Lattice models of peptide aggregation: evaluation of conformational search algorithms

We present a series of conformational search calculations on the aggregation of short peptide fragments that form fibrils similar to those seen in many protein mis-folding diseases. The proteins were represented by a face-centered cubic lattice model with the conformational energies calculated using the Miyazawa-Jernigan potential. The searches were performed using algorithms based on the Metropolis Monte Carlo method, including simulated annealing and replica exchange. We also present the results of searches using the tabu search method, an algorithm that has been used for many optimization problems, but has rarely been used in protein conformational searches. The replica exchange algorithm consistently found more stable structures then the other algorithms, and was particularly effective for the octamers and larger systems.     

β微管蛋白中紫杉醇(Taxol)结合腔的性质分析

采用多拷贝同时搜寻法(MCSS), 并结合现有微管抑制剂的SAR及3D-QSAR对β微管蛋白中Taxol(紫杉醇)结合腔的性质进行了分析. 结构研究结果表明, Taxol结合腔以疏水性质为主, 并指出官能团分布的具体位置: 在Phe270上方(Leu361-Pro272-Leu273-Leu228之间)的弧形区域、Asp26羧基下方及其与Glu22羧基之间、M-loop的中部, 以及Asp224内侧且靠近Arg276的胍基的位置. 而Asp224的内侧又是新提出的结合位点. 研究结果符合现有微管抑制剂的SAR, 为现有抗肿瘤药物的结构改造以及小分子微管抑制剂设计提供了理论依据.     

Continuous determination of carbon dioxide evolved during thermal decomposition reactions

A simple device suitable for continuous monitoring of carbon dioxide evolved during thermal decomposition reactions is described. Carbon dioxide is transported by a carrier gas through the device connected to thermoanalytical equipment and absorbed by soda lime reagent. The reaction heat released is linearly proportional to the amount of carbon dioxide absorbed.     

A MORPHOLOGICAL STUDY OF POLY（DIVINYLBENZENE-co-ACRYLIC ACID） IN CROSSLINKING PRECIPITATION POLYMERIZATION

Divinylbenzene-80 （DVB-80） and polar monomer acrylic acid （AA） having hydrogen bonding at a total monomer loading of 5 vol% were precipitated-copolymerized in a variety of organic solvents with 2,2＇-azobis（isobutyronitrile） （AIBN） as initiator. The experiments were investigated from a two-dimensional matrix, i.e., the actual crosslinking degree of DVB varying from 0 to 80% and the solvent composition varying from 0 to 100% of toluene mixture with acetonitrile, when the mixture of acetonitrile and toluene was used as the reaction solvent. Under various reaction conditions, six distinct morphologies including soluble polymers, swellable microgels, coagulum, irregular microparticles, and nano-/micrometer microspheres were formed and the structures of these polymer architectures were described. A morphological map was utilized to discuss the effects of both crosslinking degree of DVB and composition of solvent on the transitions between morphology domains. The results demonstrated that the microspheres are formed by an internal contraction due to the marginal solvency of the continuous phase and the crosslinking of the polymer network through the covalent bonding from DVB as well as the interchain hydrogen-bonding between the carboxylic acid units.     

A window fourier domain search system

A search system is presented that utilizes Fourier domain data. This system removes dominating features from the infrared absorbance data, transforms the data into the Fourier domain and performs a complete library search. The actual matching algorithm is very simple and excellent search results were attained using 16 cm^–1 resolution infrared absorbance spectra before transformation. This method can be used to distinguish very similar spectra that cannot be distinguished by many other search methods.     

Conformational analysis of [Met5]-enkephalin: Solvation and ionization considerations

[Met5]-Enkephalin has the sequence Tyr-Gly-Gly-Phe-Met. Only the extended conformation of the peptide has been observed by X-ray crystallography. Nuclear magnetic resonance spectroscopy supports the presence of a turn at Gly 3 and Phe 4 in dimethyl sulfoxide. In this study, the peptide conformational states and thermodynamic properties are understood in terms of ionization state and solvent environment. In the calculation, final conformations obtained from multiple independent Monte Carlo simulated annealing conformational searches are starting points for molecular dynamics simulations. In an aqueous environment given by the use of solvation free energy and the zwitterionic state, dominant structural motifs computed are G-P Type II bend, G-G Type II bend, and G-G Type I bend motifs, in order of increasing free energy. In the calculation of the peptide with neutral N- and C-termini and solvation free energy, the extended conformer dominates (by at least a factor of 2.5), and the conformation of another low free energy conformer superimposes well on the pharmacophoric groups of morphine. Neutralization of charge and solvation induce and stabilize the extended conformation, respectively. A mechanism of inter-conversion between the extended conformer and three bent conformers is supported by /-scatter plots, and by the conformer relative free energies. An estimate of the entropy change of receptor unbinding is 8.3 cal K-1 mol-1, which gives rise to a -2.5 kcal/mol entropy contribution to the free energy of unbinding at 25 °C. The conformational analysis methodology described here should be useful in studies on short peptides and flexible protein surface loops that have important biological implications.     

基于近红外光谱的维生素C片无损鉴别分析

基于近红外光谱技术与化学计量学方法,建立了一种国内外不同品牌维生素C片的无损鉴别方法。采集了国内外8个品牌的维生素C片共计40个样本的近红外光谱数据,比较了完整样品以及粉末样品的近红外光谱,采用连续小波变换技术消除背景干扰和基线漂移,基于标准偏差与相对标准偏差的变量筛选方法筛选出具有代表性的波数点,结合主成分分析方法对国内外不同品牌维生素C片进行鉴别分析。结果表明:原始光谱存在着明显的背景干扰和基线漂移现象,且粉末样品的重现性要优于完整样品;单纯使用原始光谱无法辨别来自不同品牌的维生素C片;连续小波变换可以有效消除背景干扰,提高模型鉴别能力;完整样品的鉴别准确率优于粉末样品,说明国内外不同品牌维生素C片主要成分基本一致,可能是辅剂和工艺上存在细微差异。通过结合近红外光谱分析技术与化学计量学方法,可实现对国产以及进口不同品牌维生素C片的鉴别分析。     

Observations of trends for singular values and eigenvectors from library searching ultraviolet-visible spectra with spectral subtraction

A promising procedure for computerized library searching and identification of ultraviolet-visible spectra for one- and two-component mixtures is evaluated. The procedure is based on singular value decomposition and utilizes band position and shape. Searching more than one library spectrum at a time is possible. Library spectra which have similar spectra (collinear) with the sample and each other are indicated by two measures. First, a large condition index must be obtained, and second, two or more large variance-decomposition proportions in the same row need to be associated with the large condition index. The searching procedure has a significant degree of differentiation between the actual sample and potential candidates and is compared with the dot product, Euclidean distance and the correlation coefficient.     

A proposal for the molecular basis of μ and δ opiate receptor differentiation based on modeling of two types of cyclic enkephalins and a narcotic alkaloid

Summary The molecular basis underlying the divergent receptor selectivity of two cyclic opioid peptides Tyr-c[N -d-Orn²-Gly-Phe-Leu-] (c-ORN) and [d-Pen², l-Cys⁵]-enkephalinamide (c-PEN) was investigated using a molecular modeling approach. Ring closure and conformational searching procedures were used to determine low-energy cyclic backbone conformers. Following reinsertion of amino acid side chains, the narcotic alkaloid 7-[(1R)-1-methyl-1-hydroxy-3-phenylpropyl]-6,14-endoethenotetrahydro oripavine (PEO) was used as a flexible template for bimolecular superpositions with each of the determined peptide ring conformers using the coplanarity and cocentricity of the phenolic rings as the minimum constraint. A vector space of PEO, accounting for all possible orientations for the C₂₁-aromatic ring of PEO served as a geometrical locus for the aromatic ring of the Phe⁴ residue in the opioid peptides. Although a vast number of polypeptide conformations satisfied the criteria of the opiate pharmacophore, they could be grouped into three classes differing in magnitude and sign of the torsional angle values of the tyrosyl side chain. Only class III conformers for both c-ORN and c-PEN, having tyramine dihedral angles ₁ =–150° ± 30° and ₂=–155° ± 20°, had significant structural and conformational properties that were mutually compatible while respecting the PEO vector space. Comparison of these properties in the context of the divergent receptor selectivity of the studied opioid peptides suggests that the increased distortion of the peptide backbone in the closure region of c-PEN together with the pendant ,-dimethyl group, combine to generate a steric volume which is absent in c-ORN and that may be incompatible with a restrictive topography of the receptor. The nature and stereo-chemistry of substituents adjacent to the closure region of the peptides could also modulate receptor selection by interacting with a charged () or neutral () subsite.     

Value function and optimality conditions for semilinear control problems

This paper is concerned with optimal control problems of Mayer and Bolza type for systems governed by a semilinear state equationx(t)=Ax(t) + f(t, x(t), u(t)), u(t) U, whereA is the infinitesimal generator of a strongly continuous semigroup in a Banach spaceX. We prove necessary and sufficient conditions for optimality and then use these conditions to investigate properties of the value function related to superdifferentials. Conversely, we use the value function to obtain criteria for optimality and feedback systems.Work (partially) supported by the Research Project Equazioni di evoluzione e applicazioni fisicomatematiche (M.U.R.S.T.-Italy).