Protein–Protein Interactions

Ubbink, Marcellus; Savino, Antonella Di

doi:10.1039/9781788013291-00134

Cited by 3 publications

(3 citation statements)

References 94 publications

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“…Therefore, PREs are powerful tools for the detection of minor states or the characterization of ensembles of conformations, such as found in intrinsically disordered proteins or encounter complexes. 33,34,584 At the same time, the strong distance dependence of the PRE adds uncertainties to distance measurements of major conformations, when minor conformations or alternative interactions featuring short distances r IS contribute disproportionally to the observed PRE. Minor species populated as low as 0.1% can be manifested in the observed PRE in this way.…”

Section: Complications In Pre-to-distance Conversionmentioning

confidence: 99%

Paramagnetic Chemical Probes for Studying Biological Macromolecules

et al. 2022

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Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.

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Section: Complications In Pre-to-distance Conversionmentioning

confidence: 99%

Paramagnetic Chemical Probes for Studying Biological Macromolecules

et al. 2022

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“…With restraints from multiple tagging sites, PCSs of backbone amide protons have been shown to be sufficient for 3D structure determinations of proteins (Schmitz et al, 2012;Yagi et al, 2013;Pilla et al, 2016Pilla et al, , 2017Cucuzza et al, 2021). Particularly appealing applications of PCSs have been the structure refinement of polypeptide segments in proteins of known 3D fold (Banci et al, 1996;Crick et al, 2015;Lescanne et al, 2018;Müntener et al, 2020) and the structural characterisation of the interfaces of protein-protein (Pintacuda et al, 2006;Keizers et al, 2010;Kobashigawa et al, 2012;Hass and Ubbink, 2014;de la Cruz et al, 2011;Brewer et al, 2015;Ubbink and Di Savino, 2018) and protein-ligand complexes (Pintacuda et al, 2007;Guan et al, 2013;Chen et al, 2016;Lescanne et al, 2018;Zimmermann et al, 2019), as the long-range nature of PCSs allows the attachment of the H. W. Orton et al: Localising nuclear spins by pseudocontact shifts from a single tagging site metal tags at a distance that is sufficiently far from the site of interest to avoid structural perturbations by the tag.…”

Section: Introductionmentioning

confidence: 99%

Localising nuclear spins by pseudocontact shifts from a single tagging site

et al. 2022

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Abstract. Ligating a protein at a specific site with a tag molecule containing a paramagnetic metal ion provides a versatile way of generating pseudocontact shifts (PCSs) in nuclear magnetic resonance (NMR) spectra. PCSs can be observed for nuclear spins far from the tagging site, and PCSs generated from multiple tagging sites have been shown to enable highly accurate structure determinations at specific sites of interest, even when using flexible tags, provided the fitted effective magnetic susceptibility anisotropy (Δχ) tensors accurately back-calculate the experimental PCSs measured in the immediate vicinity of the site of interest. The present work investigates the situation where only the local structure of a protein region or bound ligand is to be determined rather than the structure of the entire molecular system. In this case, the need for gathering structural information from tags deployed at multiple sites may be queried. Our study presents a computational simulation of the structural information available from samples produced with single tags attached at up to six different sites, up to six different tags attached to a single site, and in-between scenarios. The results indicate that the number of tags is more important than the number of tagging sites. This has important practical implications, as it is much easier to identify a single site that is suitable for tagging than multiple ones. In an initial experimental demonstration with the ubiquitin mutant S57C, PCSs generated with four different tags at a single site are shown to accurately pinpoint the location of amide protons in different segments of the protein.

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“…The use of paramagnetic metal tags for biomolecular PCS NMR was covered in numerous general reviews, − and specific aspects like dynamics, conformational changes, sparse data, in-cell NMR, tag design, protein interactions, − and domain motions have also been addressed. The current and future role of PCSs for structural life sciences was discussed in perspective contributions by Otting, , Ubbink, and others. − Several excellent recent monographs embed PCSs into the context of other biomolecular NMR methods. − …”

Section: Introductionmentioning

confidence: 99%

Pseudocontact Shifts in Biomolecular NMR Spectroscopy

et al. 2022

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Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole–dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.

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Protein–Protein Interactions

Cited by 3 publications

References 94 publications

Paramagnetic Chemical Probes for Studying Biological Macromolecules

Paramagnetic Chemical Probes for Studying Biological Macromolecules

Localising nuclear spins by pseudocontact shifts from a single tagging site

Pseudocontact Shifts in Biomolecular NMR Spectroscopy

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