软硬酸碱原则在确定取代的乙烷构象中的应用

有机化学中,在涉及有机化合物的构象分析时,只要合适,常要把这些化合物作为取代的乙烷或取代的环己烷加以考虑。这是由于在有机化合物的立体化学中,这二者得到了最深入的研究,并积累了丰富的实验数据。但是,根据已有方法进行构象分析,仍有许多情况得不到较好的解释。本文把软、硬酸碱理论的原则运用到取代的乙烷的构象分析,得到了比较满意的结果,并由此得到了一些确定取代的乙烷的优势构象的一般规则。     

构象分析初期的研究和有关的思考

简单介绍构象分析方法创建初期的研究工作,构象分析方法的2位创始人OddHassel和Derek H.R.Barton的简单情况,并分析由此给我们的启示。     

原卟啉原Ⅸ的构象分析

在合理药物设计方法中,当靶标酶的三维结构未知时,对其底物进行构象分析,特别是确定其活性构象,对阐明靶标酶活性中心的空间形状和作用位点具有十分重要的意义.我们曾利用距离比较法确定了原卟啉原氧化酶的底物-原卟啉原Ⅸ的活性构象,本文从构象分析的角度对4种不同构象的原卟啉原Ⅸ分子与二苯醚类分子的晶体学构象进行了几何参数的比较和分析,结果进一步证实了距离比较法所确定的活性构象更为可靠.     

原卟啉原IX的构象分析

在合理药物设计方法中 ,当靶标酶的三维结构未知时 ,对其底物进行构象分析 ,特别是确定其活性构象 ,对阐明靶标酶活性中心的空间形状和作用位点具有十分重要的意义。我们曾利用距离比较法确定了原卟啉原氧化酶的底物—原卟啉原IX的活性构象 ,本文从构象分析的角度对 4种不同构象的原卟啉原IX分子与二苯醚类分子的晶体学构象进行了几何参数的比较和分析 ,结果进一步证实了距离比较法所确定的活性构象更为可靠     

N-取代-α-氧代环十二烷基磺酰胶的合成及其杀菌活性

以易得的环十二酮为原料，由磺化获得中间体α-氧代环十二烷基磺酸后，再经生成磺酰、氯和胺化反应合成了一系列N-取代-α-氧代环十二烷基磺酰胺（Ⅲ）．生物活性测定结果表明，它们对小麦赤霉病菌（Gibberellazeae）的生长具有抑制作用，其中活性最高的是氮上取代有一氯苯基的化合物（Ⅲ7、Ⅲ8），通过构象分析讨论了它们的结构-活性关系．     

新型双核锌席夫碱配合物的合成及其结构表征

新型双核锌席夫碱配合物的合成及其结构表征;席夫碱; 双核锌配合物; 合成; 谱学表征; 构象分析     

分子力学应用进展

本文总结了近年来分子力学在化学研究中的应用,包括有机化合物的构象分析、化学反应机理、核磁共振谱分析、生物化学、药物分子设计和配位化学诸方面。     

立体电子效应

立体电子效应是近年来有机化学研究的一个热点，有关的研究论文逐年增多。对于立体电子效应的认识始于构象分析和异头效应。     

用硝基苯萃取法在拉曼测试中猝灭荧光

本文报道了一种测试拉曼光谱时把硝基苯掺入蛋白质溶液再加以萃取的预处理方法，该方法能迅速猝灭蛋白质分子的荧光。得到稳定清晰的拉曼图谱，而且不影响对蛋白质分子的构象分析。     

微波波谱方法与应用研究进展

综述了微波波谱法及其应用研究进展,阐述了微波波谱法的基本原理及仪器构造。对微波波谱法在分子结构及构象分析、弱相互作用体系的研究、分析化学、星际物质的探测等方面的应用进行了综述。并展望了微波波谱方法未来的发展趋势。     

Rapid identification of oxidation-induced conformational changes by kinetic analysis

Protein oxidation by reactive oxygen species is known to result in changes in the structure and function of the oxidized protein. Many proteins can tolerate multiple oxidation events before altering their conformation, while others suffer gross changes in conformation after a single oxidation event. Additionally, reactive oxygen species have been used in conjunction with mass spectrometry to map the accessible surface of proteins, often after verification that the oxidations do not alter the conformation. However, detection of oxidation-induced conformational changes by detailed kinetic oxidation analysis of individual proteolytic peptides or non-mass spectrometric analysis is labor-intensive and often requires significant amounts of sample. In this work, we describe a methodology to detect oxidation-induced conformational changes in proteins via direct analysis of the intact protein. The kinetics of addition of oxygen to unmodified protein are compared with the kinetics of addition of oxygen to the mono-oxidized protein. These changes in the rate of oxidation of the oxidized versus the non-oxidized protein are strongly correlated with increases in the random coil content as measured by the molar ellipticity at 198 nm. This methodology requires only small amounts of protein, and can be done rapidly without additional sample handling or derivatization.     

The "nearest single neighbor" method-finding families of conformations within a sample

A simple method for self-organization of conformation samples into families is presented. According to this method, any large sample of molecular conformations may be reorganized according to the nearest single root-mean-square displacement (rmsd) neighbor, starting at any chosen "seed" conformation. Following such reordering, conformational families may be determined by a novel process that maximizes family sizes while minimizing family mixing. This process eliminates much of the arbitrariness that was inherent in most of the related methods of conformation clustering. We demonstrate the construction of rmsd matrices and discuss the convergence criteria for the sample size as well as criteria for determining the cutoff value for the definition of families in each sample. The method is invariant to changes of the "seed" conformation. After applying this method, families of conformations may be more easily recognized in graphic matrices. The method has been applied to the analysis of the conformational space of two cyclic peptides. It is also shown that the "organized" conformational space, at least in those specific examples, has an energy topology that reminds of energy basins. The method is general and applicable to molecules of any type.     

简化的系统搜索法及其在构象分析中的应用

多肽的构象研究除了可以用X-射线晶体学及二维核磁共振等实验方法外,理论计算的方法有系统搜索法、蒙特卡洛方法、距离几何方法、分子动力学方法及能量极小化等.系统搜索法具有构象空间搜索彻底的特点,相对来说找到系统整体极小值的可能性较大,但由于其计算量较大,对于多肽及蛋白质很难实现.我们对系统搜索法进行了简化,不是同时旋转所有的二面角,而是成对地进行,以迭代的方法达到收敛,最后得到可能的构象.     

A new tool in peptide engineering: a photoswitchable stilbene-type beta-hairpin mimetic

Peptide secondary structure mimetics are important tools in medicinal chemistry, as they provide analogues of endogenous peptides with new physicochemical and pharmacological properties. The development, synthesis, photochemical investigation, and conformational analysis of a stilbene-type beta-hairpin mimetic capable of light-triggered conformational changes have been achieved. In addition to standard spectroscopic techniques (nuclear Overhauser effects, amide temperature coefficients, circular dichroism spectroscopy), the applicability of self-diffusion measurements (longitudinal eddy current delay pulsed-field gradient spin echo (LED-PGSE) NMR technique) in conformational studies of oligopeptides is demonstrated. The title compound shows photoisomerization of the stilbene chromophore, resulting in a change in solution conformation between an unfolded structure and a folded beta-hairpin.     

Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition

Sequence dependence of DNA conformation plays a crucial role in its recognition by proteins and ligands. To clarify the relationship between sequence and conformation, it is necessary to quantify the conformational energy and specificity of DNA. Here, we make a systematic analysis of dodecamer DNA structures including all the 136 unique tetranucleotide sequences at the center by molecular dynamics simulations. Using a simplified conformational model with six parameters to describe the geometry of adjacent base pairs and harmonic potentials along these coordinates, we estimated the equilibrium conformational parameters and the harmonic potentials of mean force for the central base-pair steps from many trajectories of the simulations. This enabled us to estimate the conformational energy and the specificity for any given DNA sequence and structure. We tested our method by using sequence-structure threading to estimate the conformational energy and the Z-score as a measure of specificity for many B-DNA and A-DNA crystal structures. The average Z-scores were negative for both kinds of structures, indicating that the potential of mean force from the simulation is capable of predicting sequence specificity for the crystal structures and that it may be used to study the sequence specificity of both types of DNA. We also estimated the positional distribution of conformational energy and Z-score within DNA and showed that they are strongly position dependent. This analysis enabled us to identify particular conformations responsible for the specificity. The presented results will provide an insight into the mechanisms of DNA sequence recognition by proteins and ligands.     

An In‐tether Chiral Center Modulates the Helicity,Cell Permeability,and Target Binding Affinity of a Peptide

The addition of a precisely positioned chiral center in the tether of a constrained peptide is reported, yielding two separable peptide diastereomers with significantly different helicity, as supported by circular dichroism (CD) and NMR spectroscopy. Single crystal X‐ray diffraction analysis suggests that the absolute configuration of the in‐tether chiral center in helical form is R, which is in agreement with theoretical simulations. The relationship between the secondary structure of the short peptides and their biochemical/biophysical properties remains elusive, largely because of the lack of proper controls. The present strategy provides the only method for investigating the influence of solely conformational differences upon the biochemical/biophysical properties of peptides. The significant differences in permeability and target binding affinity between the peptide diastereomers demonstrate the importance of helical conformation.     

Can one derive the conformational preference of a beta-peptide from its CD spectrum?

CD spectroscopy is often used to elucidate the secondary structure of peptides built from non-natural amino acids such as beta-amino acids. The interpretation of such CD spectra is not always unambiguous. Here, we present a case where two beta-hexapeptides, a dimethyl-beta-hexapeptide indicated as DM-BHP (A) and its nonmethylated analogue indicated as BHP (B), exhibit similar CD spectra, whereas they are expected to differ in secondary structure. The structural properties of both peptides were studied by molecular dynamics simulation, and from the resulting trajectories, the corresponding CD spectra were calculated. Starting from a fully extended conformation, BHP is observed to form a 3(14)-helix, while DM-BHP remains unfolded. However, even though these two peptides hardly share any conformations, their calculated CD spectra are alike and show the same features as the experimentally measured ones. Our results imply that a particular CD pattern can be induced by spatially different structures, which makes it difficult to derive the conformational preference of a peptide from its CD spectrum alone. To gain more insight into the relationship between the preferred conformation of a peptide and its CD spectrum, more accurate methods to calculate the CD spectrum for a given conformation are required.     

Prediction of peptide conformation: The adaptive simulated annealing approach

We report the application of the adaptive simulated annealing (ASA) method as a global optimization approach to biomolecular structure determination, using the ECEPP/2 (empirical conformation energy program for peptides) potential energy form. As applied to Met-enkephalin, our optimization results in a conformation that is in agreement with other studies. In addition, a dominant right-handed α-helical conformation is predicted for a 14-residue poly (L-alanine) model peptide in a limited search range. These results show that ASA is an efficient and robust algorithm for conformational analysis. © 1997 by John Wiley & Sons, Inc.     

An In‐tether Chiral Center Modulates the Helicity,Cell Permeability,and Target Binding Affinity of a Peptide

The addition of a precisely positioned chiral center in the tether of a constrained peptide is reported, yielding two separable peptide diastereomers with significantly different helicity, as supported by circular dichroism (CD) and NMR spectroscopy. Single crystal X‐ray diffraction analysis suggests that the absolute configuration of the in‐tether chiral center in helical form is R, which is in agreement with theoretical simulations. The relationship between the secondary structure of the short peptides and their biochemical/biophysical properties remains elusive, largely because of the lack of proper controls. The present strategy provides the only method for investigating the influence of solely conformational differences upon the biochemical/biophysical properties of peptides. The significant differences in permeability and target binding affinity between the peptide diastereomers demonstrate the importance of helical conformation.     

Determination of conformational preferences of dipeptides using vibrational spectroscopy

The NMR coupling constants ((3)J(H(N), H(alpha))) of dipeptides indicate that the backbone conformational preferences vary strikingly among dipeptides. These preferences are similar to those of residues in small peptides, denatured proteins, and the coil regions of native proteins. Detailed characterization of the conformational preferences of dipeptides is therefore of fundamental importance for understanding protein structure and folding. Here, we studied the conformational preferences of 13 dipeptides using infrared and Raman spectroscopy. The main advantage of vibrational spectroscopy over NMR spectroscopy is in its much shorter time scale, which enables the determination of the conformational preferences of short-lived states. Accuracy of structure determination using vibrational spectroscopy depends critically on identification of the vibrational parameters that are sensitive to changes in conformation. We show that the frequencies of the amide I band and the A12 ratio of the amide I components of dipeptides correlate with the (3)J(H(N), H(alpha)). These two infrared vibrational parameters are thus analogous to (3)J(H(N), H(alpha)), indicators for the preference for the dihedral angle phi. We also show that the intensities of the components of the amide III bands in infrared spectra and the intensities of the skeletal vibrations in Raman spectra are indicators of populations of the P(II), beta, and alpha(R) conformations. The results show that alanine dipeptide adopts predominantly a PII conformation. The population of the beta conformation increases in valine dipeptides. The populations of the alpha(R) conformation are generally small. These data are in accord with the electrostatic screening model of conformational preferences.