Kinetics of proton transfer in a green fluorescent protein: A laser-induced pH jump study

The sub-millisecond protonation dynamics of the chromophore in S65T mutant form of the green fluorescent protein (GFP) was tracked after a rapid pH jump following laser-induced proton release from the caged photolabile compoundo-nitrobenzaldehyde. Following a jump in pH from 8 to 5 (which is achieved within 2 μs), the fluorescence of S65T GFP decreased as a single exponential with a time constant of ∼90 μs. This decay is interpreted as the conversion of the deprotonated fluorescent GFP chromophore to a protonated non-fluorescent species. The protonation kinetics showed dependence on the bulk viscosity of the solvent, and therefore implicates bulk solvent-controlled protein dynamics in the protonation process. The protonation is proposed to be a sequential process involving two steps: (a) proton transfer from solvent to the chromophore, and (b) internal structural rearrangements to stabilize a protonated chromophore. The possible implications of these observations to protein dynamics in general is discussed     

The elastic theory of a single DNA molecule

We study the elastic responses of double-(ds) and single-stranded (ss) DNA at external force fields. A double-strand-polymer elastic model is constructed and solved by path integral methods and Monte Carlo simulations to understand the entropic elasticity, cooperative extensibility, and supercoiling property of dsDNA. The good agreement with experiments indicates that short-ranged base-pair stacking interaction is crucial for the stability and the high deformability of dsDNA. Hairpin-coil transition in ssDNA is studied with generating function method. A threshold force is needed to pull the ssDNA hairpin patterns, stabilized by base pairing and base-pair stacking, into random coils. This phase transition is predicted to be of first order for stacking potential higher than some critical level, in accordance with experimental observations.     

Millimeter and submillimeter wave spectroscopic investigations into the rotation-tunneling spectrum of gGg ethylene glycol, HOCH2CH2OH

The rotation-tunneling spectrum of the second most stable gGg^′ conformer of ethylene glycol (1,2-ethanediol) in its ground vibrational state has been studied in selected regions between 77 and 579 GHz. Compared to the study of the more stable aGg^′ conformer, a much larger frequency range was studied, resulting in a much extended frequency list covering similar quantum numbers, J?55 and K_a?19. While the input data were reproduced within experimental uncertainties up to moderately high values of J and K_a larger residuals remain at higher quantum numbers. The severe mixing of the states caused by the Coriolis interaction between the two tunneling substates is suggested to provide a considerable part of the explanation. In addition, a Coriolis interaction of the gGg^′ ground vibrational state with an excited state of the aGg^′ conformer may also contribute. Relative intensities of closely spaced lines have been investigated to determine the signs of the Coriolis constants between the two tunneling substates relative to the dipole moment components and to estimate the magnitudes of the dipole moment components and the energy difference between the gGg^′ and the aGg^′ conformers. Results of ab initio calculations on the total dipole moment and the vibrational spectrum were needed for these estimates. The current analysis is limited to transitions with quantum numbers J?40 and K_a?6 plus those having J?22 and K_a?17 which could be reproduced within experimental uncertainties. The results are aimed at aiding radioastronomers to search for gGg^′ ethylene glycol in comets and in interstellar space.     

Intrinsic Fluorescence of Actin

In this work actin is used to illustrate connection of protein fluorescence characteristics with its structure. On one hand, it has been demonstrated what kind of information about the contribution of each tryptophan residues to the bulk fluorescence spectrum can be obtained from the special analysis of protein three-dimensional structure. On the other hand, potentials of intrinsic fluorescence for elucidation of proteins structure, dynamics and processes of folding-unfolding are shown. In particular, using this method a new essentially unfolded kinetic intermediate state of actin was detected and characterized, and the place of inactivated actin and its kinetic predecessor in the process of folding-unfolding was determined. It has been revealed that inactivated actin is not intermediate state between the native and completely unfolded states, as it has been accepted before, but a result of protein misfolding. On the basis of the obtained data a new model of actin folding-unfolding pathway has been proposed.     

酵母蛋白质网络的动力学性质

蛋白质-蛋白质、蛋白质-DNA相互作用网络决定了细胞中各种关键功能的执行．基于芽殖酵母(budding yeast saccharomyces cerevisiae)的蛋白质-蛋白质相互作用网络数据和相关的实验文献，我们建立了调控细胞周期和生命周期(cell cycle and life cycle)的蛋白质网络，并利用离散模型研究了该网络的动力学性质，研究表明：细胞周期网络的动力学性质具有很强的稳定性，约94％的蛋白质初态将演化到对应于生物学G1基态的稳定态，使其成为惟一的全局吸引点；同时，绝大多数的初态的演化路径都通过由G1激发态到G1基态的细胞周期演化路径，使细胞周期路径成为全局性的“吸引”路径。     

Formation of Supersonic Zones and Local Separation Zones in Transonic Steady-State Flow Past Surface Roughness in the Free Interaction Regime

Within the framework of free interaction theory numerical methods are used to investigate the occurrence of supersonic zones with shocks in the outer inviscid region for flow past roughness in the lower viscous sublayer, with and without the formation of local separation zones.     

Dynamic fractal unifying interaction confirmed with magnetospheric behavior and orbital data

The solar wind makes the magnetosphere to expand and contract as indicated by the expansions and contractions of the auroral oval due to balancing of the dynamic pressure of the ambient space plasma at inner and outer magnetic lines. This self‐similar magnetospheric behavior elucidates the controversial magnetic storm‐substorm relationship and reveals the 3D‐spiral structure of magnetic interaction. The found self‐similarly evolving structure of one seen as fundamental interaction suggests dynamic fractal unifying interaction that builds a firework universe having 3D‐spiral code. The unifying interaction is described with equation drawn in new fundamental dynamic fractal framework. The equation of unifying interaction converges to the inverse square laws and the principle of uncertainty at laboratory scales. The dynamic fractal fundamental framework is made of one 3D‐spirally‐faster‐inward contracting and expanding, oscillating, basic matter. It simply accounts for observed constant speed of light and for the creation of bright and dark bands on a screen behind a tiny slit. The dynamic fractal framework is quantitatively confirmed with the orbital data for the Milky Way Galaxy, the Sun, the Earth, and the triple asteroid system 87 Sylvia. Many testable predictions are also made. The presented new fundamental dynamic fractal framework allows qualitative and quantitative modeling and simplification. © 2007 Wiley Periodicals, Inc. Complexity 12: 61–76, 2007     

复制缺陷型人泡沫病毒载体辅助质粒pΔGP的构建及转染小肠癌细胞的研究

在人泡沫病毒原病毒全长克隆pHRSV13的基础上,缺失突变gag和pol基因,并且用SV40polyA加尾信号替代人泡沫病毒的3′LTR,构建辅助质粒pΔGP.将复制缺陷型人泡沫病毒载体质粒pGPSNI EGFP和辅助质粒pΔGP分别转染和共转染小肠癌HIC细胞系,荧光显微镜检测发现共转染pGPSNI EGFP和pΔGP的HIC细胞能够强烈表达绿色荧光蛋白,转染有复制缺陷型人泡沫病毒载体质粒pGPSNI EGFP的HIC细胞能够表达少量的绿色荧光蛋白,而转染有辅助载体pΔGP的HIC细胞不表达绿色荧光.结果证明复制缺陷型人泡沫病毒载体的构建成功,表明人泡沫病毒env基因3′端的内部启动子IP具有弱启动子的活性,并且bel基因产生的调控蛋白能够反式激活人泡沫病毒内部启动子IP和5′LTR的启动子.     

使用Dreamweaver UltraDev制作

介绍了用DreamweaverUltraDev来实现动态网页的优点 ,并给出实例剖析 .     

Bending-torsion vibration of a partially submerged cylinder with an arbitrary cross-section

An analytical method is presented to investigate the bending-torsion vibration characteristics of a cylinder with an arbitrary cross-section and partially submerged in water. The compressibility and the free surface waves of the water are considered simultaneously in the analysis. The exact solution of structure–water interaction is obtained mathematically. Firstly, the analytical expression of the velocity potential of the water is derived by using the method of separation of variables. The unknown coefficients in the velocity potential are determined by the longitudinal and circumferential Fourier expansions along the outer surface of the cylinder and are expressed in the form of integral equations including the unknown dynamic bending deflection and torsional angle of the cylinder. Secondly, the force and torque acting on the cylinder per unit length, provided by the water, are obtained by integrating the water dynamic pressure along the circumference of the cylinder. The general solution of bending-torsion vibration of the cylinder under the water dynamic pressure is derived analytically. The integral equations included in the velocity potential of the water can be solved exactly. Finally, the eigenfrequency equation of cylinder–water interaction is obtained by means of the boundary conditions of the cylinder. Some numerical examples for elliptical columns partially submerged in water are provided to show the application of the present method.