Application of solid-state NMR restraint potentials in membrane protein modeling

We have developed a set of orientational restraint potentials for solid-state NMR observables including (15)N chemical shift and (15)N-(1)H dipolar coupling. Torsion angle molecular dynamics simulations with available experimental (15)N chemical shift and (15)N-(1)H dipolar coupling as target values have been performed to determine orientational information of four membrane proteins and to model the structures of some of these systems in oligomer states. The results suggest that incorporation of the orientational restraint potentials into molecular dynamics provides an efficient means to the determination of structures that optimally satisfy the experimental observables without an extensive geometrical search.     

炉膛三维温度场重建中Tikhonov正则化和截断奇异值分解算法比较

在煤粉锅炉诊断中火焰辐射能图像扮演着越来越重要的角色, 通过电荷耦合器件(CCD)获得的辐射能图像可以重建出炉内火焰三维温度场, CCD 用于获取视场角内的辐射能图像. 温度场重建的矩阵方程是一个严重病态的方程, 本文使用两种算法(Tikhonov正则化算法和截断奇异值分解(TSVD)算法)来重建温度场. 应用广义交叉检验算法来选取正确的正则化参数. 数值模拟的环境为一个10 m×10 m×10 m的三维炉膛, 系统被划分为10×10×10的1000个网格, 每个网格单元都是边长为1 m的立方体. 在正问题求解所得到的CCD接受信号基础上加上不同随机误差以模拟测量时的CCD接受信号. 研究两种算法重建后的温度重建误差、两者的重建时间, 以及最高温度的重建效果. 初步的研究结果显示, 一般情况下基于Tikhonov算法重建的温度场比基于TSVD算法重建的温度场误差要小, 计算所需时间短, 最高温度重建更准确.     

C-radiolabeling study of methanol decomposition on copper oxide modified mesoporous SBA-15 silica

¹¹C-radiolabeling technique is applied to investigate methanol decomposition on copper oxide modified SBA-15. Nitrogen physisorption, XRD, FTIR, UV-vis and TPR techniques are used for catalyst characterization. Selective adsorption coverage of the catalytic active sites with ¹¹C- and ¹²C-methanol molecules is carried out and the products of their conversion are followed. The mechanism of methyl formate, methylal and CO₂ formation from methanol is discussed.     

13C NMR Studies on 3-Aryl-4-Cyanosydnones (II). NMR Spectroscopy and the Chain-Conjugated Structure of Sydnones

Carbon-13 NMR spectra of 3-aryl-4-cyanosydnones have been analyzed to serve as an electronic structure probe of sydnones. 2-Dimensional INADEQUATE experiments and spin-lattice relaxation time measurements were employed to ascertain exact assignments. Deshielding of the phenyl carbon para to the sydnone ring manifests that N(3) bears positive charge. The electronic-rich property of C(4) is confirmed by shift data of cyano carbons, which have been found by far the most shielded cyano carbons in nitrile-containing compounds yet reported. Shift variations of C(5) resulting from the substitution at C(4) and supplementary oxygen-17 chemical shift data provide evidence in favor of the chain-conjugated structure.     

Solid-state NMR investigations of Si-29 and N-15 enriched silicon nitride

We compare ²⁹Si magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectra from the two modifications of silicon nitride, α-Si₃N₄ and β-Si₃N₄, with that of a fully (²⁹Si, ¹⁵N)-enriched sample ²⁹Si₃¹⁵N₄, as well as ¹⁵N NMR spectra of Si₃¹⁵N₄ (having ²⁹Si at natural abundance) and ²⁹Si₃¹⁵N₄. We show that the ¹⁵N NMR peak-widths from the latter are dominated by J(²⁹Si–¹⁵N) through-bond interactions, leading to significantly broader NMR signals compared to those of Si₃¹⁵N₄. By fitting calculated ²⁹Si NMR spectra to experimental ones, we obtained an estimated coupling constant J(²⁹Si–¹⁵N) of 20 Hz. We provide ²⁹Si spin-lattice (T₁) relaxation data for the ²⁹Si₃¹⁵N₄ sample and chemical shift anisotropy results for the ²⁹Si site of β-Si₃N₄. Various factors potentially contributing to the ²⁹Si and ¹⁵N NMR peak-widths of the various silicon nitride specimens are discussed. We also provide powder X-ray diffraction (XRD) and mass spectrometry data of the samples.     

Spin-State-Selective TPPI: A New Method for Suppression of Heteronuclear Coupling Constants in Multidimensional NMR Experiments

A novel multidimensional NMR pulse sequence tool, spin-state-selective time-proportional phase incrementation (S(3) TPPI), is introduced. It amounts to application of different TPPIs on the two components of doublets so that their frequencies can be manipulated independently. The chief application is for suppression of large heteronuclear one-bond coupling constants in indirect dimensions of multidimensional experiments without interchanging the two transverse magnetization components of doublets as conventional decoupling does, which is advantageous when they relax at different rates such as by partial compensation of dipolar and CSA relaxation contributions. For experimental confirmation we use a sample of (15)N-labeled neural cell adhesion molecule modules 1 and 2, a protein with a molecular weight of about 20 kDa. The new tool is general and can be combined with many multidimensional NMR experiments for proteins.     

CHHC and H–H magnetization exchange: Analysis by experimental solid-state NMR and 11-spin density-matrix simulations

A protocol is presented for correcting the effect of non-specific cross-polarization in CHHC solid-state MAS NMR experiments, thus allowing the recovery of the ¹H–¹H magnetization exchange functions from the mixing-time dependent buildup of experimental CHHC peak intensity. The presented protocol also incorporates a scaling procedure to take into account the effect of multiplicity of a CH₂ or CH₃ moiety. Experimental CHHC buildup curves are presented for l-tyrosine·HCl samples where either all or only one in 10 molecules are U–¹³C labeled. Good agreement between experiment and 11-spin SPINEVOLUTION simulation (including only isotropic ¹H chemical shifts) is demonstrated for the initial buildup (t_mix < 100 μs) of CHHC peak intensity corresponding to an intramolecular close (2.5 Å) H–H proximity. Differences in the initial CHHC buildup are observed between the one in 10 dilute and 100% samples for cases where there is a close intermolecular H–H proximity in addition to a close intramolecular H–H proximity. For the dilute sample, CHHC cross-peak intensities tended to significantly lower values for long mixing times (500 μs) as compared to the 100% sample. This difference is explained as being due to the dependence of the limiting total magnetization on the ratio N_obs/N_tot between the number of protons that are directly attached to a ¹³C nucleus and hence contribute significantly to the observed ¹³C CHHC NMR signal, and the total number of ¹H spins into the system. ¹H–¹H magnetization exchange curves extracted from CHHC spectra for the 100% l-tyrosine·HCl sample exhibit a clear sensitivity to the root sum squared dipolar coupling, with fast buildup being observed for the shortest intramolecular distances (2.5 Å) and slower, yet observable buildup for the longer intermolecular distances (up to 5 Å).     

A 15N NMR Study of Protonation and Deprotonation of 4,5-Dicyanoimidazole and Its 2-Amino Analogue

Protonation and deprotonation of the title compounds, was studied by means of ¹⁵N NMR. The shieldings of the ring nitrogen atoms are found to be very sensitive to changes in the amount of protonation. In contrast the ¹⁵N shieldings of the cyano and amino groups are found to be relatively insensitive to protonation effects and are unsuitable for estimating the degree of protonation occurring.     

14N NMR relaxation times of several protein amino acids in aqueous solution--comparison with 17O NMR data and estimation of the relative hydration numbers in the cationic and zwitterionic forms

The 14N nuclear magnetic resonance (NMR) linewidths of the alpha-amino groups of several protein amino acids were measured in aqueous solution, with and without composite proton decoupling, to estimate the effect of proton exchange and molecular weight on the linewidths. It is shown that, contrary to earlier claims, the increase in the linewidth at low pH is not exclusively due to the effect of proton exchange broadening. The 14N linewidths, under composite proton decoupling, increase with the bulk of the amino acid, and increase at low pH. Statistical treatment of the experimental 14N and literature 17O NMR data was performed assuming two models: (i) an isotropic molecular reorientation of a rigid sphere in a medium of viscosity eta, (ii) a stochastic diffusion of the amino and carboxyl groups comprising contributions from internal (tauint) and overall (taumol) motions. Assuming a single correlation time from overall molecular reorientation (taumol), then, a linear correlation was found between the linewidths and the molecular weights of the protein amino acids at the pH values 0.5 and 6.0, which are characteristic of the cationic and zwitterionic forms, respectively. The slopes of the straight-lines were found to be dependent of pH for 14N, contrary to the 17O linear correlations whose slopes were found to be independent of pH. Assuming effective correlation times of the amino and carboxyl groups, which comprise contributions from the internal (tauint) and overall (taumol) motions, then, a significant improvement of the statistics of the regression analysis was observed. The 14N relaxation data, in conjunction with 17O NMR linewidths, can be interpreted by assuming that the 14N quadrupole coupling constants (NQCCs) are influenced by the protonation state of the carboxyl group, the 17O NQCCs remain constant, and the cationic form of the amino acids is hydrated by an excess of 1-3 molecules of water relative to the zwitterionic state.     

A 15N NMR Study of Some Imidazolidine-2,4-Dichalcogen Derivatives

The ¹⁵N NMR chemical shifts and ¹(¹⁵N-¹H) coupling constants of a series of imidazolidine-2,4-dichalcogen (O, S) derivatives are reported.The ¹⁵N NMR chemical shifts show a linear correlatlon wlth the vNH stretchlng vlbratlons. The influence of the substitution of the oxygen at C₂ and/or C₄ with the sulphur, and of the hydrogen at C₅ wlth the methyls and phenyls has been considered. The ¹J(¹⁵N-¹H)'s found In thls serles of molecules agrees well with the expected values.     

Complete Analysis of the 1H and 13C NMR Spectra of 5-Isopropylsulfonyl-2-Norbornenes Through the Application of Two-Dimensional NMR Techniques

Total assignment of ¹³C and ¹H NMR spectra of the 5-isopropylsulfonyl-2-norbornenes 2 was achieved using the concerted application of two-dimensional homonuclear and heteronuclear chemical shift correlations. The stereochemistry of both the diastereoisomers endo 2a and exo 2b have been established using the magnitude of the proton coupling constants.     

Probing membrane topology by high-resolution 1H-13C heteronuclear dipolar solid-state NMR spectroscopy

Membrane topology changes introduced by the association of biologically pertinent molecules with membranes were analyzed utilizing the (1)H-(13)C heteronuclear dipolar solid-state NMR spectroscopy technique (SAMMY) on magnetically aligned phospholipid bilayers (bicelles). The phospholipids (1)H-(13)C dipolar coupling profiles lipid motions at the headgroup, glycerol backbone, and the acyl chain region. The transmembrane segment of phospholamban, the antimicrobial peptide (KIGAKI)(3) and cholesterol were incorporated into the bicelles, respectively. The lipids (1)H-(13)C dipolar coupling profiles exhibit different shifts in the dipolar coupling contour positions upon the addition of these molecules, demonstrating a variety of interaction mechanisms exist between the biological molecules and the membranes. The membrane topology changes revealed by the SAMMY pulse sequence provide a complete screening method for analyzing how these biologically active molecules interact with the membrane.     

3D NMR Experiments for MeasuringN Relaxation Data of Large Proteins: Application to the 44 kDa Ectodomain of SIV gp41

A suite of 3D NMR experiments for measuring¹⁵N–{¹H} NOE,¹⁵NT₁, and¹⁵NT_1ρvalues in large proteins, uniformly labeled with¹⁵N and¹³C, is presented. These experiments are designed for proteins that exhibit extensive spectral overlap in the 2D¹H–¹⁵N HSQC spectrum. The pulse sequences are readily applicable to perdeuterated samples, which increases the spectral resolution and signal-to-noise ratio, thereby permitting the characterization of protein dynamics to be extended to larger protein systems. Application of the pulse sequences is demonstrated on a perdeuterated¹³C/¹⁵N-labeled sample of the 44 kDa ectodomain of SIV gp41.     

In Vivo Detection of N-Coupled Protons in Rat Brain by ISIS Localization and Multiple-Quantum Editing

Three-dimensional image-selected in vivo spectroscopy (ISIS) was combined with phase-cycled ¹H–¹⁵N heteronuclear multiple-quantum coherence (HMQC) transfer NMR for localized selective observation of protons J-coupled to ¹⁵N in phantoms and in vivo. The ISIS–HMQC sequence, supplemented by jump–return water suppression, permitted localized selective observation of 2–5 μmol of [¹⁵N_indole]tryptophan, a precursor of the neurotransmitter serotonin, through the ¹⁵N-coupled proton in 20–40 min of acquisition in vitro at 4.7 T. In vivo, the amide proton of [5-¹⁵N]glutamine was selectively observed in the brain of spontaneously breathing ¹⁵NH₄⁺-infused rats, using a volume probe with homogeneous ¹H and ¹⁵N fields. Signal recovery after three-dimensional localization was 72–82% in phantoms and 59 ± 4% in vivo. The result demonstrates that localized selective observation of ¹⁵N-coupled protons, with complete cancellation of all other protons except water, can be achieved in spontaneously breathing animals by the ISIS–HMQC sequence. This sequence performs both volume selection and heteronuclear editing through an addition/subtraction scheme and predicts the highest intrinsic sensitivity for detection of ¹⁵N-coupled protons in the selected volume. The advantages and limitations of this method for in vivo application are compared to those of other localized editing techniques currently in use for non-exchanging protons.     

NMR and AM1 Study of the Tautomeric Equilibrium of Isochroman-1,2-diones

Reaction of homophtalic anhydrid with aliphatic or aryl anhydrids (or acid chlorides) and an appropriate base gives 4-acyl and 4-aroylisochroman-1,3-diones. The structure of these isochroman-1,3-diones was determined by ¹H, ¹³C and ¹⁷O NMR spectrometry. In solution, among the three possible tautomers, only the enolic one with exocyclic double bond was observed. These results are in good agreements with AMI calculations ones.     

Application of Tikhonov regularization method to wind retrieval from scatterometer data Ⅱ: cyclone wind retrieval with consideration of rain

According to the conclusion of the simulation experiments in paper I, the Tikhonov regularization method is applied to cyclone wind retrieval with a rain-effect-considering geophysical model function (called GMF+Rain). The GMF+Rain model which is based on the NASA scatterometer-2 (NSCAT2) GMF is presented to compensate for the effects of rain on cyclone wind retrieval. With the multiple solution scheme (MSS), the noise of wind retrieval is effectively suppressed, but the influence of the background increases. It will cause a large wind direction error in ambiguity removal when the background error is large. However, this can be mitigated by the new ambiguity removal method of Tikhonov regularization as proved in the simulation experiments. A case study on an extratropical cyclone of hurricane observed with SeaWinds at 25-km resolution shows that the retrieved wind speed for areas with rain is in better agreement with that derived from the best track analysis for the GMF+Rain model, but the wind direction obtained with the two-dimensional variational (2DVAR) ambiguity removal is incorrect. The new method of Tikhonov regularization effectively improves the performance of wind direction ambiguity removal through choosing appropriate regularization parameters and the retrieved wind speed is almost the same as that obtained from the 2DVAR.