Molecular physiology of rhodopsin: Computer simulation

Computer simulation is used for comparative investigation of the molecular dynamics of rhodopsin containing the chromophore group (11-cis-retinal) and free opsin. Molecular dynamics is traced within a time interval of 3000 ps; 3 × 10⁶ discrete conformational states of rhodopsin and opsin are obtained and analyzed. It is demonstrated that the presence of the chromophore group in the chromophore center of opsin influences considerably the nearest protein environment of 11-cis-retinal both in the region of the β-ionone ring and in the region of the protonated Schiff base bond. Based on simulation results, a possible intramolecular mechanism of keeping rhodopsin as a G-protein-coupled receptor in the inactive state, i.e., the chromophore function as an efficient ligand antagonist, is discussed.     

High-Temperature Phase Transition in N(CH3)4CdCl3 Studied Using Static NMR and MAS NMR

To clarify the nature of microscopic structural changes of N(CH₃)₄CdCl₃ at high temperatures, the nuclear magnetic resonance (NMR) spectra of the protons and carbons in N(CH₃)₄CdCl₃ were measured. NMR studies of the ¹H and ¹³C spin–lattice relaxation time, T _1ρ, in the rotating frame were also performed. No changes in the T _1ρ of ¹H and ¹³C associated with the N(CH₃)₄ groups were observed at the high-temperature transition from phase I to phase I′. However, the ¹⁴N NMR spectra reflected changes in the structural geometry during the transition to phase I′, indicating that this transition is driven by N(CH₃)₄.     

研究CTG和CCTG重复序列溶液结构的挑战

脱氧核糖核酸(DNA)重复序列的基因不稳定性和遗传神经退行性疾病有关. 通过在基因复制中形成异常结构,CTG和CCTG重复序列进行自我扩张,并会分别导致强直性肌营养不良类型1 (DM1) 和强直性肌营养不良类型2 (DM2). 尽管x-射线衍射晶体分析法在解决基因结构上是一个强大的技术,但是CTG和CCTG这些重复序列可能是因为其固有的灵活性,很难得到晶体,所以现在还没能成功鉴定其结构. 因此,核磁共振 (NMR) 光谱仍然是在单个脱氧核糖核酸层次上研究DNA结构的唯一技术. 最近,研究人员克服了包括由于重复系列导致的严重信号重叠、存在的多种构象及构象互换导致的光谱复杂性的挑战, 顺利运用核磁共振技术研究了CTG和CCTG重复序列的结构. 通过适当的样品设计、样品操作技术、次序修改、及/或单个脱氧核糖核酸替代实验,利用¹H 和³¹P核磁共振波谱法确定了CTG和 CCTG 重复序列的结构特点. 该综述回顾详细阐述上述研究中所采用的技术.     

27Al NMR spectroscopy of minerals and related materials

We present a review of the applications of²⁷Al NMR methods to investigations of the structures of minerals, primarily alumino-silicates, and related synthetic compounds. Such materials are ubiquitous in the earth and other terrestrial planets. Because of their diverse structures and compositions, they also provide examples of many situations in which²⁷Al NMR spectroscopy can provide useful information. Thus, they serve well as model compounds for synthetic crystalline and amorphous materials and usefully illustrate the applications of many techniques. The advent of high-field superconducting magnets (H ₀>9 T) has made application of²⁷Al NMR to solids much more effective than it was previously, and we focus primarily on these recent applications but also discuss older, single-crystal data.²⁷Al NMR methods can be used for many purposes in investigations of solids. Here we emphasize the following. 1) Determination of the Al coordination number and the polymerization of tetrahedrally coordinated Al. 2) Determination of tetrahedral Al/octahedral Al ratios. 3) Investigation of tetrahedral Al, Si order/disorder in, especially, framework-structure alumino-silicate phases. 4) Investigation of the static structural changes and dynamical behavior of crystals undergoing structural phase transitions. 5) Investigation of the local symmetry of Al-sites through the quadrupole coupling constant and asymmetry parameter.     

Structural changes of piezoelectric La3Ga5SiO14 induced by paramagnetic ions revealed by Ga multiple quantum magic angle spinning

Experimental evidence that nuclear magnetic resonance (NMR) can detect structural changes of piezoelectric La₃Ga₅SiO₁₄ induced by dilute paramagnetic ions is presented. Gd³⁺ and Eu³⁺ cations have been incorporated into La₃Ga₅SiO₁₄ monocrystals. As expected, the line-width of the tetrahedral ²⁹Si magic angle spinning (MAS) NMR spectra as well as the inverse of the T₂ relaxation time of ⁷¹Ga increases with the concentration of the paramagnetic ions. A surprising result is shown by ⁷¹Ga multiple quantum (MQ) MAS NMR spectrum, which changes with the concentration of paramagnetic ions. The changes in the ⁷¹Ga MQMAS spectra can be explained by a more ordonated distribution of Ga ions inside the oxygen tetrahedra. The ⁷¹Ga MQMAS NMR spectra allow identification of the one octahedral and two tetrahedral Ga sites.     

Structural investigation of non-stoichiometric CuInS<Subscript>2</Subscript> by <Superscript>63</Superscript>Cu and <Superscript>115</Superscript>In nuclear magnetic resonance

Results of studies of non-stoichiometric CuInS₂ semiconductor by ⁶³Cu and ¹¹⁵In nuclear magnetic resonance are presented. It was established that deviation of the composition from stoichiometry causes a quadrupolebroadened region of the NMR spectrum to change most. In this case a central peak whose shape is governed by the chemical shift anisotropy remains unaffected. NMR spectra reveal two types of structural distortions in the nearest surroundings of the In atoms.     

A 59Co NMR study to observe the effects of ball milling on small ferromagnetic cobalt particles

To demonstrate the potential of nuclear magnetic resonance (NMR) spectroscopy for investigating detailed structural properties in ferromagnetic materials, three different particle sized cobalt (Co) powders have been ball milled for 24 h are accurately characterised by internal-field ⁵⁹Co NMR. The ⁵⁹Co NMR spectra show distinct resonance bands corresponding to the different Co sites, face-centred-cubic (fcc), hexagonal-close-packed (hcp) and stacking faults (sfs), in Co metal powders. The hcp+fcc→hcp phase transition encouraged by ball-milling was observed and quantitative values for each Co environment were obtained.     

NMR and Mössbauer study of multiferroic BiFeO<Subscript>3</Subscript>

Pulse nuclear magnetic resonance (NMR) was applied in studying the effect of ⁵⁷Fe isotope content in multiferroic BiFeO₃ on the shape of NMR spectra at 4.2 K. Strong dependences of the NMR line shape on the isotope content and transverse relaxation time were found. Consideration of these effects on NMR line shape shows that there is an undisturbed (with no anharmonicity effect) space spin-modulated structure of the cycloid type in BiFeO₃. The Mössbauer effect was also used to investigate the perovskite BiFeO₃ at 650, 295, and 87 K. Experimental spectra allowed us to obtain the distribution of hyperfine fields, which was found to be consistent with studies of the NMR line shape. The local electronic and magnetic states of the iron ion were measured.     

New Multidimensional Editing Experiments for Measurement of Amide Deuterium Isotope Effects on CChemical Shifts inC,N-Labeled Proteins

Novel multidimensional NMR pulse sequences for measurement of the three- and four-bond amide deuterium isotope effect on the chemical shifts of¹³C^βin proteins are presented. The sequences result in editing into two subspectra of a heteronuclear triple resonance spectrum {ω(N), ω(C^β), ω(H^α)} according to there being a deuterium or a proton attached to¹⁵N for the pertinent correlations. The new experiments are demonstrated by an application to the first module of the¹³C,¹⁵N-labeled protein RAP 18-112 (N-terminal module of α₂-macroglobulin receptor associated protein).     

NMR Studies of Heat-Induced Transitions in Structure and Cation Binding Environments of a Strontium-Saturated Swelling Mica

In this work, we combine ²⁷Al, ²⁹Si, ¹⁹F, and ²³Na magic-angle spinning (MAS) nuclear magnetic resonance (NMR) to characterize the structure and interlayer cation environments in a strontium-saturated member of the swelling mica family before and after a heat-induced collapse of the interlayer space. The ²⁷Al and ²⁹Si MAS NMR demonstrate that the sample consists mainly of swelling mica, though the composition does not match the ideal structural formula. Aluminum NMR also shows that a portion of the aluminum shifts from a tetrahedral to an octahedral coordination environment upon heating. Changes in the ²⁹Si and ¹⁹F NMR after heating are consistent with a structural rearrangement of the tetrahedral sheet to permit the binding of larger cations in the ditrigonal cavity. The ²³Na MAS NMR results indicate the presence of three unique sodium environments before and after heating. The heat-invariant resonance is consistent with the presence of sodium carbonate. The other two resonances are associated with interlayer sodium and reflect a migration of sodium to a dominantly anhydrous ditrigonal binding structure with heating. Quantitative elemental analysis and NMR data presented here suggest strontium is bound deep within the ditrigonal cavity of the collapsed micas. Authors' address: Karl T. Mueller, 104 Chemistry Building, Penn State University, University Park, PA 16802, USA     

The Surface Metal Site in Blc. viridis Photosynthetic Bacterial Reaction Centers: Cu2+ as a Probe of Structure, Location, and Flexibility

Metal ion binding to a surface site on photosynthetic reaction centers (RCs) modulates light-induced electron and proton transfer events in the RC. Whereas many studies have elucidated aspects of metal ion modulation events in Rhodobacter sphaeroides RCs, much less is understood about the surface site in Blastochloris viridis (Blc. viridis) RCs. Interestingly, electron paramagnetic resonance studies revealed two spectroscopically distinct Cu²⁺ surface site environments in Blc. viridis RCs. Herein, Cu²⁺ has been used to spectroscopically probe the structure of these Cu²⁺ site(s) in response to freezing conditions, temperature, and charge separation. One Cu²⁺ environment in Blc. viridis RCs, termed Cu_A, exhibits temperature-dependent conformational flexibility. Different conformation states of the Cu_A²⁺ site are trapped when the RC is frozen in the dark either by fast-freeze or slow-freeze procedure. The second Cu²⁺ environment, termed Cu_B, is structurally invariant to different freezing conditions and shows resolved hyperfine coupling to three nitrogen atoms. Cu²⁺ is most likely binding at the same location on the RC, but in different coordination environments which may reflect two distinct conformational states of the isolated Blc. viridis RC protein.     

Toxic effects of anticancer drug doxorubicin to bovine serum albumin evaluated by spectroscopic methods

The aim of this present work is to investigate the interaction between doxorubicin and bovine serum albumin (BSA) in simulated physiological conditions by spectroscopic methods to reveal potential toxic effects of the drug. The results reflected that doxorubicin made the fluorescence quenching of BSA through a static quenching procedure. The binding constants at 293, 298, and 303 K were obtained as 2.53 × 10⁵, 8.13 × 10⁴, and 3.59 × 10⁴ M^–1, respectively. There may be one binding site of doxorubicin on BSA. The thermodynamic parameters indicated that the interaction between doxorubicin and BSA was driven mainly by hydrogen bonding and electrostatic forces. Synchronous fluorescence spectra and circular dichroism (CD) results showed doxorubicin binding slightly changed the conformation of BSA with secondary structural content changes. Förster resonance energy transfer (FRET) study revealed high possibility of energy transfer with doxorubicin-Trp-212 distance of 3.48 nm. The results of the present study may provide valuable information for studying the distribution, toxicological and pharmacological mechanisms of doxorubicin in vivo.     

Silicon-29 NMR Spectroscopy Study of the Effect of Tetraphenylammonium (TPA) as a Template on Distribution of Silicate Species on Alkaline Aqueous and Alcoholic Silicate Solutions

Silicon-29 nuclear magnetic resonance (NMR) spectroscopy is used to characterize aqueous and non-aqueous alkaline solutions of tetraphenylammonium (TPA) silicates. Effect of the TPA cation on the equilibrium of silicate oligomers in aqueous and non-aqueous alkaline silicate solutions is investigated using ²⁹Si NMR spectra. It was found that the TPA cation had a structural directing role, directing the silicate species to form minor amounts of high order silicate anion in the presence of a high concentration of silicon. ²⁹Si NMR spectra of TPA silicate solutions indicate that considerable changes occur by changing the Si/TPA ratio. Also the effect of different alcohols on the distribution of silicate species is investigated. The results obtained show that distribution of these species is affected by the presence of alcohols and that maximum variations in this distribution are observed in the presence of methanol.     

Multinuclear NMR Study of Structure and Mobility in Cyclic Model Lithium Conducting Systems

The transport of the lithium ions is the basis of lithium ion conductivity of currently used electrolytes. Understanding how the transport of lithium ions within the matrix is influenced by the interactions with solvating moieties is needed to improve their performance. Along these lines well-defined model compounds based on cyclotriphosphazene (CTP) and hexaphenylbenzene (HPB) cores, bearing side groups of ethylene carbonate, a common solvent for lithium salts used as electrolytes in Li-ion batteries (Thielen et al. Chem. Mater, 23, 2120, 2011) and blended with different amounts of Lithium bis(trifluoromethanesulfonyl) imide (LiTFSI) have been studied by multinuclear nuclear magnetic resonance (NMR) spectroscopy. The local dynamics of the matrix was probed by ¹H and ³¹P NMR, while the local dynamics of the Li⁺ cations was unraveled by ⁷Li and ¹³C NMR. Transport of both ions was studied by pulsed-field gradient (PFG) NMR. Based on the different temperature dependences of the dynamics the bulk ion transport is not attributed to local dynamics, but to translational diffusion best characterized by PFG NMR. Although the glass transition temperatures of the blends are low, their conductivities are only in the range of typical polymer electrolytes. The results of NMR spectroscopy are in accord with the conjecture that the coordination between the cyclic carbonate functionality and the Li⁺-ion is too tight to allow for fast ion dynamics.     

1H–13C hetero-nuclear dipole–dipole couplings of methyl groups in stationary and magic angle spinning solid-state NMR experiments of peptides and proteins

¹³C NMR of isotopically labeled methyl groups has the potential to combine spectroscopic simplicity with ease of labeling for protein NMR studies. However, in most high resolution separated local field experiments, such as polarization inversion spin exchange at the magic angle (PISEMA), that are used to measure ¹H–¹³C hetero-nuclear dipolar couplings, the four-spin system of the methyl group presents complications. In this study, the properties of the ¹H–¹³C hetero-nuclear dipolar interactions of ¹³C-labeled methyl groups are revealed through solid-state NMR experiments on a range of samples, including single crystals, stationary powders, and magic angle spinning of powders, of ¹³C₃ labeled alanine alone and incorporated into a protein. The spectral simplifications resulting from proton detected local field (PDLF) experiments are shown to enhance resolution and simplify the interpretation of results on single crystals, magnetically aligned samples, and powders. The complementarity of stationary sample and magic angle spinning (MAS) measurements of dipolar couplings is demonstrated by applying polarization inversion spin exchange at the magic angle and magic angle spinning (PISEMAMAS) to unoriented samples.     

Structural Nature of 7Li and 11B Sites by Static NMR and MAS NMR in Nonlinear Optical Material LiCsB6O10

The relationship between structure and nonlinear optical properties in LiCsB₆O₁₀ is characterized using single-crystal nuclear magnetic resonance (NMR) and magic-angle spinning (MAS) NMR. Although the quadrupole parameters for B(1) and B(2) sites were obtained using single-crystal NMR, the T ₁ values for these atomic sites could not be distinguished in this way. Thus, the structural nature of lithium and boron sites in LiCsB₆O₁₀ was investigated using MAS NMR. B(1) and B(2) sites could be distinguished based on the spectrum and T _1ρ obtained from ¹¹B MAS NMR. In addition, the T ₁ and T _1ρ values and activation energies for ⁷Li and ¹¹B are compared. No significant changes were seen in the T _1ρ at the lithium and boron nuclei in LiCsB₆O₁₀.     

Magnetic resonance study of the two-dimensional spin diffusion in the Heisenberg paramaget (C18H37NH3)2MnCl4

¹H nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) techniques were employed to study the perovskite-type layered structure compound (C₁₈H₃₇NH₃)₂MnCl₄ undergoing structural phase transitions. The spin relaxation was found to sensitively reflect the two-dimensional electron spin diffusion.     

Proton NMR studies of the NaAlH4 structure

Advanced nuclear magnetic resonance (NMR) techniques were applied to study the local environments of hydrogen in NaAlH₄. Through a combined application of the magic echo (ME) and the magic Hahn echo (MHE) sequences the hetero- and homonuclear contributions to the dipolar second moment (M₂) were determined separately. The obtained values are compared with the second moments calculated by the van Vleck formulae, using structural data determined by neutron scattering on NaAlD₄. This comparison indicates structural differences between NaAlH₄ and NaAlD₄. A model is suggested for the orientation of the [AlH₄]⁻ tetrahedra in NaAlH₄, for which the calculated second moments are in good agreement with the experimentally observed values.     

Thermodynamically Induced Conformational Changes of the Cyanobacterial Circadian Clock Protein KaiB

Site-directed spin labeling electron spin resonance (ESR) was applied to investigate the local environment of the cyanobacterial circadian clock protein KaiB. We prepared five cysteine residue-substituted mutants of KaiB labeled with maleimide spin label (MSL). By comparing the ESR spectra of KaiBs carrying MSL at different positions (Thr64, Lys67, Tyr94, Gly98, and Ala101), local conformational changes were identified. The ESR spectra of MSL-T64C and MSL-K67C showed the relatively slow motion of MSL characterized by τ?=?79 and 59?ns at 4°C, respectively. The spectra of MSL-Y94C, MSL-G98C and MSL-A101C showed relatively fast motion characterized by τ?=?8.0, 4.1 and 3.1?ns at 4°C, respectively. These differences were explained by the local environments of the position in KaiB. On incubation at 40°C for 24?h, all ESR spectra of the labeled KaiBs changed, which can be explained by the structural relaxation of KaiB.     

The influence of easy direction of magnetisation on 59Co NMR spectrum in R2(Co1−xMnx)17 compounds

The spin echo NMR spectra of ⁵⁹Co in R₂(Co_1-xMn_x)₁₇, (R = Y, Gd) measured at 4.2 K are reported. The large shift of resonance lines is observed, that is explained as caused by reorientation of easy axis of magnetisation from easy plane to easy direction (c axis). It is suggested to explain quantitatively the spectra, that only two of four Co sites (9d and 18f) in R₂Co₁₇ structure play a dominant role in determining of anisotropy energy and the Co atoms at the 6c sites (“dumb-bell” atoms) give no direct contribution to the anisotropy energy of the compound. The corresponding changes of local anisotropy energy and the orbital part of cobalt magnetic moment characteristic for each of cobalt structural sites are calculated and discussed.