Understanding Pre-Structured Motifs (PreSMos) in Intrinsically Unfolded Proteins

Abstract

Intrinsically unfolded proteins (IUPs) do not obey the golden rule of structural biology, 3D structure = function, as they manifest their inherent functions without resorting to three-dimensional structures. Absence of a compact globular topology in these proteins strongly implies that their ligand recognition processes should involve factors other than spatially well-defined binding pockets. Heteronuclear multidimensional (HetMulD) NMR spectroscopy assisted with a stable isotope labeling technology is a powerful tool for quantitatively investigating detailed structural features in IUPs. In particular, it allows us to delineate the presence and locations of pre-structured motifs (PreSMos) on a per-residue basis. PreSMos are the transient local structural elements that presage target-bound conformations and act as specificity determinants for IUP recognition by target proteins. Here, we present a brief chronicle of HetMulD NMR studies on IUPs carried out over the past two decades along with a discussion on the functional significance of PreSMos in IUPs.

A pre-structured helix in the intrinsically disordered 4EBP1

“…After the introduction of the PreSMo concept several CU type IDPs originally proposed to undergo the coilhelix IF transition were carefully re-analyzed by NMR and turned out to be MU-types, seriously weakening the basis knowledge supporting the coil -helix IF mechanism. 6 These results pointed out a need to rekindle the early idea of the potential contribution of conformational selection of a PreSMo by a target protein to IDP-target binding. 3 Nonetheless, the IF mechanism has been mostly considered in the IDP field.…”

“…[1][2][3][4][5] As the eventual function of most (B80%) IDPs is to convey biological signals by binding to various types of target molecules, such as proteins, nucleic acids, metals, or lipids, 1,6,7 delineating their target-binding mechanism is important to clearly understand IDP function. Recent studies illustrate that accurate structural knowledge of IDPs may have immediate consequences even for drug development.…”

“…[8][9][10][11] However, a coil -helix structural transition is not likely to occur if a targetbinding segment in a free IDP is already pre-structured in a conformation that presages its target-bound conformation. 6 In such a case conformational selection of the pre-structured segment by a target may be an efficient and more thermodynamically favorable event. Thus, a fundamental question concerns whether IDPs in their free state are totally unstructured down to the level of secondary structures [12][13][14] noting that even fully denatured globular proteins cannot be described by a complete random coil model.…”

“…15 A recent analysis of B50 IDPs and IDRs (intrinsically disordered regions) whose conformational details were characterized by NMR techniques revealed that B70% of them are in a mostly unstructured (MU) state rather than being in a completely unstructured (CU) state. 6 The MU-type IDPs contain the so-called pre-structured motifs (PreSMos), originally coined as local structural (lost) elements, 3 almost all of which serve as the specific determinants for target binding. After the introduction of the PreSMo concept several CU type IDPs originally proposed to undergo the coilhelix IF transition were carefully re-analyzed by NMR and turned out to be MU-types, seriously weakening the basis knowledge supporting the coil -helix IF mechanism.…”

“…17 Early reports also pointed out the pre-structuring of the target-binding segments. 6,16 The human phosphoprotein 4EBP1 is the very first IDP explicitly described to be completely or ''wholly'' disordered, 8,9 which contributed critically to the formation of a coil -helix IF concept. Interestingly, this paradigmatic IDP was not re-analyzed in the context of the PreSMo concept.…”