聚肽分子链构象转变研究

聚肽分子链在一定的条件下可发生右旋分子链构象与左旋分子链构象间的构象转变 .文中提出了一个有关这一现象的统计理论解释 ,理论包含了两个重要的参数γ、ρ .γ与右旋和左旋分子链构象间能量差别有关 ;ρ与在左旋分子链段中启始一个右旋构象的结构单元所需能量有关 .进一步考虑了体系中酸分子存在对构象转变的影响 ,以解释新近发现的聚肽左、右旋多重分子链构象转变现象 .此外 ,运用核磁共振 (NMR)手段还对这一现象做了进一步的研究 .通过与实验结果和文献中报告的数据比较 ,证明这一理论可以很好地解释聚肽分子链中发生的左、右旋分子链构象转变     

环肽纳米管的应用研究

环肽分子通过主链骨架中C=O和N-H形成分子间网络氢键,以β-片层反平行方式堆积可形成中空管状结构。通过控制环肽的结构和尺寸,或修饰具有不同功能的基团,可获得多种结构和性能的肽纳米管。本文综述了环肽分子自组装成纳米管的应用研究成果。首先介绍了带合适疏水性侧链的环肽纳米管在模拟生物跨膜离子通道方面的实验和理论研究进展,重点论及环肽纳米管的结构、极性和侧链的疏水性等对离子通道传输行为的影响以及分子动力学（MD）模拟研究水通道的进展。进而介绍了环肽纳米管用作生物传感器模板,与功能性（如电性、光学性和磁性）纳米材料合成制备生物传感器的实验研究成果,接着介绍了环肽纳米管作为药物或药物载体潜在的应用前景,特别是在某些抗菌和抗感染药物开发设计中的应用以及环肽在不同极性的环境中自组装过程微观机制的MD模拟研究,最后介绍了环肽纳米管作为模板,制备磁性、电性纳米材料方面的实验和理论研究进展。     

聚肽的结构性能及其在生物材料领域的应用

聚肽是一类由氨基酸及其衍生物通过聚合反应形成的聚合物，具有和蛋白质类似的二级结构。由于其独特的结构和性能，近年来在蛋白质结构模拟、分子链构象研究、生物医学等领域被广泛地加以研究。本文着重介绍了聚肽的合成、分子链构象、相行为、自组装行为以及在药物缓释等领域的研究和应用状况，并对聚肽在组织工程领域的应用前景进行了展望，为聚肽在生物材料领域的应用提供参考。     

两亲性聚(L-谷氨酸γ-苄基酯)-聚乙二醇接枝共聚物的自组装行为和载药性能研究

由氨基酸及其衍生物聚合形成的聚肽,因其独特的结构和性能,近年来在蛋白质结构模拟、分子链构象研究、生物医学等领域备受关注．其中两亲性聚肽共聚物的自组装行为,为开发具有生物相容性、可控释、可降解性的新型药物载体创造了条件．目前对聚肽共聚物自组装及载药性能研究主要集中于聚肽嵌段共聚物胶束,     

N-磷酰化肽酯及小肽与溶菌酶相互作用的ESI-MS研究

用ESI-MS研究了一系列结构具有可比性的N-磷酰化肽酯及小肽和溶菌酶的非共价相互作用, 比较了磷酰化肽酯及小肽分子中的不同基团对相互作用的影响. 结果表明—OH对其与溶菌酶的相互作用有较大贡献; 芳香环由于位阻原因, 对相互作用有促进和阻碍双重效应; 当—OH与芳香环相连时会发生协同效应, 可使相互作用显著增强. 磷酰化肽酯及小肽的体积大小、空间位阻对相互作用亦有显著影响. 磷酰化二肽中氨基酸残基的构型、顺序、碳链长短的变化(增加1～2个C)对其与蛋白溶菌酶之间的相互作用在质谱中没有表现出影响. 分子结构较为伸展、分子柔顺性好、空间位阻较小的磷酰化小肽更容易使蛋白在溶液中的构象趋于收缩, 而构象较为收缩的蛋白分子更易结合空间位阻较小的磷酰化小肽分子.     

2-苯基/环己基取代环十二酮肟衍生物的合成及晶体结构

以环十二酮为原料,分别与溴代环己烷或苯基锂试剂反应制得2-环己基环十二酮和2-苯基环十二酮,还意外获得了副产物1,1'-二羟基-1,1'-联环十二烷.2-环己基环十二酮和2-苯基环十二酮与盐酸羟胺反应制备了2-环己基环十二酮肟和2-苯基环十二酮肟,与亚硝酸钠-盐酸体系反应获得了3-环己基-1,2-环十二二酮单肟和3-苯基-1,2-环十二二酮单肟.在溶液中结晶获得其中四个化合物单晶并进行了X射线衍射,结果表明1-苯基环十二醇和1,1'-二羟基-1,1'-联环十二烷在晶体中的十二元环均采取[3333]构象,两个取代基在角碳上;在晶体中2-环己基环十二酮肟的十二元环采取[3333]-2-酮构象,而3-苯基-1,2-环十二二酮单肟的十二元环则改变为[4233]-3,4-二酮构象,取代基均在边碳外向位,量子力学计算的结果与晶体衍射的结果一致.1,1'-二羟基-1,1'-联环十二烷在晶体中采取摞光盘一样完全重叠的自组装排列方式.     

无机磷试剂辅助均环肽库的建立及其电喷雾质谱研究

在无机磷试剂辅助下建立了氨基酸自组装成均环肽的方法, 得到了相应的均环肽库. 均环肽库的建立增加了肽库的多样性, 为药物筛选提供了新的选择性. 采用电喷雾多级质谱技术, 对系列均环多肽 [M＋H]＋离子和[M＋Na]＋离子的质谱裂解规律进行了系统研究, 两种系列的离子具有不同的质谱裂解特征, 分别提出了其可能的质谱裂解机制. 该研究丰富了环多肽化合物的电喷雾多级质谱研究, 结果表明环肽化合物的加钠离子较加氢离子的质谱图可以更容易地用于环多肽的序列测定. 本研究为其它类似环肽化合物结构的分析鉴定及利用电喷雾质谱推测环肽序列提供了有效的质谱方法.     

环肽中酰胺键cis-/trans-异构化的相关研究进展

介绍了环肽化合物中顺式(cis-)和反式(trans-)结构特点,分别针对不含N-取代的环肽、含脯氨酸残基的环肽以及含N-甲基化残基的天然环肽,讨论了cis-或trans-结构在上述环肽及结构类似物中的研究进展,以及这种cis-或trans-结构对环肽生物活性的潜在影响.脯氨酸由于其刚性吡咯环结构而显著影响着环肽分子构象,N-甲基化残基不仅增大了空间位阻,而且能够诱导增大酰胺键cis-结构比例.     

环二肽的自组装及其荧光性能

环二肽由两个氨基酸通过肽键环合形成,在氢键相互作用驱动下具有较强的自组装倾向.本工作研究了c-SF,c-SY,c-SH及c-DF等四种环二肽的自组装行为和组装体的荧光特性.实验结果表明,c-SH为无规卷曲而其他三种环二肽均采取β-sheet二级结构,且除c-SH未形成明显组装体外,其他三种环二肽均形成不同尺寸的纳米纤维.荧光光谱检测发现环二肽在不同波长的激发下存在多个不同的荧光发射峰;对于c-SH,侧链咪唑基官能团与Zn（II）配位可以增大荧光发射的强度;对于c-SY,侧链酚羟基的氧化也可以增强荧光强度.推测在氢键作用的驱动下环二肽分子可以逐个堆叠形成纳米纤维,自组装导致的分子聚集和分子的侧链结构均可使环二肽具有可调变的荧光性能.     

Mannich型环肽的液相及固相合成比较

为了改善肽化合物的抗酶解能力，首次介绍了3肽Pro-Pro-Tyr分子的非天然环 化反应，其中分别采用液相及固相两种合成方式组装直链肽，再经过分子内 Mannich缩合，得到以Mannich碱为桥连结构的环肽5（产率5.38%)及10（产率72. 7%)。产物结构经氨基酸组分及质谱分析证明。结果表明，固相法环合可以避免分 子间反应，因此产物收率明显高于液相法。     

硝酸酯类分子力学参数的确定和应用

运用MM2(85年版)分子力学程序, 以硝酸甲酯、硝酸乙酯的实验结构为参比, 调试确定了硝酸酯类化合物的伸缩力常数(K~s)、弯曲力常数(K~b)和旋转力常数(V~1、V~2、和V~3)。用这套力场参数计算了硝酸甲酯、硝酸乙酯和硝化甘油的平衡几何构型、生成热和偶极矩, 计算结果与实验值和从头计算结果相一致。还用这套参数计算了结构未见报道的异基硝酸酯、丙烯基硝酸酯和苯基硝酸酯, 所得结果与MNDO全优化几何构型相符。     

右旋邻氯扁桃酸分子印迹聚合物的制备及结合特性研究

以右旋邻氯扁桃酸为模板分子合成了具有高选择性的分子印迹聚合物作为手性分离材料 .紫外光谱研究说明在聚合开始之前模板分子与功能单体形成了配合物 ,并用Hyperchem软件模拟其分子结构 ,结合能分别为 -1 643 7× 1 0 4 J·mol- 1 和 -4 2 799× 1 0 4 J·mol- 1 .分子印迹聚合物对模板分子的结合量高于其它类似物 ,手性分离因子α达 1 76.Scatchard分析表明分子印迹聚合物在识别右旋邻氯扁桃酸分子过程中存在两类结合位点 ,与配合物模拟结构数目一致     

Structure,strain, and reorganization energy of blue copper models in the protein

The copper coordination geometry in the blue copper proteins plastocyanin, nitrite reductase, cucumber basic protein, and azurin has been studied by combined density functional (B3LYP) and molecular mechanical methods. Compared to quantum chemical vacuum calculations, a significant improvement of the geometry is seen (toward the experimental structures) not only for the dihedral angles of the ligands but also for the bond lengths and angles around the copper ion. The flexible Cu–S_Met bond is well reproduced in the oxidized structures, whereas it is too long in some of the reduced complexes (too short in vacuum). The change in the geometry compared to the vacuum state costs 33–66 kJ/mol. If the covalent bonds between the ligands and the protein are broken, this energy decreases by ∼25 kJ/mol, which is an estimate of the covalent strain. This is similar to what is found for other proteins, so the blue copper proteins are not more strained than other metalloproteins. The inner‐sphere self‐exchange reorganization energy of all four proteins are ∼30 kJ/mol. This is 30–50 kJ/mol lower than in vacuum. The decrease is caused by dielectric and electrostatic effects in the protein, especially the hydrogen bond(s) to the cysteine copper ligands and not by covalent strain. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 335–347, 2001     

Total synthesis of prostaglandin F2alpha using nickel-catalyzed stereoselective cyclization of 1,3-diene and tethered aldehyde via transmetalation of nickelacycle with diisobutylaluminum acetylacetonate

Total synthesis of prostaglandin F2alpha utilizing a nickel(0)-catalyzed cyclization of 1,3-diene and tethered aldehyde was achieved. The cyclization proceeded via a transmetalation of nickelacycle with diisobutylaluminum acetylacetonate (iBu2-ALAC). Thus, the reaction of 19, having a side chain corresponding to the alpha-chain in PGF2alpha with Ni(cod)2 (10 mol %), PPh3 (20 mol %), and 1,3-cyclohexadiene (25 mol %) in the presence of iBu2-ALAC (1.5 eq) proceeded stereoselectively to give the cyclized product 26 in 54% yield. During the cyclization of 19, the Z-olefin at C-5 in the side chain completely retained its geometry, and the four contiguous chiral carbon centers in PGF2alpha were stereoselectively constructed. Transformation of the key intermediate 19 into PGF2alpha was successfully achieved.     

Response of a designed metalloprotein to changes in metal ion coordination, exogenous ligands, and active site volume determined by X-ray crystallography

The de novo protein DF1 is a minimal model for diiron and dimanganese metalloproteins, such as soluble methane monooxygenase. DF1 is a homodimeric four-helix bundle whose dinuclear center is formed by two bridging Glu side chains, two chelating Glu side chains, and two monodentate His ligands. Here, we report the di-Mn(II) and di-Co(II) derivatives of variants of this protein. Together with previously solved structures, 23 crystallographically independent four-helix bundle structures of DF1 variants have been determined, which differ in the bound metal ions and size of the active site cavity. For the di-Mn(II) derivatives, as the size of the cavity increases, the number and polarity of exogenous ligands increases. This collection of structures was analyzed to determine the relationship between protein conformation and the geometry of the active site. The primary mode of backbone movement involves a coordinated tilting and sliding of the first helix in the helix-loop-helix motif. Sliding depends on crystal-packing forces, the steric bulk of a critical residue that determines the dimensions of the active site access cavity, and the intermetal distance. Additionally, a torsional motion of the bridging carboxylates modulates the intermetal distance. This analysis provides a critical evaluation of how conformation, flexibility, and active site accessibility affect the geometry and ligand-binding properties of a metal center. The geometric parameters defining the DF structures were compared to natural diiron proteins; DF proteins have a restricted active site cavity, which may have implications for substrate recognition and chemical stability.     

Fe2S2Cl4^2^-电子结构的从头计算

从头计算了FeS2Cl4二价负离子,证实了Fe3d为主的分子轨道不处于前沿地位,而是属于S和Cl孤对能级原子布居数表明铁原子是4s电子的强给予体,3d电子的弱接受体,但是硫和氯原子都是P电子接受体.     

Determination of the structure of fusaproliferin by1H-NMR and distance geometry

The absolute configuration of fusaproliferin, a toxic metabolite produced byFusarium proliferation, was determined by the combined use of¹H NMR and distance geometry. The configuration of double bonds has been determined in agreement with NOESY buildup data. An R configuration for C10 was determined using Mosher's method. Processing the constraints obtained from NOESY experiments with a distance geometry program, a limited number (80) of possible structures was derived. An agglomerative nonhierarchical method of clustering was used in order to place these structures into classes suggested by the data, and not previously defined in any way. This statistical method showed that indeed the structures could be grouped in four classes. One of these classes is represented by a single structure, with the highest sum of violations and was discarded. All other structures have the same chirality; respectively S for C14 and R for C15. In solution the overall conformation is quite well defined in the region of the five-member ring and the planes of double bonds C2–C3 and C11–C12, while near to C8 and C9 internal flexibility appears evident.     

Chiral recognition of octadentate Na complex with tetra-armed cyclen by molecularly imprinted polymers

Chiral indanyl substituted tetra-armed cyclens (TAC) formed octadentate complexes with Na⁺. Since their four side arms stand up and are bundled to form quadruplicated helical structures, they can have Δ- or Λ-types enantiomers based on complex helicity. In this study, TAC-imprinted polymers were prepared using an ion-pair complex of the sodium salt of (S)-indanyl substituted TAC (TAC(S)) and 2-sulfoethyl methacrylate as a template, and ethylene glycol dimethacrylate as a cross-linker. Affinity of the obtained polymers for the TAC Na⁺ complexes was evaluated chromatographically and the imprinted polymer gave longer retention time for the template than that for its antipode where the separation factor was given to be 1.29-1.45 under the NaOH concentrations of 10-25 mM in the eluent. These results indicate that the imprinted polymer could discriminate helix structures of TAC Na⁺ complexes.     

A comparison of distance geometry and molecular dynamics simulation techniques for conformational analysis of β-cyclodextrin

Distance geometry and molecular dynamics simulation techniques were compared in their ability to search the conformational potential energy surface of β-cyclodextrin. Structures generated by the DISGEO program were minimized using three different atomic point charge sets. Some of these structures were used as starting points for molecular dynamics simulation in vacuo at 298K. The distance geometry results showed that the global features of the conformational potential energy surface were generally independent of the point charge set. The distance geometry technique was able to find structures of lower energy than those obtained by direct minimization of the X-ray or neutron diffraction structures. However, the molecular dynamics simulation technique was consistently able to find structures of lower energy than those generated by distance geometry. Root mean square fit of the trajectory structures to the starting structure showed that the simulation allowed the molecule to explore regions of the potential energy surface in the neighborhood of the starting structure. Both the distance geometry and molecular dynamics simulation techniques showed that β-cyclodextrin can adopt a wide range of conformations in the gas phase and that these conformations are much less symmetrical than the crystalline structure.     

Permeation of particle through a four-helix-bundle model channel

By using molecular dynamics simulation, the dynamic behaviors of particle permeation through a four-helix-bundle model channel are studied. The interior cavity of the four-helix-bundle provides the "routes" for particle permeation. The main structural properties of the model channel are similar to those that appear in natural four-helix-bundle proteins. It is found that the interior structure of the model channel may greatly influence the permeation process. At the narrow necks of the model channel, the particle would be trapped during the permeation. There is a threshold value for the driving force. When the driving force is larger than this threshold value, the mean first permeation time decreases sharply and tends to be saturated. Increasing the temperature of either the model channel or the particle reservoir can also facilitate the permeation. Enhancing the interaction strength between the particle and monomer on the four-helix-bundle model chain will hinder the permeation. Hence, the electrical current which is induced by the particle permeation is a function of the driving force and temperature. It is found that this current increases monotonically as the strength of the driving force or the temperature increases, but decreases as the interaction strength between the particle and monomer increases. It is also found that the larger the friction coefficient, the slower the permeation is. In addition, the multiparticle (or multi-ion) permeation process is also studied. The permeation of multiparticle is usually quicker than that of the single particle. The permeation of particle through a five-helix-bundle shows similar properties as that through a four-helix-bundle.