Intrinsic energy landscapes of amino acid side-chains

Amino acid side-chain conformational properties influence the overall structural and dynamic properties of proteins and, therefore, their biological functions. In this study, quantum mechanical (QM) potential energy surfaces for the rotation of side-chain χ(1) and χ(2) torsions in dipeptides in the alphaR, beta, and alphaL backbone conformations were calculated. The QM energy surfaces provide a broad view of the intrinsic conformational properties of each amino acid side-chain. The extent to which intrinsic energetics dictates side-chain orientation was studied through comparisons of the QM energy surfaces with χ(1) and χ(2) free energy surfaces from probability distributions obtained from a survey of high resolution crystal structures. In general, the survey probability maxima are centered in minima of the QM surfaces as expected for sp(3) (or sp(2) for χ(2) of Asn, Phe, Trp, and Tyr) atom centers with strong variations between amino acids occurring in the energies of the minima indicating intrinsic differences in rotamer preferences. High correlations between the QM and survey data were found for hydrophobic side-chains except Met, suggesting minimal influence of the protein and solution environments on their conformational distributions. Conversely, low correlations for polar or charged side-chains indicate a dominant role of the environment in stabilizing conformations that are not intrinsically favored. Data also link the presence of off-rotamers in His and Trp to favorable interactions with the backbone. Results also suggest that the intrinsic energetics of the side-chains of Phe and Tyr may play important roles in protein folding and stability. Analyses on whether intrinsic side-chain energetics can influence backbone preference identified a strong correlation for residues in the alphaL backbone conformation. It is suggested that this correlation reflects the intrinsic instability of the alphaL backbone such that assumption of this backbone conformation is facilitated by intrinsically favorable side-chain conformations. Together our results offer a broad overview of the conformational properties of amino acid side-chains and the QM data may be used as target data for force field optimization.     

In vitro metabolism of corydaline in human liver microsomes and hepatocytes using liquid chromatography-ion trap mass spectrometry

Corydaline is a pharmacologically active isoquinoline alkaloid isolated from Corydalis tubers. It exhibits the antiacetylcholinesterase, antiallergic, antinociceptive, and gastric emptying activities. The purposes of this study were to establish in vitro metabolic pathways of corydaline in human liver microsomes and hepatocytes by identification of their metabolites using liquid chromatography-ion trap mass spectrometry. Human liver microsomal incubation of corydaline in the presence of an NADPH-generating system resulted in the formation of nine metabolites, namely, four O-desmethylcorydaline [M1 (yuanhunine), M2 (9-O-desmethylcorydaline), M3 (isocorybulbine), and M4 (corybulbine)], three di-O-desmethylcorydaline [M5 (9,10-di-O-desmethylcorydaline), M6 (2,10-di-O-desmethylcorydaline), and M7 (3,10-di-O-desmethylcorydaline)], M8 (hydroxyyuanhunine), and M9 (hydroxycorydaline). Incubation of corydaline in human hepatocytes produced four metabolites including M1, M5, M6, and M9. O-Demethylation and hydroxylation were the major metabolic pathways for the metabolism of corydaline in human liver microsomes and hepatocytes.     

Cationic conjugated polyelectrolytes-triggered conformational change of molecular beacon aptamer for highly sensitive and selective potassium ion detection

We demonstrate highly sensitive and selective potassium ion detection against excess sodium ions in water, by modulating the interaction between the G-quadruplex-forming molecular beacon aptamer (MBA) and cationic conjugated polyelectrolyte (CPE). The K(+)-specific aptamer sequence in MBA is used as the molecular recognition element, and the high binding specificity of MBA for potassium ions offers selectivity against a range of metal ions. The hairpin-type MBA labeled with a fluorophore and quencher at both termini undergoes a conformational change (by complexation with CPEs) to either an open-chain form or a G-quadruplex in the absence or presence of K(+) ions. Conformational changes of MBA as well as fluorescence (of the fluorophore in MBA) quenching or amplification via fluorescence resonance energy transfer from CPEs provide clear signal turn-off and -on in the presence or absence of K(+). The detection limit of the K(+) assays is determined to be ~1.5 nM in the presence of 100 mM Na(+) ions, which is ~3 orders of magnitude lower than those reported previously. The successful detection of 5'-adenosine triphosphate (ATP) with the MBA containing an ATP-specific aptamer sequence is also demonstrated using the same sensor scheme. The scheme reported herein is applicable to the detection of other kinds of G-rich aptamer-binding chemicals and biomolecules.     

Estimating value at risk with semiparametric support vector quantile regression

Value at Risk (VaR) has been used as an important tool to measure the market risk under normal market. Usually the VaR of log returns is calculated by assuming a normal distribution. However, log returns are frequently found not normally distributed. This paper proposes the estimation approach of VaR using semiparametric support vector quantile regression (SSVQR) models which are functions of the one-step-ahead volatility forecast and the length of the holding period, and can be used regardless of the distribution. We find that the proposed models perform better overall than the variance-covariance and linear quantile regression approaches for return data on S&P 500, NIKEI 225 and KOSPI 200 indices.     

消磁场对纳米铁磁线磁畴壁动力学行为的影响

为了实现基于磁畴壁运动的自旋电子学装置, 掌握磁畴壁动力学行为是重要争论之一.研究了在外磁场驱动下L-型纳米铁磁线磁畴壁的动力学行为. 通过微磁学模拟,在各种外磁场的驱动下考察了纳米铁磁线磁畴壁的动力学特性; 在较强外磁场的驱动下, 在不同厚度纳米线上考察了纳米线表面消磁场对磁畴壁动力学行为的影响. 为了进一步证实消磁场对磁畴壁动力学的影响, 在垂直于纳米线表面的外磁场辅助下分析了磁畴壁的动力学行为变化. 结果表明, 随着纳米线厚度和外驱动磁场强度的增加, 增强了纳米线表面的消磁场的形成, 使得磁畴壁内部自旋结构发生周期性变化, 导致磁畴壁在纳米线上传播时出现Walker崩溃现象. 在垂直于纳米线表面的外磁场辅助下, 发现辅助磁场可以调节消磁场的强度和方向. 这意味着利用辅助磁场可以有效地控制纳米铁磁线磁畴壁的动力学行为.     

High-density assembly of gold nanoparticles with zwitterionic carbon nanotubes and their electrocatalytic activity in oxygen reduction reaction

Gold nanoparticles (AuNPs) were assembled with high density onto multi-walled carbon nanotubes, which were functionalized with zwitterionic poly(imidazoliumsulfonate). The AuNP/zwitterionic CNT hybrids exhibited decent electrocatalytic activity in oxygen reduction reaction as the AuNP-based catalysts.     

An asymptotic stability involving collision and avoidance

Generally it is not easy task whether the stable systems governed by nonlinear ordinary differential equations are asymptotically stable or not. This problem often appears in studying a collision and avoidance control problem based on the stability theory. In this paper we devoted to finding conditions that the stable system obtained from the collision and avoidance control problem is asymptotically stable.     

Cyclic and acyclic S2O2 donor-type ionophores. Ion-pair extraction and transport of Ag(I) picrate, and X-ray confirmation of existence of the ion-pair complex

Extraction and transport behaviors of isomeric oxathia macrocycles (L₂, ortho-; L₃, meta- and L₄, para-isomer) and their structure related open-chain compound (L₁) towards Ag(I) picrate have been examined. From the plot of log (D_Ag(I)/[pic⁻]) vs. log [L]₀ for all of the ionophores were linear with slope near unity, thereby confirming the 1:1:1 complex formations of Ag(I)/ligand/picrate ion to be extracted into the dichloromethane phase. The extractability of an acyclic ionophore was superior to those of the corresponding cyclic ones. In membrane transport experiments, the slow rate of release of Ag(I) from the membrane into the receiving phase seems to be responsible for lower transport efficiency. Upon addition of sodium thiosulfate as a stripping reagent in receiving phase, the efficiency of transport is significantly enhanced in the order of L₁ (acyclic)>L₂ (ortho-)>L₃ (meta-)>L₄ (para-) in accordance with those of log K_ex values. It is hypothesized that the ion-pair complexation of L₁ in extraction step would be more favorable in extraction and transport of Ag(I). Its structure have been confirmed by X-ray diffraction analysis of [Ag(L₁)pic], where L₁=1,10-bis(mercaptobenzylyl)-4,7-dioxadecane.     

Core ionization energies of atoms and ions calculated using the generalized Sturmian method

The physical event of the umbrella inversion of ammonia has been studied in detail by application of the formalisms of frontier orbital theory, the density functional theory, the localized molecular orbital method, and the energy partitioning analysis. An intuitive structure for the transition state and dynamics of the physical process of structural reorganization prior to inversion have been suggested. The computation starts with the CNDO/2 equilibrium geometry, and thereafter the cycle proceeds through all the conformations of ammonia obtained by varying the ∠HNH angle in steps of 2° from its equilibrium value up to the transition state. The geometry of each conformation is optimized with respect to the length of the N–H bond. The glimpses of the charge density reorganization during the movement of the molecule from equilibrium conformation toward the transition state is computed in terms of dipole moment and the quantum mechanical hybridizations of bond pair and lone pair of N atom through the localized molecular orbitals (LMOs) of all the conformations. Results demonstrate that as the geometry of the molecule begins to evolve through the reorganization of structure, the N–H bond length and the dipole moment begin to decrease, and the trend continues up to the transition state. The dipole moment of the molecule at the suggested transition state is zero. The computed nature of quantum mechanical hybridization of bond pair and lone pair of the N atom as a function of reaction coordinates of the ∠HNH angles reveals that the percentage of s character of the lone pair hybrid decreases and that of the bond pair hybrid forming the σ(N–H) bond increases during the process of geometry reorganization from the equilibrium shape to the transition state. The rationale of the zero dipole moment of the transition state for inversion is not straightforward from its point‐group symmetry, but is self‐evident from its electronic structure drawn in terms of LMOs. The electronic structure of the transition state, which may be drawn in terms of the LMOs, seems to closely reproduce its suggested intuitive structure. The pattern of variation of dipole moment and nature of the changes of the percentage of the s character in the lone pair hybrid creating dipole with the evolution of geometry during the physical process of structural reorganization for the inversion are found to be nicely correlated according to the suggestion of Coulson. The profiles of the increasing strength of the N–H bond and the increasing percentage of s character of the bond pair hybrid of N atom forming this bond as a function of reaction coordinates are also found to be correlated in accordance with the suggestion of Coulson. The profile of global hardness as a function of reaction coordinate seems to demonstrate that the dynamics of the evolution of the molecular structure from equilibrium shape to the transition state following the course of suggested mode of structural reorganization conforms to the principle of maximum hardness (PMH). The profiles of parameters like the energies of highest occupied and lowest unoccupied molecular orbital (HOMO and LUMO), the gap in energy between HOMO and LUMO, the global hardness, the global softness, and chemical potential as a function of reaction coodinates of a continuous structural evolution from equilibrium shape to the transition state mimic the potential energy diagram of the total energy. Both the frontier orbital parameters and the density functional quantities are found to be equally effective and reliable to monitor the process of necessary structural reorganization prior to the inversion of mofecules. An energy partitioning analysis demonstrates that the origin of barrier has no unique single source rather as many as four mutually exclusive but interacting one‐ and two‐center energy terms within the molecule entail the origin and the height of the barrier. From a close analysis of the results, it seems highly probable that the necessary structural reorganization prior to umbrella inversion of ammonia most realistically occurs following the course of normal modes of vibration of the molecule. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 80: 1–26, 2000     

A technique for rapid two-stage dynamic tensile loading of polymers

A method for rapid two-stage dynamic-dynamic tensile loading of polymers, based on a tensile Hopkinson bar apparatus, is established. In this technique, the initial incident wave and its reflection are used to load a specimen in quick succession. Consequently, the specimen is stressed, momentarily unloaded, then reloaded until fracture. By adopting appropriate assumptions, a procedure to obtain the associated stress-strain curves for such double-stage loading is formulated. These assumptions are examined experimentally and analytically to substantiate their validity. To verify the proposed approach, a relatively rate-insensitive material, LEXAN 141 polycarbonate, was subjected to two-stage dynamic tension. The stress-strain curves obtained via the procedure established were compared with results from static loading. Favorable correlation between the two indicates that the proposed technique can be applied to the study of load history effects on the dynamic behavior of polymeric materials.