Molecular symmetry as an aid to geometry determination in ligand protein complexes

Dipole-dipole couplings between pairs of spin 12 nuclei, which can be measured from NMR spectra in field-ordered media, offer useful constraints on the orientation of various fragments in molecular systems. However, the orientation of fragments relative to a molecule fixed reference frame is often key to complete structure determination. Here, we demonstrate that the symmetry properties of molecular complexes can aid in the definition of a reference frame. It is shown that a threefold rotational symmetry axis dictates the direction and symmetry of the experimentally determined order tensor for alpha-methyl-mannose in fast exchange among the three symmetry-related binding sites of mannose binding protein. This approach facilitates studies of the geometry of the ligand in the protein-ligand complex and also may provide a novel route to structure determination of a homomultimeric protein.     

Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings

Residual dipolar couplings for pairs of proximate magnetic nuclei in macromolecules can easily be measured using high-resolution NMR methods when the molecules are dissolved in dilute liquid crystalline media. The resulting couplings can in principle be used to constrain the relative orientation of molecular fragments in macromolecular systems to build a complete structure. However, determination of relative fragment orientations based on a single set of residual dipolar couplings is inherently hindered by the multi-valued nature of the angular dependence of the dipolar interaction. Even with unlimited dipolar data, this gives rise to a fourfold degeneracy in fragment orientations. In this Communication, we demonstrate a procedure based on an order tensor analysis that completely removes this degeneracy by combining residual dipolar coupling measurements from two alignment media. Application is demonstrated on (15)N-(1)H residual dipolar coupling data acquired on the protein zinc rubredoxin from Clostridium pasteurianum dissolved in two different bicelle media.     

Experimental results on proton diffractive dissociation

Properties of proton diffractive dissociation have been investigated for four-prong final states in proton-proton reactions at 360 GeV/c, in particular forpp→ppπ ⁺π^? mπ ⁰(m=0,1,2). Mass distributions and decay angular distributions are given. The decay of the diffractive system is seen to be very anisotropic, and largep _T is suppressed at higher masses. It is found that the “pomeron” couples with a single valence quark of the incident proton, but indications for a diquark-pomeron coupling are also found. Similarities with fragmentation in lepton-hadron deep inelastic scattering are underlined.     

Field- and phage-induced dipolar couplings in a homodimeric DNA quadruplex: relative orientation of G.(C-A) triad and G-tetrad motifs and direct determination of C2 symmetry axis orientation.

We present a new NMR procedure for determining the three-dimensional fold of C2-symmetric nucleic acid homodimers that relies on long-range orientational constraints derived from the measurement of two independent sets of residual dipolar couplings under two alignment conditions. The application is demonstrated on an (15)N/(13)C-enriched deoxyoligonucleotide sequence, d(G-G-G-T-T-C-A-G-G), shown previously to dimerize into a quadruplex in solution and form a pair of G.(C-A) triads and G-G-G-G tetrads (G-tetrad) motifs. One-bond (1)H-(15)N ((1)D(NH)) and (1)H-(13)C ((1)D(CH)) residual dipolar couplings have been measured between nuclei in the bases of these motifs using bacteriophage as an ordering medium, and under direct magnetic field alignment (800 MHz). By combining the two dipolar data sets in an order matrix analysis, the orientation of the G.(C-A) triad relative to the G-tetrad within a contiguous monomeric unit can directly be determined, even in the presence of interstrand/intrastrand NOE ambiguity. We further demonstrate that the orientation of the C2-axis of molecular symmetry in the homodimer relative to the G.(C-A) triad and G-tetrad motifs can unambiguously be determined using the two sets of independent dipolar coupling measurements. The three-dimensional fold of the homodimer determined using this procedure is very regular and in excellent agreement with a previously determined high-resolution NOE-based NMR structure, where interstrand/intrastrand NOEs were treated as ambiguous and where noncrystallographic symmetry constraints were implicitly imposed during the structure calculation.     

Structural and dynamic analysis of residual dipolar coupling data for proteins.

The measurement of residual dipolar couplings in weakly aligned proteins can potentially provide unique information on their structure and dynamics in the solution state. The challenge is to extract the information of interest from the measurements, which normally reflect a convolution of the structural and dynamic properties. We discuss here a formalism which allows a first order separation of their effects, and thus, a simultaneous extraction of structural and motional parameters from residual dipolar coupling data. We introduce some terminology, namely a generalized degree of order, which is necessary for a meaningful discussion of the effects of motion on residual dipolar coupling measurements. We also illustrate this new methodology using an extensive set of residual dipolar coupling measurements made on (15)N,(13)C-labeled human ubiquitin solvated in a dilute bicelle solution. Our results support a solution structure of ubiquitin which on average agrees well with the X-ray structure (Vijay-Kumar, et al., J. Mol. Biol. 1987, 194, 531--544) for the protein core. However, the data are also consistent with a dynamic model of ubiquitin, exhibiting variable amplitudes, and anisotropy, of internal motions. This work suggests the possibility of primary use of residual dipolar couplings in characterizing both structure and anisotropic internal motions of proteins in the solution state.     

具有几个光振荡周期的飞秒激光脉冲

从麦克斯韦方程组出发 ,推导出了具有几个光振荡周期的飞秒激光脉冲在非线性光纤中传输的方程和非线性光纤的折射率。给出了描述具有几个光振荡周期的飞秒激光脉冲在非线性光纤中传输方程的解。研究了在非线性光纤中自相位调制导致具有几个光振荡周期的飞秒激光脉冲频谱展宽 (脉宽压缩 )的详细物理过程。研究了非线性光纤中飞秒光孤子产生的条件     

新型燃料电池质子交换膜──含叔丁基的磺化聚芳醚砜

以3,3'-二磺酸钠基-4,4'-二氯二苯砜(SDCDPS)、叔丁基对苯二酚(TBHQ)、二氟二苯酮(DFBP)为原料,利用亲核缩聚反应,通过调整磺化单体(SDCDPS)和非磺化单体(DFBP)的比例与叔丁基对苯二酚(TBHQ)共聚,合成了不同磺化度的聚芳醚砜.聚合物成膜后的研究结果表明,该膜具有良好的机械性能和电化学性能,可能在质子交换膜燃料电池中得到应用.     

含联苯结构的环氧树脂固化性能的研究

以3,3′,5,5′-四甲基联苯二酚为单体,合成了一种含联苯结构的环氧树脂.用DDM和DDS为固化剂对环氧树脂的固化性能进行了研究,发现与双酚A型环氧树脂相比,含有联苯结构的环氧树脂具有更好的耐热性,同时在耐湿性方面也有很大改进.     

一种新型磺化聚醚醚酮的合成、表征和性能

以特丁基对苯二酚、3,3′-二磺酸钠基-4,4′-二氟二苯酮和4,4′-二氟二苯酮为单体,制备了具有高磺化度的聚醚醚酮.该系列聚合物可溶,并具有良好的成膜性.对聚合物及其膜的一些性能进行了研究.     

用于有机光导材料的三偶氮颜料的合成研究

以4,4′,4″ 三氨基三苯胺为母体,以含有4种不同取代基的萘酚AS为偶合组分合成了一系列三芳胺三偶氮类有机光导颜料.用元素分析、红外光谱、紫外光谱、质谱和X射线衍射光谱对结构进行了表征.研究结果表明,含硫杂环三偶氮类有机光导颜料在520-730nm之间都有较强吸收.