Journal of Molecular Biology

helical binding motifs mediate protein interactions and fold into α-helix upon binding.

database of 65 helical binding motifs and their helix content in the unbound state.

residual helices predispose the helix structure in the target-bound state.

residues that are involved in target binding also stabilise the helix structure.

leucine and leucine motifs (LxxLL) stabilise the residual helix structure.

Many examples are known of regions of intrinsically disordered proteins that fold into α-helices upon binding to their targets. These helical binding motifs (HBMs) can be partially helical also in the unbound state, and this so-called residual structure can affect binding affinity and kinetics. To investigate the underlying mechanisms governing the formation of residual helical structure, we assembled a dataset of experimental helix contents of 65 peptides containing HBM that fold-upon-binding. The average residual helicity is 17% and increases to 60% upon target binding. The helix contents of residual and target-bound structures do not correlate, however the relative location of helix elements in both states shows a strong overlap. Compared to the general disordered regions, HBMs are enriched in amino acids with high helix preference and these residues are typically involved in target binding, explaining the overlap in helix positions. In particular, we find that leucine residues and leucine motifs in HBMs are the major contributors to helix stabilization and target-binding. For the two model peptides, we show that substitution of leucine motifs to other hydrophobic residues (valine or isoleucine) leads to reduction of residual helicity, supporting the role of leucine as helix stabilizer. From the three hydrophobic residues only leucine can efficiently stabilize residual helical structure. We suggest that the high occurrence of leucine motifs and a general preference for leucine at binding interfaces in HBMs can be explained by its unique ability to stabilize helical elements.

intrinsic disorder

pre-folding

folding-upon-binding

recognition motif

leucine motif

All data is included in Supporting information

© 2024 The Author(s). Published by Elsevier Ltd.