Assessing the Coupling in cis between Disordered Regions and Ordered Domains

Abstract

A majority of intrinsically disordered regions occur in cis with ordered domains. This suggests the possibility of functional synergy between ordered domains and disordered regions. Such coupling between distinct modules opens the possibility for increased versatility in protein functions through combinatorial diversity. Despite this, the coupling between ordered domains and disordered regions has been largely unexplored. Here, we build on our growing understanding of the intrinsic conformational preferences of disordered regions to assess the degree and nature of the modulation of these preferences by cis-acting ordered domains. We use SH3/SH2 domains of NcK adapter proteins and disordered linkers attached to these domains as archetypes of ordered domains in cis with disordered regions. We use atomistic simulations to quantify the intrinsic conformational preferences of different linker sequences. In doing so, we establish that sequence permutants of linkers with similar amino acid compositions can have considerably different conformational preferences. We next use a combination of atomistic and coarse grain simulations to interrogate the nature and degree of coupling between disordered regions and ordered domains. In particular, we quantify and compare the extent of conformational coupling between ordered SH2/SH3 domains for different linker sequences of fixed amino acid compositions and linker sequences with different compositions. We show how insights from the resultant conformational phase diagram are relevant for explaining the phase behavior of copolymers of ordered domains connected by linkers and for heterotypic interactions in signaling pathways that are mediated through synergy between SH2/SH3 domains and their disordered linkers.