Structure and dynamics of the Abeta(21-30) peptide from the interplay of NMR experiments and molecular simulations

We combine molecular dynamics simulations and new high-field NMR experiments to describe the solution structure of the Abeta(21-30) peptide fragment that may be relevant for understanding structural mechanisms related to Alzheimer's disease. By using two different empirical force-field combinations, we provide predictions of the three-bond scalar coupling constants ((3)J(H(N)H(alpha))), chemical-shift values, (13)C relaxation parameters, and rotating-frame nuclear Overhauser effect spectroscopy (ROESY) crosspeaks that can then be compared directly to the same observables measured in the corresponding NMR experiment of Abeta(21-30). We find robust prediction of the (13)C relaxation parameters and medium-range ROESY crosspeaks by using new generation TIP4P-Ew water and Amber ff99SB protein force fields, in which the NMR validates that the simulation yields both a structurally and dynamically correct ensemble over the entire Abeta(21-30) peptide. Analysis of the simulated ensemble shows that all medium-range ROE restraints are not satisfied simultaneously and demonstrates the structural diversity of the Abeta(21-30) conformations more completely than when determined from the experimental medium-range ROE restraints alone. We find that the structural ensemble of the Abeta(21-30) peptide involves a majority population (approximately 60%) of unstructured conformers, lacking any secondary structure or persistent hydrogen-bonding networks. However, the remaining minority population contains a substantial percentage of conformers with a beta-turn centered at Val24 and Gly25, as well as evidence of the Asp23 to Lys28 salt bridge important to the fibril structure. This study sets the stage for robust theoretical work on Abeta(1-40) and Abeta(1-42), for which collection of detailed NMR data on the monomer will be more challenging because of aggregation and fibril formation on experimental timescales at physiological conditions. In addition, we believe that the interplay of modern molecular simulation and high-quality NMR experiments has reached a fruitful stage for characterizing structural ensembles of disordered peptides and proteins in general.     

How hot? Systematic convergence of the replica exchange method using multiple reservoirs

We have devised a systematic approach to converge a replica exchange molecular dynamics simulation by dividing the full temperature range into a series of higher temperature reservoirs and a finite number of lower temperature subreplicas. A defined highest temperature reservoir of equilibrium conformations is used to help converge a lower but still hot temperature subreplica, which in turn serves as the high‐temperature reservoir for the next set of lower temperature subreplicas. The process is continued until an optimal temperature reservoir is reached to converge the simulation at the target temperature. This gradual convergence of subreplicas allows for better and faster convergence at the temperature of interest and all intermediate temperatures for thermodynamic analysis, as well as optimizing the use of multiple processors. We illustrate the overall effectiveness of our multiple reservoir replica exchange strategy by comparing sampling and computational efficiency with respect to replica exchange, as well as comparing methods when converging the structural ensemble of the disordered Aβ_21‐30 peptide simulated with explicit water by comparing calculated Rotating Overhauser Effect Spectroscopy intensities to experimentally measured values. © 2009 Wiley Periodicals, Inc. J Comput Chem 31: 620–627, 2010     

苯二酚异构体的电动毛细管色谱-玻碳微电极柱上安培检测分析方法研究

在玻碳纤维微电极上研究了电解液中β－环糊精（ＣＤ）的浓度对邻、间、对苯二酚的循环伏安特性的影响,从实验结果和分子结构水平方面考察了β－ＣＤ与邻、间、对苯二酚的包结作用。研究结果表明,β－ＣＤ与邻、间、对苯二酚的包结作用强弱顺序为间苯二酚、邻苯二酚、对苯二酚。讨论了电泳缓冲液中ΝΗ４Ｃｌ,ＳＤＳ,β－ＣＤ的浓度及ｐＨ值对邻、间、对苯二酚迁移时间的影响。建立了苯二酚异构体胶束电动毛细管色谱－玻碳微电极柱上安培检测分析方法,方法的回收率在９８％～１０３％之间。     

Mass spectra of aminoacyl adenylate pentacoordinated phosphorus compounds

Aminoacyl adenylate pentacoordinated phosphorus compounds were analyzed by field desorption (FD) and fast atom bombardment (FAB) mass spectrometries, together with the B/E linked scan technique, and their mass spectral fragmentation pathways were investigated. For the five bonds (one P-N bond, three P-O bonds and one mixed anhydride bond P-O-CO), the cleavage usually occurred more on the P-N bond, the mixed anhydride bond and the O-C bond adjacent to the P-O bond, and less on the P-O bond. Ion YH(+), corresponding to water loss from protonated 2',3'-O-isopropylidene-adenosine, was the base peak. The results reflect the structural characteristics of aminoacyl adenylate pentacoordinated phosphorus compounds. Copyright 1999 John Wiley & Sons, Ltd.     

奥伯斯佯谬浅析

给出满足宇宙学原理的宇宙模型中计算星体视光度的一般公式，作为特例，导出“稳恒态”和“大爆炸”模型中星体视光度的表达式，结果表明这些模型是可以避免奥伯斯佯谬的。