NMR characterization of solvent accessibility and transient structure in intrinsically disordered proteins

Abstract

In order to understand the conformational behavior of intrinsically disordered proteins (IDPs) and their biological interaction networks, the detection of residual structure and long-range interactions is required. However, the large number of degrees of conformational freedom of disordered proteins require the integration of extensive sets of experimental data, which are difficult to obtain. Here, we provide a straightforward approach for the detection of residual structure and long-range interactions in IDPs under near-native conditions using solvent paramagnetic relaxation enhancement (sPRE). Our data indicate that for the general case of an unfolded chain, with a local flexibility described by the overwhelming majority of available combinations, sPREs of non-exchangeable protons can be accurately predicted through an ensemble-based fragment approach. We show for the disordered protein α-synuclein and disordered regions of the proteins FOXO4 and p53 that deviation from random coil behavior can be interpreted in terms of intrinsic propensity to populate local structure in interaction sites of these proteins and to adopt transient long-range structure. The presented modification-free approach promises to be applicable to study conformational dynamics of IDPs and other dynamic biomolecules in an integrative approach. Electronic supplementary material The online version of this article (10.1007/s10858-019-00248-2) contains supplementary material, which is available to authorized users.

Metal‐Chelated Polymer Nanodiscs for NMR Studies

“…Removing the salt increases the strength of the interactions between the nanodiscs and G‐quadruplexes and consequently increases the PRE effect (Figure ). This interesting result suggests that DOTA functionalized nanodiscs could potentially be used to structurally and dynamically probe surfaces of biomolecules similar to previously applied solvent PRE techniques …”

“…This interesting result suggests that DOTAf unctionalized nanodiscs could potentially be used to structurally and dynamically probe surfaces of biomolecules similar to previously applied solvent PRE techniques. [36][37][38][39][40] In conclusion, we have demonstrated the functionalization of am etal-chelating polymer and its ability to form nanodiscs,w hich can be used as as table,r elatively noninteracting system for PRE enhancement of biomolecules for fast NMR acquisition. We show,u sing inverse recovery experiments,u pt oa7 decrease of T 1 rates of polymerlipid nanodiscs.W ea lso show the compatibility of nanodiscs and structured DNAm olecules (G-quadruplexes) and up to 3 reduction in T 1 times.W ee xpect this approach to be valuable in the NMR structural studies of large size RNAthat exhibit avery long T 1 values for protons; [41] and could enable multidimensional NMR experimental studies on membraneassociated peptides and proteins that may not be available in large quantity and/or sensitive to heat for long data acquisition.…”

Multiple regulatory intrinsically disordered motifs control FOXO4 transcription factor binding and function

“…b-catenin binds multiple sites on FOXO4 involving the FH domain and the intrinsically disordered C terminus Human FOXO4 is composed of a short N-terminal disordered region (residues 1-85) followed by a folded DNA binding domain, the FH domain (residues 91-188) and a long, disordered, C-terminal region (residues 189-505) (Bourgeois and Madl, 2018;Hartlm€ uller et al, 2019). Among the FOXO proteins, three disordered regions localized within the N and C termini have been reported to be conserved and called CR1 (residues 16-40 in FOXO4), CR2 (residues 278-374 in FOXO4), and CR3 (469-503 in FOXO4), respectively (Wang et al, 2012) (Figure 1A).…”

Trendbericht: Kernmagnetische Resonanz

“…34) Weitere Entwicklungen mit paramagnetischen Gruppen sind etwa die ultraempfindliche aminosäurespezifische Detektion durch Gadolinium-Markierungen, 35) die 300-fache Empfindlichkeitssteigerung bei der Detektion der Iminoprotonen in RNA und DNA durch hyperpolarisiertes Wasser 36) sowie die Detektion von Lösungsmittelzugänglichkeit und damit vorübergehend existierender Strukturelemente in intrinsisch ungeordneten Proteinen (IDPs) durch Gadolinium-dotiertes Wasser. 37 41) Kürzlich ist es gelungen, die Struktur der transmembranen Domäne und einer Wirkstoffbindungsstelle des Sars-Cov-2-Virus-Hüllproteins E mit 2,1 Å Genauigkeit zu bestimmen. 42) An Bedeutung gewinnt die direkte Kombination von MAS-NMR mit Kryoelektronmikroskopie (Cryo-EM).…”