Identifying intrinsically disordered protein regions likely to undergo binding-induced helical transitions

Abstract

Many proteins contain intrinsically disordered regions (IDRs) lacking stable secondary and ordered tertiary structure. IDRs are often implicated in macromolecular interactions, and may undergo structural transitions upon binding to interaction partners. However, as binding partners of many protein IDRs are unknown, these structural transitions are difficult to verify and often are poorly understood. In this study we describe a method to identify IDRs that are likely to undergo helical transitions upon binding. This method combines bioinformatics analyses followed by circular dichroism spectroscopy to monitor 2,2,2-trifluoroethanol (TFE)-induced changes in secondary structure content of these IDRs. Our results demonstrate that there is no significant change in the helicity of IDRs that are not predicted to fold upon binding. IDRs that are predicted to fold fall into two groups: one group does not become helical in the presence of TFE and includes examples of IDRs that form β-strands upon binding, while the other group becomes more helical and includes examples that are known to fold into helices upon binding. Therefore, we propose that bioinformatics analyses combined with experimental evaluation using TFE may provide a general method to identify IDRs that undergo binding-induced disorder-to-helix transitions.

Conformational flexibility of BECN1: Essential to its key role in autophagy and beyond

“…76 Similar methodology shows that residues 76-105, which include the second Anchor region, is likely also an aMoRF. 76 Flexible helical domain (residues 141-171)…”

“…The BH3D, comprising residues 105‐130 and encompassing the third Anchor region, was the first BECN1 αMoRF identified . The BH3D is disordered, even in BECN1 constructs including adjacent structured domains, but folds into a helix upon binding to various BCL2 homologs or in the presence of 2,2,2‐trifluoroethanol (TFE), a chemical that induces helicity in αMoRFs even in the absence of their binding partners . Similar methodology shows that residues 76–105, which include the second Anchor region, is likely also an αMoRF …”

“…It has now been conclusively shown that the BECN1 BH3D is part of a larger IDR . Notably, residues toward the BH3D C‐terminus (residues 116‐123) comprise an Anchor region . Mutation of these Anchor region residues abolishes BCL2 binding and abrogates binding‐induced helical transition within the BH3D .…”

The Un(f)told Story of General Anesthesia

“…The number and relative proportion of hydrophobic and disorder‐promoting polar/charged residues may seriously alter, amplify, or reduce the helix‐stabilization potency of fluoroalcohols. Several examples are known in which the limited or missing structure‐forming activity of either TFE or HFIP on particular ID sequences has been demonstrated …”

“…As already demonstrated, helicogenicity is the inherent feature of these compounds, that is, the induction and stabilization of helix structures, especially for ID sequences (Table ). By exploiting this ability, a TFE‐based general method was developed to unveil the ID preferences of peptides and proteins . Even though fluorinated cosolvents are generally considered as helix‐inducing agents, they can promote and stabilize molten globule‐like folding intermediates, β‐hairpin‐like structures, and even β‐sheets …”