多粘菌素-B的溶液构象研究

利用核磁共振技术对多粘菌素－Ｂ在溶液中的构象进行测定。多粘菌素－Ｂ的全部质子信号及３ＪＨＮα均得到归属和确认。大部分存在于环肽及侧链的分子间ＮＯＥ得到归属,并以此为依据对多粘菌素－Ｂ的溶液构象进行了计算     

水稻条纹病毒RNA4基因间隔区的分子变异

应用反转录－聚合酶链式反应（RT－PCR）和单链构象多态性（single-strand conformation polymorphism,SSCP)技术快速检测我国水稻条纹病毒（RSV）RNA4基因间隔区（intergenic region,IR)的分子变异,结果表明,我国RSV RNA4 IR存在分子变异。供试的7个分离物共有4种泳动带型,其中YL、BS、JD、LY分离物完全一致,而YL、BS、YL及JD4个分离物序列完全一致;JN、PJ、SQ3个分离各不一样,序列之间的同源性均在92％－94％之间.IR序列内部具有两个重要的结构特征：（1）有两处反向重复序列,可形成两个明显的发夹结构,其中一个序列比较保守,形成的发夹结构稳定;但中一个发夹结构由于碱基变异导致其稳定性在各个分离物中差异较大;（2）具有插入序列,相对于日本M分离物,我国7个分离物都有一段长19bp的插入序列,这段插入序列比较保守,各分离物之间仅有1－2个碱基的差异。     

利用回归模型筛选出近天然的抗原-抗体对接模拟结构

在抗原-抗体分子对接模拟所生成的大量计算生成构象中筛选出近天然结构,即接近真实情况的抗原-抗体结合模式。借鉴QSAR原理,定义抗原-抗体接触面描述符并利用Discovery Studio 4.5软件平台计算出各对接模拟构象的接触面描述符和能量参数。构造训练集数据进行回归分析,建立预测对接模拟构象是否是近天然结构的数学模型。通过测试集和实际应用情况检验该数学模型。通过回归分析所建立的数学模型能够在成百上千的抗原-抗体对接模拟构象中有效筛选出其中的近天然结构,在测试集验证和4G7抗体结合模式预测应用中具有良好的表现,验证了该数学模型的有效性和实用性。经验性的抗原-抗体接触面特征如氢键密度、氨基酸对偏好性指数等以及能量参数能够共同有效表征近天然结构,所建立的数学模型有效增强了通过分子对接预测抗原-抗体结合模式的可行性。     

新型平均势函数在蛋白质反向折叠中的应用

利用蛋白质主链的极性分数及主链二面角为参量,构建了一种基于蛋白质结构数据库的势函数。将该势函数应用于蛋白质反向折叠研究中,发现该函数可成功地将蛋白质分子的天然构象从构建的构象库中识别出来;将一目标序列与构象库的每一可能的构象匹配,并用该势函数计算相应的能量,结果表明对绝大多数蛋白质分子来说,天然的构象的能量值总是最低。此外,该函数还将一些序列相似性较低,而结构相似性较高的蛋白质分子识别出来。我们认     

左手螺旋Z-DNA的研究 Ⅴ 环境因子对Oligo-d(G-C)_6构象的影响

脱氧寡聚核苷酸ｄ（Ｇ－Ｃ）６是迄今所报道的同类脱氧多聚核苷酸中能形成左手螺旋ＤＮＡ（Ｚ－ＤＮＡ）的最短序列。环境因子如ＰＨ,温度和离子的类别与浓度对ｄ（Ｇ－Ｃ）６在溶液中的Ｚ－构象的形成和Ｂ－、Ｚ－构象的相对稳定性有着明显的影响。在合适的条件下,ｄ（Ｇ－Ｃ）６在溶液中可呈现Ｂ－构象区,Ｚ－构象相对稳定区和Ｂ－、Ｚ－构象跃迁过渡区。     

α（1→4）连接的半乳糖醛酸构象的量子化学研究

本文采用量子化学ＳＣＦ－ＭＯ－ＬＣＡＯ半经验方法,对二聚半乳糖醛酸的构象从理论上进行了研究。在势能面上存在多个构象区域稳定点,最稳定的构象形式在Φ＝６０．０°,ψ＝－１２０．０°位置。从量子化学的前线分子轨道、电荷布后以及双中心作用能分析探讨了稳定构象与水解易于发生的可能构象间的联系。为生物化学研究提供了必要的信息。     

应用量子化学方法研究茶多酚类抗氧化剂的构效关系

采用分子力学和量子化学从头计算方法,研究了不同结构茶多酚（Green tea polyphenol,GTP)抗氧化活性的构效关系。计算结果表明,茶多酚类的抗氧化活性与其释放活泼氢生成苯氧自由基的能力有关,添生大小与O－H间的Mulliken集居数、前线轨道能量、反应终态能量下降量及苯氧自由基稳定性有关。     

左手螺旋Z—DNA的研究：V 环境因子对Oligo—d（G—C）6构象的影响

脱氧寡聚核苷酸ｄ（Ｇ－Ｃ）６是迄今所报道的同类脱氧多聚核苷酸中能形成左手螺旋ＤＮＡ（Ｚ－ＤＮＡ）的最短序列。环境因子如ＰＨ,温度和离子的类别与浓度对ｄ（Ｇ－Ｃ）６在溶液中的Ｚ－构象的形成和Ｂ－、Ｚ－构象的相对稳定性有着明显的影响。在合适的条件,ｄ（Ｇ－Ｃ）６在溶液中可呈现Ｂ－构象区,Ｚ－构象相对稳定区和Ｂ－、Ｚ－构象跃迁过渡区。     

高峰淀粉酶的分子可及性的研究

依据高峰淀粉酶的晶体结构数据对它的分子可及性进行了计算和分析,得到了极性与非极性氨基酸的分布、极性原子与非级性原子对可及性的贡献、催化活性中心裂隙的构象、Ｃ末端结构域空间拓扑等信息。活性部位氨基酸残基的可及性研究结果与酶－底物复合物模型相符。     

去七肽胰岛素的分子动力学研究

本文用分子动力学的方法对去七肽胰岛素(DHPI)分子的构象进行了研究,首先用分子动力学方法对晶体胰岛素分子的构象能进行了优化,然后除去B链C端的最后七个残基(B24—B30),做分子动力学模拟,得到了DHPI的平衡构象和均方差波动。胰岛素分子的X射线晶体衍射结构和能量优化构象之间的均方根偏差为0.1;所得DHPI构象和胰岛素能量优化构象间C原子间的均方根偏差为1.8。变化最大的区域是A8—A10,A18—A21,B1—B41和B18—B23。     

Does conformational free energy distinguish loop conformations in proteins?

Limitations in protein homology modeling often arise from the inability to adequately model loops. In this paper we focus on the selection of loop conformations. We present a complete computational treatment that allows the screening of loop conformations to identify those that best fit a molecular model. The stability of a loop in a protein is evaluated via computations of conformational free energies in solution, i.e., the free energy difference between the reference structure and the modeled one. A thermodynamic cycle is used for calculation of the conformational free energy, in which the total free energy of the reference state (i.e., gas phase) is the CHARMm potential energy. The electrostatic contribution of the solvation free energy is obtained from solving the finite-difference Poisson-Boltzmann equation. The nonpolar contribution is based on a surface area-based expression. We applied this computational scheme to a simple but well-characterized system, the antibody hypervariable loop (complementarity-determining region, CDR). Instead of creating loop conformations, we generated a database of loops extracted from high-resolution crystal structures of proteins, which display geometrical similarities with antibody CDRs. We inserted loops from our database into a framework of an antibody; then we calculated the conformational free energies of each loop. Results show that we successfully identified loops with a "reference-like" CDR geometry, with the lowest conformational free energy in gas phase only. Surprisingly, the solvation energy term plays a confusing role, sometimes discriminating "reference-like" CDR geometry and many times allowing "non-reference-like" conformations to have the lowest conformational free energies (for short loops). Most "reference-like" loop conformations are separated from others by a gap in the gas phase conformational free energy scale. Naturally, loops from antibody molecules are found to be the best models for long CDRs (> or = 6 residues), mainly because of a better packing of backbone atoms into the framework of the antibody model.     

Solution conformations of amphidinolide H

Solution conformations of amphidinolide H (1), a 26-membered macrolide exhibiting potent cytotoxic and antitumor activity, in CDCl3 and DMSO-d6 were investigated on the basis of NMR data, distance geometry calculation, and restrained energy minimization. Three-dimensional conformations in CDCl3 were suggested to be close to the X-ray structure of 1, while those in DMSO-d6 were indicated to be different from both those in CDCl3 and the X-ray structure.     

Anti-insulin antibody structure and conformation. II. Molecular dynamics with explicit solvent.

Molecular dynamics at 300 K was used as a conformation searching tool to analyze a knowledge-based structure prediction of an anti-insulin antibody. Solvation effects were modeled by packing water molecules around the antigen binding loops. Some loops underwent backbone and side-chain conformational changes during the 95-ps equilibration, and most of these new, lower potential energy conformations were stable during the subsequent 200-ps simulation. Alterations to the model include changes in the intraloop, main-chain hydrogen bonding network of loop H3, and adjustments of Tyr and Lys side chains of H3 induced by hydrogen bonding to water molecules. The structures observed during molecular dynamics support the conclusion of the previous paper that hydrogen bonding will play the dominant role in antibody-insulin recognition. Determination of the structure of the antibody by x-ray crystallography is currently being pursued to provide an experimental test of these results. The simulation appears to improve the model, but longer simulations at higher temperatures should be performed.     

Plant-growth-promoting traits and antifungal potential of the Bacillus amyloliquefaciens YL-25

Biological control of plant soil-borne diseases has been shown as an attractive and an environment friendly alternative to chemical fungicides. Different microbial strains have been reported effective in controlling plant pathogens. Among those, Bacillus strains have their own importance. Bacillus amyloliquefaciens strain YL-25, isolated from the rhizosphere of healthy banana plant, was evaluated as bio-organic fertiliser (BIO) for its ability to promote plant growth and suppress Fusarium wilt of banana in pot experiment. The results showed that the application of the BIO containing strain YL-25 significantly promoted the growth of banana plants and decreased the incidence of Fusarium wilt compared to the organic fertiliser and chemical fertiliser (CF). In order to explore the beneficial mechanisms of strain YL-25, experiments were conducted in vitro. The phytohormones including indole-3-acetic acid and gibberellin A3 and stable antifungal compounds three homologous of iturin A were identified in the culture broth of strain YL-25. The strain YL-25 also showed the ability to degrade extracellular phytate in plate experiment. Owing to its innate multiple functional traits and biocontrol activity, the strain YL-25 may be used as plant-growth-promoting rhizobacterium and biocontrol agent against Fusarium wilt of banana.     

Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations

The energy landscape of a peptide [Ace-Lys-Gln-Cys-Arg-Glu-Arg-Ala-Nme] in explicit water was studied with a multicanonical molecular dynamics simulation, and the AMBER parm96 force field was used for the energy calculation. The peptide was taken from the recognition helix of the DNA-binding protein, c-MYB: A rugged energy landscape was obtained, in which the random-coil conformations were dominant at room temperature. The CD spectra of the synthesized peptide revealed that it is in the random state at room temperature. However, the 300 K canonical ensemble, Q(300K), contained alpha-helix, 3(10)-helix, beta-turn, and beta-hairpin structures with small but notable probabilities of existence. The complete alpha-helix, imperfect alpha-helix, and random-coil conformations were separated from one another in the conformational space. This means that the peptide must overcome energy barriers to form the alpha-helix. The overcoming process may correspond to the hydrogen-bond rearrangements from peptide-water to peptide-peptide interactions. The beta-turn, imperfect 3(10)-helix, and beta-hairpin structures, among which there are no energy barriers at 300 K, were embedded in the ensemble of the random-coil conformations. Two types of beta-hairpin with different beta-turn regions were observed in Q(300K). The two beta-hairpin structures may have different mechanisms for the beta-hairpin formation. The current study proposes a scheme that the random state of this peptide consists of both ordered and disordered conformations. In contrast, the energy landscape obtained from the parm94 force field was funnel like, in which the peptide formed the helical conformation at room temperature and random coil at high temperature.     

Location of proline derivatives in conformational space. I. Conformational calculations; optical activity and NMR experiments

In order to develop methods of analysis applicable to the determination of the conformation of biological polymers in solution, a series of proline derivatives was studied. The steric constraints of the pyrrolidine ring limit these compounds to a relatively small set of conformations. This set was further reduced by eliminating conformations with large computed conformational energy. Computations revealed that the conformational energy of the proline derivatives fits into one of three classes, depending on the bulk and the polarity of the C-terminal group. Three analogous classes of optical activity were observed. The optical activity data were analyzed in terms of conformations computed to be of low energy. In some cases qualitative theoretical considerations enabled molecular groups to be located. For example, solvent-dependent isomerization of the carboxyl hydrogen of N-acetyl-L -proline was detected. Nuclear magnetic resonance provided an experimental measure of the fraction of molecules which had cis unsymmetrically-substituted tertiary amide groups. This information aided and confirmed the other measures of molecular conformation.     

Improving conformational searches by geometric screening

MOTIVATION: Conformational searches in molecular docking are a time-consuming process with wide range of applications. Favorable conformations of the ligands that successfully bind with receptors are sought to form stable ligand-receptor complexes. Usually a large number of conformations are generated and their binding energies are examined. We propose adding a geometric screening phase before an energy minimization procedure so that only conformations that geometrically fit in the binding site will be prompted for energy calculation. RESULTS: Geometric screening can drastically reduce the number of conformations to be examined from millions (or higher) to thousands (or lower). The method can also handle cases when there are more variables than geometric constraints. An early-stage implementation is able to finish the geometric filtering of conformations for molecules with up to nine variables in 1 min. To the best of our knowledge, this is the first time such results are reported deterministically. CONTACT: mzhang@mdanderson.org.     

Enhanced conformational diversity search of CDR-H3 in antibodies: role of the first CDR-H3 residue

Through a conformation search by a simulation calculation, the relationships between the amino acid sequences and the conformations of the third complementarity-determining region of the antibody heavy chain (CDR-H3) were investigated to characterize the large conformational varieties of antibodies. Here, we focused on the structural role of the first CDR-H3 residue, and we selected two antibodies, 28B4 and PLG, whose CDR-H3 conformations are significantly different, having Trp and Gly at the first position, respectively. Multicanonical molecular dynamics simulations, with the advantage of enhanced sampling efficiency, were performed for the CDR-H3 fragments of 28B4 and PLG, and a modified CDR-H3 model of 28B4, where the first Trp residue was substituted with Gly. When the first CDR-H3 residue is Trp, almost all of the observed CDR-H3 loops were bent at the first residue. In contrast, when the first residue is Gly, large varieties of loop conformations were observed. The structural role of this Gly residue is discussed from the perspective of the other antibody structures in the database. When the surrounding residues were included in the calculations, CDR-H3 loop structures similar to those in the crystal structures were reproduced as the major conformations for both the 28B4 and PLG antibodies.     

Molecular simulation uncovers the conformational space of the λ Cro dimer in solution

The significant variation among solved structures of the λ Cro dimer suggests its flexibility. However, contacts in the crystal lattice could have stabilized a conformation which is unrepresentative of its dominant solution form. Here we report on the conformational space of the Cro dimer in solution using replica exchange molecular dynamics in explicit solvent. The simulated ensemble shows remarkable correlation with available x-ray structures. Network analysis and a free energy surface reveal the predominance of closed and semi-open dimers, with a modest barrier separating these two states. The fully open conformation lies higher in free energy, indicating that it requires stabilization by DNA or crystal contacts. Most NMR models are found to be unstable conformations in solution. Intersubunit salt bridging between Arg⁴ and Glu⁵³ during simulation stabilizes closed conformations. Because a semi-open state is among the low-energy conformations sampled in simulation, we propose that Cro-DNA binding may not entail a large conformational change relative to the dominant dimer forms in solution.     

Conformational analysis of phosphatides: Mapping and minimization of the intramolecular energy

Empirical intramolecular energy calculations were carried out on molecular fragments related to phosphatides in order to find the preferred conformations. The energy was mapped as a function of several pairs of torsional angles in progressively larger molecular fragments, with energy minimization being carried out at each map point with respect to other significant variables. The energy mapping results were used as starting points for energy minimization on diheptanoyl L-α-phosphatidic acid-C, which consisted of the named molecule plus a carbon atom attached to one of the phosphate oxygens. It was found that there are 6 pairs of values for 2 of the torsional angles at the 3-way branch point in the glyceryl group which give sterically acceptable conformations; only 4 of these are compatible with lipid bilayer structure in that they can give a parallel arrangement of the acyl chains. The several acceptable conformations of the phosphate and acyl ester groups within each of these conformational classes are enumerated. The results obtained may be used as a guide for further experimental and theoretical work on phosphatide structures.