Theoretical electrical conductivity of hydrogen-bonded benzamide-derived molecules and single DNA bases

A benzamide molecule is used as a “reader” molecule to form hydrogen bonds with five single DNA bases, i.e., four normal single DNA bases A,T,C,G and one for 5methylC. The whole molecule is then attached to the gold surface so that a meta-molecule junction is formed. We calculate the transmission function and conductance for the five metal–molecule systems, with the implementation of density functional theory-based non-equilibrium Green function method. Our results show that each DNA base exhibits a unique conductance and most of them are on the pS level. The distinguishable conductance of each DNA base provides a way for the fast sequencing of DNA. We also investigate the dependence of conductivity of such a metal–molecule system on the hydrogen bond length between the “reader” molecule and DNA base, which shows that conductance follows an exponential decay as the hydrogen bond length increases, i.e., the conductivity is highly sensitive to the change in hydrogen bond length.     

Probing the effect of electric field in 9,10-dimethoxy-2,6-bis(2-p-tolylethynyl)anthracene molecular nanowire using quantum chemical and charge density analysis

The effect of electric field (EF) in a newly designed molecular nanowire 9,10-dimethoxy-2,6-bis(2-p-tolylethynyl)anthracene has been analysed theoretically from the structural and electronic charge transport properties using quantum chemical and charge density calculations. The applied EF (0–0.36 VÅ^? 1) alters the molecular conformation, charge density distribution, electrostatic properties and the electronic energy levels of the molecule. Furthermore, the applied EF decreases the highest occupied molecular orbital–lowest unoccupied molecular orbital gap significantly from 1.775 to 0.258 eV and it also induces polarisation in the molecule, which leads to increase the dipole moment of the molecule. The electrostatic potential for various levels of applied EF reveals the charge-accumulated regions of the molecule. The I–V characteristics of the molecule have been studied against various applied fields using Landauer formalism.     

Analysis of the electrophoretic migration of DNA frayed wires

We analyzed the electrophoretic behaviour of the unusual multi-stranded DNA complexes, frayed wires, in polyacrylamide gels under non-denaturing conditions. Frayed wires arise from the association of several strands of a parent oligonucleotide that possesses long terminal runs of consecutive guanines. According to the structural model proposed for frayed wires, there are two distinct conformational domains, a guanine stem and single stranded arms displaced from the stem. The presence of the two domains affects the electrophoretic migration of the frayed wires, resulting in a greater retardation compared to that of double stranded DNA of the same molecular weight. The degree of retardation is determined by the relative length of the stem and the arms; the complexes with longer arms display a stronger dependence on the total molecular weight. Reptation plots (mobility x molecular weight vs. molecular weight) were used to study the electrophoretic behaviour of frayed wires that arise from the different parent oligonucleotides. The plots are unique for each type of frayed wire. The characteristic parameter, the position of the maximum of the reptation plot, depends on the type of the frayed wire as well as the total gel concentration. The plots become similar when we replot the mobility data taking into account only the single stranded arms of the frayed wires. The positions of the maximum and the overall shape are very close for the four types of frayed wires studied.     

西南大西洋阿根廷滑柔鱼雄性个体的有效繁殖力特性研究

对西南大西洋阿根廷滑柔鱼(Illex argentinus)雄性个体的有效繁殖力特性, 以及有效繁殖力与个体生长发育关系进行了研究。结果表明, 阿根廷滑柔鱼雄性个体的胴长、体重的生物学最小型分别为207.79 mm和162.55 g; 个体有效繁殖力为(374±280.33)条精荚, 胴长相对有效繁殖力为(179.18±117.66)条/mm; 精荚的平均长度为(21.57±4.17) mm, 是胴长的(10.22±1.82)%。随着性腺发育, 个体有效繁殖力和精荚长度均增长显著(P<0.05), 前者在功能性成熟期达到最大值, 为(811±181.34)条精荚; 后者在繁殖产卵期达到最大值, 为(23.89±3.87) mm。同时, 个体有效繁殖力和精荚长度均与胴长、体重呈显著的线性函数关系(P<0.05)。回归拟合数据集比较分析和多元线性回归分析显示, 个体有效繁殖力与胴长、体重之间的线性关系不存在显著性差异(P>0.05), 但是体重对个体有效繁殖力的影响更为显著(P<0.001); 精荚长度与胴长、体重之间的线性关系存在显著性差异(P<0.001), 并且胴长、体重两者对精荚长度具有一致的影响效应(P<0.001)。以上结果表明, 阿根廷滑柔鱼雄性个体随着性腺发育持续产生并存储精荚, 精荚长度也随之显著增加, 并且与个体大小密切相关。     

叶肉细胞导度研究进展

叶肉细胞导度指叶片叶肉细胞内部的CO2扩散能力,在植物生理生态及全球气候变化和陆地生态系统相互关系的研究中具有重要作用。系统介绍了叶肉细胞导度的发现、发展过程及其研究进展、几种目前国际上常用的叶肉细胞导度测度方法的原理、计算过程;强调了叶肉细胞导度作为光合作用扩散过程一部分的重要意义,明确了叶肉细胞导度的定义及分布范围。并探讨了不同方法的优缺点及注意事项。总结分析了叶肉细胞导度对不同环境因子(温度、水分及环境中CO2和O3浓度等)的响应,从不同角度对叶肉细胞导度的生态学意义进行了简单的概括。对叶肉细胞导度的未来研究进行了展望。     

Pressure dependence on electronic structures,charge distribution and bond orders of solid nitromethane using nonlocal DFT functional

The electronic properties of solid nitromethane are studied using nonlocal exchange-correlation functional (optPBE–vdW) under hydrostatic compression up to 40?GPa. We found that the optPBE–vdW functional can reproduce well the crystalline structures compared with the experiments, and an isomorphic phase transition has been verified by their P–V curve. Bader’s charge analysis shows the electron flows from CH₃ group to NO₂ group with the pressure. Moreover, the calculated bond orders show that the pressure only strengthens the intermolecular C–N bond and intermolecular C–H···O hydrogen bonds though it shortens all bond lengths. Furthermore, the electronic structure and its pressure dependence have also been discussed in detail.     

Molecular dynamics study of methane in water: diffusion and structure

In this study, theoretical analysis on the geometries and electronic properties of various conjugated oligomers based on thiophene (Th) or bicyclic non-classical Th units is reported. The dihedral angle, bond length, bond-length alternation, bond critical point (BCP) properties, nucleus-independent chemical shift (NICS) and Wiberg bond index (WBIs) are analysed and correlated with conduction properties. The changes of bond length, BCP properties, NICS and WBIs all show that the conjugational degree is increased systematically with main chain extension. As a result, the highest occupied molecular orbital–lowest unoccupied molecular orbital energy separation (E _g) is decreased upon chain elongation. The E _g of oligomers based on bicyclic non-classical Th unit is much lower than that of Th-based oligomers due to the narrower E _g of bicyclic non-classical Ths compared to Th, which indicates that the narrow E _g of the bicyclic non-classical Ths can be carried over to their polymers by using them as building blocks for the polymers. The band structures and density of states analysis show that the four polymers all have small band gap ( < 0.9 eV), wide highest occupied bandwidth and relatively small effective mass of hole, which indicate that those proposed polymers may be potential conductors.     

Determinants of conductance of a bacterial voltage-gated sodium channel

Through molecular dynamics (MD) and free energy simulations in electric fields, we examine the factors influencing conductance of bacterial voltage-gated sodium channel Na_vMs. The channel utilizes four glutamic acid residues in the selectivity filter (SF). Previously, we have shown, through constant pH and free energy calculations of pKa values, that fully deprotonated, singly protonated, and doubly protonated states are all feasible at physiological pH, depending on how many ions are bound in the SF. With 173 MD simulations of 450 or 500 ns and additional free energy simulations, we determine that the conductance is highest for the deprotonated state and decreases with each additional proton bound. We also determine that the pKa value of the four glutamic residues for the transition between deprotonated and singly protonated states is close to the physiological pH and that there is a small voltage dependence. The pKa value and conductance trends are in agreement with experimental work on bacterial Na_v channels, which show a decrease in maximal conductance with lowering of pH, with pKa in the physiological range. We examine binding sites for Na⁺ in the SF, compare with previous work, and note a dependence on starting structures. We find that narrowing of the gate backbone to values lower than the crystal structure's backbone radius reduces the conductance, whereas increasing the gate radius further does not affect the conductance. Simulations with some amount of negatively charged lipids as opposed to purely neutral lipids increases the conductance, as do simulations at higher voltages.     

DNA frayed wires: Differential polymerization of d(AnGm) oligonucleotides

Oligodeoxyribonucleotides with terminal runs of contiguous guanines, d(A_nG_m), spontaneously associate into high molecular weight complexes that resolve on polyacrylamide gels as a regular ladder pattern of bands with low mobility. The aggregates, which we call frayed wires, arise from the interaction between the guanine residues of the oligonucleotides; the adenine tracts are single stranded and can take part in Watson–Crick interactions. Oligonucleotides, with different arm‐to‐stem ratios and total length, readily associate in the presence of Mg²⁺ to form aggregates consisting of an integer number of strands. The type of the observed aggregates is determined by the length of the guanine run. Oligonucleotides with six guanines form four‐ and eight‐stranded complexes; there is no further polymerization. An increase in the number of guanine residues to 10 and 15 leads to polymerization resulting in a ladder pattern of up to 9 bands and an intense signal at the top of the gel. The relative population of any given species in a frayed wire sample is governed by the guanine stem length and is not affected to any substantial extent by arms up to 40 bases long. The type and concentration of the cation in the solution affect the degree of aggregation, with Na⁺ and K⁺ promoting the formation of complexes comprised of 2–4 strands and Mg²⁺ being the most effective in facilitating polymerization. The electrophoretic behavior of frayed wires was analyzed in the framework of the Ogston theory. The free mobility of frayed wires in the solution is close to the values reported for single‐stranded DNA, indicating the equivalence of the charge density of the two conformations. The retardation coefficients for frayed wires arising from a single kind of parent strand increase with the introduction of each additional strand. There is no correlation between the retardation coefficient and the type of parent strand; rather, the magnitude of the retardation coefficient is determined by the total molecular weight of the complex. The values of the retardation coefficients are consistently higher than those for double‐stranded DNA and they display much stronger dependence on the total molecular weight. Presumably, the distinct structural and dynamic characteristics of the two conformations account for their different electrophoretic behavior. © 1999 John Wiley & Sons, Inc. Biopoly 49: 287–295, 1999     

Conformation-dependent conductance through a molecular break junction

Ab initio molecular dynamics simulations have been performed of a gold—1,4-benzenedithiol (BDT)—gold nanojunction under mechanical stress. For three different pulling rates between 10 and 40 m s^-1, it is found that the nanowire always ruptures between the second and third Au atom from the thiol sulfur. Larger rupture forces and longer extensions are required at higher pulling rates and vice versa. The electrical conductance was calculated along a pulling trajectory using the DFT-NEGF method to study the effect of thermal and stress-induced structural changes on the electrical transport properties. While the mechanically induced stretching of the junction is seen to lower the time-averaged conductance, thermal conformational changes are capable of altering the conductance by one order of magnitude. No single geometric quantity could be identified as the main contributor to the conductance fluctuations. Small modulations, however, can be explained in terms of C=C double bond vibrations in the BDT molecule. The dependence of the conductance on different geometric variables has further been investigated systematically by performing constrained geometry optimizations along a number of angle and dihedral coordinates. The largest changes in the conductance are observed when the Au-S-C angle and the Au-S-C-C dihedral are simultaneously constrained.

The molecular density of states in bacterial nanowires

The recent discovery of electrically conductive bacterial appendages has significant physiological, ecological, and biotechnological implications, but the mechanism of electron transport in these nanostructures remains unclear. We here report quantitative measurements of transport across bacterial nanowires produced by the dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1, whose electron transport system is being investigated for renewable energy recovery in microbial fuel cells and bioremediation of heavy metals and radionuclides. The Shewanella nanowires display a surprising nonlinear electrical transport behavior, where the voltage dependence of the conductance reveals peaks indicating discrete energy levels with higher electronic density of states. Our results indicate that the molecular constituents along the Shewanella nanowires possess an intricate electronic structure that plays a role in mediating transport.     

Molecular and functional properties of the psychrophilic elongation factor G from the Antarctic Eubacterium <Emphasis Type="Italic">Pseudoalteromonas haloplanktis</Emphasis> TAC 125

The molecular and functional properties of the elongation factor (EF) G from the psychrophilic Antarctic eubacterium Pseudoalteromonas haloplanktis (Ph) were studied. PhEF-G catalyzed protein synthesis in vitro that was inhibited by fusidic acid, an antibiotic specifically acting on EF-G. The EF interacted with GDP only in the presence of P. haloplanktis ribosome and fusidic acid with an affinity similar to that displayed by Escherichia coli EF-G. The psychrophilic translocase elicited a ribosome-dependent GTPase that was competitively inhibited by GDP, the slowly hydrolyzable GTP analog GppNHp, and the protein synthesis inhibitor ppGDP. The temperature dependence of the activity of PhEF-G reached its maximum at least 26°C beyond the growth temperature of P. haloplanktis (4–20°C). The heat inactivation profile of the ribosome-dependent GTPase of PhEF-G gave a temperature for half inactivation (46°C), significantly lower than that for half denaturation measured by either UV- (57°C) or fluorescence-melting (62°C). This finding was attributed to a different effect of the temperature on the catalytic domain with respect to that elicited on the other domains constituting the EF, thus confirming the differential molecular flexibility present in psychrophilic enzymes. A molecular model, based on the 3D coordinates of a thermophilic EF-G, showed differences only in connecting loops. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Intermediate state trapping of a voltage sensor

Voltage sensor domains (VSDs) regulate ion channels and enzymes by undergoing conformational changes depending on membrane electrical signals. The molecular mechanisms underlying the VSD transitions are not fully understood. Here, we show that some mutations of I241 in the S1 segment of the Shaker Kv channel positively shift the voltage dependence of the VSD movement and alter the functional coupling between VSD and pore domains. Among the I241 mutants, I241W immobilized the VSD movement during activation and deactivation, approximately halfway between the resting and active states, and drastically shifted the voltage activation of the ionic conductance. This phenotype, which is consistent with a stabilization of an intermediate VSD conformation by the I241W mutation, was diminished by the charge-conserving R2K mutation but not by the charge-neutralizing R2Q mutation. Interestingly, most of these effects were reproduced by the F244W mutation located one helical turn above I241. Electrophysiology recordings using nonnatural indole derivatives ruled out the involvement of cation-Π interactions for the effects of the Trp inserted at positions I241 and F244 on the channel’s conductance, but showed that the indole nitrogen was important for the I241W phenotype. Insight into the molecular mechanisms responsible for the stabilization of the intermediate state were investigated by creating in silico the mutations I241W, I241W/R2K, and F244W in intermediate conformations obtained from a computational VSD transition pathway determined using the string method. The experimental results and computational analysis suggest that the phenotype of I241W may originate in the formation of a hydrogen bond between the indole nitrogen atom and the backbone carbonyl of R2. This work provides new information on intermediate states in voltage-gated ion channels with an approach that produces minimum chemical perturbation.     

不同生长阶段遮荫对番茄光合作用、干物质分配与叶N、P、K的影响

对番茄植株做了两种不同程度的遮荫处理,观测了夏季午间遮荫对光合速率,干物质积累量及其在根,茎,叶之间的分配,和叶N,P,K的含量以及经济产量的影响,发现不同时期遮荫影响不同。（1）遮荫增加三个阶段（开花早期,盛花期和开花后期）的气孔导度和胞间CO2浓度,显著降低开花早期中午的净化合速率,但盛花期中度遮荫（40%遮荫）使净光合速率随着时间的增加逐渐上升,在开花后期表现更加明显,平均净光合速率比对照高20%以上,蒸腾速率也增加较多。（2）开花早期和盛花期重度遮荫（如本实验中的75%遮荫）显著降低根,茎的干重,而开花后期中度遮荫的根,茎干重高于对照,但遮荫对叶干重的影响不明显。（3）开花早期和盛花期遮荫不明显影响叶片中N,P,K的含量,但开花后期中度遮荫使N,P,K含量增加,（4）开花早期两种遮荫对果实产量影响较小,但盛花期重度遮荫使产量降低,全部产量中无效部分所占的比例上升,开花后期中度遮荫的总产量和有效产量增加,单果重也增加,这些结果表明,在某些时期中度遮荫可以克服夏天辐射过强,气温过高对番茄的不良影响,对番茄生长,干物质积累和提高产量等有利,在生产上有意义。     

MD Simulations of Anthrax Edema Factor: Calmodulin Complexes with Mutations in the Edema Factor “Switch A” Region and Docking of 3′-deoxy ATP into the Adenylyl Cyclase Active Site of Wild-Type and Mutant Edema Factor Variants

Abstract

Bacillus anthracis, a spore-forming infectious bacterium, produces an exotoxin, called the edema factor (EF), that functions in part by disrupting internal signalling pathways. When complexed with human host cell calmodulin (CaM), EF becomes an active adenylyl cyclase, producing the internal signal substance cyclic-AMP in an uncontrolled fashion. Recently, the crystal structures for uncomplexed EF and EF:CaM complexes in the presence and absence of a substrate analog (3′-deoxy-ATP), were reported. EF mutational studies have implicated a number of residues important in CaM binding and/or in the generation of the adenylyl cyclase active site, formed by the movements of the EF switch A, B and C regions upon CaM binding. Here we report on the results of molecular dynamics (MD) simulations on two EF:CaM complexes, one containing wild-type EF and the other containing EF in which a cluster of residues in the switch A region (L523, K525, Q526 and V529) have been mutated to alanine. The switch A mutations cause a large increase in the flexibility of the switch C region, the rupture of a number of EF-CaM interactions, an expansion of the car-boxyl-terminal domain of CaM, and a change in the Ca²⁺ ion binding abilities of the CaM that is in complex with EF. The results indicate the importance of the mutated switch A residues in maintaining a compact EF:CaM complex that appears to be a prerequisite for the generation of a fully-functional adenylyl cyclase active site. The effects of mutating key residues (K346, K353, H577, E588, D590 and N639) in the active site region of EF (to alanine) on the ability of EF to bind the 3′-deoxy-ATP substrate analog were also examined. Active-site residue substitutions at positions 583 (N583A) and 577 (H577A) were found to be particularly distruptive for the placement of the adenine ring moiety into the position found in the x-ray crystal structure of the ligand-protein complex.     

A simple method for the determination of the pore radius of ion channels in planar lipid bilayer membranes

Abstract A new method of pore size determination is presented. The results of applying this simple method to ion channels formed by staphylococcal α-toxin and its N-terminal fragment as well as to cholera toxin channels are shown. The advantages and the difficulties of this method are discussed. It was found that (i) the mobility of ions in solutions depends only on the percentage of concentration of added non-electrolytes and practically not on their chemical nature (sugars or polyglycols) and molecular size; (ii) the proportional change of both ion channel conductance and bulk solution conductivity by low M . non-electrolytes may be used as an indication of a diffusion mechanism of ion transport through channels; (iii) the slope of the dependence of the ion channel conductance on the bulk conductivity of solutions containing different concentrations of non-electrolyte is a good measure of channel permeability for non-electrolytes.     

Hydrogen bonds in galactopyranoside and glucopyranoside: a density functional theory study

Density functional theory calculations on two glycosides, namely, n-octyl-β-D-glucopyranoside (C₈O-β-Glc) and n-octyl-β-D-galactopyranoside (C₈O-β-Gal) were performed for geometry optimization at the B3LYP/6-31G level. Both molecules are stereoisomers (epimers) differing only in the orientation of the hydroxyl group at the C4 position. Thus it is interesting to investigate electronically the effect of the direction (axial/equatorial) of the hydroxyl group at the C4 position. The structure parameters of X-H???Y intramolecular hydrogen bonds were analyzed, while the nature of these bonds and the intramolecular interactions were considered using the atoms in molecules (AIM) approach. Natural bond orbital analysis (NBO) was used to determine bond orders, charge and lone pair electrons on each atom and effective non-bonding interactions. We have also reported electronic energy and dipole moment in gas and solution phases. Further, the electronic properties such as the highest occupied molecular orbital, lowest unoccupied molecular orbital, ionization energy, electron affinity, electronic chemical potential, chemical hardness, softness and electrophilicity index, are also presented here for both C₈O-β-Glc and C₈O-β-Gal. These results show that, while C₈O-β-Glc possess– only one hydrogen bond, C₈O-β-Gal has two intramolecular hydrogen bonds, which further confirms the anomalous stability of the latter in self-assembly phenomena.     

Vacuum-ultraviolet photochemically initiated modification of polystyrene surfaces: morphological changes and mechanistic investigations.

Vacuum-ultraviolet (VUV) irradiation (lambda(exc): 172 +/- 12 nm) of polystyrene films in the presence of oxygen produced not only oxidatively functionalized surfaces, but generated also morphological changes. Whereas OH- and C[double bond, length as m-dash]O-functionalized surfaces might be used for e.g. secondary functionalization, enhanced aggregation or printing, processes leading to morphological changes open new possibilities of microstructurization. Series of experiments made under different experimental conditions brought evidence of two different reaction pathways: introduction of OH- and C[double bond, length as m-dash]O-groups at the polystyrene pathways is mainly due to the reaction of reactive oxygen species (hydroxyl radicals, atomic oxygen, ozone) produced in the gas phase between the VUV-radiation source and the substrate. However, oxidative fragmentation leading to morphological changes, oxidation products of low molecular weight and eventually to mineralization of the organic substrate is initiated by electronic excitation of the polymer leading to C-C-bond homolysis and to a complex oxidation manifold after trapping of the C-centred radicals by molecular oxygen. The pathways of oxidative functionalization or fragmentation could be differentiated by FTIR-ATR analysis of irradiated polystyrene surfaces before and after washing with acetonitrile and microscopic fluorescence analysis of the surfaces secondarily functionalized with the N,N,N-tridodecyl-triaza-triangulenium (TATA) cation. Ozonization of the polystyrene leads to oxidative functionalization of the polymer surface but cannot initiate the fragmentation of the polymer backbone. Oxidative fragmentation is initiated by electronic excitation of the polymer (contact-mode AFM analysis), and evidence of the generation of intermediate C-centred radicals is given e.g. by experiments in the absence of oxygen leading to cross-linking (solubility effects, optical microscopy, friction-mode AFM) and disproportionation (fluorescence).     

Structural Study of Cell Attachment Peptide Derived from Laminin by Molecular Dynamics Simulation

Peptides with cell attachment activity are beneficial component of biomaterials for tissue engineering. Conformational structure is one of the important factors for the biological activities. The EF1 peptide (DYATLQLQEGRLHFMFDLG) derived from laminin promotes cell spreading and cell attachment activity mediated by α2β1 integrin. Although the sequence of the EF2 peptide (DFATVQLRNGFPYFSYDLG) is homologous sequence to that of EF1, EF2 does not promote cell attachment activity. To determine whether there are structural differences between EF1 and EF2, we performed replica exchange molecular dynamics (REMD) simulations and conventional molecular dynamics (MD) simulations. We found that EF1 and EF2 had β-sheet structure as a secondary structure around the global minimum. However, EF2 had variety of structures around the global minimum compared with EF1 and has easily escaped from the bottom of free energy. The structural fluctuation of the EF1 is smaller than that of the EF2. The structural variation of EF2 is related to these differences in the structural fluctuation and the number of the hydrogen bonds (H-bonds). From the analysis of H-bonds in the β-sheet, the number of H-bonds in EF1 is larger than that in EF2 in the time scale of the conventional MD simulation, suggesting that the formation of H-bonds is related to the differences in the structural fluctuation between EF1 and EF2. From the analysis of other non-covalent interactions in the amino acid sequences of EF1 and EF2, EF1 has three pairs of residues with hydrophobic interaction, and EF2 has two pairs. These results indicate that several non-covalent interactions are important for structural stabilization. Consequently, the structure of EF1 is stabilized by H-bonds and pairs of hydrophobic amino acids in the terminals. Hence, we propose that non-covalent interactions around N-terminal and C-terminal of the peptides are crucial for maintaining the β-sheet structure of the peptides.