Protein Structural Ensembles Visualized by Solvent Paramagnetic Relaxation Enhancement

Abstract

A protein can be in different conformations when fulfilling its function. Yet depiction of protein structural ensembles remains difficult. Here we show that the accurate measurement of solvent paramagnetic relaxation enhancement (sPRE) in the presence of an inert paramagnetic cosolute allows the assessment of protein dynamics. Demonstrated with two multi-domain proteins, we present a method to characterize protein microsecond-millisecond dynamics based on the analysis of the sPRE. Provided with the known structures of a protein, our method uncovers an ensemble of structures that fully accounts for the observed sPRE. In conjunction with molecular dynamics simulations, our method can identify protein alternative conformation that has only been theorized before. Together, our method expands the application of sPRE beyond structural characterization of rigid proteins and complements the established PRE NMR technique.

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

“…The most commonly used paramagnetic agent for measuring sPRE data is the inert complex Gd(DTPA-BMA) (gadolinium diethylenetriaminepenta-acetic acid bismethylamide, commercially available as ‘Omniscan’), that is known to not specifically interact on protein surfaces (Guttler et al 2010; Madl et al 2009, 2011; Pintacuda and Otting 2002; Wang et al 2012; Respondek et al 2007; Zangger et al 2009; Göbl et al 2010). Previously, we and others could show that sPRE data provide in-depth structural and dynamic data for IDP analysis (Madl et al 2009; Sun et al 2011; Gong et al 2017; Emmanouilidis et al 2017; Johansson et al 2014). For example, sPRE data helped to characterize α-helical propensity in a previously postulated flexible region in the folded 42 kDa maltodextrin binding protein (Madl et al 2009), and dynamic ligand binding to the human “survival of motor neuron” protein (Emmanouilidis et al 2017).…”

“…We and others have proposed applications of soluble paramagnetic agents to obtain structural information by NMR without any modifications of the molecules of interest (Gobl et al 2014; Guttler et al 2010; Hartlmuller et al 2016; Hocking et al 2013; Madl et al 2009, 2011; Respondek et al 2007; Zangger et al 2009; Pintacuda and Otting 2002; Bernini et al 2009; Wang et al 2012; Sun et al 2011; Gong et al 2017; Gu et al 2014; Hartlmuller et al 2017). The addition of soluble paramagnetic compounds leads to a concentration-dependent and therefore tunable increase of relaxation rates, the so-called paramagnetic relaxation enhancement (here denoted as solvent PRE, sPRE; also known as co-solute PRE, Fig.…”

“…The nuclei on the surface are affected the strongest by the sPRE effect, and this approach has been shown to correlate well with biomolecular structure in the case of proteins and RNA (Madl et al 2009; Pintacuda and Otting 2002; Bernini et al 2009; Hartlmuller et al 2017). sPREs have gained popularity for structural studies of biomolecules, including in the structure determination of proteins (Madl et al 2009; Wang et al 2012), docking of protein complexes (Madl et al 2011), and qualitative detection of dynamics (Hocking et al 2013; Sun et al 2011; Gong et al 2017; Gu et al 2014).

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NMR-based investigations into target DNA search processes of proteins

“…Random collisions with paramagnetic co-solute molecules (e.g., gadolinium-diethylenetriamine pentaacettic acid bismethylamide [Gd-DTPA-BME] and 4-hydroxy-2,2,6,6-tetramethylpiperidin-1-oxyl [TEMPOL]) at relatively high concentrations cause sizable PRE for 1 H nuclei of proteins [80–84]. This type of PRE, referred to as solvent PRE, is stronger for 1 H nuclei near the molecular surface accessible to solvent and can be used to identify molecular interfaces.…”

Conformational Space Sampled by Domain Reorientation of Linear Diubiquitin Reflected in Its Binding Mode for Target Proteins

“…PREs are sensitive to distances between paramagnetic metal ions and the observed nuclei, [17] while RDCs report on the orientation of internuclear vectors, such as NÀ H in a molecular frame. PCSs depend on both the distance and orientation.…”