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.     

Protein Unfolding: 1H‐NMR Studies of Paramagnetic Ferricytochrome c‐550 from Horse Heart

Electronic transfer protein cytochrome c‐550 from horse heart is studied in the unfolded state by means of paramagnetic ¹H NMR. The protein contains 104 aminoacid residues and a heme group with low spin Fe^III ion in the oxidized form of protein. The global secondary structure is of the α‐helix type as occurs in the case of very other cytochromes c investigated such as cyt c‐550 from Thiobacillus versutus or cyt c‐551 from Pseudomonas aeruginosa. We have studied the coordination characteristic and electronic properties of heme iron horse heart ferricytochrome c‐550 at increasing denaturing conditions (up to 3.1 M GuHCl and 288‐323 K). The ¹H T₁ values of the signals were measured and some resonance assignments made based on EXSY experiments. The electronic structure of the iron(III) is discussed on the basis of the temperature dependence of the isotropic shifts and relaxation times. These results show that it is produced a change of spin, from low‐spin iron(III) (²T₂, S=1/2) in the folded state to high‐spin iron(III) (⁶A₁, S=5/2) in the unfolded state. It seems to be possible that in the opened structure the ferricyt c‐550 loses one axial ligand (His/‐) appearing the spin transition.     

Installation of a Rigid EDTA‐Like Motif into a Protein α‐Helix for Paramagnetic NMR Spectroscopy with Cobalt(II) Ions

Coupling two copies of an iminodiacetic acid–cysteine hybrid ligand to a pair of cysteine residues positioned in an i, i+4 arrangement within a protein α‐helix leads to generation of an EDTA‐like metal ion‐binding motif. Rigid binding of a Co^II ion by this motif produces pseudo‐contact shifts suitable for paramagnetic NMR structural studies.     

Solid‐State NMR Correlation Experiments and Distance Measurements in Paramagnetic Metalorganics Exemplified by Cu‐Cyclam

We show how to record and analyze solid‐state NMR spectra of organic paramagnetic complexes with moderate hyperfine interactions using the Cu‐cyclam complex as an example. Assignment of the ¹³C signals was performed with the help of density functional theory (DFT) calculations. An initial assignment of the ¹H signals was done by means of ¹H–¹³C correlation spectra. The possibility of recording a dipolar HSQC spectrum with the advantage of direct ¹H acquisition is discussed. Owing to the paramagnetic shifting the resolution of such paramagnetic ¹H spectra is generally better than for diamagnetic solid samples, and we exploit this advantage by recording ¹H–¹H correlation spectra with a simple and short pulse sequence. This experiment, along with a Karplus relation, allowed for the completion of the ¹H signal assignment. On the basis of these data, we measured the distances of the carbon atoms to the copper center in Cu‐cyclam by means of ¹³C R₂ relaxation experiments combined with the electronic relaxation determined by EPR.     

Apo‐CopC and CopC‐Cu(II) Unfolding Characteristics in GuHCl Solution

The stability of CopC, a copper resistant protein with a Greek β‐barrel motif, in GuHCl solution was investigated by fluorescence spectra. Parameter A, characterizing position and shape of the fluorescence spectra, "phase diagram" method of fluorescence, and cupric binding capacity in GuHCl solution of different concentration showed that the denaturation transition of apo‐CopC and CopC‐Cu(II) might be fitted to a simple two‐state model. According to a two‐state model, the free energy of stabilization for apo‐CopC and CopC‐Cu(II), (17.08±0.35) and (23.81±0.45) kJ·mol^‐1 respectively, was obtained. Copper(II) increased the stability of apo‐CopC. The higher thermodynamics stability of CopC‐Cu(II) was revealed to originate in both the faster folding and the slower unfolding rates by unfolding kinetics.     

Physicochemical characterization of α‐chitin, β‐chitin,and γ‐chitin separated from natural resources

We isolated α‐chitin, β‐chitin, and γ‐chitin from natural resources by a chemical method to investigate the crystalline structure of chitin. Its characteristics were identified with Fourier transform infrared (FTIR) and solid‐state cross‐polarization/magic‐angle‐spinning (CP–MAS) ¹³C NMR spectrophotometers. The average molecular weights of α‐chitin, β‐chitin, and γ‐chitin, calculated with the relative viscosity, were about 701, 612, and 524 kDa, respectively. In the FTIR spectra, α‐chitin, β‐chitin, and γ‐chitin showed a doublet, a singlet, and a semidoublet at the amide I band, respectively. The solid‐state CP–MAS ¹³C NMR spectra revealed that α‐chitin was sharply resolved around 73 and 75 ppm and that β‐chitin had a singlet around 74 ppm. For γ‐chitin, two signals appeared around 73 and 75 ppm. From the X‐ray diffraction results, α‐chitin was observed to have four crystalline reflections at 9.6, 19.6, 21.1, and 23.7 by the crystalline structure. Also, β‐chitin was observed to have two crystalline reflections at 9.1 and 20.3 by the crystalline structure. γ‐Chitin, having an antiparallel and parallel structure, was similar in its X‐ray diffraction patterns to α‐chitin. The exothermic peaks of α‐chitin, β‐chitin, and γ‐chitin appeared at 330, 230, and 310, respectively. The thermal decomposition activation energies of α‐chitin, β‐chitin, and γ‐chitin, calculated by thermogravimetric analysis, were 60.56, 58.16, and 59.26 kJ mol^?1, respectively. With the Arrhenius law, ln β was plotted against the reciprocal of the maximum decomposition temperature as a straight line; there was a large slope for large activation energies and a small slope for small activation energies. α‐Chitin with high activation energies was very temperature‐sensitive; β‐Chitin with low activation energies was relatively temperature‐insensitive. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 3423–3432, 2004     

Solid‐State 17O NMR Spectroscopy of Paramagnetic Coordination Compounds

High‐quality solid‐state ¹⁷O (I=5/2) NMR spectra can be successfully obtained for paramagnetic coordination compounds in which oxygen atoms are directly bonded to the paramagnetic metal centers. For complexes containing V^III (S=1), Cu^II (S=1/2), and Mn^III (S=2) metal centers, the ¹⁷O isotropic paramagnetic shifts were found to span a range of more than 10 000 ppm. In several cases, high‐resolution ¹⁷O NMR spectra were recorded under very fast magic‐angle spinning (MAS) conditions at 21.1 T. Quantum‐chemical computations using density functional theory (DFT) qualitatively reproduced the experimental ¹⁷O hyperfine shift tensors.     

Proton high‐field NMR study of tomato juice

A detailed analysis of the proton high‐field (600 MHz) NMR spectra of tomato juice and pulp is reported for the first time. A combination of J‐resolved, COSY, TOCSY, DOSY, ¹H–¹³C HSQC and ¹H–¹³C HMBC 2D sequences was used to assign each spin system and to separate the components of the complex patterns in the 1D overlapped proton spectra. To obtain resolved proton spectra of tomato pulps the high‐resolution magic angle spinning technique was used; a comparison with the liquid‐state NMR spectra of the corresponding juices was accomplished. On the basis of the assignments made, the chemical composition of tomato juices from two cultivars (Red Setter and Ciliegino) was determined. Copyright © 2003 John Wiley & Sons, Ltd.     

N7‐ and N9‐substituted purine derivatives: a 15N NMR study

The ¹⁵N NMR chemical shifts of N⁷‐ and N⁹‐substituted purine derivatives were investigated systematically at the natural abundance level of the ¹⁵N isotope. The NMR chemical shifts were determined and assigned using GSQMBC, GHMBC, GHMQC and GHSQC experiments in solution. ¹⁵N cross‐polarization magic angle spinning data were recorded for selected compounds in order to study the principal values of the ¹⁵N chemical shifts. Geometric parameters obtained by using RHF/6–31G** and single‐crystal x‐ray structural analysis were used to calculate the chemical‐shielding constants (GIAO and IGLO) which were then used to assign the nitrogen resonances observed in the solid‐state NMR spectra and to determine the orientation of the principal components of the shift tensors. Copyright © 2002 John Wiley & Sons, Ltd.     

NMR Analysis of Apo Glutamine‐Binding Protein Exposes Challenges in the Study of Interdomain Dynamics

Glutamine‐binding protein (GlnBP) displays an apo, “open” and a holo, “closed” crystal form, mutually related by a rigid‐body reorientation of its domains. A fundamental question about such large‐scale conformational transitions, whether the closed state exists in the absence of ligand, is controversial in the case of GlnBP. NMR observations have indicated no evidence of the closed form, whereas experimentally validated computations have suggested a remarkable ca. 40 % population. Herein, a paramagnetic NMR strategy designed to detect the putative apo‐closed species shows that a major population of the latter is highly improbable. Further, NMR residual dipolar couplings collected under three anisotropic conditions do not reveal differential domain alignment and establish that the average solution conformation is satisfied by the apo‐open crystal structure. Our results indicate that the computational prediction of large‐scale interdomain motions is not trivial and may lead to erroneous conclusions without proper experimental validation.     

Coordination‐Induced Spin‐State Switching of an Aminyl‐Radical‐Bridged Nickel(II) Porphyrin Dimer between Doublet and Sextet States

A bis(Ni^II‐porphyrinyl)aminyl radical with meso‐C₆F₅ groups was prepared as a spin‐delocalized stable aminyl radical with a doublet spin state. Upon addition of pyridine, both Ni^II centers became hexacoordinated by accepting two axial pyridines, which triggered a spin‐state change of the Ni^II centers from diamagnetic (S=0) to paramagnetic (S=1). The resulting high‐spin Ni^II centers interact with the aminyl radical ferromagnetically to give rise to an overall sextet state (S=5/2). Importantly, this coordination‐induced spin‐state switching can be conducted in a reversible manner, in that washing of the high‐spin radical with aqueous hydrochloric acid regenerates the original doublet radical in good yield.     

NMR “Crystallography” for Uniformly (13C, 15N)‐Labeled Oriented Membrane Proteins

In oriented‐sample (OS) solid‐state NMR of membrane proteins, the angular‐dependent dipolar couplings and chemical shifts provide a direct input for structure calculations. However, so far only ¹H–¹⁵N dipolar couplings and ¹⁵N chemical shifts have been routinely assessed in oriented ¹⁵N‐labeled samples. The main obstacle for extending this technique to membrane proteins of arbitrary topology has remained in the lack of additional experimental restraints. We have developed a new experimental triple‐resonance NMR technique, which was applied to uniformly doubly (¹⁵N, ¹³C)‐labeled Pf1 coat protein in magnetically aligned DMPC/DHPC bicelles. The previously inaccessible ¹H_α–¹³C_α dipolar couplings have been measured, which make it possible to determine the torsion angles between the peptide planes without assuming α‐helical structure a priori. The fitting of three angular restraints per peptide plane and filtering by Rosetta scoring functions has yielded a consensus α‐helical transmembrane structure for Pf1 protein.     

NMR analysis of 6‐(2′,3′‐dihydro‐1′H‐inden‐1′‐yl)‐1H‐indene

¹H, ¹³C and two‐dimensional NMR analyses were applied to determine the NMR parameters of 6‐(2′,3′‐dihydro‐1′H‐inden‐1′‐yl)‐1H‐indene. The measurements were accomplished with 0.5 mg of the substance, this quantity being sufficient to determine the chemical shifts of all the H and C atoms, and also the appropriate coupling constants and to give the complete NMR resonance assignments of the molecule. The predicted patterns of the four different H atoms of the methylene groups of the indane structural element coincided completely with the complex patterns in the NMR spectra. Copyright © 2002 John Wiley & Sons, Ltd.     

Bacteriophage Tail‐Tube Assembly Studied by Proton‐Detected 4D Solid‐State NMR

Obtaining unambiguous resonance assignments remains a major bottleneck in solid‐state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three‐dimensional (3D) spectra are used. Here, we present a proton‐detected 4D solid‐state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non‐uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH, (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail‐tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.     

Solid‐state NMR Study of the YadA Membrane‐Anchor Domain in the Bacterial Outer Membrane

MAS‐NMR was used to study the structure and dynamics at ambient temperatures of the membrane‐anchor domain of YadA (YadA‐M) in a pellet of the outer membrane of E. coli in which it was expressed. YadA is an adhesin from the pathogen Yersinia enterocolitica that is involved in interactions with the host cell, and it is a model protein for studying the autotransport process. Existing assignments were sucessfully transferred to a large part of the YadA‐M protein in the E. coli lipid environment by using ¹³C‐¹³C DARR and PDSD spectra at different mixing times. The chemical shifts in most regions of YadA‐M are unchanged relative to those in microcrystalline YadA‐M preparations from which a structure has previously been solved, including the ASSA region that is proposed to be involved in transition‐state hairpin formation for transport of the soluble domain. Comparisons of the dynamics between the microcrystalline and membrane‐embedded samples indicate greater flexibility of the ASSA region in the outer‐membrane preparation at physiological temperatures. This study will pave the way towards MAS‐NMR structure determination of membrane proteins, and a better understanding of functionally important dynamic residues in native membrane environments.     

Solid‐state NMR and EPR Spectroscopy of Mn2+‐Substituted ATP‐Fueled Protein Engines

Paramagnetic metal ions deliver structural information both in EPR and solid‐state NMR experiments, offering a profitable synergetic approach to study bio‐macromolecules. We demonstrate the spectral consequences of Mg²⁺/ Mn²⁺ substitution and the resulting information contents for two different ATP:Mg²⁺‐fueled protein engines, a DnaB helicase from Helicobacter pylori active in the bacterial replisome, and the ABC transporter BmrA, a bacterial efflux pump. We show that, while EPR spectra report on metal binding and provide information on the geometry of the metal centers in the proteins, paramagnetic relaxation enhancements identified in the NMR spectra can be used to localize residues at the binding site. Protein engines are ubiquitous and the methods described herein should be applicable in a broad context.     

2,4‐Dinitrophenol‐Catalyzed α‐C(sp3)−H and C(sp)−H Bond Functionalization of Cyclic Amines and Alkynes: Highly Regio‐/Diastereoselective Synthesis of α‐Alkynyl‐3‐Amino‐2‐Oxindoles

A transition‐metal‐ and oxidant‐free DNP (2,4‐dinitrophenol)‐catalyzed atom‐economical regio‐ and diastereoselective synthesis of monofunctionalized α‐alkynyl‐3‐amino‐2‐oxindole derivatives by C?H bond functionalization of cyclic amines and alkynes with indoline‐2,3‐diones has been developed. This cascade event sequentially involves the reductive amination of indoline‐2,3‐dione by imine formation and cross coupling between C(sp³)?H and C(sp)?H of the cyclic amines and alkynes. This reaction offers an efficient and attractive pathway to different types of α‐alkynyl‐3‐amino‐2‐oxindole derivatives in good yields with a wide tolerance of functional groups. The salient feature of this methodology is that it completely suppresses the homocoupling of alkynes. To the best of our knowledge, this is the first example of a DNP‐catalyzed metal‐free direct C(sp³)?H and C(sp)?H bond functionalization providing biologically active α‐alkynyl‐3‐amino‐2‐oxindole scaffolds.     

Construction of a Metal‐Free Electron Spin System by Encapsulation of an NO Molecule Inside an Open‐Cage Fullerene C60 Derivative

A reactive radical species, nitric oxide (NO), was encapsulated in a unimolecular form inside an open‐cage fullerene derivative under high‐pressure conditions in the solid state. Surprisingly, the molecular complex showed sharp ¹H NMR signals despite the existence of the paramagnetic species inside the carbon cage. Owing to the paramagnetic shifts, the escape rate of the NO was determined experimentally. After constructing a stopper on the rim of the opening, the NO was found to stay inside the cage even at 50 °C. The ESR measurements of the powdery sample showed paramagnetic properties at low temperature. The single‐crystal X‐ray structure analysis clearly demonstrated the existence of the encapsulated NO molecule, suggesting rapid rotation inside the cage. The ¹H NMR chemical shifts displayed a large temperature dependence owing to the paramagnetic effects.     

Solid‐state 13C, 15N and 29Si NMR characterization of block copolymers with CO2 capture properties

Natural abundance solid‐state multinuclear (¹³C, ¹⁵N and ²⁹Si) cross‐polarization magic‐angle‐spinning NMR was used to study structures of three block copolymers based on polyamide and dimethylsiloxane and two polyamides, one of which including ferrocene in its structure. Assignment of most of the resonance lines in ¹³C, ¹⁵N and ²⁹Si cross‐polarization magic‐angle‐spinning NMR spectra were suggested. A comparative analysis of ¹³C isotropic chemical shifts of polyamides with and without ferrocene has revealed a systematic shift towards higher δ ‐values (de‐shielding) explained as the incorporation of paramagnetic ferrocene into the polyamide backbone. In addition, the ¹³C NMR resonance lines for ferrocene‐based polyamide were significantly broadened, because of paramagnetic effects from ferrocene incorporated in the structure of this polyamide polymer. Single resonance lines with chemical shifts ranging from 88.1 to 91.5 ppm were observed for ¹⁵N sites in all of studied polyamide samples. ²⁹Si chemical shifts were found to be around ?22.4 ppm in polydimethylsiloxane samples that falls in the range of chemical shifts for alkylsiloxane compounds. The CO₂ capture performance of polyamide‐dimethylsiloxane‐based block copolymers was measured as a function of temperature and pressure. The data revealed that these polymeric materials have potential to uptake CO₂ (up to 9.6 cm³ g^?1) at ambient pressures and in the temperature interval 30–40 °C. Copyright © 2016 John Wiley & Sons, Ltd.     

Spectroscopic and thermal characterization of the host–guest interactions between α‐, β‐ and γ‐cyclodextrins and vanadocene dichloride

Host–guest interactions between α‐, β‐ and γ‐cyclodextrins and vanadocene dichloride (Cp₂VCl₂) have been investigated by a combination of thermogravimetric analysis, differential scanning calorimetry, powder X‐ray diffraction and solid‐state and solution electron paramagnetic resonance (EPR) spectroscopy. The solid‐state results demonstrated that only β‐ and γ‐cyclodextrins form 1:1 inclusion complexes, while α‐cyclodextrin does not form an inclusion complex with Cp₂VCl₂. The β‐ and γ‐CD–Cp₂VCl₂ inclusion complexes exhibited anisotropic electron‐⁵¹V (I = 7/2) hyperfine coupling constants whereas the α‐CD–Cp₂VCl₂ system showed only an asymmetric peak with no anisotropic hyperfine constant. On the other hand, solution EPR spectroscopy showed that α‐cyclodextrin (α‐CD) may be involved in weak host–guest interactions in equilibrium with free vanadocene species. Copyright © 2008 John Wiley & Sons, Ltd.