抑制剂G4G与HIV-1蛋白酶作用模式的结合自由能计算研究

本文采用分子动力学模拟和结合自由能计算研究了抑制剂G4G与HIV-1蛋白酶的作用机制。研究结果表明范德华作用主导了抑制剂G4G与HIV-1蛋白酶的结合。基于残基的自由能计算表明残基Gly49、Ile50、Val82、Ile84、Gly27′、Ala28′、Ile50′和Ile84′与G4G产生了较强的相互作用,同时研究也表明CH-π,CH-O相互作用和氢键是其主要的作用形式。该研究能为以HIV-1蛋白酶为靶标的抗艾滋病药物设计提供理论上的指导。     

HIV-1 蛋白酶与抑制剂3G3相互作用机制的分子动力学研究

HIV-1蛋白酶已经成为艾滋病治疗药物设计的重要靶标。本文采用分子动力学模拟和MM-PB/SA方法计算了抑制剂3G3与HIV-1蛋白酶的结合自由能,结果表明范德华作用驱动了3G3与蛋白酶的结合。同时也采用了基于残基的自由能分解方法计算了抑制剂-残基相互作用,结果证明残基Ala28,Val32/Val32′,Ile47,Gly49,Ile50/Ile50′,Ile84/Ile84′和Pro81′ 能与蛋白酶产生较为强烈的相互作用,同时也表明CH-π,π-π和 CH-O相互作用控制了3G3与蛋白酶的结合。我们期望这个研究能为抗艾滋病的药物设计提供理论上的指导。     

HIV-1蛋白酶与抑制剂BEG相互作用的分子对接计算研究

本文使用分子对接方法和MM/PBSA方法计算抑制剂BEG与HIV-1蛋白酶的结合自由能,结果表明范德华相互作用主宰了BEG与HIV-1蛋白酶的结合,同时计算还证明分子对接采用的分子力场相比于Amber力场更适合于BEG-HIV蛋白酶系统。这篇论文还采用基于残基的自由能分解方法计算了抑制剂-残基相互作用,结果表明残基Leu23、Gly49、Ile50、Val82、Ile84、Asp25′、Gly27′、Ala28′、Gly49′、Ile50′和Ile84′与BEG产生了较强的相互作用,同时也证明CH-π和CH-O相互作用驱动了抑制剂BEG与HIV-1蛋白酶的结合。我们期望这个研究能为艾滋病治疗药物的合理化设计提供理论上的指导和实验上的参考。     

分子动力学研究抑制剂APV与HIV-1蛋白酶的作用机制

采用分子动力学模拟和结合自由能计算研究了抑制剂APV与HIV-1蛋白酶的作用机制. 研究结果表明范德瓦尔斯作用主控了APV与HIV-1蛋白酶的结合. 采用基于残基的自由能分解方法计算了抑制剂-残基相互作用,结果表明9个残基Gly27、Ile32、Val47、Ile50、Ile84、Ala28′、Gly49′、Ile50′和Arg87′与APV产生了大于1.0 kcal/mol的强相互作用,而且证明CH-π,CH-O相互作用和极性作用是其结合的主要形式. 期待该结果可以为以HIV-1蛋白酶为靶标的抗艾滋病药物设计提供理论上的指导.     

分子动力学研究抑制剂APV与HIV-1蛋白酶的作用机制

采用分子动力学模拟和结合自由能计算研究了抑制剂APV与HIV-1蛋白酶的作用机制. 研究结果表明范德瓦尔斯作用主控了APV与HIV-1蛋白酶的结合. 采用基于残基的自由能分解方法计算了抑制剂-残基相互作用,结果表明9个残基Gly27、Ile32、Val47、Ile50、Ile84、Ala28′、Gly49′、Ile50′和Arg87′与APV产生了大于1.0 kcal/mol的强相互作用,而且证明CH-π,CH-O相互作用和极性作用是其结合的主要形式. 期待该结果可以为以HIV-1蛋白酶为靶标的抗艾滋病药物设计提供理论上的指导.     

分子动力学研究抑制剂APV与HIV-1蛋白酶的作用机制

采用分子动力学模拟和结合自由能计算研究了抑制剂APV与HIV-1蛋白酶的作用机制.研究结果表明范德瓦尔斯作用主控了APV与HIV-1蛋白酶的结合.采用基于残基的自由能分解方法计算了抑制剂-残基相互作用,结果表明9个残基Gly27、Ile32、Val47、Ile50、Ile84、Ala28'、Gly49'、Ile50'和Arg87'与APV产生了大于1.0 kcal/mol的强相互作用,而且证明CH-π,CH-O相互作用和极性作用是其结合的主要形式.期待该结果可以为以HIV-1蛋白酶为靶标的抗艾滋病药物设计提供理论上的指导.     

I50V变异对HIV-1蛋白酶抑制剂Amprenavir抗药机制的分子动力学研究

HIV-1蛋白酶PR(HIV-1 protease)的变异对抑制剂产生抗药性,严重消弱抗艾滋病的治疗效果.I50V变异是HIV-1蛋白酶残基变异中最重要的一个.采用分子动力学模拟和溶解相互作用能方法SIE(solvated interaction energy)研究I50V变异对抑制剂APV(amprenavir)抗药机制.分子动力学分析表明I50V变异诱导HIV-1蛋白酶整体柔性的增加,影响了抑制剂与蛋白酶的相互作用.结合自由能计算表明范德华作用的下降驱动了I50V变异对APV的抗药性.基于残基的能量分解证明V50/V50'与APV的相互作用相对于野生型的I50/I50'明显减弱,诱导了抗药性.本研究能为高效的缓解抗药性抑制剂的研发提供一定的理论指导.     

抑制剂Benzamidine与胰岛素作用机制的分子动力学和结合自由能计算研究

氢键和极性相互作用在抑制剂-蛋白结合专一性识别过程中起到重要作用. 抑制剂Benzamidine(BEN)与胰岛素trypsin相互作用机制的阐明有助于胰岛素高效抑制剂的研发.本文采用分子动力学模拟和MM-PBSA(molecular mechanics-Poisson Boltzmann surface area)从原子层次上研究BEN与胰岛素的结合模式.结果表明抑制剂BEN的脒基不仅与Asp189的羰基产生静电相互作用，而且与残基Ser190和Gly214形成氢键相互作用.基于残基能量分解的计算表明抑制剂的苯基与残基His58, Cys191, Gln192, Trp211, Gly212和Cys215形成有利于抑制剂结合的疏水性相互作用.期望当前的研究能为胰岛素有效抑制剂的研发提供重要的理论指导.     

抑制剂Benzamidine与胰岛素作用机制的分子动力学和结合自由能计算研究

氢键和极性相互作用在抑制剂-蛋白结合专一性识别过程中起到重要作用.抑制剂Benzamidine(BEN)与胰岛素trypsin相互作用机制的阐明有助于胰岛素高效抑制剂的研发.本文采用分子动力学模拟和MM-PBSA(molecular mechanics-Poisson Boltzmann surface area)从原子层次上研究BEN与胰岛素的结合模式.结果表明抑制剂BEN的脒基不仅与Asp189的羰基产生静电相互作用,而且与残基Ser190和Gly214形成氢键相互作用.基于残基能量分解的计算表明抑制剂的苯基与残基His58,Cys191,Gln192,Trp211,Gly212和Cys215形成有利于抑制剂结合的疏水性相互作用.期望当前的研究能为胰岛素有效抑制剂的研发提供重要的理论指导.     

抑制剂8Q9和8QC与bromodomain结构域蛋白4作用机理的分子动力学研究

Bromodomain结构域蛋白4（bromodomain-containing protein 4,BRD4）已成为治疗多种疾病药物设计的重要靶标. 最近在实验上发现了几种有效的靶向BRD4的抑制剂,但具体的抑制机理尚不清楚．此工作采用分子动力学模拟,动态相关性分析和结合自由能计算研究抑制剂8Q9和8QC与BRD4(1)的结合模式．分子动力学分析表明抑制剂结合对BRD4(1)的结构柔性产生重大影响．同时动态相关性分析进一步表明抑制剂结合极大地改变了BRD4(1)的运动模式．结合自由能计算结果表明范德华相互作用是抑制剂与BRD4(1)结合的主要驱动力．采用基于残基的自由能分解方法评估了分离残基对抑制剂结合的贡献,数据表明氢键相互作用和疏水相互作用是影响抑制剂与BRD4(1)结合的关键因素．本研究有望为设计和开发靶向BRD4的抑制剂提供有意义的理论指导．     

Boundary G/G Theory and Topological Poisson–Lie Sigma Model

We study a boundary version of the gauged WZW model with a Poisson–Lie group G as the target. The Poisson–Lie structure of G is used to define the Wess–Zumino term of the action on surfaces with boundary. We clarify the relation of the model to the topological Poisson sigma model with the dual Poisson–Lie group G ^* as the target and show that the phase space of the theory on a strip is essentially the Heisenberg double of G introduced by Semenov–Tian–Shansky.     

Tests for Varying G

In this note we consider a variable G cosmology which is consistent with observation and which had successfully predicted an ever expanding accelerating universe with a small cosmological constant amongst other things. Three further tests are proposed in this note: First, the inexplicable anomalous accelerations of the Pioneer spacecrafts can be explained. It is then shown that the observed shortening of the orbital periods of binary pulsars is in good agreement with this model. Finally, more general changes in orbital parameters are deduced, which may be observed in the future.     

（G′/G）-Expansion Method Equivalent to Extended Tanh Function Method

In a recent article [Physics Letters A 372 （2008） 417], Wang et al. proposed a method, which is called the （G′/G）-expansion method, to look for travelling wave solutions of nonlinear evolution equations. The travelling wave solutions involving parameters of the KdV equation, the mKdV equation, the variant Boussinesq equations, and the Hirota-Satsuma equations are obtained by using this method. They think the （G′/G）-expansion method is a new method and more travelling wave solutions of many nonlinear evolution equations can be obtained. In this paper, we will show that the （G′/G）-expansion method is equivalent to the extended tanh function method.     

LTE-Advanced and the evolution to Beyond 4G (B4G) systems

Cellular networks have been undergoing an extraordinarily fast evolution in the past years. With commercial deployments of Release 8 (Rel-8) Long Term Evolution (LTE) already being carried out worldwide, a significant effort is being put forth by the research and standardization communities on the development and specification of LTE-Advanced. The work started in Rel-10 by the Third Generation Partnership Project (3GPP) had the initial objective of meeting the International Mobile Telecommunications-Advanced (IMT-Advanced) requirements set by the International Telecommunications Union (ITU) which defined fourth generation (4G) systems. However, predictions based on the wireless traffic explosion in recent years indicate a need for more advanced technologies and higher performance. Hence, 3GPP’s efforts have continued through Rel-11 and now Rel-12. This paper provides a state-of-the-art comprehensive view on the key enabling technologies for LTE-Advanced systems. Already consolidated technologies developed for Rel-10 and Rel-11 are reviewed while novel approaches and enhancements currently under consideration for Rel-12 are also discussed. Technical challenges for each of the main areas of study are pointed out as an encouragement for the research community to participate in this collective effort.     

万有引力常量G的测量

介绍了测量万有引力常量G的意义、历史与现状.具体讨论测量万有引力常量G的几种方法,着重阐述周期法测G的基本原理及原子干涉法测G的新进展.     

Vibrational symmetry classification and torsional tunneling splitting patterns in G6(EM), G12, and G36(EM) molecules

It is shown that the torsional splitting patterns in methanol-like molecules, with the excitation of small amplitude vibrational modes in the methyl group, are determined by mechanisms that can be formulated in an almost identical fashion to that for ethane-like molecules. This is achieved by treating ethane-like molecules by the internal axis method (IAM) and methanol-like molecules by the principal axis method (PAM) or rho-axis method (RAM). Using the extended molecular groups G₆(EM) or C_6v(M) for methanol and G₃₆(EM) for ethane, vibrations perpendicular to the internal rotation axis are conveniently described by modes of higher degeneracy (E for methanol and G_s for ethane) in the absence of coupling of top and frame. Head–tail coupling operators, except the cos-type barrier terms, lower the degeneracy, causing vibrational splittings. Coupled vibrational pairs with torsional splitting patterns that we call ‘regular’ (pure A₁, A₂ pairs for methanol and pure E_1d, E_2d pairs for ethane) or ‘inverted’ (pure B₁, B₂ pairs for methanol and pure E_1s, E_2s pairs for ethane) can be formed as limit cases. Actual splitting patterns occur between the above limits, and are basically determined by torsional Coriolis coupling, which can tune more or less to resonance pairs of uncoupled basis levels linked by specific head-tail coupling operators. The inversion of torsional splitting patterns, observed in perpendicular vibrational modes of the methyl group of methanol, can be predicted by these theoretical considerations. Similar considerations apply to molecules of G₁₂ symmetry.     

Generalised G 2–Manifolds

We define new Riemannian structures on 7–manifolds by a differential form of mixed degree which is the critical point of a (possibly constrained) variational problem over a fixed cohomology class. The unconstrained critical points generalise the notion of a manifold of holonomy G ₂, while the constrained ones give rise to a new geometry without a classical counterpart. We characterise these structures by means of spinors and show the integrability conditions to be equivalent to the supersymmetry equations on spinors in type II supergravity theory with bosonic background fields. In particular, this geometry can be described by two linear metric connections with skew–symmetric torsion. Finally, we construct explicit examples by introducing the device of T–duality.On leave at: Centre de Mathématiques Ecole Polytechnique 91128 Palaiseau, France. E-mail: fwitt@math.polytechnique.fr     

Visualizing Görtler vortices

The development of Görtler vortices with pre-set wavelength of 15 mm has been visualized in the boundary-layer on a concave surface of 2.0 m radius of curvature at a free-stream velocity of 3.0 m/s. The wavelength of vortices was pre-set by vertical wires of 0.2 mm diameter located 10 mm upstream of the concave surface leading edge. The velocity contours in the cross-sectional planes at several streamwise locations show the growth and breakdown of the vortices. Three different regions can be identified based on different growth rate of the vortices. The occurrence of a secondary instability mode is indicated by the formation of a small horseshoe eddies generated between the two neighboring vortices traveling streamwise, to form mushroom-like structures as a consequence of the non-linear growth of the Görtler vortices.