Comparative Analysis of Intrinsically Disordered Proteins

Recent experimental results and bioinformatic analyses suggest that many proteins or protein regions are lacking a defined tertiary structure and are thus `unstructured` or `intrinsically disordered` (IDPs/IDRs). These proteins exist and function as rapidly interconverting structural ensembles Bioinformatics predictors suggest that about 10-35% of the residues in prokaryotic proteins and about 15-45% of residues in eukaryotic proteomes fall into locally disordered regions. IDPs/IDRs function either directly by way of their disorder or via molecular recognition, when they bind to a partner molecule and undergo induced folding upon binding. These binding modes confer several functional advantages to the IDPs over globular proteins, when they can `reach out` for interaction partners in a mechanism, which can be described as `fly-casting` Molecular recognition is most often associated with short peptide-like recognition motifs, which are often found in regions of local disorder. These recognition motifs do show certain general features. They are strongly correlated with local structural disorder, and they are enriched in hydrophobic amino acids interspersed with flexible and charged residues, which allow for flexibility in their free state. IDPs are also represented in amyloidogenic regions of proteins which are often exposed hydrophobic stretches of disordered chains and thus prone to aggregation and fibril formation. Additionally, linear epitopes (antigenic regions) are short peptide stretches recognized by antibodies of the immune system. These regions also appear to occur in locally disordered regions and correlate with local hydrophobicity. To understand how these opposing demands have shaped the three motif types, we plan to initiate a comparative and collaborative research project, based on combining computational and experimental structural analyses. In these, we plan to (i) assemble and compare datasets of the three motif types with regards to specific features of sequence and dynamics, (ii) predict and evaluate their structural and meta-structural similarities and differences, and (iii) investigate differences in their structural propensities and dynamics by NMR and studying effects of mutations on their interaction preferences, complemented by biophysical characterization of their interacting potential. Our results will unveil thus far hidden, subtle elements of sequence/structure relationships in the three types of short binding modules, which will have benefits of IDP research, motif prediction and its application in biomedicine.

Many proteins or protein regions are lacking a defined tertiary structure and are thus 'unstructured' or 'intrinsically disordered' (IDPs/IDRs). These proteins exist and function as dynamically interconverting structural ensembles. About 10-35% of the residues in prokaryotic proteins and about 15-45% of residues in eukaryotic proteomes fall into locally disordered regions. Due to their lack of a defined structure NMR is the only technique capable of characterizing them at atomic resolution. Using NMR as the principal research tool in 'unstructured biology' it is possible to discover regions of partial or residual structure in such proteins. In some cases, IDPs can fold upon binding i.e. they assume a structure in the presence of a suitable binding partner. A number of such protein motifs were studied in this project to investigate to what extent this structure of the complex is already encoded and present in the free form. From the study of a few examples, it could be concluded that NMR observables in the free form point already towards their values expected for their complexed form and some structure is already preformed.