19F NMR studies of the native and denatured states of green fluorescent protein

Biosynthetic preparation and (19)F NMR experiments on uniformly 3-fluorotyrosine-labeled green fluorescent protein (GFP) are described. The (19)F NMR signals of all 10 fluorotyrosines are resolved in the protein spectrum with signals spread over 10 ppm. Each tyrosine in GFP was mutated in turn to phenylalanine. The spectra of the Tyr --> Phe mutants, in conjunction with relaxation data and results from (19)F photo-CIDNP (chemically induced dynamic nuclear polarization) experiments, yielded a full (19)F NMR assignment. Two (19)F-Tyr residues (Y92 and Y143) were found to yield pairs of signals originating from ring-flip conformers; these two residues must therefore be immobilized in the native structure and have (19)F nuclei in two magnetically distinct positions depending on the orientation of the aromatic ring. Photo-CIDNP experiments were undertaken to probe further the structure of the native and denatured states. The observed NMR signal enhancements were found to be consistent with calculations of the HOMO (highest occupied molecular orbital) accessibilities of the tyrosine residues. The photo-CIDNP spectrum of native GFP shows four peaks corresponding to the four tyrosine residues that have solvent-exposed HOMOs. In contrast, the photo-CIDNP spectra of various denatured states of GFP show only two peaks corresponding to the (19)F-labeled tyrosine side chains and the (19)F-labeled Y66 of the chromophore. These data suggest that the pH-denatured and GdnDCl-denatured states are similar in terms of the chemical environments of the tyrosine residues. Further analysis of the sign and amplitude of the photo-CIDNP effect, however, provided strong evidence that the denatured state at pH 2.9 has significantly different properties and appears to be heterogeneous, containing subensembles with significantly different rotational correlation times.     

NMR of fd coat protein.

The conformations of the major coat protein of a filamentous bacteriophage can be described by nuclear magnetic resonance spectroscopy of the protein and the virus. The NMR experiments involve detection of the 13C and 1H nuclei of the coat protein. Both the 13C and 1H nuclear magnetic resonance (NMR) spectra show that regions of the polypeptide chain have substantially more motion than a typical globular protein. The fd coat protein was purified by gel chromatography of the SDA solubilized virus. Natural abundance 13C NMR spectra at 38 MHz resolve all of the nonprotonated aromatic carbons from the three phenylalanines, two tyrosines, and one tryptophan of the coat protein. The alpha carbons of the coat protein show at least two different classes of relaxation behavior, indicative of substantial variation in the motion of the backbone carbons in contrast to the rigidity of the alpha carbons of globular proteins. The 1H spectrum at 360 MHz shows all of the aromatic carbons and many of the amide protons. Titration of a 1H spectra gives the pKas for the tyrosines.     

Rapid sample-mixing technique for transient NMR and photo-CIDNP spectroscopy: applications to real-time protein folding

We describe the development and application of a novel rapid sample-mixing technique for real-time NMR (nuclear magnetic resonance) spectroscopy. The apparatus consists of an insert inside a conventional NMR tube coupled to a rapid injection syringe outside the NMR magnet. Efficient and homogeneous mixing of solutions in the NMR tube is achieved with a dead time of tens of milliseconds, without modification of the NMR probe or additional hardware inside the magnet. Provision is made for the inclusion of an optical fiber to allow in situ laser irradiation of samples, for example to generate photo-CIDNP (chemically induced dynamic nuclear polarization). An NMR water suppression method has been implemented to allow experiments in H(2)O as well as in deuterated solvents. The performance of the device has been tested and optimized by a variety of methods, including sensitive detection of residual pH gradients and the use of NMR imaging to monitor the extent of mixing in real time. The potential utility of this device, in conjunction with the sensitivity and selectivity of photo-CIDNP, is demonstrated by experiments on the protein hen lysozyme. These measurements involve the direct detection of spectra during real-time refolding, and the use of CIDNP pulse labeling to study a partially unfolded state of the protein under equilibrium conditions. Magnetization transfer from this disordered state to the well-characterized native state provides evidence for the remarkable persistence of nativelike elements of structure under conditions in which the protein is partially denatured and aggregation prone.     

Modulation of structure and dynamics by disulfide bond formation in unfolded states

During oxidative folding, the formation of disulfide bonds has profound effects on guiding the protein folding pathway. Until now, comparatively little is known about the changes in the conformational dynamics in folding intermediates of proteins that contain only a subset of their native disulfide bonds. In this comprehensive study, we probe the conformational landscape of non-native states of lysozyme containing a single native disulfide bond utilizing nuclear magnetic resonance (NMR) spectroscopy, small-angle X-ray scattering (SAXS), circular dichroism (CD) data, and modeling approaches. The impact on conformational dynamics varies widely depending on the loop size of the single disulfide variants and deviates significantly from random coil predictions for both NMR and SAXS data. From these experiments, we conclude that the introduction of single disulfides spanning a large portion of the polypeptide chain shifts the structure and dynamics of hydrophobic core residues of the protein so that these regions exhibit levels of order comparable to the native state on the nanosecond time scale.     

芳香环状聚酯二聚体的结构表征

通过基质辅助激光解析电离飞行时间质谱以及核磁共振技术对芳香环状聚酯二聚体的结构进行了表征.质谱分析结果发现除了目标化合物的质子化分子离子峰外,未出现更多的碎片峰,而核磁共振结果对芳香环状齐聚物的氢以及碳的位置给予了确认.从而为芳香环状齐聚物的结构分析提供了一种新的分析方法.     

Structures behind the amyloid aggregation of α-synuclein: an NMR based approach

The misfolding of proteins into a toxic conformation is proposed to be at the molecular foundation of a number of neurodegenerative disorders including Alzheimer's and Parkinson's diseases. Evidence that α-synuclein amyloidogenesis plays a causative role in the development of Parkinson's disease is furnished by a variety of genetic, neuropathological and biochemical studies. There is a major interest in understanding the structural and toxicity features of the various species populated along the aggregation pathway of this protein. The development of multidimensional nuclear magnetic resonance (NMR) spectroscopy in liquid and solid state over the last decade has significantly increased the scope of molecules that are amenable for structural studies. The aim of this review is to provide a picture of how NMR tools were used in concert to decipher the structural and dynamic properties of the intrinsically disordered protein α-synuclein in its native, oligomeric, fibril and membrane-bound states. Understanding the structural and molecular basis behind the aggregation pathway of α-synuclein is key to advance in the design of a therapeutic strategy.     

Temperature dependence of domain motions of calmodulin probed by NMR relaxation at multiple fields

Interdomain motions of Ca(2+)-ligated calmodulin were characterized by analyzing the nuclear magnetic resonance (15)N longitudinal relaxation rate R(1), transverse relaxation rate R(2), and steady-state {(1)H}-(15)N NOE of the backbone amide group at three different magnetic field strengths (18.8, 14.1, and 8.5 T) and four different temperatures (21, 27, 35, and 43 degrees C). Between 35 and 43 degrees C, a larger than expected change in the amplitude and the time scale of the interdomain motion for both N- and C-domains was observed. We attribute this to the shift in population of four residues (74-77) in the central linker from predominantly helical to random coil in this temperature range. This is consistent with the conformation of these residues in the calmodulin-peptide complex, where they are nonhelical. The doubling of the disordered region of the central helix (residues 78-81 at room temperature) when temperature is raised from 35 to 43 degrees C results in larger amplitude interdomain motion. Our analysis of the NMR relaxation data quantifies subtle changes in the interdomain dynamics and provides an additional tool to monitor conformational changes in multidomain proteins.     

Differentiation of the local structure around tryptophan 51 and 64 in recombinant human erythropoietin by tryptophan phosphorescence

Abstract Recombinant human erythropoietin is a 4-helix bundle, glycosylated cytokine containing three tryptophan residues at positions 51, 64 and 88 whose phosphorescence emission may represent a sensitive probe of the structure at multiple sites near or at the protein surface. This report characterizes the phosphorescence properties (spectral energy, thermal spectral relaxation and phosphorescence lifetime), from low temperature glasses to ambient temperature, of the native protein plus that of three single point mutation analogs where each Trp was replaced by Phe. The structural information inferred from the phosphorescence parameters was essentially in good agreement with the structure of the Escherichia coli-produced nonglycosylated protein determined by nuclear magnetic resonance (Cheetham et al., Nat Struct Biol [1998] 5:861). The results showed that the fluorescence and phosphorescence spectra of the native protein were entirely due to independent contributions of Trp51 and Trp64 and that Trp88 was quenched under all conditions. The phosphorescence emissions of Trp51 and Trp64 were differentiated by their unique spectra at 77 K with Trp64 exhibiting an unusually blueshifted spectrum likely due to the attractive interaction of Arg110 and Lys116 with the ground state dipole of Trp64. In the native protein the room temperature phosphorescence lifetime of Trp64 was relatively short with a time of 1.62 ms whereas the lifetime of Trp51 was five-fold longer. Characterization of the single point mutation analogs showed that each lifetime was composed of multiple components revealing the presence of multiple stable conformations of the protein at these surface sites.     

Billion‐Fold Enhancement in Sensitivity of Nuclear Magnetic Resonance Spectroscopy for Magnesium Ions in Solution

β‐nuclear magnetic resonance (NMR) spectroscopy is highly sensitive compared to conventional NMR spectroscopy, and may be applied for several elements across the periodic table. β‐NMR has previously been successfully applied in the fields of nuclear and solid‐state physics. In this work, β‐NMR is applied, for the first time, to record an NMR spectrum for a species in solution. ³¹Mg β‐NMR spectra are measured for as few as 10⁷ magnesium ions in ionic liquid (EMIM‐Ac) within minutes, as a prototypical test case. Resonances are observed at 3882.9 and 3887.2 kHz in an external field of 0.3 T. The key achievement of the current work is to demonstrate that β‐NMR is applicable for the analysis of species in solution, and thus represents a novel spectroscopic technique for use in general chemistry and potentially in biochemistry.     

Insight into the structure of silver cyanide from (13)C and (15)N solid-state NMR spectroscopy

The structure of silver cyanide has been investigated by solid-state multinuclear magnetic resonance spectroscopy. Carbon-13 and nitrogen-15 NMR spectra of magic-angle-spinning (MAS) and stationary powder samples of isotopically enriched Ag(13)CN, Ag(13)C(15)N, and AgC(15)N have been acquired at the external applied magnetic field strengths 4.7, 7.05, and 9.4 T. Axially symmetric carbon and nitrogen chemical shift (CS) tensors provide evidence for linearity of the polymeric (-Ag-CN-)(n)() chains. A two-site model is required to successfully simulate the (13)C MAS NMR line shape, which is dominated by indirect nuclear spin-spin coupling between (109/107)Ag and (13)C nuclei. In combination with relativistic zeroth-order regular approximation density functional theory (ZORA-DFT) calculations on model AgCN fragments, the (13)C MAS NMR results show that 30 +/- 10% of the silver sites are disordered, that is, either -NC-Ag-CN- or -CN-Ag-NC-, and 70 +/- 10% of the silver sites are ordered, that is, -NC-Ag-NC-. Effective dipolar coupling data extracted from (13)C NMR spectra of stationary samples allow an upper limit of 1.194 A to be placed on the carbon-nitrogen internuclear distance. After incorporation of the effects of anisotropic indirect nuclear spin-spin coupling and motional averaging on the NMR-derived distance, a corrected value of r(CN) = 1.16 +/- 0.03 A is obtained. This work provides an example of the type of information which may be obtained from solid-state NMR studies of disordered materials and how such information may complement that available from diffraction studies.     

Ground- and excited-state aromaticity and antiaromaticity in benzene and cyclobutadiene

The aromaticity and antiaromaticity of the ground state (S 0), lowest triplet state (T 1), and first singlet excited state (S 1) of benzene, and the ground states (S 0), lowest triplet states (T 1), and the first and second singlet excited states (S 1 and S 2) of square and rectangular cyclobutadiene are assessed using various magnetic criteria including nucleus-independent chemical shifts (NICS), proton shieldings, and magnetic susceptibilities calculated using complete-active-space self-consistent field (CASSCF) wave functions constructed from gauge-including atomic orbitals (GIAOs). These magnetic criteria strongly suggest that, in contrast to the well-known aromaticity of the S 0 state of benzene, the T 1 and S 1 states of this molecule are antiaromatic. In square cyclobutadiene, which is shown to be considerably more antiaromatic than rectangular cyclobutadiene, the magnetic properties of the T 1 and S 1 states allow these to be classified as aromatic. According to the computed magnetic criteria, the T 1 state of rectangular cyclobutadiene is still aromatic, but the S 1 state is antiaromatic, just as the S 2 state of square cyclobutadiene; the S 2 state of rectangular cyclobutadiene is nonaromatic. The results demonstrate that the well-known "triplet aromaticity" of cyclic conjugated hydrocarbons represents a particular case of a broader concept of excited-state aromaticity and antiaromaticity. It is shown that while electronic excitation may lead to increased nuclear shieldings in certain low-lying electronic states, in general its main effect can be expected to be nuclear deshielding, which can be substantial for heavier nuclei.     

Mass spectrometry assisted assignment of NMR resonances in reductively 13C-methylated proteins

Reductive 13C-methylation of proteins has been used as an isotope labeling strategy to study protein structure, function, and dynamics by nuclear magnetic resonance (NMR) spectroscopy. However, assigning the resulting 13C-dimethylamine peaks in a 1H-13C NMR spectrum has proved to be difficult, but it is important to expand the scope of the method. The assignment strategy presented here utilizes mass spectrometry (MS) for sequence identification and varying 13C/12C isotope ratios to correlate with NMR data. The site-specific reactivity of the lysines and N-terminal amine of a protein is exploited to produce a sample with varying 13C/12C ratios at each dimethylamine. MS and NMR are used to quantitate and correlate these ratios in order to assign peaks in the 1H-13C NMR spectrum. Hen egg white lysozyme was used as a model protein to demonstrate this assignment strategy.     

Solution 1H NMR of the molecular and electronic structure of the heme cavity and substrate binding pocket of high-spin ferric horseradish peroxidase: effect of His42Ala mutation.

Solution 1H NMR has been used to assign a major portion of the heme environment and the substrate-binding pocket of resting state horseradish peroxidase, HRP, despite the high-spin iron(III) paramagnetism, and a quantitative interpretive basis of the hyperfine shifts is established. The effective assignment protocol included 2D NMR over a wide range of temperatures to locate residues shifted by paramagnetism, relaxation analysis, and use of dipolar shifts predicted from the crystal structure by an axial paramagnetic susceptibility tensor normal to the heme. The most effective use of the dipolar shifts, however, is in the form of their temperature gradients, rather than by their direct estimation as the difference of observed and diamagnetic shifts. The extensive assignments allowed the quantitative determination of the axial magnetic anisotropy, Deltachi(ax) = -2.50 x 10(-8) m(3)/mol, oriented essentially normal to the heme. The value of Deltachi(ax) together with the confirmed T(-2) dependence allow an estimate of the zero-field splitting constant D = 15.3 cm(-1), which is consistent with pentacoordination of HRP. The solution structure was generally indistinguishable from that in the crystal (Gajhede, M.; Schuller, D. J.; Henriksen, A.; Smith, A. T.; Poulos, T. L. Nature Structural Biology 1997, 4, 1032-1038) except for Phe68 of the substrate-binding pocket, which was found turned into the pocket as found in the crystal only upon substrate binding (Henriksen, A.; Schuller, D. J.; Meno, K.; Welinder, K. G.; Smith, A. T.; Gajhede, M. Biochemistry 1998, 37, 8054-8060). The reorientation of several rings in the aromatic cluster adjacent to the proximal His170 is found to be slow on the NMR time scale, confirming a dense, closely packed, and dynamically stable proximal side up to 55 degrees C. Similar assignments on the H42A-HRP mutant reveal conserved orientations for the majority of residues, and only a very small decrease in Deltachi(ax) or D, which dictates that five-coordination is retained in the mutant. The two residues adjacent to residue 42, Ile53 and Leu138, reorient slightly in the mutant H42A protein. It is concluded that effective and very informative 1H NMR studies of the effect of either substrate binding or mutation can be carried out on resting state heme peroxidases.     

Characterization of dextrin hydrogels by FTIR spectroscopy and solid state NMR spectroscopy

Fourier transform infrared (FTIR) and ¹³C solid state nuclear magnetic resonance (NMR) spectroscopy were used to study dextrin structural changes occurring upon hydrogel formation by vinyl acrylate (VA) grafting and subsequent free radical polymerization. The degrees of VA substitution (DS) and polymerization (DP) were quantified up to 40%VA by FTIR intensity measurements and partial least squares (PLS)/FTIR, the latter being a faster and less error-prone method. Above 40%VA, both parameters are underestimated by FTIR. A spin counting NMR experiment showed high carbon observabilities for hydrogels and improved PLS/NMR models were achieved for DS and DP determination. Alternative NMR integration methods are hindered by the broad VA peaks and need for area correction, due to their CP dynamics. NMR changes in C1 profile showed that a single helical conformation predominates at lower %VA, being replaced by disordered conformations as %VA increases. Furthermore, a correlation FTIR/NMR study indicated that ring conformations are significantly affected in hydrogels, compared to unpolymerized dextrin.     

Weak and Transient Protein Interactions Determined by Solid‐State NMR

Despite their roles in controlling many cellular processes, weak and transient interactions between large structured macromolecules and disordered protein segments cannot currently be characterized at atomic resolution by X‐ray crystallography or solution NMR. Solid‐state NMR does not suffer from the molecular size limitations affecting solution NMR, and it can be applied to molecules in different aggregation states, including non‐crystalline precipitates and sediments. A solid‐state NMR approach based on high magnetic fields, fast magic‐angle sample spinning, and deuteration provides chemical‐shift and relaxation mapping that enabled the characterization of the structure and dynamics of the transient association between two regions in an 80 kDa protein assembly. This led to direct verification of a mechanism of regulation of E. coli DNA metabolism.     

Conformations of Carnosine in Aqueous Solutions by All-Atom Molecular Dynamics Simulations and 2D-NOSEY Spectrum

All-atom molecular simulations and two-dimensional nuclear overhauser effect spectrum have been used to study the conformations of carnosine in aqueous solution. Intramolecular distances, root-mean-square deviation, radius of gyration, and solvent-accessible surface are used to characterize the properties of the carnosine. Carnosine can shift between extended and folded states, but exists mostly in extended state in water. Its preference for extension in pure water has been proven by the 2D nuclear magnetic resonance (NMR) experiment. The NMR experimental results are consistent with the molecular dynamics simulations.     

巴比妥酸楔形棒状液晶分子的合成、性质及与三嗪衍生物的氢键识别组装体

合成了一端含巴比妥酸, 另一端含带三条烷基链苯甲酸酯楔形单元, 中间为苯乙烯共轭单元的棒状分子5-{4-[3,4,5-三(十二烷氧基)苯甲酸酯]苯乙烯}-(1H,3H)-2,4,6嘧啶三酮(BA³/12); 采用偏光显微镜(POM)、 示差扫描量热法(DSC)、 X射线衍射(XRD)、 扫描电子显微镜(SEM)、 红外光谱(IR)、 核磁共振波谱(NMR)和荧光光谱等对其进行了表征. 结果表明, BA³/12能自组装形成晶格结构为c2mm的长方柱相液晶; 红外光谱及核磁共振氢谱表征数据初步证实了BA³/12与三嗪化合物6-(5-{4-[3,4-双(十二烷氧基)]苄氧基}苯基)噻吩-2,4-二氨基-1,3,5三嗪(1T²/12)形成的等摩尔氢键复合物BA/T的结构; BA/T不仅具有液晶性质且能形成具有三维网络状结构的超分子凝胶.     

An investigation of complexes of some model tripeptides containing phenylalanine and tyrosine residues with DNA by Fourier1H NMR spectroscopy

Complexes of native and denatured DNA with model tripeptides containing phenylalanine or tyrosine residues flanked by lysine or arginine residues, respectively have been investigated by pulsed Fourier¹H NMR spectroscopy. The existence of shifts into the strong-field region of the signals of aromatic protons of the model tripeptides in the complexes both with native and with denatured DNA has been shown. Results have been obtained that indicate the possibility of the intercalation of the side chains of aromatic amino acid residues into the DNA double helix.     

Chemical,Thermal and Antioxidant Properties of Lignins Solubilized during Soda/AQ Pulping of Orange and Olive Tree Pruning Residues

Some agroforestry residues such as orange and olive tree pruning have been extensively evaluated for their valorization due to its high carbohydrates content. However, lignin-enriched residues generated during carbohydrates valorization are normally incinerated to produce energy. In order to find alternative high added-value applications for these lignins, a depth characterization of them is required. In this study, lignins isolated from the black liquors produced during soda/anthraquinone (soda/AQ) pulping of orange and olive tree pruning residues were analyzed by analytical standard methods and Fourier-transform infrared spectroscopy (FTIR), nuclear magnetic resonance (solid state ¹³C NMR and 2D NMR) and size exclusion chromatography (SEC). Thermal analysis (thermogravimetric analysis (TGA), differential scanning calorimetry (DSC)) and antioxidant capacity (Trolox equivalent antioxidant capacity) were also evaluated. Both lignins showed a high OH phenolic content as consequence of a wide breakdown of β-aryl ether linkages. This extensive degradation yielded lignins with low molecular weights and polydispersity values. Moreover, both lignins exhibited an enrichment of syringyl units together with different native as well as soda/AQ lignin derived units. Based on these chemical properties, orange and olive lignins showed relatively high thermal stability and good antioxidant activities. These results make them potential additives to enhance the thermo-oxidation stability of synthetic polymers.     

Latex‐state NMR spectroscopy for quantitative analysis of epoxidized deproteinized natural rubber

Method of quantitative analysis through latex‐state ¹³C NMR spectroscopy was established for in situ determination of epoxy group content of epoxidized natural rubber in latex stage. The epoxidized natural rubber latex was prepared by epoxidation of deproteinized natural rubber with freshly prepared peracetic acid in latex stage. The resulting epoxidized deproteinized natural rubber (EDPNR) latex was characterized through latex‐state ¹³C NMR spectroscopy. Chemical shift values of signals of latex‐state ¹³C NMR spectrum for EDPNR were similar to those of solution‐state ¹³C NMR spectrum for EDPNR. Resolution of latex‐state ¹³C NMR spectrum was gradually improved as temperature for the nuclear magnetic resonance (NMR) measurement increased to 70°C. Signal‐to‐noise ratio of latex‐state ¹³C NMR measurement was similar to that of solution‐state ¹³C NMR measurement at temperature above 50°C. The epoxy group content determined through latex‐state NMR spectroscopy was proved to be the same as that determined through solution‐state NMR spectroscopy. Copyright © 2017 John Wiley & Sons, Ltd.