3‐Mercapto‐2,6‐Pyridinedicarboxylic Acid: A Small Lanthanide‐Binding Tag for Protein Studies by NMR Spectroscopy

Paramagnetic effects from lanthanide ions present powerful tools for protein studies by nuclear magnetic resonance (NMR) spectroscopy provided that the lanthanide can be site‐specifically and rigidly attached to the protein. A new, particularly small and rigid lanthanide‐binding tag, 3‐mercapto‐2,6‐pyridinedicarboxylic acid (3MDPA), was synthesized and attached to two different proteins via a disulfide bond. The complexes of the N‐terminal domain of the E. coli arginine repressor (ArgN) with seven different paramagnetic lanthanide ions and Co²⁺ were analyzed in detail by NMR spectroscopy. The magnetic susceptibility anisotropy (Δχ) tensors and metal position were determined from pseudocontact shifts. The 3MDPA tag generated very different Δχ tensor orientations compared to the previously studied 4‐mercaptomethyl‐DPA tag, making it a highly complementary and useful tool for protein NMR studies.     

Two Histidines in an α‐Helix: A Rigid Co2+‐Binding Motif for PCS Measurements by NMR Spectroscopy

Pseudocontact shifts (PCS) generated by paramagnetic metal ions present valuable long‐range information in the study of protein structural biology by nuclear magnetic resonance (NMR) spectroscopy. Faithful interpretation of PCSs, however, requires complete immobilization of the metal ion relative to the protein, which is difficult to achieve with synthetic metal tags. We show that two histidine residues in sequential turns of an α‐helix provide a binding site for a Co²⁺ ion, which positions the metal ion in a uniquely well‐defined and predictable location. Exchange between the bound and free cobalt is slow on the timescale defined by chemical shifts, but the NMR resonance assignments are nonetheless readily transferred from the diamagnetic to the paramagnetic NMR spectrum by an I_zS_z‐exchange experiment. The double‐histidine‐Co²⁺ motif offers a straightforward, inexpensive, and convenient way of generating precision PCSs in proteins.     

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 Tb³⁺ 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.     

4,4'-dithiobisdipicolinic acid: a small and convenient lanthanide binding tag for protein NMR spectroscopy

Pseudocontact shifts (PCS) from paramagnetic lanthanide ions present powerful long-range structure restraints for studies of proteins by nuclear magnetic resonance spectroscopy. To elicit PCSs, the lanthanide must be attached site-specifically to the target protein. In addition, it needs to be attached rigidly to avoid averaging of the PCSs due to mobility with respect to the protein and it must not interfere with the function of the protein. Here, we present a dipicolinic acid reagent that spontaneously forms a disulfide bond with thiol groups of accessible cysteine residues. A minimal number of rotatable bonds between the cysteine side chain and the tag helps to minimise mobility. Combined with the small size of the tag and quantitative tagging yields, these features make it a highly attractive tool for generating structure restraints by paramagnetic lanthanides.     

Pseudo‐Contact NMR Shifts over the Paramagnetic Metalloprotein CoMMP‐12 from First Principles

Long‐range pseudo‐contact NMR shifts (PCSs) provide important restraints for the structure refinement of proteins when a paramagnetic metal center is present, either naturally or introduced artificially. Here we show that ab initio quantum‐chemical methods and a modern version of the Kurland–McGarvey approach for paramagnetic NMR (pNMR) shifts in the presence of zero‐field splitting (ZFS) together provide accurate predictions of all PCSs in a metalloprotein (high‐spin cobalt‐substituted MMP‐12 as a test case). Computations of 314 ¹³C PCSs using g‐ and ZFS tensors based on multi‐reference methods provide a reliable bridge between EPR‐parameter‐ and susceptibility‐based pNMR formalisms. Due to the high sensitivity of PCSs to even small structural differences, local structures based either on X‐ray diffraction or on various DFT optimizations could be evaluated critically by comparing computed and experimental PCSs. Many DFT functionals provide insufficiently accurate structures. We also found the available 1RMZ PDB X‐ray structure to exhibit deficiencies related to binding of a hydroxamate inhibitor. This has led to a newly refined PDB structure for MMP‐12 (5LAB) that provides a more accurate coordination arrangement and PCSs.     

A dipicolinic acid tag for rigid lanthanide tagging of proteins and paramagnetic NMR spectroscopy

A new lanthanide tag was designed for site-specific labeling of proteins with paramagnetic lanthanide ions. The tag, 4-mercaptomethyl-dipicolinic acid, binds lanthanide ions with nanomolar affinity, is readily attached to proteins via a disulfide bond, and avoids the problems of diastereomer formation associated with most of the conventional lanthanide tags. The high lanthanide affinity of the tag opens the possibility to measure residual dipolar couplings in a single sample containing a mixture of paramagnetic and diamagnetic lanthanides. Using the DNA-binding domain of the E. coli arginine repressor as an example, it is demonstrated that the tag allows immobilization of the lanthanide ion in close proximity of the protein by additional coordination of the lanthanide by a carboxyl group of the protein. The close proximity of the lanthanide ion promotes accurate determinations of magnetic susceptibility anisotropy tensors. In addition, the small size of the tag makes it highly suitable for studies of intermolecular interactions.     

Iron(III) Located in the Dinuclear Metallo‐β‐Lactamase IMP‐1 by Pseudocontact Shifts

Heterodinuclear metalloenzymes are an important class of metalloproteins, but determining the location of the different metal ions can be difficult. Herein we present a new NMR spectroscopy method that uses pseudocontact shifts (PCS) to achieve this without assumptions about the coordinating ligands. The approach is illustrated with the dinuclear [FeZn] complex of IMP‐1, which is a prototypical metallo‐β‐lactamase (MβL) that confers resistance to β‐lactam antibiotics. Results from single‐crystal X‐ray diffraction were compromised by degradation during crystallization. With [GaZn]‐IMP‐1 as diamagnetic reference, the PCSs unambiguously identified the iron binding site in fresh samples of [FeZn]‐IMP‐1, even though the two metal centers are less than 3.8 Å apart and the iron is high‐spin Fe³⁺, which produces only small PCSs. [FeZn]‐MβLs may be important drug targets, as [FeZn]‐IMP‐1 is enzymatically active and readily produced in the presence of small amounts of Fe³⁺.     

A Chiral Lanthanide Tag for Stable and Rigid Attachment to Single Cysteine Residues in Proteins for NMR,EPR and Time-Resolved Luminescence Studies

A lanthanide-binding tag site-specifically attached to a protein presents a tool to probe the protein by multiple spectroscopic techniques, including nuclear magnetic resonance, electron paramagnetic resonance and time-resolved luminescence spectroscopy. Here a new stable chiral Ln^III tag, referred to as C12 , is presented for spontaneous and quantitative reaction with a cysteine residue to generate a stable thioether bond. The synthetic protocol of the tag is relatively straightforward, and the tag is stable for storage and shipping. It displays greatly enhanced reactivity towards selenocysteine, opening a route towards selective tagging of selenocysteine in proteins containing cysteine residues. Loaded with Tb^III or Tm^III ions, the C12 tag readily generates pseudocontact shifts (PCS) in protein NMR spectra. It produces a relatively rigid tether between lanthanide and protein, which is beneficial for interpretation of the PCSs by single magnetic susceptibility anisotropy tensors, and it is suitable for measuring distance distributions in double electron–electron resonance experiments. Upon reaction with cysteine or other thiol compounds, the Tb^III complex exhibits a 100-fold enhancement in luminescence quantum yield, affording a highly sensitive turn-on luminescence probe for time-resolved FRET assays and enzyme reaction monitoring.     

Macrocyclization of polymers via ring‐closing metathesis and azide/alkyne‐“click”‐reactions: An approach to cyclic polyisobutylenes

The end‐to‐end cyclization of telechelic polyisobutylenes (PIB's) toward cyclic polyisobutylenes is reported, using either ring‐closing metathesis (RCM) or the azide/alkyne‐“click”‐reaction. The first approach uses bisallyl‐telchelic PIB's (M_n = 1650, 3680, 9770 g mol^?1) and Grubbs 1st‐, 2nd‐, and 3rd‐generation catalyst leading to cyclic PIB's in 60–80% yield, with narrow polydispersities (M_w/M_n = 1.25). Azide/alkyne‐“click”‐reactions of bisalkyne‐telechelic PIB's (M_n = 3840 and 9820 g mol^?1) with excess of 1,11‐diazido‐undecane leads to the formation of mixtures of linear/cyclic PIB's under formation of oligomeric cycles. Subsequent reaction of the residual azide‐moieties in the linear PIB's with excess of alkyne‐telechelic PEO enables the chromatographic removal of the resulting linear PEO‐PIB‐block copolymers by column chromatography. Thus pure cyclic PIB's can be obtained using this double‐“click”‐method, devoid of linear contaminants. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 671–680, 2010     

Stimuli‐responsive diblock copolymer brushes via combination of “click chemistry” and living radical polymerization

pH‐ and temperature‐responsive poly(N‐isopropylacrylamide‐block?4‐vinylbenzoic acid) (poly(NIPAAm‐b‐VBA)) diblock copolymer brushes on silicon wafers have been successfully prepared by combining click reaction, single‐electron transfer‐living radical polymerization (SET‐LRP), and reversible addition‐fragmentation chain‐transfer (RAFT) polymerization. Azide‐terminated poly(NIPAAm) brushes were obtained by SET‐LRP followed by reaction with sodium azide. A click reaction was utilized to exchange the azide end group of a poly(NIPAAm) brushes to form a surface‐immobilized macro‐RAFT agent, which was successfully chain extended via RAFT polymerization to produce poly(NIPAAm‐b‐VBA) brushes. The addition of sacrificial initiator and/or chain‐transfer agent permitted the formation of well‐defined diblock copolymer brushes and free polymer chains in solution. The free polymer chains were isolated and used to estimate the molecular weights and polydispersity index of chains attached to the surface. Ellipsometry, contact angle measurements, grazing angle‐Fourier transform infrared spectroscopy, and X‐ray photoelectron spectroscopy were used to characterize the immobilization of initiator on the silicon wafer, poly(NIPAAm) brush formation via SET‐LRP, click reaction, and poly(NIPAAm‐b‐VBA) brush formation via RAFT polymerization. The poly(NIPAAm‐b‐VBA) brushes demonstrate stimuli‐responsive behavior with respect to pH and temperature. The swollen brush thickness of poly(NIPAAm‐b‐VBA) brush increases with increasing pH, and decreases with increasing temperature. These results can provide guidance for the design of smart materials based on copolymer brushes. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 2677–2685     

Noncovalent Tagging Proteins with Paramagnetic Lanthanide Complexes for Protein Study

The site‐specific labeling of proteins with paramagnetic lanthanides offers unique opportunities for NMR spectroscopic analysis in structural biology. Herein, we report an interesting way of obtaining paramagnetic structural restraints by employing noncovalent interaction between a lanthanide metal complex, [Ln(L)₃]^n? (L=derivative of dipicolinic acid, DPA), and a protein. These complexes formed by lanthanides and DPA derivatives, which have different substitution patterns on the DPA derivatives, produce diverse thermodynamic and paramagnetic properties when interacting with proteins. The binding affinity of [Ln(L)₃]^n? with proteins, as well as the determined paramagnetic tensor, are tunable by changing the substituents on the ligands. These noncovalent interactions between [Ln(L)₃]^n? and proteins offer great opportunities in the tagging of proteins with paramagnetic lanthanides. We expect that this method will be useful for obtaining multiple angles and distance restraints of proteins in structural biology.     

Thiol-ene reaction: a versatile tool in site-specific labelling of proteins with chemically inert tags for paramagnetic NMR

Site-specific tagging of proteins with paramagnetic lanthanides generates valuable long-range structure restraints for structural biology by NMR spectroscopy. We show that the thiol-ene addition reaction offers a powerful tool for tagging proteins in a chemically stable manner with very small lanthanide tags.     

Binding of low molecular weight inhibitors promotes large conformational changes in the dengue virus NS2B-NS3 protease: fold analysis by pseudocontact shifts

The two-component dengue virus NS2B-NS3 protease (DEN NS2B-NS3pro) is an established drug target, but inhibitor design is hampered by the lack of a crystal structure of the protease in its fully active form. In solution and without inhibitors, the functionally important C-terminal segment of the NS2B cofactor is dissociated from DEN NS3pro ("open state"), necessitating a large structural change to produce the "closed state" thought to underpin activity. We analyzed the fold of DEN NS2B-NS3pro in solution with and without bound inhibitor by nuclear magnetic resonance (NMR) spectroscopy. Multiple paramagnetic lanthanide tags were attached to different sites to generate pseudocontact shifts (PCS). In the face of severe spectral overlap and broadening of many signals by conformational exchange, methods for assignment of (15)N-HSQC cross-peaks included selective mutation, combinatorial isotope labeling, and comparison of experimental PCSs and PCSs back-calculated for a structural model of the closed conformation built by using the structure of the related West Nile virus (WNV) protease as a template. The PCSs show that, in the presence of a positively charged low-molecular weight inhibitor, the enzyme assumes a closed state that is very similar to the closed state previously observed for the WNV protease. Therefore, a model of the protease built on the closed conformation of the WNV protease is a better template for rational drug design than available crystal structures, at least for positively charged inhibitors. To assess the open state, we created a binding site for a Gd(3+) complex and measured paramagnetic relaxation enhancements. The results show that the specific open conformation displayed in the crystal of DEN NS2B-NS3pro is barely populated in solution. The techniques used open an avenue to the fold analysis of proteins that yield poor NMR spectra, as PCSs from multiple sites in combination with model building generate powerful information even from incompletely assigned (15)N-HSQC spectra.     

“Click polyester”: Synthesis of polyesters containing triazole units in the main chain via safe and rapid “click” chemistry and their properties

Click Cu(I)‐catalyzed polymerizations of diynes that contained ester linkages and diazides were performed to produce polyesters (click polyesters) of large molecular weights [(～1.0–7.0 ) × 10⁴], that contained main‐chain 1,4‐disubstitued triazoles in excellent yields. Incorporation of triazole improved the thermal properties and magnified the even‐odd effect of the methylene chain length. We also found that, by changing the positions of the triazole rings, the thermal properties of the polyesters could be controlled. The use of in situ azidation was a safe reaction, as explosive diazides are not used. In addition, the microwave heating was found to accelerate the polymerization rates. This is the first study that has applied click chemistry for the synthesis of a series of polyesters. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 4207–4218, 2010     

Synthesis and functionalization of dendron‐polymer conjugate based hydrogels via sequential thiol‐ene “click” reactions

Fabrication and functionalization of hydrogels from well‐defined dendron‐polymer‐dendron conjugates is accomplished using sequential radical thiol‐ene “click” reactions. The dendron‐polymer conjugates were synthesized using an azide‐alkyne “click” reaction of alkene‐containing polyester dendrons bearing an alkyne group at their focal point with linear poly(ethylene glycol)‐bisazides. Thiol‐ene “click” reaction was used for crosslinking these alkene functionalized dendron‐polymer conjugates using a tetrathiol‐based crosslinker to provide clear and transparent hydrogels. Hydrogels with residual alkene groups at crosslinking sites were obtained by tuning the alkene‐thiol stoichiometry. The residual alkene groups allow efficient postfunctionalization of these hydrogel matrices with thiol‐containing molecules via a subsequent radical thiol‐ene reaction. The photochemical nature of radical thiol‐ene reaction was exploited to fabricate micropatterned hydrogels. Tunability of functionalization of these hydrogels, by varying dendron generation and polymer chain length was demonstrated by conjugation of a thiol‐containing fluorescent dye. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 926–934     

Fluorine Pseudocontact Shifts Used for Characterizing the Protein–Ligand Interaction Mode in the Limit of NMR Intermediate Exchange

The characterization of protein–ligand interaction modes becomes recalcitrant in the NMR intermediate exchange regime as the interface resonances are broadened beyond detection. Here, we determined the ¹⁹F low‐populated bound‐state pseudocontact shifts (PCSs) of mono‐ and di‐fluorinated inhibitors of the BRM bromodomain using a highly skewed protein/ligand ratio. The bound‐state ¹⁹F PCSs were retrieved from ¹⁹F chemical exchange saturation transfer (CEST) in the presence of the lanthanide‐labeled protein, which was termed the ¹⁹F PCS‐CEST approach. These PCSs enriched in spatial information enabled the identification of best‐fitting poses, which agree well with the crystal structure of a more soluble analog in complex with the BRM bromodomain. This approach fills the gap of the NMR structural characterization of lead‐like inhibitors with moderate affinities to target proteins, which are essential for structure‐guided hit‐to‐lead evolution.     

Photo‐initiated thiol–ene “click” hydrogels from RAFT‐synthesized poly(N‐isopropylacrylamide)

Despite the efficiency and robustness of the widely used copper‐catalyzed 1,3‐dipolar cycloaddition reaction, the use of copper as a catalyst is often not attractive, particularly for materials intended for biological systems. The use of photo‐initiated thiol‐ene as an alternative “click” reaction to synthesize “model networks” is investigated here. Poly(N‐isopropylacrylamide) precursors were synthesized by reversible addition fragmentation chain transfer (RAFT) polymerization and were designed to have trithiocarbonate moieties as end groups. This structure design provides opportunity for subsequent end‐group modifications in preparation for thiol‐ene “click.” Two reaction routes have been proposed and studied to yield thiol and ene moieties. The advantages and disadvantages of each reaction path were investigated to propose a simple but efficient route to prepare copper‐free “click” hydrogels. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013 , 51, 4626–4636     

Synthesis of AB3‐type miktoarm star polymers with steroid core via a combination of “Click” chemistry and ring opening polymerization techniques

Well‐defined AB₃‐type miktoarm star‐shaped polymers with cholic acid (CA) core were fabricated with a combination of “click” chemistry and ring opening polymerization (ROP) methods. Firstly, azide end‐functional poly(ethylene glycol) (mPEG), poly(methyl methacrylate) (PMMA), polystyrene (PS), and poly(ε‐caprolactone) (PCL) polymers were prepared via controlled polymerization and chemical modification methods. Then, CA moieties containing three OH groups were introduced to these polymers as the end groups via Cu(I)‐catalyzed click reaction between azide end‐functional groups of the polymers ( mPEG‐N₃ , PMMA‐N₃ , PS‐N₃ , and PCL‐N₃ ) and ethynyl‐functional CA under ambient conditions, yielding CA end‐functional polymers ( mPEG‐Cholic , PMMA‐Cholic , PS‐Cholic , and PCL‐Cholic ). Finally, the obtained CA end‐capped polymers were employed as the macroinitiators in the ROP of ε‐caprolactone (ε‐CL) yielding AB₃‐type miktoarm star polymers ( mPEG‐Cholic‐PCL₃ , PMMA‐Cholic‐PCL₃ , and PS‐Cholic‐PCL₃ ) and asymmetric star polymer [ Cholic‐(PCL)₄ ]. The chemical structures of the obtained intermediates and polymers were confirmed via Fourier transform infrared and ¹H nuclear magnetic resonance spectroscopic techniques. Thermal decomposition behaviors and phase transitions were studied in detail using thermogravimetric analysis and differential scanning calorimetry experiments. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52, 3390–3399     

Cyclic poly(ε‐caprolactone) synthesized by combination of ring‐opening polymerization with ring‐closing metathesis,ring closing enyne metathesis,or “click” reaction

This article described the synthesis of cyclic poly(ε‐caprolactone) (PCL) via ring‐closing metathesis (RCM), ring closing enyne metathesis (RCEM), and “click” reaction of different difunctional linear PCL. Linear PCL precursors were prepared by ring‐opening polymerization (ROP) of ε‐caprolactone in bulk using 10‐undecen‐1‐ol or propargyl alcohol as the initiator, followed by reacting with corresponding acyl chloride containing vinyl or azido end group. The subsequent end‐to‐end intramolecular coupling reactions were performed under high dilution conditions. The successful transformation of linear PCL precursor to cyclic PCL was confirmed by Gel permeation chromatography, ¹H NMR, and Fourier transform infrared measurements. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 3022–3033, 2009     

Synthesis,Structure, and Fluorescent Properties of Lanthanide Complexes Based on 8‐Hydroxyquinoline‐7‐carboxylic Acid

The lanthanide complex [Eu₃(8‐HQCA)₃(COOH)(OH)₂(H₂O)₃]_n · nH₂O (8‐HQCA = 8‐hydroxyquinoline‐7‐carboxylic acid) was synthesized and characterized. Single‐crystal X‐ray diffraction shows that the trinuclear structures are linked by ligands to form 2D layers. The results of DFT calculation shows that energy can be transferred effectively from the ligand to Eu^III ions. A series of heteronuclear complexes {[(Eu_1–xY_x)₃(8‐HQCA)₃(COOH) (OH)₂(H₂O)₃]_n · nH₂O (x = 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8)} were synthesized and their luminescent properties were studied. The results showed that the doping of Y^III ions could change the fluorescent intensity of the Eu^III complex, but could not change their positions.