In order to overcome these limitations, it was therefore suggested to use meta-structure derived compactness data to identify suitable sites of spin label attachment .
Since residue-specific compactness values quantify the spatial environment of individual residues in 3D protein structures the sites of spin label attachment should therefore be selected based on small compactness values as for these regions tight side chain interactions or packing can safely be neglected. Fig. 4 shows compactness and PRE data for the IDP Osteopontin . In addition to their innate conformational flexibility Epigenetic inhibitor chemical structure (plasticity) IDPs are also sensitive to changes of environmental parameters (e.g. temperature, pH values, presence of interacting ligands). For example, it was shown that although the thymic hormone Prothymosin-α and α-Synuclein remain natively unfolded under acidic conditions, local secondary structure propensities in proximity to acidic residues
change upon variations in pH and the conformational ensemble becomes enriched in compact structures with pronounced local rigidity of the protein backbone. In a recent study, we showed that intrinsically disordered human proteins fold under acidic Doramapimod price conditions into more compact structures with higher α-helical content largely due to reduced electrostatic repulsion of negatively charged side chains . This finding suggests that IDP recognition elements can be stabilized by favorable electrostatic interactions across the interaction interface check details (between proton acceptor located at the surface of the IDP and the acidic proton donor of the interaction partner). In this study NMR spectroscopy was used to verify theoretical predictions . Structural compaction was experimentally verified employing PFG-DOSY experiments together with SOFAST-HMQC techniques (Fig. 5) . SOFAST-HMQC experiments efficiently
probe 1H–1H spin diffusion or NOE effects, when a selective inversion pulse (Hsat) is applied on aliphatic protons before the start of the pulse sequence. In this experiment, two data sets are recorded with (Isat) and without (Iref) the inversion pulse Hsat. The intensity ratio (λNOE = Isat/Iref) depends on spin diffusion effects and quantitatively probes the structural dynamics of proton spin networks . In well-structured, globular proteins spin diffusion is highly efficient leading to λNOE ≪ 1, while in loosely folded proteins (random coils, molten globules) λNOE ≈ 1. In BASP1 (Brain Acid Soluble Protein 1) a significant decrease of λNOE was observed upon lowering pH (0.75–0.60) corroborating the predicted structural compaction of BASP1 under acidic conditions. Given its ease of implementation and reliability of quantitative analysis the SOFAST-HMQC technique will be important for future studies of IDPs’ structural adaptations under varying experimental conditions.