Noncovalent Tagging Proteins with Paramagnetic Lanthanide Complexes for Protein Study

One touch is all it takes: the supramolecular interaction between ubiquitin and lanthanide complexes revisited by paramagnetic NMR and molecular dynamics

The supramolecular interaction between lanthanide complexes and proteins is at the heart of numerous chemical and biological studies. Some of these complexes have demonstrated remarkable interaction properties with proteins or peptides in solution and in the crystalline state. Here we have used the paramagnetism of lanthanide ions to characterize the affinity of two lanthanide complexes for ubiquitin. As the interaction process is dynamic, the acquired NMR data only reflect the time average of the different steps. We have used molecular dynamics (MD) simulations to get a deeper insight into the detailed interaction scenario at the microsecond scale. This NMR/MD approach enabled us to establish that the tris-dipicolinate complex interacts specifically with arginines and lysines, while the crystallophore explores the protein surface through weak interactions with carboxylates. These observations shed new light on the dynamic interaction properties of these complexes, which will ultimately enable us to propose a crystallization mechanism.

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.

Paramagnetic spin labeling of a bacterial DnaB helicase for solid-state NMR

Labeling of biomolecules with a paramagnetic probe for nuclear magnetic resonance (NMR) spectroscopy enables determining long-range distance restraints, which are otherwise not accessible by classically used dipolar coupling-based NMR approaches. Distance restraints derived from paramagnetic relaxation enhancements (PREs) can facilitate the structure determination of large proteins and protein complexes. We herein present the site-directed labeling of the large oligomeric bacterial DnaB helicase from Helicobacter pylori with cysteine-reactive maleimide tags carrying either a nitroxide radical or a lanthanide ion. The success of the labeling reaction was followed by quantitative continuous-wave electron paramagnetic resonance (EPR) experiments performed on the nitroxide-labeled protein. PREs were extracted site-specifically from 2D and 3D solid-state NMR spectra. A good agreement with predicted PRE values, derived by computational modeling of nitroxide and Gd³⁺ tags in the low-resolution DnaB crystal structure, was found. Comparison of experimental PREs and model-predicted spin label-nucleus distances indicated that the size of the "blind sphere" around the paramagnetic center, in which NMR resonances are not detected, is slightly larger for Gd³⁺ (∼14 Å) than for nitroxide (∼11 Å) in ¹³C-detected 2D spectra of DnaB. We also present Gd³⁺-Gd³⁺ dipolar electron-electron resonance EPR experiments on DnaB supporting the conclusion that DnaB was present as a hexameric assembly.

Capturing the dynamic association between a tris-dipicolinate lanthanide complex and a decapeptide: a combined paramagnetic NMR and molecular dynamics exploration

In the realm of biomolecules, peptides can present a large diversity of structures. Our study sheds new light on the structural interplay between a tris-dipicolinate lanthanide probe and a decapeptide SASYKTLPRG. Although a rather trivial, electrostatically driven interaction was expected, the combination of paramagnetic NMR and molecular dynamics simulations reveals a highly dynamic association process and allows for providing extensive insights into the interaction sites and their occupancy. This study highlights the importance of a large conformational sampling to reconcile characteristic time in NMR with molecular dynamics simulations, where sampling in the microsecond range is needed. This study opens the door for a detailed mechanistic elucidation of the early steps of lanthanide complex-peptide or lanthanide complex-protein interaction or self-assembly processes.

Structure of micelle bound cationic peptides by NMR spectroscopy using a lanthanide shift reagent

[Tm(DPA)₃]^3- was used to generate multiple, paramagnetic nuclear Overhauser effect NMR spectra of cationic peptides when weakly bound to a lipopolysaccharide micelle. Increased spectral resolution combined with a marked increase in the number of distance restraints yielded high resolution structures of polymyxin and MSI-594 in the liposaccharide bound state.

Luminescent and Chiroptical Properties of 1 : 1 Eu (III) : Tetracycline Species Probed by Circularly Polarized Luminescence

This study investigates the significantly different luminescent and chiroptical properties of tetracycline (TC) when coordinated to Eu(III). The approach involves understanding the 1) speciation of TC and 2) conformation and species formed between Eu(III) and TC in a ratio of 1 : 1 in a dimethylformamide (DMF) solution and as a function of the pH value. By identifying the conformational changes of the various 1 : 1 Eu(III) : TC species, the results from this study explain information on the local microenvironment about the Eu(III) metal center. In particular, ⁵ D₀ ←⁷ F₀ Eu(III) laser excitation spectroscopy was employed to distinguish the different types of species found in solution in order to understand the interaction between Eu(III) and TC. On the other hand, circularly polarized luminescence (CPL) spectroscopy was used to understand the structural changes within the 1 : 1 Eu(III) : TC complex that could be related to the chirality of the Eu(III)-containing species. The CPL spectrum serves as a "fingerprint" to indicate the conformational changes within the 1 : 1 Eu(III) : TC complex as a result of the chiroptical signal arising from the various Eu(III) : TC species.

Crystal structure of catena-poly[μ2-4,4′-bipyridine-κ2N:N′)-tetrakis(μ2-2-((3,5,6-trichloropyridin-2-yl)oxy)acetato-κ2O:O′)dicobalt(II)], C19H10Cl6CoN3O6

C19H10Cl6CoN3O6, tetragonal, I4̄ (no. 82), a = 13.1152(4) Å, c = 14.2497(6) Å, V = 2451.07(18) Å3, Z = 4, Rgt(F) = 0.0359, wRref(F2) = 0.0843, T = 293.2(3) K.

Two-Color Three-State Luminescent Lanthanide Core-Shell Crystals

Luminescent core-shell crystals based on lanthanide tris-dipicolinate complexes were obtained from the successive growing of two different lanthanide complex layers. Selective or simultaneous emission of each part of the crystal can be achieved by a careful choice of the excitation wavelength.

An encodable lanthanide binding tag with reduced size and flexibility for measuring residual dipolar couplings and pseudocontact shifts in large proteins

Metal ions serve important roles in structural biology applications from long-range perturbations seen in magnetic resonance experiments to electron-dense signatures in X-ray crystallography data; however, the metal ion must be secured in a molecular framework to achieve the maximum benefit. Polypeptide-based lanthanide-binding tags (LBTs) represent one option that can be directly encoded within a recombinant protein expression construct. However, LBTs often exhibit significant mobility relative to the target molecule. Here we report the characterization of improved LBTs sequences for insertion into a protein loop. These LBTs were inserted to connect two parallel alpha helices of an immunoglobulin G (IgG)-binding Z domain platform. Variants A and B bound Tb(3+) with high affinity (0.70 and 0.13 μM, respectively) and displayed restricted LBT motion. Compared to the parent construct, the metal-bound A experienced a 2.5-fold reduction in tag motion as measured by magnetic field-induced residual dipolar couplings and was further studied in a 72.2 kDa complex with the human IgG1 fragment crystallizable (IgG1 Fc) glycoprotein. The appearance of both pseudo-contact shifts (-0.221 to 0.081 ppm) and residual dipolar couplings (-7.6 to 14.3 Hz) of IgG1 Fc resonances in the IgG1 Fc:(variant A:Tb(3+))2 complex indicated structural restriction of the LBT with respect to the Fc. These studies highlight the applicability of improved LBT sequences with reduced mobility to probe the structure of macromolecular systems.

Paramagnetic Ligand Tagging To Identify Protein Binding Sites

Transient biomolecular interactions are the cornerstones of the cellular machinery. The identification of the binding sites for low affinity molecular encounters is essential for the development of high affinity pharmaceuticals from weakly binding leads but is hindered by the lack of robust methodologies for characterization of weakly binding complexes. We introduce a paramagnetic ligand tagging approach that enables localization of low affinity protein–ligand binding clefts by detection and analysis of intermolecular protein NMR pseudocontact shifts, which are invoked by the covalent attachment of a paramagnetic lanthanoid chelating tag to the ligand of interest. The methodology is corroborated by identification of the low millimolar volatile anesthetic interaction site of the calcium sensor protein calmodulin. It presents an efficient route to binding site localization for low affinity complexes and is applicable to rapid screening of protein–ligand systems with varying binding affinity.

Hybrid luminescence materials assembled by [Ln(DPA)3](3-) and mesoporous host through ion-pairing interactions with high quantum efficiencies and long lifetimes

A kind of mesoporous hybrid luminescence material was assembled through the ion exchange method between [Ln(DPA)₃]³⁻ and ionic liquid functionalized SBA-15. [Ln(DPA)₃]³⁻ was successfully anchored onto positive-charge modified SBA-15 by the strong electrostatic interaction. In [Ln(DPA)₃]³⁻, Ln³⁺ ions are in 9-fold coordination through six oxygen atoms of carboxyl groups and three nitrogen atoms of pyridine units, leaving no coordination site for water molecules. Therefore the hybrids possess prominent luminescent properties, SBA-15-IMI-Tb(DPA)₃ and SBA-15-IMI-Eu(DPA)₃ exhibit high quantum yield values of 63% and 79%, and long lifetimes values of 2.38 ms and 2.34 ms, respectively. Especially, SBA-15-IMI-Eu(DPA)₃ presents a high color purity, and the red/orange intensity ratio is as high as 7.6. The excellent luminescence properties and ordered mesoporous structures give rise to many potential applications in optical and electronic areas.

Bioconjugation of proteins with a paramagnetic NMR and fluorescent tag

Site-specific labeling of proteins with lanthanide ions offers great opportunities for investigating the structure, function, and dynamics of proteins by virtue of the unique properties of lanthanides. Lanthanide-tagged proteins can be studied by NMR, X-ray, fluorescence, and EPR spectroscopy. However, the rigidity of a lanthanide tag in labeling of proteins plays a key role in the determination of protein structures and interactions. Pseudocontact shift (PCS) and paramagnetic relaxation enhancement (PRE) are valuable long-range structure restraints in structural-biology NMR spectroscopy. Generation of these paramagnetic restraints generally relies on site-specific tagging of the target proteins with paramagnetic species. To avoid nonspecific interaction between the target protein and paramagnetic tag and achieve reliable paramagnetic effects, the rigidity, stability, and size of lanthanide tag is highly important in paramagnetic labeling of proteins. Here 4'-mercapto-2,2':6',2''-terpyridine-6,6''-dicarboxylic acid (4MTDA) is introduced as a a rigid paramagnetic and fluorescent tag which can be site-specifically attached to a protein by formation of a disulfide bond. 4MTDA can be readily immobilized by coordination of the protein side chain to the lanthanide ion. Large PCSs and RDCs were observed for 4MTDA-tagged proteins in complexes with paramagnetic lanthanide ions. At an excitation wavelength of 340 nm, the complex formed by protein-4MTDA and Tb(3+) produces high fluorescence with the main emission at 545 nm. These interesting features of 4MTDA make it a very promising tag that can be exploited in NMR, fluorescence, and EPR spectroscopic studies on protein structure, interaction, and dynamics.