Large-scale motions in the adenylate kinase solution ensemble: coarse-grained simulations and comparison with solution X-ray scattering [0.03%]
腺苷酸激酶溶液构象 Ensemble中的大尺度运动：粗粒化模拟及溶液X射线散射结果的比较
Michael D Daily,Lee Makowski,George N Phillips Jr et al.
Michael D Daily et al.
While coarse-grained (CG) simulations provide an efficient approach to identify small- and large-scale motions important to protein conformational transitions, coupling with appropriate experimental validation is essential. Here, by compari...
Likelihood functions for the analysis of single-molecule binned photon sequences [0.03%]
单分子光子计数序列的似然函数分析方法
Irina V Gopich
Irina V Gopich
We consider the analysis of a class of experiments in which the number of photons in consecutive time intervals is recorded. Sequence of photon counts or, alternatively, of FRET efficiencies can be studied using likelihood-based methods. Fo...
Structural distributions from single-molecule measurements as a tool for molecular mechanics [0.03%]
基于单分子测量的构象分布作为分子力学工具的能力
Jeffrey A Hanson,Jason Brokaw,Carl C Hayden et al.
Jeffrey A Hanson et al.
A mechanical view provides an attractive alternative for predicting the behavior of complex systems since it circumvents the resource-intensive requirements of atomistic models; however, it remains extremely challenging to characterize the ...
Water Diffusion In And Out Of The β-Barrel Of GFP and The Fast Maturing Fluorescent Protein, TurboGFP [0.03%]
荧光蛋白GFP和快速成熟的荧光蛋白TurboGFP中β-桶状结构的水分子扩散研究
Binsen Li,Ramza Shahid,Paola Peshkepija et al.
Binsen Li et al.
The chromophore of fluorescent proteins is formed by an internal cyclization of the tripeptide 65SYG67 fragment and a subsequent oxidation. The oxidation is slow - the kinetics of this step is presumably improved in fast maturing GFPs. Wate...
A method to estimate the elastic energy stored in braided DNA molecules using hydrodynamic equations [0.03%]
基于流体动力学方程估计编织DNA分子中存储的弹性能量的方法
Mónica Fernández-Sierra,Violeta Delgado-Martí,Jorge E Colón-García et al.
Mónica Fernández-Sierra et al.
We present a single-molecule method for measuring the torque exerted by braided DNA molecules undergoing spontaneous unbraiding while attached to a paramagnetic dumbbell in the absence of external manipulation. A magnetic tweezers setup is ...
Stark Absorption Spectroscopy of Peridinin and Allene-Modified Analogues [0.03%]
丙二烯修饰类化合物及原绿素的斯塔克吸收光谱研究
Toshiyuki Kusumoto,Tomoko Horibe,Takayuki Kajikawa et al.
Toshiyuki Kusumoto et al.
Stark absorption spectra of peridinin (Per) and five allene-modified analogues and their angular dependence as a function of an externally applied electric field were measured in methyl methacrylate polymer at 77K. In all cases, the energet...
Hadrien Bosetti,Harald A Posch
Hadrien Bosetti
We carry out extensive computer simulations to study the Lyapunov instability of a two-dimensional hard-disk system in a rectangular box with periodic boundary conditions. The system is large enough to allow the formation of Lyapunov modes ...
Modeling temperature dependent kinetic isotope effects for hydrogen transfer in a series of soybean lipoxygenase mutants: The effect of anharmonicity upon transfer distance [0.03%]
利用一系列大豆血红素加氧酶突变体模拟氢转移的温度依赖性的同位素效应：非谐振性对转移距离的影响
Matthew P Meyer,Judith P Klinman
Matthew P Meyer
Soybean lipoxygenase-1 (SLO) catalyzes the oxidation of linoleic acid. The rate-limiting step in this transformation is the net abstraction of the pro-S hydrogen atom from the center of the 1,5-pentadienyl moiety in linoleic acid. The large...
Fluxes of non-interacting and strongly repelling particles through a single conical channel: Analytical results and their numerical tests [0.03%]
非相互作用和强烈排斥粒子通过单个圆锥形通道的通量：解析结果及其数值检验
Alexander M Berezhkovskii,Mark A Pustovoit,Sergey M Bezrukov
Alexander M Berezhkovskii
Using a diffusion model of particle dynamics in the channel, we study entropic effects in channel-facilitated transport. We derive general expressions for the fluxes of non-interacting particles and particles that strongly repel each other ...
Ultrafast Time-resolved Absorption Spectroscopy of Geometric Isomers of Xanthophylls [0.03%]
类胡萝卜素几何异构体的超快时间共振吸收光谱研究
Dariusz M Niedzwiedzki,Miriam M Enriquez,Amy M Lafountain et al.
Dariusz M Niedzwiedzki et al.
This paper presents an ultrafast optical spectroscopic investigation of the excited state energies, lifetimes and spectra of specific geometric isomers of neoxanthin, violaxanthin, lutein, and zeaxanthin. All-trans- and 15,15'-cis-beta-caro...