Rigid, Highly Reactive and Stable DOTA-like Tags Containing a Thiol-Specific Phenylsulfonyl Pyridine Moiety for Protein Modification and NMR Analysis*

Excellent Fe(II) Binding Tag in Protein Paramagnetic NMR Spectroscopy

Most first series of transition metal ions have one or more unpaired electrons and show great variations in the paramagnetic property. The magnetic anisotropy of some transition metal ions, including Co(II), as well as lanthanide ions [Ln(III)], has been well examined in proteins by NMR. In contrast, few examples of Fe(II) complexes reporting the magnetic anisotropy were analyzed in proteins, except for the ones containing a heme motif or iron-sulfur clusters. Here, we showed that [2,2':6',2″-terpyridine]-6,6″-dicarboxylic acid (TDA) is an excellent iron-binding ligand. It forms a stable iron complex in aqueous solution and demonstrates distinct iron-binding properties. TDA forms a 1:1 stable complex with both Fe(II) and Fe(III), but Fe(II) presents a high-spin state in the complex. The TDA moiety can be site-specifically attached to a protein, and its protein conjugate generates sizable pseudocontact shifts (PCSs) in complex with Fe(II), which are larger than those of commonly used metal binding tags. In contrast, the protein-TDA-Fe(III) complex produces negligible paramagnetic relaxation enhancement (PRE) effects in the protein signals, indicating a low-spin state of Fe(III) in the protein-TDA complex. The high stability of the protein-TDA-Fe(II) complex allows one to measure accurate PCSs in cell lysate even in the presence of other transition metal ions and an excess of GSH.

Systematic kinetic assay of phenylsulfonyl pyridine derivatives with free thiol for site-specific modification of proteins

Site-specific modification of proteins with functional groups is a powerful way of understanding the dynamics and functions of proteins. Recently reported phenylsulfonyl pyridine is a thiol-specific moiety and is of great interest for the use of high resolution nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) in structural biology. However, the reactivity of phenylsulfonyl pyridines to free thiols was barely understood, especially considering the effect of the substituent groups in pyridine on the kinetic activity. In this work, we used a number of phenylsulfonyl pyridine derivatives and systematically evaluated the kinetic properties of these compounds with free cysteine at different pHs by means of NMR and UV spectroscopy. The experimental results show that the reactivity of phenylsulfonyl pyridines with free thiols can be tuned by substitution of pyridine or metal ion coordination, with a range of reaction rates from one to five orders of magnitude. These kinetic parameters provide valuable insights into the protein site-specific modification by the phenylsulfonyl pyridine moiety, as demonstrated in the present study.

The evolution of paramagnetic NMR as a tool in structural biology

Paramagnetic NMR data contain extremely accurate long-range information on metalloprotein structures and, when used in the frame of integrative structural biology approaches, they allow for the retrieval of structural details to a resolution that is not achievable using other techniques. Paramagnetic data thus represent an extremely powerful tool to refine protein models in solution, especially when coupled to X-ray or cryoelectron microscopy data, to monitor the formation of complexes and determine the relative arrangements of their components, and to highlight the presence of conformational heterogeneity. More recently, theoretical and computational advancements in quantum chemical calculations of paramagnetic NMR observables are progressively opening new routes in structural biology, because they allow for the determination of the structure within the coordination sphere of the metal center, thus acting as a loupe on sites that are difficult to observe but very important for protein function.

Paramagnetic Chemical Probes for Studying Biological Macromolecules

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.

Localising nuclear spins by pseudocontact shifts from a single tagging site

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 (Δ χ ) 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.