Lanthanide complexes of 3-methoxy-salicylaldehyde

The reaction of a lanthanide(III) nitrate (Ln = Pr, Nd, Gd, Dy, Er) with 3-methoxy-salicylaldehyde(3-OCH₃-saloH), afforded neutral complexes of the general formula [Ln(3-OCH₃-salo)₃], which were characterized by means of elemental analysis, FT-IR spectra, TG-DTA curves, and magnetic measurements. The released products, due to the thermal decomposition were analyzed by on-line coupling MS spectrometer to the thermobalance in argon, allowed to prove the proposed decomposition stages. In order to confirm the stability scale provided on the basis of the onset decomposition temperature, a kinetic analysis of the three decomposition stages was made using the Kissinger equation, while the complex nature of the decomposition kinetics was revealed by the isoconvertional Ozawa–Flynn–Wall method.     

Using oxidative crosslinking and proximity labeling to quantitatively characterize protein-protein and protein-Peptide complexes

The quantitative analysis of protein-protein and protein-peptide complexes is of fundamental importance in biochemistry. We report here that nickel-catalyzed proximity biotinylation and Ru(II)(bpy)(3)(2+)-mediated oxidative crosslinking can be used to measure the equilibrium dissociation constant and stoichiometry of protein complexes. Only small amounts of protein are required, neither of the binding partners must be immobilized on a surface, and no special instrumentation is necessary. This chemistry should provide a useful complement to existing methods for the analysis of protein-protein and protein-peptide interactions.     

Use of selective Trp side chain labeling to characterize protein-protein and protein-ligand interactions by NMR spectroscopy

Recent studies on amino acid occurrence in protein binding sites suggest that only a reduced number of residues are responsible for most interaction energy in protein-protein and protein-ligand interactions. Above all, tryptophan (Trp) seems to be the most frequent residue in protein's hot spots. Here we report a novel, efficient, and cost-effective method to selectively incorporate specific isotope labels into the side chains of Trp residues in recombinant proteins. We show that the method proposed allows selective NMR observation of Trp side chains that enables studies of ligand binding, protein-protein interactions, hydrogen binding, protein folding, and side chain dynamics. Examples with the protein BIR3 will be given.     

A new approach in 1D and 2D 13C high-resolution solid-state NMR spectroscopy of paramagnetic organometallic complexes by very fast magic-angle spinning

Novel 1D and multidimensional solid-state NMR (SSNMR) methods using very fast magic-angle spinning (VFMAS) (spinning speed > 20 kHz) for performing 13C high-resolution SSNMR of paramagnetic organometallic complexes are discussed. VFMAS removes a majority of 13C-1H and 1H-1H dipolar couplings, which are often difficult to remove by RF pulse techniques in paramagnetic complexes because of large paramagnetic shifts. In the first systematic approach using the unique feature of VFMAS for paramagnetic complexes, we demonstrate a means of obtaining well-resolved 1D and multidimensional 13C SSNMR spectra, sensitivity enhancements via cross polarization, and signal assignments, and applications of dipolar recoupling methods for nonlabeled paramagnetic organometallic complexes of moderate paramagnetic shifts ( approximately 800 ppm). Experimental results for powder samples of small nonlabeled coordination complexes at 1H frequencies of 400.2-400.3 MHz show that highly resolved 13C SSNMR spectra can be obtained under VFMAS, without requirements of 1H decoupling. Sensitivity enhancement in 13C SSNMR via cross polarization from 1H spins was demonstrated with an amplitude-sweep high-power CP sequence using strong RF fields ( approximately 100 kHz) available in the VFMAS probe. 13C CPMAS spectra of nonlabeled Cu(II)(dl-alanine)2.(H2O) and V(III)(acetylacetonate)3 (V(acac)3) show that it is possible to obtain high-resolution spectra for a small quantity ( approximately 15 mg) of nonlabeled paramagnetic organometal complexes within a few minutes under VFMAS. Experiments on Cu(II)(dl-alanine)2.(H2O) demonstrated that 1H-13C dipolar recoupling for paramagnetic organometal complexes can be performed under VFMAS by application of rotor-synchronous pi-pulses to 1H and 13C spins. The results also showed that signal assignments for 13CH, 13CH3, and 13CO groups in paramagnetic complexes are possible on the basis of the amount of 13C-1H dipolar dephasing induced by dipolar recoupling. Furthermore, the experimental 2D 13C/1H chemical-shift correlation NMR spectrum obtained for nonlabeled V(acac)3 exhibits well-resolved lines, which overlap in 1D 13C and 1H spectra. Signals for different chemical groups in the 2D spectrum are distinguished by the 13C-1H dipolar dephasing method combined with the 2D 13C/1H correlation NMR. The assignments offer information on the existence of nonequivalent ligands in the coordination complex in solids, without requiring a single-crystal sample.     

Protein 3D structure determination by high-resolution solid-state NMR

Developments in NMR technology, sample preparation, pulse sequence methodology and structure calculation protocols have recently allowed one to progress towards structure determination at high-resolution of proteins by solid-state NMR spectroscopy. We here report solid-state NMR protocols based on magic-angle-spinning experiments, combined with modified structure calculation protocols, for structure determination of uniformly ¹³C, ¹⁵N isotopically labeled proteins. We demonstrate the use of these protocols to obtain high-resolution structures for the example of the microcrystalline Crh protein. The CHHC, DARR and PAR solid-state NMR experiments, as well as the calculation protocols using the program ARIA, are presented.     

Lanthanide complexes with polyaminopolycarboxylates as prospective NMR/MRI diagnostic probes: peculiarities of molecular structure,dynamics and paramagnetic properties

Journal of Inclusion Phenomena and Macrocyclic Chemistry - The paramagnetic lanthanide complexes with polyaminopolycarboxylate (PAPC) ligands attract considerable attention from the standpoint of...     

Measurement of NMR cross-polarization (CP) rate constants in the slow CP regime: relevance to structure determinations of zeolite-sorbate and other complexes by cp magic-angle spinning NMR

When analyzing I --> S variable contact time cross-polarization (CP) curves, the spin dynamics are usually assumed to be describable in the "fast CP regime" in which the growth of the S spin magnetization is governed by the rate of cross polarization while its decay is governed by the rate of I spin T1rho relaxation. However, in the investigation of the structures of zeolite-sorbate and other complexes by polarization transfer this will not necessarily be the case. We discuss the measurement of I --> S CP rate constants under the "slow CP regime" in which the rate of T1rho relaxation is fast compared to the rate of cross polarization, leading to a reversal of the usual assumptions such that the rate or growth is governed by the rate of I spin T1rho relaxation while the decay is governed by the rate of cross polarization (and the S spin T1rho relaxation). It is very important to recognize when a system is in the slow CP regime, as an analysis assuming the normal fast CP will lead to erroneous data. However, even when the slow CP regime is recognized, it is difficult to obtain absolute values for the CP rate constants from fits to standard CP curves, since the CP rate constant is correlated to the scaling factor, the contribution from 29Si T1rho relaxation is ignored, and it is difficult to obtain reliable data at very long contact times. The use of a 29Si{1H} CP "drain" or "depolarization" experiment, which measures absolute values of the CP rate constants, is therefore proposed as being most appropriate for theses situations. To illustrate the importance of these observations, measurements of the 1H-29Si CP rate constants in the p-dichlorobenzene/ZSM-5 sorbate-zeolite complex by 29Si{1H} CP and CP drain magic-angle spinning (MAS) NMR experiments are presented and compared and used to determine the location of the guest sorbate molecules in the cavities of the host zeolite framework.     

"Multi-scan single shot" quantitative 2D NMR: a valuable alternative to fast conventional quantitative 2D NMR

Quantitative Ultrafast (UF) 2D NMR is a very promising methodology enabling the acquisition of 2D spectra in a single scan. The analytical performances of UF 2D NMR have been highly increased in the last few years, however little is known about the sensitivity of ultrafast experiments versus conventional 2D NMR. A fair and relevant comparison has to consider the Signal-to-Noise Ratio (SNR) per unit of time, in order to answer the following question: for a given experiment time, should we run a conventional 2D experiment or is it preferable to accumulate ultrafast acquisitions? To answer this question, we perform here a systematic comparison between accumulated ultrafast experiments and conventional ones, for different experiment durations. Sensitivity issues and other analytical aspects are discussed for the COSY experiment in the context of quantitative analysis. The comparison is first carried out on a model sample, and then extended to model metabolic mixtures. The results highlight the high analytical performance of the "multi-scan single shot" approach versus conventional 2D NMR acquisitions. This result is attributed to the absence of t(1) noise in spatially encoded experiments. The multi-scan single shot approach is particularly interesting for quantitative applications of 2D NMR, whose occurrence in the literature has been greatly increasing in the last few years.     

Studying molecular 3D structure and dynamics by high-resolution solid-state NMR: Application to L-tyrosine-ethylester

A unified approach to the study of 3D conformation and molecular dynamics using magic-angle-spinning solid-state NMR is demonstrated on a uniformly 13C-labeled sample of L-tyrosine-ethylester.     

^1^3C NMR研究稀土柠檬酸配合物的溶液配位结构

用稀土离子诱导位移和顺磁弛豫时间测定等NMR方法研究了稀土柠檬酸配合物在pH 7.4的溶液中的配位结构。结果表明稀土离子通过3-羟基和3-羧基与柠檬酸配体形成1:2的配合物, 两个端羧基没有参与配位。通过计算稀土离子和柠檬酸配体中各个碳原子间的空间距离的相对比, 建立了稀土离子与柠檬酸配体配位的新模式。     

镧系离子与α-氨基丙酸配合物的^1^3C NMR波谱及其的结构研究

本文以XL-200型超导核磁共振谱仪对镧系离子与α-氨基丙酸配合物体系进行了研究, 测得微酸性条件下配合物中各^1^3C核的诱导化学位移值, 以独立结构法将诱导位移进行分离得到配合物生成位移、接触位移及准接触位移。分析这些不同性质的位移贡献得出镧系离子在磁学性质上同样存在"四分组现象”及"钆断效应”。以准接触位移为依据, 对配合物的结构进行计算机模拟, 取得了一些有意义的结果。     

Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex

Nuclear magnetic resonance (NMR) spectroscopy provides a range of powerful techniques for determining the structures and the dynamics of proteins. The high-resolution determination of the structures of protein-protein complexes, however, is still a challenging problem for this approach, since it can normally provide only a limited amount of structural information at protein-protein interfaces. We present here the determination using NMR chemical shifts of the structure (PDB code 2K5X) of the cytotoxic endonuclease domain from bacterial toxin colicin (E9) in complex with its cognate immunity protein (Im9). In order to achieve this result, we introduce the CamDock method, which combines a flexible docking procedure with a refinement that exploits the structural information provided by chemical shifts. The results that we report thus indicate that chemical shifts can be used as structural restraints for the determination of the conformations of protein complexes that are difficult to obtain by more standard NMR approaches.     

NMR methods for molecular structure studies of paramagnetic lanthanide complexes in solutions. Applications to crown ether complexes

The literature data on NMR spectroscopic methods for investigation of the spatial structure and molecular dynamics of lanthanide complexes with macrocyclic potyethers in solutions are reviewed. Translated fromZhumal Strukturnoi Khimii, Vol. 39, No. 4, pp. 714–730, July–August, 1998.     

3D structure determination of the Crh protein from highly ambiguous solid-state NMR restraints

In a wide variety of proteins, insolubility presents a challenge to structural biology, as X-ray crystallography and liquid-state NMR are unsuitable. Indeed, no general approach is available as of today for studying the three-dimensional structures of membrane proteins and protein fibrils. We here demonstrate, at the example of the microcrystalline model protein Crh, how high-resolution 3D structures can be derived from magic-angle spinning solid-state NMR distance restraints for fully labeled protein samples. First, we show that proton-mediated rare-spin correlation spectra, as well as carbon-13 spin diffusion experiments, provide enough short, medium, and long-range structural restraints to obtain high-resolution structures of this 2 x 10.4 kDa dimeric protein. Nevertheless, the large number of 13C/15N spins present in this protein, combined with solid-state NMR line widths of about 0.5-1 ppm, induces substantial ambiguities in resonance assignments, preventing 3D structure determination by using distance restraints uniquely assigned on the basis of their chemical shifts. In the second part, we thus demonstrate that an automated iterative assignment algorithm implemented in a dedicated solid-state NMR version of the program ARIA permits to resolve the majority of ambiguities and to calculate a de novo 3D structure from highly ambiguous solid-state NMR data, using a unique fully labeled protein sample. We present, using distance restraints obtained through the iterative assignment process, as well as dihedral angle restraints predicted from chemical shifts, the 3D structure of the fully labeled Crh dimer refined at a root-mean-square deviation of 1.33 A.     

Structures of protein-protein complexes are docked using only NMR restraints from residual dipolar coupling and chemical shift perturbations

NMR structures of protein-protein and protein-ligand complexes rely heavily on intermolecular NOEs. Recent work has shown that if no significant conformational changes occur upon complex formation residual dipolar coupling can replace most of the NOE restraints in protein-protein complexes, while restraints derived from chemical shift perturbations can largely replace intermolecular NOEs in protein-ligand structures. By combining restraints from chemical shift perturbations with orientation restraints derived from measurements of residual dipolar couplings, we show that the structure of the EIN-HPr complex can be calculated without NOE restraints. The final structure, built from the crystal structures of EIN and HPr in their uncomplexed form and docked only with NMR restraints, places HPr within 2.5 A of the position determined from the mean NMR structure of the complex.     

Elucidation of lignin structure by quantitative 2D NMR

Quick quantitative HSQC (QQ‐HSQC) was applied to quantitative evaluation of different inter‐unit linkages in an array of milled softwood and hardwood and technical lignins by using the guaiacyl C2 and syringyl C2–C6 signals as internal standards. The results were found to be highly reproducible and comparable with earlier literature reports. The advantage of QQ‐HSQC NMR analysis of lignin is contemporary detection and quantification of lignin inter‐unit linkages with a direct, non‐destructive method requiring short acquisition times.     

NMR Characterization of Lanthanide(3+) Complexes of Tetraazatetrakisphosphinato and Tetraazatetra­kisphosphonato Ligands

The three‐dimensional structures in aqueous solution of the entire series of the Ln³⁺ complexes [Ln(DOTP*‐Et)]^? (formed from the free ligand P,P′,P″,P′′′‐[1,4,7,10‐tetraazacyclododecane‐1,4,7,10‐tetrayltetrakis(methylene)]tetrakis[P‐ethylphosphinic acid] (H₄DOTP*‐Et) were studied by NMR techniques to rationalize the parameters governing the relaxivity of the Gd³⁺ complex and evaluate its potential as MRI contrast agent. From the ¹H‐ and ³¹P‐NMR lanthanide‐induced‐shift (LIS) values, especially of the [Yb(DOTP*‐Et)]^? complex, it was concluded that the [Ln(DOTP*‐Et)]^? complexes adopt in solution twisted square antiprismatic coordination geometries which change gradually their coordination‐cage structure along the lanthanide series. These complexes have no inner‐sphere‐H₂O coordination, and preferentially have the (R,R,R,R) configuration of the P‐atoms in the pendant arms. Self‐association was observed in aqueous solution for the tetraazatetrakisphosphonic acid ester complexes [Ln(DOTP*‐OEt)]^? (=[Ln(DOTP‐Et)]^?) and [Ln(DOTP*‐OBu)]^? (=[Ln(DOTP‐Bu)]^?) at and above 5 mM concentration, through analysis of ³¹P‐NMR, EPR, vapor‐pressure‐osmometry, and luminescence‐spectroscopic data. The presence of the cationic detergent cetylpyridinium chloride (CPC; but not of neutral surfactants) shifts the isomer equilibrium of [Eu(DOTP*‐OBu)]^? to the (S,S,S,S) form which selectively binds to the cationic micelle surface.     

Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data

In many cases of protein structure determination by NMR a high-quality structure is required. An important contribution to structural precision is stereospecific assignment of magnetically nonequivalent prochiral methylene and methyl groups, eliminating the need for introducing pseudoatoms and pseudoatom corrections in distance restraint lists. Here, we introduce the stereospecific assignment program that uses the resonance assignment, a preliminary 3D structure and 2D and/or 3D nuclear Overhauser effect spectroscopy peak lists for stereospecific assignment. For each prochiral group the algorithm automatically calculates a score for the two different stereospecific assignment possibilities, taking into account the presence and intensity of the nuclear Overhauser effect (NOE) peaks that are expected from the local environment of each prochiral group (i.e., the close neighbors). The performance of the algorithm has been tested and used on NMR data of alpha-helical and beta-sheet proteins using homology models and/or X-ray structures. The program produced no erroneous stereospecific assignments provided the NOEs were carefully picked and the 3D model was sufficiently accurate. The set of NOE distance restraints produced by nmr2st using the results of the SSA module was superior in generating good-quality ensembles of NMR structures (low deviations from upper limits in conjunction with low root-mean-square-deviation values) in the first round of structure calculations. The program uses a novel approach that employs the entire 3D structure of the protein to obtain stereospecific assignment; it can be used to speed up the NMR structure refinement and to increase the quality of the final NMR ensemble even when no scalar or residual dipolar coupling information is available.