Coupled Folding and Binding with α-Helix-Forming Molecular Recognition Elements

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Abstract
Many protein−protein and protein−nucleic acid interactions involve coupled folding and binding of at least one of the partners. Here, we propose a protein structural element or feature that mediates the binding events of initially disordered regions. This element consists of a short region that undergoes coupled binding and folding within a longer region of disorder. We call these features “molecular recognition elements” (MoREs). Examples of MoREs bound to their partners can be found in the α-helix, β-strand, polyproline II helix, or irregular secondary structure conformations, and in various mixtures of the four structural forms. Here we describe an algorithm that identifies regions having propensities to become α-helix-forming molecular recognition elements (α-MoREs) based on a discriminant function that indicates such regions while giving a low false-positive error rate on a large collection of structured proteins. Application of this algorithm to databases of genomics and functionally annotated proteins indicates that α-MoREs are likely to play important roles protein−protein interactions involved in signaling events.