Interdomain Dynamics Explored by Paramagnetic NMR

Russo, Luca; Maestre-Martínez, Mitcheell; Wolff, Sebastian; Becker, Stefan; Griesinger, Christian

doi:10.1021/ja408143f

Cited by 68 publications

(87 citation statements)

References 83 publications

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“…These methods require the introduction of spin-labels (Tamm et al 2007;Schiemann and Prisner 2007;Keizers and Ubbink 2011;Yagi et al 2011;Loscha et al 2012;Russo et al 2013) attached to or within a protein. In NMR-spectroscopic studies, attachment of a single paramagnetic lanthanide center (Keizers and Ubbink 2011) with an anisotropic Dv-tensor (Bertini et al 2002) has been employed to obtain PCSs, which report on the distance and radial coordinates of a nuclear spin with respect to the paramagnetic center.…”

Section: Introductionmentioning

confidence: 99%

Encoded loop-lanthanide-binding tags for long-range distance measurements in proteins by NMR and EPR spectroscopy

et al. 2015

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We recently engineered encodable lanthanide binding tags (LBTs) into proteins and demonstrated their applicability in Nuclear Magnetic Resonance (NMR) spectroscopy, X-ray crystallography and luminescence studies. Here, we engineered two-loop-LBTs into the model protein interleukin-1b (IL1b) and measured 1 H, 15 Npseudocontact shifts (PCSs) by NMR spectroscopy. We determined the Dv-tensors associated with each Tm 3? -loaded loop-LBT and show that the experimental PCSs yield structural information at the interface between the two metal ion centers at atomic resolution. Such information is very valuable for the determination of the sites of interfaces in protein-protein-complexes. Combining the experimental PCSs of the two-loop-LBT construct IL1b-S2R2 and the respective single-loop-LBT constructs IL1b-S2, IL1b-R2 we additionally determined the distance between the metal ion centers. Further, we explore the use of two-loop LBTs loaded with Gd 3? as a novel tool for distance determination by Electron Paramagnetic Resonance spectroscopy and show the NMR-derived distances to be remarkably consistent with distances derived from Pulsed Electron-Electron Dipolar Resonance.

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Section: Introductionmentioning

confidence: 99%

Encoded loop-lanthanide-binding tags for long-range distance measurements in proteins by NMR and EPR spectroscopy

et al. 2015

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“…Characterization of such rearrangements and the relevant conformational states can provide important clues about the mechanisms underlying biological function. This however is a challenging task because the system is underdetermined, implying a large degeneracy in the reconstructed solutions, and requires extensive experimental work often involving multiple techniques (Bonvin and Brunger, 1996; Choy and Forman-Kay, 2001; Svergun et al, 2001; Burgi et al, 2001; Clore and Schwieters, 2004; Schroeder et al, 2004; Iwahara et al, 2004; Bertini et al, 2004a; Blackledge, 2005; Lindorff-Larsen et al, 2005; Fragai et al, 2006; Tolman and Ruan, 2006; Boehr et al, 2006; Ryabov and Fushman, 2006; Chen et al, 2007; Bernadò et al, 2007; Bertini et al, 2007; Ryabov and Fushman, 2007; Lange et al, 2008; Hulsker et al, 2008; Korzhnev and Kay, 2008; Nodet et al, 2009; Boehr et al, 2009; Stelzer et al, 2009; Huang and Grzesiek, 2010; Fisher et al, 2010; Bashir et al, 2010; Rinnenthal et al, 2011; Bothe et al, 2011; Fisher and Stultz, 2011; Berlin et al, 2013; Russo et al, 2013; Guerry et al, 2013; Kukic et al, 2014; Ravera et al, 2014; Torchia, 2015). Therefore, it is important to know the information content provided by various experimental methods in order to decide on an optimal set of experiments a priori .…”

Section: Introductionmentioning

confidence: 99%

Information content of long-range NMR data for the characterization of conformational heterogeneity

et al. 2015

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Long-range NMR data, namely residual dipolar couplings (RDCs) from external alignment and paramagnetic data, are becoming increasingly popular for the characterization of conformational heterogeneity of multidomain biomacromolecules and protein complexes. The question addressed here is how much information is contained in these averaged data. We have analyzed and compared the information content of conformationally averaged RDCs caused by steric alignment and of both RDCs and pseudocontact shifts caused by paramagnetic alignment, and found that, despite the substantial differences, they contain a similar amount of information. Furthermore, using several synthetic tests we find that both sets of data are equally good towards recovering the major state(s) in conformational distributions.

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“…These multiple sets can be obtained by alternative replacement of the paramagnetic ion with other paramagnetic ions with different magnetic susceptibility anisotropy tensors or by attaching, once at a time, paramagnetic tags in different points (Bertini et al 2001;Pintacuda et al 2006;Otting 2010;Liu et al 2012). Finally, PCSs and RDCs can provide information on interdomain mobility in multidomain proteins or internal mobility in protein-protein complexes, whenever internal consistency of all PCSs and RDCs arising from each paramagnetic metal with its own magnetic susceptibility anisotropy tensor cannot be achieved by assuming a single rigid structure (Gardner et al 2005;Longinetti et al 2006;Bertini et al 2007Bertini et al , 2010Bertini et al , 2012bRusso et al 2013;Ravera et al 2014;Andralojc et al 2014).…”

Section: Introductionmentioning

confidence: 99%

FANTEN: a new web-based interface for the analysis of magnetic anisotropy-induced NMR data

et al. 2014

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Pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) arising from the presence of paramagnetic metal ions in proteins as well as RDCs due to partial orientation induced by external orienting media are nowadays routinely measured as a part of the NMR characterization of biologically relevant systems. PCSs and RDCs are becoming more and more popular as restraints (1) to determine and/or refine protein structures in solution, (2) to monitor the extent of conformational heterogeneity in systems composed of rigid domains which can reorient with respect to one another, and (3) to obtain structural information in protein-protein complexes. The use of both PCSs and RDCs proceeds through the determination of the anisotropy tensors which are at the origin of these NMR observables. A new user-friendly web tool, called FANTEN (Finding ANisotropy TENsors), has been developed for the determination of the anisotropy tensors related to PCSs and RDCs and has been made freely available through the WeNMR ( http://fanten-enmr.cerm.unifi.it:8080 ) gateway. The program has many new features not available in other existing programs, among which the possibility of a joint analysis of several sets of PCS and RDC data and the possibility to perform rigid body minimizations.

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Interdomain Dynamics Explored by Paramagnetic NMR

Cited by 68 publications

References 83 publications

Encoded loop-lanthanide-binding tags for long-range distance measurements in proteins by NMR and EPR spectroscopy

Encoded loop-lanthanide-binding tags for long-range distance measurements in proteins by NMR and EPR spectroscopy

Information content of long-range NMR data for the characterization of conformational heterogeneity

FANTEN: a new web-based interface for the analysis of magnetic anisotropy-induced NMR data

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