Distance distributions and dynamics of a zinc finger peptide from fluorescence resonance energy transfer measurements

Time-resolved fluorescence resonance energy transfer (FRET) measurements were used to measure distance distributions and intramolecular dynamics (site-to-site diffusion) of a 28-residue single-domain zinc finger peptide in the absence and presence of zinc ion. Energy transfer was measured between TRP₁₄ and a N-terminal DNS group. As expected, the TRP-to-DNS distance distribution for zinc-bound peptide is shorter and narrower (R _av=11.2 Å,hw=2.8 Å) than the metal-free peptide (R _av=20.1 Å,hw=14.5 Å). The degree of mutual donor-to-acceptor diffusion (D) was also determined for these distributions. For zinc-bound peptide there is no detectible diffusion (D0.2 Ų/ns), whereas for metal-free peptide a considerable amount of motion is occurring between the donor and the acceptor (D=12 Ų/ns). These results indicate that the zinc-bound peptide folds into a unique, well-defined conformation, whereas the metal-free conformation is flexible and rapidly changing. The absence of detectible mutual site-to-site diffusion between the donor and the acceptor in the metal-bound zinc finger peptide indicates that intramolecular motion is essentially frozen out, on the FRET time scale, as a consequence of zinc coordination.Dedicated to the memory of Barbara D. Wells.     

Investigation of the dissociative adsorption for cyclopropane on the copper surface by density functional theory and quantum chemical molecular dynamics method

The dissociative adsorption of cyclopropane on the copper surface was studied using quantum chemical molecular dynamics method with “Colors-Excite” code and density functional theory by Amsterdam Density Functional program (ADF2000). The excited state of cyclopropane was used as adsorbate to simulate the dissociated adsorption under an irradiation energy of ca. 10 eV. One of the C-C bonds in cyclopropane was broken and the two new bonds between cyclopropane and copper surface were formed. The electrons transferred from the copper atoms to cyclopropane with a value of about 0.2e. The shorter distances between the carbons and surface copper atoms showed the existence of strong interaction. Consistently, the results indicated metallacyclopentane was the most possible intermediate species in dissociative adsorption by ADF2000 and “Colors-Excite” method.     

Survivor statistics and damage spreading on social network with power-law degree distributions

Damage spreading(DS) of the random graph networks with power-law degree distributions is investigated using Glauber dynamics. Various subgraphs defined by the probability of acquaintance show distinct features in DS as measured by Hamming distance. A heuristic understanding of the long-time value of damage is achieved through an analysis of the survivor statistics. All survivors are dynamical, flipping in unison for the controlled sample and the damaged sample. Verification of these dynamic survivors is achieved through the introduction of a new measure of self-damage.     

Traffic dispersion induced by noise in off-lattice model

We study the dispersion of vehicles induced by speed fluctuation on a single-lane highway under open boundary. We extend the cellular automaton model on one-dimensional lattice to the real-variable model on off-lattice (continuous-in space model) in order to take into account the fluctuation of vehicular speed. Vehicles extend over the highway when moving forward. The characteristics of traffic dispersion are derived. It is shown that vehicular traffic exhibits scaling property. When a vehicle accelerates for following the vehicle ahead, vehicles move forming a cluster without dispersion. The relationship between the width of vehicular cluster and acceleration rate is clarified.     

巨共振激发的相对论效应

在相对论量子场论(QHD)的框架下,得到了相对论线性Vlasov方程.基此计算了球形核¹⁶O、⁴⁰Ca、⁹⁰Zr及²⁰⁸Pb的巨偶极共振的强度函数分布.计算得到的巨共振中心能量,与实验结果比较有较好的符合.对计算结果作了简要的讨论,发现核子有效质量m^*和平均场自旋轨道耦合力对巨共振能量有着重要的效应.     

细菌视紫红质激发态动力学过程的实验与数值分析

本文采用差异吸收光谱法对化学增强型细菌视紫红质的状态变化进行了实验研究.发现在585 nm处明显存在一个稳定的中间过程.从分子动力学和实验出发,提出了一个适用于差异吸收光谱研究方法的数学模型,对菌紫质受激以后的动力学过程进行了模拟与数值分析.     

7-Hydroxy-4-methyl-8-(4′-methylpiperazine-1′-yl)methyl coumarin: An efficient probe for fluorescence resonance energy transfer to a bioactive indoloquinolizine system

Solvatochromic effects on the fluorescence behavior of 7-hydroxy-4-methyl-8-(4′-methyl-piperazine-1′ yl)methylcoumarin (HMMC) was studied in different solvents. The fluorescence of HMMC was found to be highly sensitive to both the polarity and the protic character of the solvent. Exploiting the polarity-sensitive fluorescence property of HMMC, its excited-state dipole moment has been determined. Fluorescence (Förster) resonance energy transfer (FRET) process from HMMC to a potent bioactive molecule 3-acetyl-4-oxo-6,7-dihydro-12 H indolo-[2,3-a] quinolizine (AODIQ) was studied. From the determined K_SV and R₀ values, it is argued that a long-range dipole-dipole interaction is operating for the energy transfer mechanism. The energy transfer efficiency (E) and the distance between the acceptor and the donor (r₀) have been determined.     

Structure of zinc-borate low-melting glasses derived from IR spectroscopy data

The IR spectra of glasses of the ZnO—SrO—B₂O₃ system with constant additions of PbO, Al₂O₃, and Li₂O (20 mol. % in sum) were studied. It is established that on replacement of B₂O₃ by ZnO, the structure of the glasses is characterized by the presence of groupings with the bridge bonds B^III— O—B^III, B^III—O—B^IV, B^IV—O—B^IV and end groups B^III— O⁻; ZnO practically exerts no influence on the coordination transition [BO₃] → [BO₄]. At a high content of ZnO, zinc ions are present in both a six-and a four-coordinated state. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 72, No. 6, pp. 778–781, November–December, 2005.     

Membrane Organization and Dynamics of the G-Protein-Coupled Serotonin<Subscript>1A</Subscript> Receptor Monitored Using Fluorescence-Based Approaches

The G-protein-coupled receptor (GPCR) superfamily represents one of the largest classes of molecules involved in signal transduction across the plasma membrane. Fluorescence-based approaches have provided valuable insights into GPCR functions such as receptor–receptor and receptor–ligand interactions, real-time assessment of signal transduction, receptor dynamics on the plasma membrane, and intracellular trafficking of receptors. This has largely been possible with the use of fluorescent probes such as the green fluorescent protein (GFP) from the jellyfish Aequoria victoria and its variants. We discuss the potential of fluorescence-based approaches in providing novel information on the membrane organization and dynamics of the G-protein-coupled serotonin_1A receptor tagged to the enhanced yellow fluorescent protein (EYFP). These authors contributed equally to the work.