Analysis of Lanthanide-Induced Conformational Change of the C-Terminal Domain on Centrin

Centrin, an EF-hand calcium-binding protein with high homology to calmodulin (CaM), is an essential component of microtubule-organizing center (MTOC). Lanthanide (Ln) ions can improve the stability, increase the amount and enhance the orderliness of microtubules, which are components of cytoskeleton. In order to investigate the structural basis of Ln ions on enhancing orderliness of microtubules, we characterized the binding properties of Ln ions with the isolated C-terminal domain of the Euplotes centrin (C-EoCen). Results suggested that Ln ions may occupy the canonical Ca²⁺ binding sites on C-EoCen with middle affinity. Near- and far-UV CD spectra of C-EoCen displayed pronounced differences before and after additing Ln ions. The asymmetry of microenvironments of Phe on C-EoCen was changed. Using 2-p-toluidinylnaphthalene-6- sulfonate (TNS) as probe, Ln ions induced C-EoCen to undergo conformational changes from closed state to open state, resulting in exposing hydrophobic patches to external environments. Ln ions have more obvious effect on the conformation of centrin than Ca²⁺. The differences found in the interactions of centrin binding with Ln ions/Ca²⁺ maybe provide some insights for structural basis of centrin functions in vivo.     

粗粒化自由能模拟研究ABC输出蛋白质构象态转变

本文应用了粗粒化分子动力学方法模拟计算了ATP结合盒式输出蛋白沿其构象转变途径反应坐标的平均力势，这个反应坐标被定义为内门和外门质量中心距离之差. 计算得到的平均力势能很好地描述不同的向内构象态、向外构象态和阻塞构象状态，以及它们之间的转变. 粗粒化分子动力学自由能模拟显示，在向内构象态到向外构象态转变过程中，内门在外门打开之前先行关闭；反之，在向外构象态到向内构象态转变过程中，外门在内门大开之前先行关闭. 因此，在向内构象态和向外构象态两种转变过程中，都经过了阻塞构象状态. 模拟结果揭示了ATP结合盒式输出蛋白的传输单向性，这种特性在生命体系功能实现中具有十分重要的意义. 这些结果与先前晶体结构实验［Proc. Natl. Acad. Sci. USA 104，19005 (2007)］发现有根本的不同，这些实验结果显示了内外门同时打开的不合理结果. 本文通过计算模拟阐明了ABC输出蛋白构象态变化的分子机理.     

Quantum ergodicity and energy flow in molecules

We review a theory for coupled many-nonlinear oscillator systems that describes quantum ergodicity and energy flow in molecules. The theory exploits the isomorphism between quantum energy flow in Fock space, that is, vibrational state space, and single-particle quantum transport in disordered solid-state systems. The quantum ergodicity transition in molecules is thereby analogous to the Anderson transition in disordered solids. The theory reviewed here, local random matrix theory (LRMT), describes the nature of the quantum ergodicity transition, statistical properties of vibrational eigenstates, and quantum energy flow through the vibrational states of molecules. Predictions of LRMT have been observed in computational studies of coupled nonlinear oscillator systems, which are summarized here. We also review applications of LRMT to molecular spectroscopy and chemical reaction rate theory, including adoption of LRMT in theories that predict rates of conformational change of molecules taking place at energies corresponding to those below and above the quantum ergodicity transition. A number of specific examples are reviewed, including the application of LRMT to predict (1) dilution factors of IR spectra of organic molecules, (2) rates of conformational change in chemical and photochemical reactions, (3) conformational dynamics of biological molecules in molecular beams, (4) rates of hydrogen bond breaking and rearrangement in clusters of biological molecules and water, and (5) excited state proton transfer reactions in proteins.     

Effect of Oxide Content of Graphene Oxide Membrane on Remarkable Adsorption for Calcium Ions

Graphene oxide membranes(GOMs), as one of the most promising novel materials, have gained great interest in the field of adsorption. However, the oxygen content of graphene oxide is directly related to its adsorption properties, such as suspension stability, adsorption capacity, and reusability of GOMs. Here, a series of reduced GOMs with oxygen content from 28% to 12% were conveniently prepared by the thermally reduced and the corresponding interlayer spacing of these membranes changed from 8.0 ? to 3.7 ?. These prepared GOMs have remarkable Ca~(2+) adsorption capacity, which increases with the oxygen content or interlayer spacing of GOMs.Importantly, the max adsorption capacity of the mass ratio between adsorbed Ca~(2+)and pristine GOMs can reach up to 0.481 g/g, which is about one order of magnitude higher than the adsorption capacity of activated sludge,magnetic Fe_3 O_4, functionalized silica, zeolite molecular sieve, and other reported previously. Moreover, GOMs show excellent stability and the Ca~(2+) can be easily desorbed by water, so that the GOMs can be reused. Our previous theoretical analysis suggests that this remarkable adsorption is attributable to the strong interactions between Ca~(2+) and GO sheets, including the ion- interactions between Ca~(2+) and aromatic graphitic rings as well as the electrostatic interaction between Ca~(2+) and oxygen-containing groups.     

Current-induced conformational switching in single-molecule junctions

Current-induced conformational switching in single-molecule junctions constitutes a fundamental process in molecular electronics. Motivated by recent experiments on azobenzene derivatives, we study this process for molecules which exhibit two (meta)stable conformations in the neutral state but only a single stable conformation in the ionic state. We derive and analyze appropriate Fokker–Planck equations obtained from a density-matrix formalism starting from a generic model and present comprehensive analytical and numerical results for the switching dynamics in general and the quantum yield in particular.     

稀土离子Tb3+与拟南芥钙调素相互作用的荧光光谱及分析应用

钙调素 (CaM)是一种普遍存在的钙受体蛋白 ,它调节了许多细胞生物学功能。钙调素分子有 4个金属结合位点 ,而植物钙调素Ⅰ ,Ⅱ ,Ⅲ位点不含酪氨酸残基 ,只有第 4位点含一个酪氨酸残基。与动物体不同的是 ,植物能表达多种功能不同的钙调素亚型。文章利用Tb3 荧光探针 ,采用直接激发 ( 2 2 1nm)或敏化激发 ( 2 80nm)并测量 5 4 5nm处的荧光发射强度 ,研究拟南芥CaM与Tb3 的结合作用及分析应用。直接激发 ( 2 2 1nm)Tb3 CaM络合物时 ,Tb3 的发光显著增强 ,这归因于CaM中配位基取代了Tb3 的配位水分子 ,从而导致荧光速率常数增加。直接激发滴定曲线中 ,当cTb3 /cCaM <4时 ,荧光强度呈不断上升的直线 ,之后出现平台区 ,这与CaM只结合 4个钙离子的结论一致。而间接激发滴定曲线近似为S型 ,且荧光强度较弱 ;其中当cTb3 /cCaM≤ 2时 ,荧光强度增加较弱 ;当 2 相似文献   

Current–Voltage Characteristics of the Aziridine-Based Nano-Molecular Wires: a Light-Driven Molecular Switch

Using nonequilibrium Green's function formalism combined first-principles density functional theory, we analyze the transport properties of a 4,4-dimethyl-6-(4-nitrophenyl)-2-phenyl-3,5-diaza-bicyclo[3.1.0]hex-2-ene molecular optical switch. The title molecule can convert between closed and open forms by visible or ultraviolet irradiation. The I-V characteristics, differential conductance, on-off ratio, electronic transmission coefficients, spatial distribution of molecular projected self-consistent Hamiltonian orbitals, HOMO-LUMO gaps, effect of electrode materials Y(111)(Y =Au, Ag and Pt) on electronic transport and different molecular geometries corresponding to the closed and open forms through the molecular device are discussed in detail. Based on the results, as soon as possible the open form translates to the closed form, and there is a switch from the ON state to the OFF state(low resistance switches to high resistance). Theoretical results show that the donor/acceptor substituent plays an important role in the electronic transport of molecular devices. The switching performance can be improved to some extent through suitable donor and acceptor substituents.     

铽离子发光探针研究pH诱导的植物钙调素构象变化

利用脱钙钙调素(apo-CaM),Tb.CaM和Ca.CaM系统的荧光光谱及酪氨酸-铽离子(Tyr-Tb3 )敏化荧光光谱,研究了pH诱导钙调素构象的改变.随着pH值的降低,apo-CaM的荧光强度下降并出现蓝移,Ca.CaM系统的荧光强度较Tb.CaM下降显著,Tyr-Tb3 敏化荧光光谱也有相当程度的降低.对荧光强度的变化与钙调素分子结构和构象的关系和pH诱导钙调素构象改变的机理作了详细的解释,H 可通过与Ca2 和Tb3 产生竞争结合,影响金属离子与钙调素的结合作用,还可以通过正电相斥或与肽链上带负电荷原子相结合而使CaM分子的极性增强,改变CaM表面的疏水性,降低CaM的活性.文章对pH诱导钙调素构象改变在胞外钙调素信号转导机制中的重要意义进行了阐述.     

Influence of amphotericin B on liquid crystal state of the Cholesterol/Dipalmitoylphosphatidylcholine monolayer in the presence of different metal cations

Amphotericin B is a very effective antifungal drug,but it has an adverse reaction to the membrane of mammals' cells.The interaction between Am B and cholesterol(Chol) causes the formation of pores on the membrane to destroy its integrity.In particular,Am B has a significant effect on the permeability of membrane for K~+ions.It has been reported that Na+ions and Ca~(2+)ions may have some influence on the interaction between amphotericin B and lipid molecules.In this work,the effects of these metal cations on the physical state and intermolecular interaction of the Cholesterol/Dipalmitoylphosphatidylcholine(Chol/DPPC) monolayer with and without Am B have been investigated.The addition of Am B induces the change of physical state of the lipid monolayer from liquid-gel phase to liquid phase.Different metal cations could influence the phase transition of the Am B-lipid monolayer.The K~+ions and Ca2+ions make the obvious phase transition disappear.However,the presence of Na+ions has little influence on the phase transition of the Am B-lipid monolayer.The addition of Am B and the presence of different metal cations weaken the attractive force on the monolayers.After addition of Am B,the force between the molecules is the strongest in the environment of K+ions,thus is the weakest in the environment of Ca~(2+)ions,which may be due to the distribution of these metal cations inside and outside of cells.A large number of K+ions distribute inside of the cells,thus most of Na+and Ca~(2+)ions exist out of the cells.Hence,it may be possible that when Am B molecules are out of the cells,the reaction between the drug and lipid molecules is weaker than that inside the cells.These results may have a great reference value for further studying the toxicity mechanism of Am B and the influence of metal cations on the membrane.     

The alternating access mechanism of transport as observed in the sodium-hydantoin transporter Mhp1

Secondary active transporters move molecules across cell membranes by coupling this process to the energetically favourable downhill movement of ions or protons along an electrochemical gradient. They function by the alternating access model of transport in which, through conformational changes, the substrate binding site alternately faces either side of the membrane. Owing to the difficulties in obtaining the crystal structure of a single transporter in different conformational states, relatively little structural information is known to explain how this process occurs. Here, the structure of the sodium-benzylhydantoin transporter, Mhp1, from Microbacterium liquefaciens, has been determined in three conformational states; from this a mechanism is proposed for switching from the outward-facing open conformation through an occluded structure to the inward-facing open state.     

Nonlinear signal transduction network with multistate

Signal transduction is an important and basic mechanism to cell life activities. The stochastic state transition of receptor induces the release of signaling molecular, which triggers the state transition of other receptors. It constructs a nonlinear sigaling network, and leads to robust switchlike properties which are critical to biological function. Network architectures and state transitions of receptor affect the performance of this biological network. In this work, we perform a study of nonlinear signaling on biological polymorphic network by analyzing network dynamics of the Ca²⁺-induced Ca²⁺ release (CICR) mechanism, where fast and slow processes are involved and the receptor has four conformational states. Three types of networks, Erdös-Rényi (ER) network, Watts-Strogatz (WS) network, and BaraBási-Albert (BA) network, are considered with different parameters. The dynamics of the biological networks exhibit different patterns at different time scales. At short time scale, the second open state is essential to reproduce the quasi-bistable regime, which emerges at a critical strength of connection for all three states involved in the fast processes and disappears at another critical point. The pattern at short time scale is not sensitive to the network architecture. At long time scale, only monostable regime is observed, and difference of network architectures affects the results more seriously. Our finding identifies features of nonlinear signaling networks with multistate that may underlie their biological function.     

Chaos control in biological system using recursive backstepping sliding mode control

This paper puts forward the control of chaos in the biological system. A new controller based on recursive backstepping sliding mode control is proposed such that it can control the chaotic dynamics in the biological system to stabilize at any position or to track any trajectory that is a smooth function of time. A proportional integral switching surface is proposed to achieve the stability condition of the error dynamics. Unlike the open loop and open plus closed loop control techniques, the design of proposed controller does not require the parameter perturbation. The required stability condition is derived based on Lyapunov stability theory. Simulation is achieved in MATLAB environment. Numerical simulation results are presented in order to show the effective verification of the proposed controller design. Simulation results correspond that the objective of chaos control is achieved successfully.     

Photoinduced reversible changes in the electronic structure of photochromic diarylethene films

The change in the valence electronic structure upon switching of two photochromic diarylethene derivatives, i.e. 1,2-bis(2-methyl-5-p-tolylthiophen-3-yl)cyclopent-1-ene (DAE1) and 1,2-bis(5-(4-hexyloxycarbonylphenyl)-2-methylthiophen-3-yl)cyclopent-1-ene (DAE2), was measured by photoelectron spectroscopy. Switching between open and closed forms was followed in situ upon illumination. The increase of the ionization energy from the closed to the open form was 0.85 eV for DAE1 and 0.80 eV for DAE2. For DAE1, the work function also decreased by 0.25 eV upon switching, which is explained by a decrease of the intrinsic molecular dipole moment and a preferential orientation of molecules in thin films.     

From molecular flexibility to shape, curvature and thermotropic transitions in pure surfaces

A material surface of pure constituents with a flexible molecular chain (amphiphilics) is considered; thermodynamic behaviour is studied in the chain length-temperature plane. The Hamiltonian of the system is modelled as the sum of a formation term which refers to the polymer nature of the chain, and of a fluctuation term with a specific elastic form. For closed systems the model exhibits phases with uniform curvature and conformational order/disorder or, alternatively, modulated phases; a critical chain length is found for the existence of modulated phases; the dependence of transition temperature on energy parameters is determined. A critical region is found for open systems, where conformational disorder drives spontaneous generation of curvature; this lies above a characteristic chain length and around the shape transition temperature. Received: 13 November 1996 / Revised: 9 May 1997 / Received in final form: 4 November 1997 / Accepted: 10 November 1997     

Effect of electrolyte concentration on DNA A—B conformational transition:An unrestrained molecular dynamics simulation study

<正>The DNA conformational transition depends on both the DNA sequences and environment such as solvent as well as electrolyte in the solution.This paper uses the AMBER8 package to investigate the electrolyte concentration influence on the dynamics of the A→B conformational transition of DNA duplex d(CGCGAATTCGCG)_2.The results from the restrained molecular dynamics(MD) simulations indicate that the total energies of the systems for A-DNA are always higher than those for B-DNA,and that the A→B conformational transition in aqueous NaCl solution is a downhill process.The results from the unrestrained MD simulations,as judged by the average distance between the C5' atoms(average helical rise per ten base pair),show that the concentrated NaCl solution slows down the A→B conformational transition.This observation can be well understood by analyses of the difference between the counterion distributions around A-DNA and B-DNA.     

Tm(3+)/Ho(3+) codoped tellurite fiber laser

Continuous-wave and Q-switched lasing from a Tm(3+)/Ho(3+) codoped tellurite fiber is reported. An Yb(3+)/Er(3+)-doped silica fiber laser operating at 1.6 microm was used as an in-band pump source, exciting the Tm(3+) ions into the (3)F(4) level. Energy is then nonradiatively transferred to the upper laser level, the (5)I(7) state of Ho(3+). The laser transition is from the (5)I(7) level to the (5)I(8) level, and the resulting emission is at 2.1 microm. For continuous wave operation, the slope efficiency was 62% and the threshold 0.1 W; the maximum output demonstrated was 0.16 W. Mechanical Q switching resulted in a pulse of 0.65 microJ energy and 160 ns duration at a repetition rate of 19.4 kHz.     

Interface water-induced hydrophobic carbon chain unfolding in water

The folding and unfolding of the carbon chain, which is the basic constitutional unit of polymers,are important to the performance of the material. However, it is difficult to regulate conformational transition of the carbon chain, especially in an aqueous environment. In this paper, we propose a strategy to regulate the conformational transition of the carbon chain in water based on the all-atom molecular dynamics simulations. It is shown that the unfolded carbon chain will spontaneously collapse into the folded state, while the folded carbon chain will unfold with an external electric field. The regulation ability of the electric field is attributed to the electric field-induced redistribution of interface water molecules near the carbon chain. The demonstrated method of regulating conformational transition of the carbon chain in water in this study provides an insight into regulating hydrophobic molecules in water, and has great potential in drug molecule design and new polymer material development.     

类立方烷过渡金属簇合物(n-Bu4N)3[MoAg3BrI3S4]激发态寿命测量

本文在类立方烷过渡金属簇合物(n-Bu₄N)₃[MoAg₃BrI₃S₄]空气饱和乙氰溶液中实现了瞬态全光开关.由开关时间推断出这种材料的激发态寿命约600ns,约为C₆₀三重态第一激发态在空气饱和甲苯溶液中寿命的2倍.     

(Sr,Ca)4Si3O8Cl4基质中Eu2+的发光特性研究

采用高温固相法合成Sr4-xCaxSi3O8Cl4：Eu^2＋荧光材料,利用Van Uitert公式讨论Sr4-xCaxSi3O8Cl4：Eu^2＋中yEu^2＋的晶格环境和发光特性,确定晶体中有蓝色和黄绿色两种发光中心,并讨论了它们与光谱结构的对应关系。当0〈x〈0．5,Ca^2＋固溶入Sr4Si3O8Cl4基质晶格,Eu^2＋占据八配位Si^2＋格位,晶体主要产生蓝色中心的蓝绿色发射;当0．5〈x〈2,较大的Ca^2＋掺杂使晶胞参数变小,品格中的杂质束缚激子态的束缚增强,Eu^2＋处于杂质束缚激子中心所形成的激发态能量进一步降低,发射位于长波段方向并具有较大的Stokes位移,Sr4-xCaxSi3O8Cl4：yEu^2＋主要产生黄绿色中心的黄绿色发射光。     

Interpretation of protein structure and dynamics from the statistics of the open and closed times measured in a single ion-channel protein

Ion channels are proteins in the lipid cell membrane. They spontaneously fluctuate between conformational shapes that are open or closed to the passage of ions. The ionic currents through an individual channel can be resolved by the patch clamp technique. Thus, the time sequence of open and closed conformational states can be measured in one channel molecule. The probability density function of the dwell times in the open and closed states displays scaling functions that may arise from: (1) a large number of conformational substates having a continuous distribution of activation energy barriers, (2) time-dependent changes in the energy barriers between states, or (3) local interactions that constrain local structures which interact hierarchically to form global structure.