So far, however, paramagnetic relaxation enhancement (PREs) was the most common experimental parameter used for the analysis of IDPs’ tertiary structures in solution. The presence of the paramagnetic spin label (e.g. nitroxide moiety, TEMPO or MTSL) leads to an enhancement

in the transverse relaxation rates R2 depending on the inverse sixth power of the distance (1/r6) between the unpaired electron and the observed nucleus. For the quantitative analysis of PRE data two approaches have been proposed. In the first approach PRE data are converted into distances using well-established methodology [28] that can subsequently be used in, for example, MD simulations to calculate conformational ensembles [29]. A second approach involves a more sophisticated selleck chemical extended model-free model for the time–dependency of PRE effects [25]. Several applications to IDPs have been reported demonstrating the validity of the approach [30], [31], [32] and [33]. Despite the popularity and the robustness of the PRE approach applications to IDPs are still far from trivial. Firstly, the identification of suitable spin label attachment sites without prior knowledge of the compact

structure is not a trivial task as the introduction of the spacious spin label at positions that are relevant for the compact tertiary structure will inevitably perturb the structures. In the worst case, as observed for globular proteins, single point mutations selleck chemicals llc can have detrimental effects on the structural stability of proteins. Thus, additional, http://www.selleck.co.jp/products/Nutlin-3.html entirely primary sequence-based analysis tools are

needed for the reliable definition of attachment sites. Secondly, it has been shown that the pronounced distance dependence of PREs can lead to significant bias in the derived ensemble, although this can be partly improved by invoking independent, complementary experimental data (e.g. SAXS) [30]. Recent studies provided some insight into the molecular details of the conformational ensembles populated by IDPs in solution and call for a reassessment of the binary description scheme proposed for proteins lacking a stable tertiary structure [34]. Although proteins differ in terms of tertiary structure stability both ordered and disordered proteins share similar protein folding funnels encoded by the primary sequence leading to distinct residue–residue interaction patterns. The fundamental differences between ordered and disordered proteins are thus merely the heights of energy barriers and the different distributions of thermally accessible conformational substates. As globular proteins can partly populate different unfolded states, conversely in structural ensembles of disordered proteins a significant number of compact structures can also exist stabilized by enthalpically favored long-range interaction patterns similar to stable protein folds.