Sample Optimization and Identification of Signal Patterns of Amino Acid Side Chains in 2D RFDR Spectra of the α-Spectrin SH3 Domain

Future structural investigations of proteins by solid-state CPMAS NMR will rely on uniformly labeled protein samples showing spectra with an excellent resolution. NMR samples of the solid α-spectrin SH3 domain were generated in four different ways, and their ¹³C CPMAS spectra were compared. The spectrum of a [u-¹³C, ¹⁵N]-labeled sample generated by precipitation shows very narrow ¹³C signals and resolved scalar carbon–carbon couplings. Linewidths of 16–19 Hz were found for the three alanine C^β signals of a selectively labeled [70% 3-¹³C]alanine-enriched SH3 sample. The signal pattern of the isoleucine, of all prolines, valines, alanines, and serines, and of three of the four threonines were identified in 2D ¹³C–¹³C RFDR spectra of the [u-¹³C,¹⁵N]-labeled SH3 sample. A comparison of the ¹³C chemical shifts of the found signal patterns with the ¹³C assignment obtained in solution shows an intriguing match.     

Elasticity-driven spontaneous curvature of a 2D comb-like polymer with repulsive interactions in the side chains

We have shown that the rectilinear conformation of a 2D comb-like polymer with symmetrical left-right distribution of the side chains relative to the backbone is thermodynamically unstable. The minimum of the free energy of the comb molecule per unit of its length is attained at asymmetrical distribution of the side chains accompanied by the bending of the backbone. The curved conformation is characterized by a lower elastic energy of the side chains.Received: 11 August 2003, Published online: 4 November 2003PACS: 82.35.Jk Copolymers, phase transitions, structure - 89.75.Fb Structures and organization in complex systems     

3D HCCH(3)-TOCSY for resonance assignment of methyl-containing side chains in (13)C-labeled proteins

Two 3D experiments, (H)CCH(3)-TOCSY and H(C)CH(3)-TOCSY, are proposed for resonance assignment of methyl-containing amino acid side chains. After the initial proton-carbon INEPT step, during which either carbon or proton chemical shift labeling is achieved (t(1)), the magnetization is spread along the amino acid side chains by a carbon spin lock. The chemical shifts of methyl carbons are labeled (t(2)) during the following constant time interval. Finally the magnetization is transferred, in a reversed INEPT step, to methyl protons for detection (t(3)). The proposed experiments are characterized by high digital resolution in the methyl carbon dimension (t(2max) = 28.6 ms), optimum sensitivity due to the use of proton decoupling during the long constant time interval, and an optional removal of CH(2), or CH(2) and CH, resonances from the F(2)F(3) planes. The building blocks used in these experiments can be implemented in a range of heteronuclear experiments focusing on methyl resonances in proteins. The techniques are illustrated using a (15)N, (13)C-labeled E93D mutant of Schizosacharomyces pombe phosphoglycerate mutase (23.7 kDa).     

Use of continuous optimization methods to find carbon links in 2D INADEQUATE spectra

The 2-D INADEQUATE experiment is a useful experiment for determining carbon structures of organic molecules, which is known for having low signal-to-noise ratios. A non-linear optimization method for solving low-signal spectra resulting from this experiment is introduced to compensate. The method relies on the peak locations defined by the INADEQUATE experiment to create boxes around these areas and measure the signal in each. By measuring pairs of these boxes and applying penalty functions that represent a priori information, we are able to quickly and reliably solve spectra with an acquisition time approximately a quarter of that required by traditional methods. Examples are shown using the spectrum of sucrose.     

Modeling of recognition sites of nucleic acid bases aaand amide side chains of amino acids. Combination of experimental and theoretical approaches

A combined experimental-theoretical approach to modeling of building blocks of recognition complexes formed by nucleic acid bases and the amino-acids side-chain amino group is reviewed. The approach includes the temperature dependent field-ionization mass spectrometry and ab initio quantum chemical calculations. The mass spectrometric technique allows determination of interaction enthalpies of biomolecules in the gas phase, and the results it produces are directly comparable to the results obtained through theoretical modeling. In our works we have analyzed both thermodynamic and structural aspects of the recognition complexes of four canonical nucleic acid bases and acrylamide, which models the side chain of asparagine and glutamine. It has been shown that all bases can interact with amide group of the amino acids via their Watson-Crick sites when being incorporated into a single strand DNA or RNA. Stability of the complexes studied, expressed as - ΔH (kJ mole^-1) decreases as: m⁹Gua (- 59.5) > m ¹Cyt (- 57.0) > m ⁹Ade (- 52.0) ≫m ¹Ura (- 40.6). We have determined that in the double stranded DNA only purine bases can be recognized. Received 5 February 2002 and Received in final form 14 March 2002 Published online 13 September 2002     

Far infrared spectra of the D2 and the D2-He systems

The rototranslational absorption spectra of D₂ and D₂ - He at 92K have been measured at different densities and different D₂ concentrations. From these spectra we have derived the translational line-shape; the observed density effects and, in particular, the relevance of the two-body and the three-body contributions have been discussed by comparing the line-shape derived from the D₂ spectra with the two-body term obtained from the analysis of the D₂ - He spectra.     

Magnetic resonance image reconstruction using trained geometric directions in 2D redundant wavelets domain and non-convex optimization

Reducing scanning time is significantly important for MRI. Compressed sensing has shown promising results by undersampling the k-space data to speed up imaging. Sparsity of an image plays an important role in compressed sensing MRI to reduce the image artifacts. Recently, the method of patch-based directional wavelets (PBDW) which trains geometric directions from undersampled data has been proposed. It has better performance in preserving image edges than conventional sparsifying transforms. However, obvious artifacts are presented in the smooth region when the data are highly undersampled. In addition, the original PBDW-based method does not hold obvious improvement for radial and fully 2D random sampling patterns. In this paper, the PBDW-based MRI reconstruction is improved from two aspects: 1) An efficient non-convex minimization algorithm is modified to enhance image quality; 2) PBDW are extended into shift-invariant discrete wavelet domain to enhance the ability of transform on sparsifying piecewise smooth image features. Numerical simulation results on vivo magnetic resonance images demonstrate that the proposed method outperforms the original PBDW in terms of removing artifacts and preserving edges.     

密度泛函理论研究具有手性侧链的卟啉液晶分子几何结构与电子光谱

采用量子化学密度泛函理论方法在B3LYP/6-31G水平上对具有手性侧链的卟啉液晶分子进行几何结构优化,在此基础上使用含时密度泛函理论方法计算了分子第一激发态的电子垂直跃迁能,得到最大吸收波长λmax.计算表明,手性侧链取代基对λmax的影响不大,Zn络合导致最大吸收波长兰移,与实验结果一致.     

Microwave spectra of deuterated arsines: Distortion moment transitions of AsD3, microwave spectra of AsH2D and AsHD2, and the structure of arsine

Microwave spectra of three deuterated arsines have been measured and analysed. For AsD₃ distortion moment transitions have been observed for the first time, in the form of the K = ±1 ← ∓2 cluster; their frequencies have been combined with those of previously observed “normal” transitions to give rotational, centrifugal distortion, and ⁷⁵As hyperfine constants. For AsH₂D and AsHD₂, the measurements have been extended considerably and now include for the first time R-branch transitions; similar spectroscopic constants have been evaluated. The data have been combined with earlier results for AsH₃ and with vibrational data in a harmonic force field analysis. Both ground state average (r_z) and equilbbrium (r_e) structures have been estimated.     

Amino acid type identification in NMR spectra of proteins via beta- and gamma-carbon edited experiments

In this work, we introduce a set of pulse sequences that provide amino acid type identification of the NH correlation signals of proteins. The first pulse sequence is a modification of the CBCA(CO)NH experiment that exploits spin-coupling topologies to differentiate between amino acid types. A set of eight 2D ¹H–¹⁵N correlation spectra is recorded where the sign of the cross-peaks change from one spectrum to another according to the amino acid type of the preceding residue in the protein sequence. Linear combination of these eight data sets produces four subspectra. Taking also into account the sign of the correlation signals, this method allows the classification of the NH signals into six different groups, depending on the character of the preceding residue. This sequence is complemented with a (CGCBCACO)NH experiment that allows the subdivision of the largest of these groups into two smaller ones. Finally, a modification of the CBCANH experiment led to a similar classification of NH signals into six different groups, but now depending on the type of its own amino acid. The set of pulse sequences is demonstrated with two proteins of small to moderate size.     

Characteristic patterns in microwave spectra of quasi-symmetric top molecules of the WH3XYZ type

Characteristic patterns in microwave spectra of quasi-symmetric top molecules of the WH₃XYZ type are discussed in terms of the quasi-symmetric top model accounting for the large-amplitude WXY bending motion, and internal and overall rotation. The molecules SiH₃NCS, SiH₃NCO, CH₃NCS, CH₃NCO, and CH₃SCN, exemplifying the symmetric, quasi-symmetric, and asymmetric top molecules, are considered. The correlation parameter γ_v is defined to quantify the position of a WH₃XYZ molecule between the two symmetric and asymmetric top limiting cases. The quasi-symmetric top model is compared to the usual approach to the rotational-vibrational problem of symmetric top molecules.     

High resolution,rotation, vibration spectra of D2O in the region ofν 1 andν 3 bands

The infrared spectrum of D₂O from 2400 to 3000 cm⁻¹ has been analysed at a resolution better than 0·02 cm⁻¹. It was recorded at the Fourier transform spectrometer of the Kitt Peak National Observatory, Tucson. Ground state constants of the reduced Watson-Hamiltonian, ground state energies and transition for theν ₁ andν ₃ bands are reported. The effect of strong Coriolis resonances on the spectra is discussed. Work done at the Jet Propulsion Laboratory, Division of Stratospheric and Planetary Research California Institute of Technology, Pasadena, Ca (U.S.A.)     

Steady state signal in the limit of weak optical pumping with D1 or D2 line

The simplified rate equations for electronic polarization of alkali atoms in the hyperfine ground states are shown for circularly polarizedD ₁ andD ₂ lines in the limit of weak pumping. The rate equations include effects due to collisional and spin exchange relaxation of atoms in the ground state. Analytical forms of the repopulation pumping terms are shown assuming the standardJ-randomization model for relaxation of alkali atoms in resonant² P _J states and neglecting energy transfer. Analyses of the analytical steady state solutions have been performed to determine the conditions at which the longitudinal electronic orientation of alkali atoms 〈S _z〉 and the orientation of atoms in hyperfine sublevels 〈S _z〉 _f pass through zero.     

用光谱和EPR谱确定CsMgBr3:Ni2+的局域结构

本文采用半自洽场(semi-SCF)自由Ni2 的3d轨道波函数、点电荷—偶极子模型和Ni2 -6X-(X=F,Cl,Br,I)络合物的μ-κ-α模型,建立了结构参数与光谱、EPR谱之间的定量关系,利用完全对角化方法,由光谱和电子顺磁共振(EPR)谱,确定了CsMgBr3:Ni2 晶体在77K温度时的局域结构参数,统一解释了CsMgBr3:Ni2 晶体的局域结构、光谱和EPR谱。所得理论结果与实验值符合得很好。此外,还讨论了晶体局域结构发生畸变的原因。     

2D and 3D electrically switchable hexagonal photonic crystal in the ultraviolet range

Two holographic lithography systems are demonstrated for easy and large-area fabrication of 2D and 3D photonic crystal (PhC) microstructures in a polymer dispersed liquid crystal (PDLC) by applying a single top-cut hexagon prism. A six-beam system has been used to produce 2D hexagonal PhCs. By adding an additional mirror, a twelve-beam system is demonstrated to fabricate 3D PhCs with ultraviolet (UV) band-gap along the z direction. A good agreement is obtained for measured PhCs structure and theoretical results. Far-field diffraction patterns and electrical switching characteristics of the 2D and 3D PhC HPDLC films have been investigated. PACS 42.15.Eq; 42.40.Eq