The different dependencies observed for BASP1 ( Fig. 6) convincingly illustrate the potential of the methodology

to probe differential side-chain dynamics in IDPs. In future applications it is planned to extend the methodology to higher frequency dimensions exploiting non-uniform sampling techniques. Details of the sequence and results will be reported elsewhere (manuscript in preparation). IDPs are involved in fundamental biological (physiological) processes and are, therefore, of great interest to medical and pharmaceutical PF-02341066 order research [40]. Their inherent structural flexibility allows them to accommodate different binding partners exploiting different binding modes (e.g. folding-upon binding or formation of fuzzy complexes). Despite limitations due to their unfolded nature several successful studies have been reported demonstrating that IDPs are indeed amenable to drug development programs [41]. However, the dynamic nature of IDPs impairs the application of conventional structure-based drug design strategies. The lack of 3D structures as bottleneck in the pharmaceutical industry is widely recognized and was recently addressed by a combination of information-rich

selleck chemicals NMR and new protein sequence analysis tools (e.g. meta-structure) [34] and [42]. It was already demonstrated that the meta-structure analysis provides valid starting points for ligand development by revealing information about the construction of suitable fragment libraries and ligand binding modes [42]. Given the fact that only primary sequence information is needed, valuable applications also to ligand

identification for IDPs can be anticipated. A prototypical application to IDPs is given with the example of Osteopontin (OPN), an extracellular matrix protein associated with metastasis of several kinds of cancer. The meta-structure analysis revealed a similarity to the (folded) protein Staurosporine antithrombin. The naturally occurring, highly sulfated glycosaminoglycan heparin is an established ligand for antithrombin. Heparin binding to OPN was verified using NMR spectroscopy [37]. It was shown that heparin binding to OPN causes significant and specific chemical shift changes. This example illustrates how the combined usage of meta-structure and NMR data can be used to create valid starting points for drug development programs involving IDPs. In subsequent steps NMR spectroscopy can be used to provide additional information about binding modes and orientations of bound ligands [42]. Naturally, a comprehensive analysis has to address both structural and dynamical changes. In a recent NMR analysis we have employed both PRE and 15N NMR relaxation data to analyze the interaction between the IDP Osteopontin (OPN) and heparin (manuscript in preparation). Fig. 7 shows differential PREs and 15N relaxation parameters (15N-T2 and 1HN–15N NOE).