Effect of Dimer Structure and Inhomogeneous Broadening of Energy Levels on the Action of Flavomononucleotide in Rigid Polyvinyl Alcohol Films

The results of time-resolved fluorescence measurements of flavin mononucleotide (FMN) in rigid polyvinyl alcohol films (PVA) demonstrate that fluorescence intensity decays are strongly accelerated in the presence of fluorescent dimers and nonradiative energy transfer processes. The fluorescence decay originating both from H and J dimer states of FMN was experimentally observed for the first time. The mean fluorescence lifetimes for FMN dimers were obtained: τfl = 2.66 ns (at λ_exc = 445 nm) and τfl = 2.02 (at λ_exc = 487 nm) at λ_obs = 600 nm and T = 253 K from H and J state of dimers, respectively. We show that inhomogeneous orientational broadening of energy levels (IOBEL) affects the shape of the fluorescence decay and leads to the dependence of the average monomer fluorescence lifetime on excitation wavelength. IOBEL affected the nonradiative energy transfer and indicated that different flavin positioning in the protein pocket could (1) change the spectroscopic properties of flavins due to the existence of “blue” and “red” fluorescence centers, and (2) diminish the effectiveness of energy transfer between FMN molecules.     

Crystal Structure of CYP3A4 Complexed with Fluorol Identifies the Substrate Access Channel as a High-Affinity Ligand Binding Site

Cytochrome P450 3A4 (CYP3A4) is a major human drug-metabolizing enzyme, notoriously known for its extreme substrate promiscuity, allosteric behavior, and implications in drug–drug interactions. Despite extensive investigations, the mechanism of ligand binding to CYP3A4 is not fully understood. We determined the crystal structure of CYP3A4 complexed with fluorol, a small fluorescent dye that can undergo hydroxylation. In the structure, fluorol associates to the substrate channel, well suited for the binding of planar polyaromatic molecules bearing polar groups, through which stabilizing H-bonds with the polar channel residues, such as Thr224 and Arg372, can be established. Mutagenesis, spectral, kinetic, and functional data confirmed the involvement but not strict requirement of Thr224 for the association of fluorol. Collectively, our data identify the substrate channel as a high-affinity ligand binding site and support the notion that hydrophobic ligands first dock to the nearby peripheral surface, before migrating to the channel and, subsequently, into the active site.     

胭脂红阴离子插层Mg/Al-LDH晶体结构的研究

用液相共沉淀法制备胭脂红插层Mg/Al双氢氧化物,对产物晶化成核以及胭脂红阴离子插层的机理进行探讨,对不同条件下晶化成核LDH的晶体结构、晶面生长选择性和晶粒尺寸等结构参数进行分析比较,得出不同反应条件对晶体形成的影响规律。根据LDH层间距和胭脂红离子的几何尺度,推算出胭脂红阴离子在双氢氧化物层间的配置方式为单层平卧。     

Crystal Structures of the Clostridium botulinum Neurotoxin A6 Cell Binding Domain Alone and in Complex with GD1a Reveal Significant Conformational Flexibility

Clostridium botulinum neurotoxin A (BoNT/A) targets the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex, by cleaving synaptosomal-associated protein of 25 kDa size (SNAP-25). Cleavage of SNAP-25 results in flaccid paralysis due to repression of synaptic transmission at the neuromuscular junction. This activity has been exploited to treat a range of diseases associated with hypersecretion of neurotransmitters, with formulations of BoNT/A commercially available as therapeutics. Generally, BoNT activity is facilitated by three essential domains within the molecule, the cell binding domain (H_C), the translocation domain (H_N), and the catalytic domain (LC). The H_C, which consists of an N-terminal (H_CN) and a C-terminal (H_CC) subdomain, is responsible for BoNT’s high target specificity where it forms a dual-receptor complex with synaptic vesicle protein 2 (SV2) and a ganglioside receptor on the surface of motor neurons. In this study, we have determined the crystal structure of botulinum neurotoxin A6 cell binding domain (H_C/A6) in complex with GD1a and describe the interactions involved in ganglioside binding. We also present a new crystal form of wild type H_C/A6 (crystal form II) where a large ‘hinge motion’ between the H_CN and H_CC subdomains is observed. These structures, along with a comparison to the previously determined wild type crystal structure of H_C/A6 (crystal form I), reveals the degree of conformational flexibility exhibited by H_C/A6.     

Crystal Structure of the Recombination Mediator Protein RecO from Campylobacter jejuni and Its Interaction with DNA and a Zinc Ion

Homologous recombination is involved in repairing DNA damage, contributing to maintaining the integrity and stability of viral and cellular genomes. In bacteria, the recombination mediator proteins RecO and RecR are required to load the RecA recombinase on ssDNA for homologous recombination. To structurally and functionally characterize RecO, we determined the crystal structure of RecO from Campylobacter jejuni (cjRecO) at a 1.8 Å resolution and biochemically assessed its capacity to interact with DNA and a metal ion. cjRecO folds into a curved rod-like structure that consists of an N-terminal domain (NTD), C-terminal domain (CTD), and Zn²⁺-binding domain (ZnD). The ZnD at the end of the rod-like structure coordinates three cysteine residues and one histidine residue to accommodate a Zn²⁺ ion. Based on an extensive comparative analysis of RecO structures and sequences, we propose that the Zn²⁺-binding consensus sequence of RecO is CxxC…C/HxxC/H/D. The interaction with Zn²⁺ is indispensable for the protein stability of cjRecO but does not seem to be required for the recombination mediator function. cjRecO also interacts with ssDNA as part of its biological function, potentially using the positively charged patch in the NTD and CTD. However, cjRecO displays a low ssDNA-binding affinity, suggesting that cjRecO requires RecR to efficiently recognize ssDNA for homologous recombination.     

Crystal Structure of a Phospholipase D from the Plant-Associated Bacteria Serratia plymuthica Strain AS9 Reveals a Unique Arrangement of Catalytic Pocket

Phospholipases D (PLDs) play important roles in different organisms and in vitro phospholipid modifications, which attract strong interests for investigation. However, the lack of PLD structural information has seriously hampered both the understanding of their structure–function relationships and the structure-based bioengineering of this enzyme. Herein, we presented the crystal structure of a PLD from the plant-associated bacteria Serratia plymuthica strain AS9 (SpPLD) at a resolution of 1.79 Å. Two classical HxKxxxxD (HKD) motifs were found in SpPLD and have shown high structural consistence with several PLDs in the same family. While comparing the structure of SpPLD with the previous resolved PLDs from the same family, several unique conformations on the C-terminus of the HKD motif were demonstrated to participate in the arrangement of the catalytic pocket of SpPLD. In SpPLD, an extented loop conformation between β9 and α9 (aa228–246) was found. Moreover, electrostatic surface potential showed that this loop region in SpPLD was positively charged while the corresponding loops in the two Streptomyces originated PLDs (PDB ID: 1F0I, 2ZE4/2ZE9) were neutral. The shortened loop between α10 and α11 (aa272–275) made the SpPLD unable to form the gate-like structure which existed specically in the two Streptomyces originated PLDs (PDB ID: 1F0I, 2ZE4/2ZE9) and functioned to stabilize the substrates. In contrast, the shortened loop conformation at this corresponding segment was more alike to several nucleases (Nuc, Zuc, mZuc, NucT) within the same family. Moreover, the loop composition between β11 and β12 was also different from the two Streptomyces originated PLDs (PDB ID: 1F0I, 2ZE4/2ZE9), which formed the entrance of the catalytic pocket and were closely related to substrate recognition. So far, SpPLD was the only structurally characterized PLD enzyme from Serratia. The structural information derived here not only helps for the understanding of the biological function of this enzyme in plant protection, but also helps for the understanding of the rational design of the mutant, with potential application in phospholipid modification.     

Synthesis, Characterization and Crystal Structure of a Novel One-Dimensional Supramolecular Dimethyltin (IV) Compound

A novel one-dimensional (1D) supramolecular dimethyltin compound of (Me₂SnO)₂(Me₂SnOCH₃)(O₂CCH₂SC₄H₃N₂-2,6)[Me₂Sn(O₂CCH₂SC₄H₃N₂-2,6)₂]·CH₃OH was prepared by the reaction of (CH₃)₂SnCl₂ with (2-pyrimidylthio)acetic acid with CH₃ONa as a base. The title compound contained four different tin atom environments. Among them, Sn(1) and Sn(2) were both five-coordinate with distorted trigonal bipyramidal geometries, Sn(3) was six-coordinate with a distorted octahedral geometry and Sn(4) was seven-coordinate with pentagonal bipyramidal geometry. Meanwhile, the compound was stabilized in a 1D infinite chain by intermolecular Sn–O bonds. An erratum to this article can be found at     

Distributions of Crystal Size from DSC Melting Traces for Polyethylenes

Melting curves, obtained by differential scanning calorimetry, are used to estimate crystal size distributions. The proposed theoretical analysis is applied to different types of polyethylene, including high‐density polyethylene (HDPE), metallocene catalyzed linear low‐density polyethylenes (m‐LLDPE), blends of m‐LLDPEs, and Ziegler‐Natta catalyzed LLDPEs (ZN‐LLDPE). Theoretical predictions are in agreement with experimental results. A generalized melting temperature equation successfully predicts the melting temperatures of all the LLDPEs, although it was initially proposed for homogeneous copolymers with excluded comonomers. A new definition of the heat of fusion for pure crystals is proposed. This heat of fusion can be calculated from the average crystal size or the crystal size number distribution.     

Crystal structure of the poly(ethylene oxide)–p-nitrophenol molecular complex

A crystalline complex of poly(ethylene oxide) (PEO) and p-nitrophenol (PNP) was studied by differential scanning calorimetry, X-ray diffraction, and FTIR spectroscopy, The phase diagram of this system is characterized by a peritectic reaction, and reveals the formation of a new crystal form different from those of PEO, and PNP. The triclinic unit cell of the complex was determined from the X-ray diffraction patterns of differently oriented samples obtained by mechanical deformations or spherulitic crystallizations. Finally, the molecular packing and the conformation adopted by the PEO chains were determined by FTIR spectroscopy. Polarization measurements have shown that the aromatic rings are very nearly normal to the c parameter (chain axis) and that the 1–4 axes of PNP molecules are parallel to the a^* reciprocal parameter (spherulitic growth direction). Finally, a new (t₂ gt₂ gt₃) conformation is proposed for the PEO chains on the basis of a normal mode analysis and the calculation of the intramolecular energy.     

三维锌孔道配位聚合物的合成及结构

在DMF/H2O/C2H5OH混合体系中,以2-(4-吡啶)-咪唑二羧酸为有机连接体与Zn2+反应得到了一个新的含有孔道的三维锌配位聚合物,分子式为:Zn3(HL)3(DMF)2.2DMF,H3L=2-(4’-吡啶)-咪唑二甲酸,DMF=N,N-二甲基甲酰胺。单晶X射线分析显示1是带有一维矩形孔道的三维开骨架结构,孔道直径大小为18.28×6.952。     

Self-Assembly Syntheses and Crystal Structure of a New Organotin(IV) Schiff Base Complex Containing a Novel Sn<Subscript>5</Subscript>O<Subscript>5</Subscript> Hydrolysis Ladder

A new organotin(IV) Schiff base complex 4 containing a novel Sn₅O₅ hydrolysis ladder and a disulfide group has been synthesized through a self-assembly reaction. The complex 4 has been characterized by elemental analysis, IR, ¹H-, ¹³C-, and ¹¹⁹Sn-NMR spectra and X-ray crystallography diffraction analyses. The study of the supramolecular structure of complex 4 found that there exist two kinds of C–H···S and C–H···O intermolecular hydrogen bonds. The two kinds of intermolecular hydrogen bonds force the complex 4 into a 2-dimensional “wave” network. The geometry about each tin atom involved is distorted trigonal bipyramid.     

Cu(NH3)2(FOX-7)2的晶体结构和热行为

用l,1-二氨基-2,2-二硝基乙烯的钾盐[K(FOX-7)·H2O]和硝酸铜在氨水体系中合成了Cu( NH3)2(FOX-7)2,并培养得到了单晶.该晶体为单斜晶系,空间群P21/c,a=0.68818(7)nm,b=O.73083 (8) nm,c=1.319 66(14)nm,β=95.986°,V=0.6600...     

Structure and processability of iodinated poly(vinyl alcohol). IV. Drawability of the films iodinated at solution before casting

The drawability of iodinated at solution before casting (IBC) polyvinyl alcohol films prepared by casting aqueous solutions of 10 wt % PVA containing 15.2, 39.8, 83.2, 117.0, and 140.1% was examined with a tensile tester at 20–60°C. The tensile behavior of IBC films showed that the yield and breaking loads were much lower, and the breaking elongation was even higher than those of the unoriented iodinated after casting (IAC) films as well as the untreated PVA films. The maximum draw ratios of the films with the weight gain of 15.2, 39.8, 83.2, 117, and 140.1% were 4.5, 5.5, 8.5, 8.0, and 7.5, respectively, which were achieved at 20°C in all. The crystallinity of all films increased by the maximum draw, regardless of crystallinity before drawing. The crystalline structure was recovered to the original PVA crystalline lattice by deiodination. Amorphous orientation and initial moduli increased with the maximum draw ratio, while the orientation of crystals was constant. The orientation and moduli increased up to the weight gain of 83.2%, whose highest draw ratio and initial modulus were 8.5 and of 7.1 GPa, respectively, and then decreased. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2008     

Crystal and molecular structure of the thioether-analogue of PEEK from X-ray powder data and diffraction-modelling

Analysis of X-ray powder data for the melt-crystallisable aromatic poly(thioether thioether ketone) [-S-Ar-S-Ar-CO-Ar]_n, (‘PTTK’, Ar=1,4-phenylene), reveals that it adopts a crystal structure very different from that established for its ether-analogue PEEK. Molecular modelling and diffraction-simulation studies of PTTK show that the structure of this polymer is analogous to that of melt-crystallised poly(thioetherketone) [-S-Ar-CO-Ar]_n in which the carbonyl linkages in symmetry-related chains are aligned anti-parallel to one another, and that these bridging units are crystallographically interchangeable. The final model for the crystal structure of PTTK is thus disordered, in the monoclinic space group I2/a (two chains per unit cell), with cell dimensions a=7.83, b=6.06, c=10.35 Å, β=93.47°.     

Crystal Structure and Biochemical Analysis of a Cytochrome P450 CYP101D5 from Sphingomonas echinoides

Cytochrome P450 enzymes (CYPs) are heme-containing enzymes that catalyze hydroxylation with a variety of biological molecules. Despite their diverse activity and substrates, the structures of CYPs are limited to a tertiary structure that is similar across all the enzymes. It has been presumed that CYPs overcome substrate selectivity with highly flexible loops and divergent sequences around the substrate entrance region. Here, we report the newly identified CYP101D5 from Sphingomonas echinoides. CYP101D5 catalyzes the hydroxylation of β-ionone and flavonoids, including naringenin and apigenin, and causes the dehydrogenation of α-ionone. A structural investigation and comparison with other CYP101 families indicated that spatial constraints at the substrate-recognition site originate from the B/C loop. Furthermore, charge distribution at the substrate binding site may be important for substrate selectivity and the preference for CYP101D5.     

石英晶体微天平对硫辛酸自组装成膜动力学的研究

用石英晶体微天平 (QCM)在线监测了硫辛酸 (TA)在金电极上自组装成膜动力学过程。探讨了温度、浓度对成膜过程的影响及 TA膜在不同 p H值下的稳定性 ,给出了有关自组装成膜动力学信息。结果表明 :成膜动力学过程符合 Langmuir吸附速率方程 ,TA膜在 p H值为 5 .4～ 7.6间比较稳定。     

Rational Design of CYP3A4 Inhibitors: A One-Atom Linker Elongation in Ritonavir-Like Compounds Leads to a Marked Improvement in the Binding Strength

Inhibition of the major human drug-metabolizing cytochrome P450 3A4 (CYP3A4) by pharmaceuticals and other xenobiotics could lead to toxicity, drug–drug interactions and other adverse effects, as well as pharmacoenhancement. Despite serious clinical implications, the structural basis and attributes required for the potent inhibition of CYP3A4 remain to be established. We utilized a rational inhibitor design to investigate the structure–activity relationships in the analogues of ritonavir, the most potent CYP3A4 inhibitor in clinical use. This study elucidated the optimal length of the head-group spacer using eleven (series V) analogues with the R₁/R₂ side-groups as phenyls or R₁–phenyl/R₂–indole/naphthalene in various stereo configurations. Spectral, functional and structural characterization of the inhibitory complexes showed that a one-atom head-group linker elongation, from pyridyl–ethyl to pyridyl–propyl, was beneficial and markedly improved K_s, IC₅₀ and thermostability of CYP3A4. In contrast, a two-atom linker extension led to a multi-fold decrease in the binding and inhibitory strength, possibly due to spatial and/or conformational constraints. The lead compound, 3h, was among the best inhibitors designed so far and overall, the strongest binder (K_s and IC₅₀ of 0.007 and 0.090 µM, respectively). 3h was the fourth structurally simpler inhibitor superior to ritonavir, which further demonstrates the power of our approach.     

复合材料储能飞轮分层结构研究

采用有限元数值分析，分析了复合材料飞轮内部应力及应变，并结合复合材料缠绕成型工艺，提出一种新的复合材料飞轮分层结构。利用张力缠绕成型的分层结构的复合材料飞轮，最高转速可从28662r／min提高到63057r／min。     

5-(4-叠氮呋咱基)-[1,2,3]三唑[4,5-c]并呋咱内盐的合成、晶体结构及性能

以3,4-二氨基呋咱为原料,经重氮化-叠氮化、氧化-环化等反应合成了一种新型无氢富氮含能材料5-(4-叠氮呋咱基)-[1,2,3]三唑[4,5-c]并呋咱内盐(AFTF);采用红外光谱、核磁共振、元素分析等方法表征了目标物的结构;获得了AFTF的单晶并进行了晶体结构解析;采用DSC方法研究了AFTF的热稳定性,初步探讨了氧化-环化反应机理;采用Gaussian 09程序CBS-QB3方法计算了AFTF的固相生成热,基于晶体密度和固相生成热,利用EXPLO5爆轰软件预估了AFTF的爆轰性能。结果表明,化合物AFTF晶体为正交晶系,空间群为P 2(1)2(1)2(1),晶胞参数为:a=8.1782(17),b=8.6446(18),c=11.521(2),V=814.5(3)3,Z=4,μ=0.151 mm^-1,F(000)=440;AFTF的熔点为101.02℃,热分解温度为186.39℃;AFTF晶体密度为1.795 g/cm 3(296 K),氮含量为63.6%,理论爆速为8.982 km/s,爆压为33.5 GPa,生成热为1178.9 kJ/mol,爆热为6450.8 kJ/kg,表明AFTF是一种爆轰性能优良的无氢富氮高能量密度化合物,有望应用于高能推进剂或气体发生剂领域;低熔点特性有望使其作为熔铸炸药载体使用。