发展尿素与丙氨酸二肽相互作用的ABEEM/MM可极化力场

基于ABEEM/MM浮动电荷模型，尝试建立了一个新的可合理描述尿素-丙氨酸二肽-水分子之间相互作用的可极化力场.采用量子力学(QM)ωB97X-D/6-311++G(3df, 2p)//MP2/aug-cc-pVTZ方法对(Urea)(Ala)₂的结构、电荷分布及结合能进行计算，以及HF/STO-3G方法计算电荷分布.构建尿素-丙氨酸二肽-水体系的ABEEM/MM势能函数，基于QM计算结果，优选确定相关参数.结果表明，与QM相比，ABEEM/MM获得的(Urea)(Ala)₂的键长、键角、二面角和结合能的AAD(平均绝对偏差),RMSD(均方根偏差)和RRMSD(相对均方根偏差)分别为0.000 8 nm, 0.001 4 nm, 1.2%;1.36°,1.72°,1.5%;4.10°,5.56°,5.0%;6.07 kJ·mol^-1,6.82 kJ·mol^-1和10.2%,电荷分布的线性相关系数为0.988.将上述势能函数应用于(Ala)₂(Urea)₂...     

固体核磁碳结构参数的修正及其在煤结构分析中的应用

为消除~(13)C CP/M AS/TOSS NM R测试中碳核NOE效应,获得相对准确的碳结构参数,考察了不同模型化合物的碳核NOE效应强度。结果表明,不同模型化合物碳谱分峰拟合的测试值与样品碳结构参数的理论值之间存在明显误差,其中,脂肪碳在25%-125%、芳香碳为4%-50%,NOE效应在固体核磁碳谱测试中影响显著。为此,将模型化合物脂肪碳和芳香碳的实测值和理论值进行回归分析,得到非线性回归方程。用该方程对9,10-二甲基蒽进行碳结构修正,发现修正后脂肪碳实测值与理论值之间误差由不修正时的119.60%减小至7.84%,芳香碳误差为由不修正时的-17.10%到1.11%,修正后误差均在10%以内;同时用该回归方程修正了不同煤的碳结构参数,发现不同煤未修正的H/C原子比与其元素分析H/C原子比误差在45%-53%,修正后误差只有4%-13%,与元素分析结果具有一致性,表明非线性回归方程能够方便、准确地消除固体核磁NOE效应,为煤中碳结构分析提供新的技术支撑。     

土壤总氮近红外光谱分析的波段优选

利用移动窗口偏最小二乘( MWPLS)和Savitzky-Golay(SG)平滑方法优选土壤总氮的近红外(NIR)光谱分析模型.从全部97个土壤样品中随机选出35个样品作为检验集;基于偏最小二乘交叉检验预测偏差(PLSPB),将余下62个样品划分为具有相似性的建模定标集(37个样品)、建模预测集(25个样品).最优波段为1692～2138 nm,SG平滑的导数阶数(OD)、多项式次数(DP)、平滑点数(NSP)分别为0,6,69,PLS因子数为11,建模预测均方根偏差(M-RMSEP)、建模预测相关系数(M-Rp)分别为0.015％,0.931,检验预测均方根偏差(V-RM-SEP)、检验预测相关系数(V-RP)分别为0.018％,0.882.其结果可为设计专用NIR仪器提供有价值的参考.     

四氟菊酯的核磁共振法分析

采用^1HNMR、^13C NMR、无畸变增强极化转移实验(DEPT)、^1H—^1H相关谱(COSY)、^1H检测异核多量子相关谱(HMQC)、^1H检测的异核多键相关谱(HMBC)等方法，对四氟菊酯的^1H和^13C NMR谱信号进行了归属；并用奥氏核效应(NOE)差谱法确定了该化合物的立体结构，为其结构鉴定和生产过程中的质量控制提供了重要依据。     

大麻素Ⅰ型受体拮抗剂的结构特征

以92个具有大麻素受体Ⅰ(CB1)拮抗活性的化合物为训练集, 39个化合物为测试集, 采用Discovery Studio V2.5(DS)软件中的3D构效关系药效团产生(QSAR Pharmacophore Generation)模块建立药效团模型. 获得的最佳药效团模型的构成为一个氢键受体(HBA)、 一个疏水基团(HY)和二个芳环中心(RA), 采用费用函数(Cost function)评价药效团模型, 该模型的Δcost为119.32, 相关性为0.921, 均方根偏差为0.730, Configuration cost为16.1229, 表明模型能较好地预测化合物的活性. 同时针对目前已知的近450个化合物的12种结构类型进行了探讨, 所得结果为进一步设计CB1拮抗剂提供了理论依据.     

Mn2+掺杂对低温生长ZnS的形貌及光致发光性能的影响

以Zn粉和S粉为原料,Au纳米颗粒为催化剂,采用低温(450℃)化学气相沉积法(CVD),在Si(100)衬底上制备了未掺杂和Mn2+掺杂的ZnS微纳米结构.利用X射线衍射仪(XRD)、能量弥散X射线谱(EDS)、场发射扫描电子显微镜(SEM)和光致发光光谱(PL)等测试手段对样品的结构、成分、形貌和发光性能进行了分析.结果表明,所得ZnS样品均为六方纤锌矿结构,未掺杂的ZnS为微纳米球,在波长为450和463 nm处有2个发光强度较大的蓝光峰;Mn2+掺杂ZnS为纳米线,在波长479和587 nm处分别有1个微弱的蓝光峰和1个强度相对较大的红光峰.此外,还对ZnS微纳米结构的形成过程进行了探讨,并提出了可能的形成机理.     

孤啡肽OFQ的溶液构象研究

应用近代NMR波谱技术对孤啡肽OFQ及其片段OFQ_(8-17)的溶液结构进行了比较 研究，测定了孤啡肽OFQ和片段OFQ_(8-17)在H_2O和TEF/H_2O两种溶剂条件下的2D －DQF－COSY，2D－TOCSY，2D－NOSESY(ROESY)谱，完成了它们氨基酸残基的处旋 系统识别和序列特异性归属，获得分子中质子化学位移的完全归属，根据NOE特征 和主链偶合常数等结构参数确定了它们的特征二级结构，以NOE提供的距离约束， 进行何，分子力学和分子动力学模拟，得到了孤啡肽OFQ在不同溶剂条件下的溶液 结构。在H_2O溶济中，孤啡肽OFQ在G3－F4－T5－G6处形成一复合型转角结构。在 TFE/H_2O溶剂中，OFQ整个分子形成两新性α－螺旋结构。而孤啡肽片OFO_(8-17) 在这两种环境中均为伸展的无规结构。孤啡肽OFQ在类似膜环境(TFE/H_2O)下的α 螺旋结构可能为其活性构象。     

锈毛野桐化学成分的研究 III: 玫瑰烷型二萜成分的分离与结构

从海南特有植物锈毛野桐Mallotus anomalus meer et Chun的地上部分又分得三个新的对映一玫瑰烷(rosane)型三环二萜类成分: 锈毛醇酮, 异锈毛醇酮, 锈毛双醇酮。根据其理化数据和核磁共振NOE及二维谱技术推定了它们的结构。     

锈毛野桐化学成分的研究 III: 玫瑰烷型二萜成分的分离与结构

从海南特有植物锈毛野桐Mallotus anomalus meer et Chun的地上部分又分得三个新的对映一玫瑰烷(rosane)型三环二萜类成分: 锈毛醇酮, 异锈毛醇酮, 锈毛双醇酮。根据其理化数据和核磁共振NOE及二维谱技术推定了它们的结构。     

从头算和ABEEMσπ/MM对(CH_3OH)_n(n=3～12)和[Na(CH_3OH)_n]~+(n=3～6)体系的研究

采用从头算方法(ab initio)和原子-键电负性均衡浮动电荷分子力场方法(ABEEMσπ/MM),对甲醇团簇(CH_3OH)n(n=3~12)和[Na(CH_3OH)_n]~+(n=3~6)体系的结构、电荷分布和结合能进行研究.依据从头算结果构建上述体系的ABEEMσπ/MM浮动电荷势能函数,并确定相关参数.结果表明,ABEEMσπ/MM所获得的结构和结合能等均优于OPLS/AA力场,并与从头算结果相符,其中键长的平均绝对偏差(AAD)小于0.004 nm,键长、键角和结合能的相对均方根偏差(RRMSD)分别小于3.8%,1.7%和6.8%;电荷分布与从头算结果的线性相关系数均大于0.99.     

NMR structure of a cyclic polyamide-DNA complex

The solution structure of a cyclic polyamide ligand complexed to a DNA oligomer, derived from NMR restrained molecular mechanics, is presented. The polyamide, cyclo-gamma-ImPyPy-gamma-PyPyPy-, binds to target DNA with a nanomolar dissociation constant as characterized by quantitative footprinting previously reported. 2D (1)H NMR data were used to generate distance restraints defining the structure of this cyclic polyamide with the DNA duplex d(5'-GCCTGTTAGCG-3'):d(5'-CGCTAACAGGC-3'). Data interpretation used complete relaxation matrix analysis of the NOESY cross-peak intensities with the program MARDIGRAS. The NMR-based distance restraints (276 total) were applied in restrained molecular dynamics calculations using a solvent model, yielding structures with an rmsd for the ligand and binding site of approximately 1 A. The resulting structures indicate some distortion of the DNA in the binding site. The constraints from cyclization lead to altered stacking of the rings in the halves of the cyclic ligand relative to unlinked complexes. Despite this, the interactions with DNA are very similar to what has been found in unlinked complexes. Measurements of ligand amide and DNA imino proton exchange rates indicate very slow dissociation of the ligand and show that the DNA can undergo opening fluctuations while the ligand is bound although the presence of the ligand decreases their frequency relative to the free DNA.     

多肽IS4溶液构象的进一步NMR研究

利用二维核磁共振技术对多肽IS4中除Ser-1外的所有残基质子进行了指认.积分NOESY谱中的相关峰可得到距离约束.二面角的约束来自偶合常数³J_NHα.由慢交换质子可得到氢键的约束.在进行距离几何程序计算时利用这些约束可得到一组构象,用能量最优化程序优化后的结果表明,多肽IS4在CF₃CD₂OH中的构象为α-螺旋.     

GAPE: an improved genetic algorithm for pharmacophore elucidation

Prediction of the binding mode for a series of active compounds, in the absence of known protein structure, is a problem of paramount importance in rational drug design. GAPE (genetic algorithm for pharmacophore elucidation) is an automated multicompound overlay creation program, based on the original GASP program, that uses a genetic algorithm to fully explore the conformational space of the input structures and their alignments, so as to elucidate a pharmacophore. The software was evaluated on 13 test systems from nine protein targets using overlaid ligands extracted from the PDB. Using objective rmsd criteria and starting from 2D structures, in the absence of any protein information, GAPE was observed in eight systems to approximate the crystallographically observed binding mode. In the predicted alignments for each of those eight systems, at least half the input structures were within 2 ? rmsd of the crystal structure coordinates. Further analysis, using stricter subjective criteria, showed considerable success in five systems. For example, the prediction for a set of 12 ligands targeting P38 had 11 ligands with a 1.8 ? rmsd to crystal structure coordinates. Finally, the algorithm was favorably compared with the current GASP and Galahad programs.     

The importance of including local correlation times in the calculation of inter-proton distances from NMR measurements: ignoring local correlation times leads to significant errors in the conformational analysis of the Glc alpha1-2Glc alpha linkage by NMR spectroscopy

The experimental determination of oligosaccharide conformations has traditionally used cross-linkage 1H-1H NOE/ROEs. As relatively few NOEs are observed, to provide sufficient conformational constraints this method relies on: accurate quantification of NOE intensities (positive constraints); analysis of absent NOEs (negative constraints); and hence calculation of inter-proton distances using the two-spin approximation. We have compared the results obtained by using 1H 2D NOESY, ROESY and T-ROESY experiments at 500 and 700 MHz to determine the conformation of the terminal Glc alpha1-2Glc alpha linkage in a dodecasaccharide and a related tetrasaccharide. For the tetrasaccharide, the NOESY and ROESY spectra produced the same qualitative pattern of linkage cross-peaks but the quantitative pattern, the relative peak intensities, was different. For the dodecasaccharide, the NOESY and ROESY spectra at 500 MHz produced a different qualitative pattern of linkage cross-peaks, with fewer peaks in the NOESY spectrum. At 700 MHz, the NOESY and ROESY spectra of the dodecasaccharide produced the same qualitative pattern of peaks, but again the relative peak intensities were different. These differences are due to very significant differences in the local correlation times for different proton pairs across this glycosidic linkage. The local correlation time for each proton pair was measured using the ratio of the NOESY and T-ROESY cross-relaxation rates, leaving the NOESY and ROESY as independent data sets for calculating the inter-proton distances. The inter-proton distances calculated including the effects of differences in local correlation times give much more consistent results.     

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.     

Structural Studies of Antarctic Fish Antifreeze Glycoproteins by One- and Two-Dimensional NMR Spectroscopy

Abstract

The solution structure of antifreeze glycoproteins (AFGP's) of the polar fish Tetramatomus borchgrevinki has been investigated by 2D ¹ H NMR spectroscopy as well as molecular modeling calculations (MM2). The simple glycotripeptide repeating structure in the shorter AFGP's (fractions 7 & 8) makes the structural analysis amenable. The resonance assignments of AFGP's 7 & 8 were determined by two-dimensional NMR techniques (COSY, Relayed-COSY, Phase Sensitive DQCOSY, NOESY). Information about the protein secondary structure was obtained by the coupling constants between the back-bone amide and α-carbon protons (obtained by phase sensitive COSY). Additional three dimensional constraints were obtained from NOESY through-space connectivities. The three dimensional solution structures of several AFGP's glycotripeptide fragments were based on MM2 calculations. The model structure was compared with the experimental data. Exchange rates of amide protons measured by dynamical spectroscopy show that the threonine and some of the alanine amide protons have two different and distinct exchange rates. GalNAc and the C-terminal Ala' amide protons appear to show relatively slow exchznge rates. The results suggets that the amide protons are not involved in any strong intramolecular hydrogen bonding.     

环十二肽溶液构象的二维核磁共振研究

利用二维核磁共振方法及距离几何计算研究了在片段组装法全新蛋白质合成中用作底座分子的环十二肽的溶液构象. 研究结果表明在环十二肽分子主链中包含四个转角结构,四个赖氨酸侧链均位于环的同一侧.环肽的构象为以环肽为模板组装四螺旋束分子提供了有利的条件     

Solution structure of folic acid. Molecular mechanics and NMR investigation

The structure of folic acid in solution was investigated by nuclear magnetic resonance (NMR) and theoretical calculations. Dynamical information and geometrical constraints were obtained by carbon-13 relaxation study, homo-nuclear NOESY spectra and hetero-nuclear 1H-13C NOE experiments. This set of experimental data was used for the molecular mechanics and molecular dynamic calculations. The accuracy of the final structure was established by the R(NMR) factor, which was calculated comparing the experimental NOESY cross-peaks intensities and the corresponding values simulated by using the complete relaxation matrix analysis (CORMA) approach.     

蒙特卡洛模拟退火与距离限制相结合的方法在多肽溶液构象分析中的应用

多维核磁共振技术的飞速发展议得其在生物大分子结构测定方面的应用已经达到可以与【射线晶体学并驾齐驱的地步．蛋白质结构堆积紧密，较适合于用核磁共振方法给出确定的结构．与蛋白质不同的是多肽的柔性较大，在溶液中可能存在多种构象，核磁共振实验给出的只是平均信息＊．利用核磁，（振数据构建分子结构模型常用的方法有距离几何、分子动力学等，在由核磁共振NOESZ得到的距离信息足够多时可以给出较好的结果问．由于多肽本身的特点：柔性较大，由核磁共振得到的距离信息较少等，利用距离几何、分子动力学方法进行构象搜索时容易陷入…     

蒙特卡洛模拟退火与距离限制相结合的方法——在多肽溶液构象分析中的应用

Distance geometry and molecular dynamics are currently employed in determining molecular structures with interatomic distances from NMR NOESY experiment. Because of the flexibility of peptide, distances obtained from NMR are usually not sufficient to confine its structure. Both distance geometry and molecular dynamics will bias in the conformational space at this circumstance. Constraint Monte Carlo simulated annealing was established to solve this problem. Distance constraints were included into the ECEPP/2 force field by introducing a harmonic energy term. Conformational analysis of a pentapeptide with eight interatomic distances from NMR was carried out as a test. By comparison of the 100 conformers obtained from constraint simulated annealing and the 100 conformers from distance geometry calculation, it was found that constraint simulated annealing can cover the outcomes of distance geometry and at the same time give more con-formers fitting to the experimental data. The result shows that constraint Monte-Carlo simulated annealing is more valid in constructing peptide structures from NMR distances than currently employed methods when no sufficient distances from NMR are available.