EXPERIMENTAL FIGURE 3-8 Intrinsically disordered proteins: mechanisms of binding to well-ordered proteins and identification based on hydrophobicity and net charge. (a) The binding of an intrinsically disordered protein (PUMA, blue) to a well-ordered protein (MCL1, gray) results in the formation of a well-defined structure in the previously disordered protein. PUMA and MCL1 are intracellular proteins that can influence the regulated process of cell death called apoptosis (see Chapter 21). Two mechanisms have been proposed for generating a bound complex in which both proteins are structured: conformational selection (top pathway) and induced fit (bottom pathway). In conformational selection, the disordered protein (PUMA) occasionally and transiently adopts in solution the structure it would have in the bound state. The well-ordered binding partner (MLC1) can then bind to (select) PUMA in that transient, ordered conformation, forming a relatively stable bound complex. In induced fit, the disordered protein begins to bind to the well-ordered partner while still disordered and then, while bound, is induced to form the ordered conformation present in the relatively stable, heterodimeric complex. Recent experiments suggest that the induced fit mechanism best describes the binding of PUMA and MCL1. (b) The sequences of 275 well-ordered, monomeric globular proteins (gray squares) and 91 intrinsically disordered proteins (black and yellow circles) were used to calculate the mean hydrophobicity per residue in each protein using a scale of 0 (least hydrophobic) to 1 (most hydrophobic, x axis), and the mean net charge per residue at pH 7.0 (y axis). With only three exceptions (black circles), the proteins define two distinct distributions: low hydrophobicity, high net charge (intrinsically disordered, yellow circles) and high hydrophobicity, low net charge (well-ordered, gray squares). The three disordered proteins (black circles) that overlap with the well-ordered population each contain substantial segments predicted to be disordered (low hydrophobicity, high net charge) that apparently overwhelm the rest of the proteins’ sequences that might otherwise result in a well-ordered conformation.

[Part (a) from Rogers, J. et al., “Folding and Binding of an Intrinsically Disordered Protein: Fast, but Not ‘Diffusion-Limited,’” J. Am. Chem. Soc., 2013, 135 (4), pp1415-1422. http://pubs.acs.org/doi/pdf/10.1021/ja309527h. Part (b) data from V. N. Uversky, J. R. Gillespie, and A. L. Fink, 2000, Proteins 41:415–427.]