Abstract
The transient folding of domain 4 of an E. coli RNA polymerase sigma^{70} subunit (r{text{EC}}sigma_{4}^{70}) induced by an increasing concentration of 2,2,2-trifluoroethanol (TFE) in an aqueous solution was monitored by means of CD and heteronuclear NMR spectroscopy. NMR data, collected at a 30 % TFE, allowed the estimation of the population of a locally folded r{text{EC}}sigma_{4}^{70} structure (CSI descriptors) and of local backbone dynamics (15N relaxation). The spontaneous organization of the helical regions of the initially unfolded protein into a TFE-induced 3D structure was revealed from structural constraints deduced from 15N- to 13C-edited NOESY spectra. In accordance with all the applied criteria, three highly populated α-helical regions, separated by much more flexible fragments, form a transient HLHTH motif resembling those found in PDB structures resolved for homologous proteins. All the data taken together demonstrate that TFE induces a transient native-like structure in the intrinsically disordered protein.Electronic supplementary materialThe online version of this article (doi:10.1007/s00249-014-0987-4) contains supplementary material, which is available to authorized users.
Highlights
Disordered proteins (IDPs) are involved in the essential processes of the living cell (Pancsa and Tompa 2012)
Does ECσ470 in a solution resemble a sigma factor from E. coli RNA polymerase (RNAP) much more than the homologous domains of Thermus aquaticus (Campbell et al 2002) and Thermus thermophilus (Vassylyev et al 2002), or the solution structure of T. maritime (Lambert et al 2004), and that of a distant one, σ454, from Axuifex aeolicus (2ahq) (Doucleff et al 2005)? In this work, on the basis of further CD and NMR studies, we show a lowresolution model of E. coli σ470 fold induced by a 30 % TFE, and we analyze the internal motions of the protein backbone with the use of 15N relaxation
It should be stressed that 100 mM NDSB195 does not preserve the protein structure for rECσ470 concentrations exceeding 2 μM, so this solvent system could not be used for heteronuclear NMR studies
Summary
Disordered proteins (IDPs) are involved in the essential processes of the living cell (Pancsa and Tompa 2012). Their sequences are generally enriched in polar and charged residues, but deficient in hydrophobic groups (Uversky 2002, 2011; Das and Pappu 2013). Free IDPs in a solution are highly flexible and do not display a stable secondary/tertiary structure (Dyson and Wright 2005; Tompa 2002). A global and/or local flexibility provides the structural plasticity of IDPs, facilitating specific interactions with various partners (Wright and Dyson 2009), the thermodynamics of partner-induced IDP folding must be linked directly to the intrinsic conformational properties (Uversky 2002, 2011; Das and Pappu 2013; Dima and Thirumalai 2004). IDPs, among others, are prominently represented in proteins associated with mRNA processing (Fu 1995; Buljan et al 2012), apoptosis (Rautureau et al 2010), signal transduction (Galea et al 2008; Moncoq et al 2003) and transcription regulation (Tompa 2002; Tompa 2005; Liu et al 2006; Ozbudak et al 2002; Wright and Dyson 1999)
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