特殊氢方法预测丙氨酸-α-四肽构象稳定性

使用B3LYP/6-31G*方法优化得到了丙氨酸-α-四肽分子的48个稳定构象.定义了丙氨酸-α-多肽中的特殊氢原子,对构象中与特殊氢原子有关的主要非键相互作用进行分析,提出了使用与特殊氢原子有关的非键相互作用来预测多肽构象的相对稳定性,并将之称为特殊氢方法.基于丙氨酸-α-二肽分子的5个构象和三肽分子的7个构象,确定了特殊氢方法中的与特殊氢原子有关的非键相互作用参数.利用特殊氢方法预测丙氨酸-α-四肽分子的48个构象的相对稳定性,与B3LYP/6-31G*方法的相对能量比较,得到了满意的结果.特殊氢方法得到的相对能量(Y)和B3LYP/6-31G*方法得到的相对能量(X)的线性相关方程为Y=0.9296X 2.2041,相关系数R=0.9532,标准偏差为3.0kJ/mol,偏差绝对值≤4.18kJ/mol的构象占87.5%.     

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     

聚偏二氯乙烯构象分布的理论研究

在MP2/6-311++G**水平下, 对2,2,4,4-四氯戊烷与2,2,4,4,6,6-六氯庚烷旋转异构体构象进行几何优化和能量计算. 结果表明, 对于2,2,4,4-四氯戊烷, 采用gauche-gauche排列的旋转异构体的能量较低; 2,2,4,4,6,6-六氯庚烷旋转异构体中, 采用trans-gauche-trans-gauche排列的构象能量较低. 反之, 完全采用trans-trans排列的旋转异构体构象能量较高, 不稳定. 通过比较模型分子不同旋转异构体构象的能量差值可以得到一级和二级特征的相互作用能差, 进而计算统计权重参数. 在此基础上, 应用计算得到的模型分子的几何构型与统计权重参数, 分别构建针对—CH2—和—CCl2—中心的聚偏二氯乙烯的6态旋转异构态模型. 通过旋转异构态模型可以计算聚偏二氯乙烯分子中各种构象的分布.     

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。     

拉链型脂肽的温控开关效应

亮氨酸拉链型脂肽是由两条肽链以螺旋结构依靠疏水作用并列结合形成的二聚体,当温度升至其相变温度时,其螺旋结构解旋继而变为无序链状结构。利用该类脂肽的温敏性能,本文设计、合成得到一组具有温敏性的拉链型脂肽,将其与磷脂混合制备温敏性脂质体。用圆二色谱测定磷脂双分子层上脂肽的二级结构,动态光散射测定脂肽-脂质体的粒径及电位;荧光偏振法测定脂质体膜的流动性;采用紫外分光光度计考察阿霉素(DOX)在37.0、45.0°C下的释放行为。结果表明,含有脂肽的脂质体具备较好的温敏性,胆固醇含量、脂质体膜的流动性,对脂肽的温控开关效应有一定的影响。脂肽-脂质体作为一种新型的温敏性药物载体展现了其较好的应用前景。     

含氧有机物脂水分配系数与结构参数的关系

应用半经验量子化学AM1方法得到了108种含氧有机分子的优势构象,利用AM1方法和分子图形学技术获得了它们的电子结构和几何结构参数,并将这些参数与脂水分配系数相关联,采用逐步回归分析方法,成功地建立了拟合度高、物理意义明确、预测能力强的含氧有机分子脂水分配系数-结构参数定量关系方程,找出了影响含氧有机分子脂水分配系数的主要结构因素.     

含过渡金属和柔性配体催化体系的构象搜索

采用密度泛函理论对含有过渡金属和柔性配体的分子进行优化时,通常只能将初始结构优化到势能面上的局部最小点,而确定反应势能面上各中间体和过渡态的最低能量构象是准确描述一个催化反应最优路径的关键.使用Cr/PCCP体系催化乙烯选择性三聚/四聚反应路径中的关键过渡态(TS1,TS2,TS3)作为分子模型,对基于Tinker软件包和CREST软件包的两种构象搜索方法进行了对比测试.使用两种构象搜索方法均成功找到了三个分子模型的最低能量构象,并且两种方法获得的构象数量总数相差不大.与基于Tinker软件包的构象搜索方法相比,使用CREST软件包进行构象搜索的计算流程更加简单,并且大大减少了计算时间.     

烷基链长及肽链电荷分布对脂肽双亲分子自组装及水凝胶化的影响

为阐明脂肽分子烷基链长及肽链电荷分布对其自组装及水凝胶化的影响, 设计合成了C_nV₃K₂ (n=12, 14, 16) 和C_mKV₃K (m=14, 16)两个系列的脂肽分子. 原子力显微镜(AFM)和透射电镜(TEM)结果表明, 两个系列的脂肽分子都可以自组装成一维纳米带结构. 圆二色(CD)光谱结果表明, C_nV₃K₂系列自组装体的二级结构为β折叠; C_mKV₃K系列自组装体中包括α螺旋和β折叠两种二级结构, 其中C14KV3K的α螺旋结构较多, C16KV3K的β折叠结构占优. 烷基链疏水作用的增强会抑制β折叠结构侧向堆积, 使纳米带随烷基链的变长而变窄; 电荷分布于肽链部分的两端有利于纳米带结构的侧向生长. 流变性测试结果表明, 在浓度10 mmol·L^-1、pH 8.4下, 脂肽分子可以形成自支撑水凝胶, 相比烷基链长度, 肽链部分的电荷分布对水凝胶性能影响更大.     

ABEEMσп/MM力场模型下的多肽构象

在ABEEM/MM蛋白质浮动电荷力场模型的基础上,加入孤对电子和π电荷位点,从而能够体现多肽和蛋白质分子中一些重要的各向异性极化性质,允许非化学键方向的电子转移和极化.利用从头计算数据拟合模型相关参数.计算得到的小分子团簇结合能、偶极矩、氢键键长等性质与从头计算结果符合很好.该经典极化模型力场能够重复量子场下丙氨酸二肽、丙氨酸四肽、甘氨酸三肽的各稳定构象,其稳定性顺序与精密从头计算结果相一致,其结构和能量性质较以往模型有一定提高,并优于其他力场模型.     

快速确定丙氨酸-α-多肽构象稳定性的新方法

使用B3LYP／6—31G^*方法优化得到了丙氨酸二肽和三肽分子的23个稳定构象．定义了丙氨酸多肽中的特殊氢原子．对构象中与特殊氢原子有关的主要弱相互作用进行了分析,提出了一种快速确定多肽构象稳定性的新方法．确定了相应的弱相互作用参数．将新方法应用于三肽分子构象相对稳定性的预测,得到了满意的结果．     

Importance of the single amino acid potential in water for secondary and tertiary structures of proteins

The structure of a protein molecule is considered to be primarily determined by the inter-amino-acid nonbonded interactions, such as hydrogen bonds. However, the conformational space of the polypeptide chain should be simultaneously restricted by the intrinsic conformational preferences of the individual amino acids. We present here precise single amino acid potential (SAAP) surfaces for glycine (For-Gly-NH(2)) and alanine (For-Ala-NH(2)) in water (epsilon = 78.39) and ether (epsilon = 4.335), which were calculated at the HF/6-31+G(d,p) level applying the self-consistent isodensity polarizable continuum model (SCIPCM) reaction field with geometry optimization in the corresponding solvents. The obtained Ramachandran potential surfaces in water showed distinct potential wells in the alpha- and beta-regions. The profiles were in almost perfect agreement with the Ramachandran plots of glycine and alanine residues in folded proteins, suggesting the Boltzmann distributions on the SAAP surfaces. Molecular simulations of polyalanines (For-Ala(n)-NH(2); n = 3-5) by using the SAAP force field equipped with the SCIPCM potentials revealed that the polyalanines readily form 3(10)-helical structures in water but not in vacuo. In ether (hydrophobic environments), the helical structures were relatively stable, but the most stable structure was assigned to a different one. These results indicated that the intrinsic conformational preferences of the individual amino acids (i.e., the SAAPs) in water are of significant importance not only for describing conformations of a polypeptide chain in the random coil state but also for understanding the folding to the secondary and tertiary structures.     

Inherent flexibility and protein function: The open/closed conformational transition in the N-terminal domain of calmodulin

The key to understand a protein's function often lies in its conformational dynamics. We develop a coarse-grained variational model to investigate the interplay between structural transitions, conformational flexibility, and function of the N-terminal calmodulin domain (nCaM). In this model, two energy basins corresponding to the "closed" apo conformation and "open" holo conformation of nCaM are coupled by a uniform interpolation parameter. The resulting detailed transition route from our model is largely consistent with the recently proposed EFbeta-scaffold mechanism in EF-hand family proteins. We find that the N-terminal parts of the calcium binding loops shows higher flexibility than the C-terminal parts which form this EFbeta-scaffold structure. The structural transition of binding loops I and II are compared in detail. Our model predicts that binding loop II, with higher flexibility and earlier structural change than binding loop I, dominates the open/closed conformational transition in nCaM.     

Combined vibrational,conformational energy and electron diffraction studies of trans-2-decalone

The structure of trans-2-decalone was investigated by combined gas phase electron diffraction, conformational energy and vibrational analyses. In this study first the minimum energy conformations for trans-2-decalone were calculated by molecular mechanics techniques using a force field described in the literature; the same field and the minimum energy conformations were then used in subsequent vibrational analyses to calculate the mean amplitudes of vibration for each minimum energy conformation of trans-2-decalone; these mean amplitudes and the corresponding internuclear distances were then used to calculate theoretical electron diffraction radial distribution curves which were compared to the experimental curves. Four conformational energy minima were investigated with one or both rings in a chair or non-chair form. The results of the combined investigations indicate that the molecule exists in the conformation which has both rings in a distorted chair form.     

Folding of the 25 residue Abeta(12-36) peptide in TFE/water: temperature-dependent transition from a funneled free-energy landscape to a rugged one

The free-energy landscape of the Alzheimer beta-amyloid peptide Abeta(12-36) in a 40% (v/v) 2,2,2-trifluoroethanol (TFE)/water solution was determined by using multicanonical molecular dynamics simulations. Simulations using this enhanced conformational sampling technique were initiated from a random unfolded polypeptide conformation. Our simulations reliably folded the peptide to the experimental NMR structure, which consists of two linked helices. The shape of the free energy landscape for folding was found to be strongly dependent on temperature: Above 325 K, the overall shape was funnel-like, with the bottom of the funnel coinciding exactly with the NMR structure. Below 325 K, on the other hand, the landscape became increasingly rugged, with the emergence of new conformational clusters connected by low free-energy pathways. Finally, our simulations reveal that water and TFE solvate the polypeptide in different ways: The hydrogen bond formation between TFE and Abeta was enhanced with decreasing temperature, while that between water and Abeta was depressed.     

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.     

Conformations of hydrophobic polyelectrolytes

Recent studies on the (hypercoiled) compact conformation and the pH-induced conformational transition to the extended coil of the hydrophobic poly(acids or bases), which have been well used in industrial and medical circles, are summarized, especially on the basis of our studies on poly(alpha-alkyl acrylic acids) and maleic acid copolymers with hydrophobic aromatic monomers. The stability of the compact conformation and values of various thermodynamic parameters of the transition of the hydrophobic polyelectrolytes suggest the importance of hydrophobic interaction among the side chains to form the compact conformation. Characterization of various physicochemical methods, including 1H-NMR measurements, gives a model of the compact conformation with a more expanded structure than in globular proteins, a free-draining property of the solvent, the conformation fluctuation, etc. Also, the apparent two-state character of each segment in the transition region, a life-time in each state and the cooperative parameter for the compact form formation are discussed. A review of our conformational studies on the hydrophobic-hydrophilic polypeptides is also given. For the anion-induced conformation transition in basic homopoly(alpha-amino acids), hydrophobic characters of the anion and the side chain in the polypeptide are shown to be important, especially in terms of solvation. The difference in the induced conformation by the anion between random and alternating basic copolypeptides is explained by introducing a model which shows the importance of the sequence of hydrophobic and hydrophilic residues in the polypeptide to induce the ordered conformation of the anions. Also, we attempt to explain the difference between the induction of ordered conformation in the basic homo- or copolypeptide in reversed micelles with a large sulfonate (AOT) vs. that in aqueous AOT in terms of the hydrophobic character of the side chains in the polypeptides, AOT and the medium.     

SCF-MO study of the polyglycine II structure

Summary In order to get insight into the conditions that make polyglycine (PG)II a stable structure, the conformational features of three model molecules closely related to the PGII conformation were investigated. The model molecules selected were glycine dipeptide (AGN), glycine tripeptide (AGGN), and glycine tetrapeptide (AGGGN). Environmental effects were mimicked by means of formaldehyde molecules. The calculations were carried out at the SCF semiempirical level, using the AM1 method. The calculations show that of the three systems considered, only the AGGGN molecule presents a minimum energy conformation which corresponds to a PGII structure. The environmental conditions in which this conformation is found were also analyzed.     

A Multifaceted Secondary Structure Mimic Based On Piperidine‐piperidinones

Minimalist secondary structure mimics are typically made to resemble one interface in a protein–protein interaction (PPI), and thus perturb it. We recently proposed suitable chemotypes can be matched with interface regions directly, without regard for secondary structures. Here we describe a modular synthesis of a new chemotype 1 , simulation of its solution‐state conformational ensemble, and correlation of that with ideal secondary structures and real interface regions in PPIs. Scaffold 1 presents amino acid side‐chains that are quite separated from each other, in orientations that closely resemble ideal sheet or helical structures, similar non‐ideal structures at PPI interfaces, and regions of other PPI interfaces where the mimic conformation does not resemble any secondary structure. 68 different PPIs where conformations of 1 matched well were identified. A new method is also presented to determine the relevance of a minimalist mimic crystal structure to its solution conformations. Thus dld ‐ 1 faf crystallized in a conformation that is estimated to be 0.91 kcal mol^?1 above the minimum energy solution state.     

Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition

Quantifying the density of conformations over phase space (the conformational distribution) is needed to model important macromolecular processes such as protein folding. In this work, we quantify the conformational distribution for a simple polypeptide (N-mer polyalanine) using the cumulative distribution function (CDF), which gives the probability that two randomly selected conformations are separated by less than a "conformational" distance and whose inverse gives conformation counts as a function of conformational radius. An important finding is that the conformation counts obtained by the CDF inverse depend critically on the assignment of a conformation's distance span and the ensemble (e.g., unfolded state model): varying ensemble and conformation definition (1 --> 2 A) varies the CDF-based conformation counts for Ala(50) from 10(11) to 10(69). In particular, relatively short molecular dynamics (MD) relaxation of Ala(50)'s random-walk ensemble reduces the number of conformers from 10(55) to 10(14) (using a 1 A root-mean-square-deviation radius conformation definition) pointing to potential disconnections in comparing the results from simplified models of unfolded proteins with those from all-atom MD simulations. Explicit waters are found to roughen the landscape considerably. Under some common conformation definitions, the results herein provide (i) an upper limit to the number of accessible conformations that compose unfolded states of proteins, (ii) the optimal clustering radius/conformation radius for counting conformations for a given energy and solvent model, (iii) a means of comparing various studies, and (iv) an assessment of the applicability of random search in protein folding.