SS-map

*Correspondence to: Ramon Crehuet; Email: [email protected] Submitted: 05/07/13; Revised: 06/03/13; Accepted: 06/08/13 http://dx.doi.org/10.4161/idp.25323 Citation: Iglesias J, Sanchez-Martinez M, Crehuet R. SS-map: Visualizing cooperative secondary structure elements in protein ensembles. Intrinsically Disordered Proteins 2013; 1:e25323; http://dx.doi.org/10.4161/idp.25323 Intrinsically Disordered Proteins (IDPs) exist in solution as ensembles of structures. This raises a challenge to us, humans, as we tend to understand structures by visualizing them, and we lack ways to represent ensembles. Ensembles contain structural information, even when IDPs satisfy random-coil statistics. Some regions of IDPs can adopt secondary structures, at least for a transient time. This can be probed with experimental techniques such as NMR, in particular with Residual Dipolar Couplings (RDCs). Structured regions, termed MoRFs, are key to recognition processes mediated by coupled folding-binding events. The interpretation of data derived from NMR is usually done by stating that a certain segment of the protein chain adopts a certain secondary structure in a percentage of the total ensemble, but this conveys information in a difficult way for scientists not familiar with these interpretations. How can the ensembles be represented to better unveil their structure? When studying protein folding, ensembles coming from computations are represented along the reaction coordinate of native contacts. This shows that for many (small) proteins, folding is a 2-state process. Thus, it is a cooperative event where most of the ensemble at a given temperature is either folded or unfolded. Victor Muñoz has pioneered the study of downhill folders, which fold in a progressive manner. How do MoRFs of IDPs behave? Contact order discriminates between 2-state and downhill folders, but it cannot be used in IDPs because it is based on the 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 SS-map Visualizing cooperative secondary structure elements in protein ensembles