

BETA
NMR
protein folding
of circular

Software Mentioned

matplotlib
Stride
SS
Biopython
map
Flexible Meccano
Profasi
Flexible Meccano code

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