Molecular dynamics simulations of DNA in solutions with different counter-ions

Molecular dynamics simulations of the [d(ATGCAGTCAG]2 fragment of DNA, in water and in the presence of three different counter-ions (Li+, Na+ and Cs+) are reported. Three-dimensional hydration structure and ion distribution have been calculated using spatial distribution functions for a detailed picture of local concentrations of ions and water molecules around DNA. According to the simulations, Cs+ ions bind directly to the bases in the minor groove, Na+ ions bind prevailing to the bases in the minor groove through one water molecule, whereas Li+ ions bind directly to the phosphate oxygens. The different behavior of the counter-ions is explained by specific hydration structures around the DNA and the ions. It is proposed how the observed differences in the ion binding to DNA may explain different conformational behavior of DNA. Calculated self-diffusion coefficients for the ions agree well with the available NMR data.     

Affecting proton mobility in activated peptide and whole protein ions via lysine guanidination

We have evaluated the effect of lysine guanidination in peptides and proteins on the dissociation of protonated ions in the gas phase. The dissociation of guanidinated model peptide ions compared to their unmodified forms showed behavior consistent with concepts of proton mobility as a major factor in determining favored fragmentation channels. Reduction of proton mobility associated with lysine guanidination was reflected by a relative increase in cleavages occurring C-terminal to aspartic acid residues as well as increases in small molecule losses. To evaluate the effect of guanidination on the dissociation behavior of whole protein ions, bovine ubiquitin was selected as a model. Essentially, all of the amide bond cleavages associated with the +10 charge state of fully guanidinated ubiquitin were observed to occur C-terminal to aspartic acid residues, unlike the dissociation behavior of the +10 ion of the unmodified protein, where competing cleavage N-terminal to proline and nonspecific amide bond cleavages were also observed. The +8 and lower charge states of the guanidinated protein showed prominent losses of small neutral molecules. This overall fragmentation behavior is consistent with current hypotheses regarding whole protein dissociation that consider proton mobility and intramolecular charge solvation as important factors in determining favored dissociation channels, and are also consistent with the fragmentation behaviors observed for the guanidinated model peptide ions. Further evaluation of the utility of condensed phase guanidination of whole proteins is necessary but the results described here confirm that guanidination can be an effective strategy for enhancing C-terminal aspartic acid cleavages. Gas phase dissociation exclusively at aspartic acid residues, especially for whole protein ions, could be useful in identifying and characterizing proteins via tandem mass spectrometry of whole protein ions.     

Selected biologically relevant ions at the air/water interface: a comparative molecular dynamics study

Interfacial behavior of selected biologically and technologically relevant ions is studied using molecular dynamics simulations employing polarizable potentials. Propensities of choline, tetraalkylammonium (TAA), and sodium cations, and sulfate and chloride anions for the air/water interface are analyzed by means of density profiles. Affinity of TAA ions for the interface increases with their increasing hydrophobicity. Tetramethylammonium favors bulk solvation, whereas cations with propyl and butyl chains behave as surfactants. The choice of counter-anions has only a weak effect on the behavior of these cations. For choline, sodium, chloride and sulfate, the behavior at the air/water interface was compared to the results of our recent study on the segregation of these ions at protein surfaces. No analogy between these two interfaces in terms of ion segregation is found.     

Amino acid side chain interaction with chelate-liganded crosslinked dextran, agarose and TSK gel. A mini review of recent work.

Protein adsorption and retention data collected from recent chromatographic studies on hydrophilic gels substituted with chelate-bonded metal ions are discussed. Attempts are made to interpret the adsorption behavior in terms of molecular events caused by the affinity for the immobilized metal ions.     

Dissecting the metal ion dependence of DNA binding by PvuII endonuclease.

Divalent cations can provide an effective means of modulating the behavior of nucleic acid binding proteins. As a result, there is strong interest in understanding the role of metal ions in the function of both nucleic acid binding proteins and their enzymes. We have applied complementary fluorescence spectroscopic and nitrocellulose filter binding assays to quantitate the role of metal ions in mediating DNA binding and sequence specificity by the representative PvuII endonuclease. At pH 7.5 in the presence of the catalytically nonsupportive Ca(II), this enzyme binds the PvuII target sequence with a K(d) of 50 pM. Under strict metal-free conditions, the enzyme exhibits a K(d) of only 300 nM for the cognate sequence, an affinity which is weak relative to those measured for other systems in the absence of metal ions. This represents a 6000-fold increase in PvuII affinity for cognate DNA upon the addition of Ca(II). The pH dependences of both metal ion-dependent and metal ion-independent DNA binding are remarkably shallow throughout the physiological range; other characterized restriction enzymes exhibit more pronounced pH dependences of DNA binding even in the absence of metal ions. Similar measurements with noncognate sequences indicate that divalent metal ions are not important to nonspecific DNA binding; K(d) values are approximately equal to 200 nM throughout the physiological pH range, a behavior shared with other endonucleases. While some of these results extend somewhat the range of expected behavior for restriction enzymes, these results indicate that PvuII endonuclease shares with other characterized systems a mechanism by which cognate affinity and sequence discrimination are most effectively achieved in the presence of divalent metal ions.     

A comparison of the influence of potassium and ammonium ions on the phosphofructokinases from rabbit muscle and rat erythrocytes.

Phosphofructokinases from rat erythrocytes and rabbit muscle have been compared in their kinetic behavior with respect to monovalent cation activation and ATP inhibition. Both ammonium and potassium ions affect the muscle enzyme in a two-fold manner: they act both as activators and effectors. On the other hand only ammonium exerts the two-fold effects on the erythrocyte enzyme, while the potassium ions activate without affecting cooperativity. The lower ATP inhibition of muscle phosphofructokinase may be partially explained by the action of potassium ions on the cooperative behavior of the enzyme. The differences between the phosphofructokinases from erythrocytes and muscle in the potassium type-II activation and ATP inhibition represent an organ specifity. Furthermore, the inhibition constants for 2, 3-bisphosphoglycerate differ by 10-fold between the two enzymes.     

The polyelectrolyte behavior of actin filaments: a 25Mg NMR study.

Under physiological conditions, filamentous actin (F-actin) is a polyanionic protein filament. Key features of the behavior of F-actin are shared with other well-characterized polyelectrolytes, in particular, duplex DNA. For example, the bundle formation of F-actin by polyvalent cations, including divalent metal ions such as Mg2+, has been proposed to be a natural consequence of the polyelectrolyte nature of actin filaments [Tang and Janmey (1996) J. Biol. Chem. 271, 8556-8563]. This recently proposed model also suggests that weak interactions between F-actin and Mg2+ ions reflect a nonspecific trapping of counterions in the electric field surrounding F-actin due to its polyelectrolyte nature. To test this hypothesis, we have performed 25Mg NMR measurements in F-actin solutions. Based on the NMR data, we estimate that the rotational correlation times of Mg2+ are independent of the overall rotational dynamics of the actin filaments. Moreover, competitive binding experiments demonstrate a facile displacement of F-actin-bound Mg2+ by Co(NH3)63+. At higher Co(NH3)63+ concentrations, a fraction of the magnesium ions are trapped as actin filaments aggregate. ATP also competes effectively with actin filaments for binding to Mg2+. These results support the hypothesis that magnesium ions bind loosely and nonspecifically to actin filaments, and thus show a behavior typical of counterions in polyelectrolyte solutions. The observed features mimic to some extent the well-documented behavior of counterions in DNA solutions.     

Effect of ions on the dielectric relaxation of DNA

The dielectric relaxation of DNA solutions has been investigated with and without extraneous ions covering a wide frequency range. The effect of monovalent ions such as Na, K, and Li as well as divalent ions such as Mg, Ca, and Hg have been included in the study. These ions are found to have a profound effect on the dielectric increment and the relaxation time without affecting the molecular dimension drastically. This dielectric effect is interpreted as indicating the importance of counterion fluctuation on the low frequency dielectric constant of DNA in solution. The effect of an organic ion, tetra-methylammoniun bromide, has also been studied. This ion has no noticeable effect. A simple theory is derived on the basis of a microscopic model to account for the effect of external ions on the dielectric behavior of solutions of DNA.     

Renaturation of copper solutions of DNA. I. Phenomenological analysis

A study of the kinetics of renaturation of cupric DNA solutions has been carried out by two physical properties methods. The use of a purely phenomenological analysis leads nevertheless to interesting conclusions concerning the transformation mechanism. We have found that: in the presence of Cu⁺⁺ ions, different. DNA samples exhibit an equivalent kinetic behavior; the system can be decomposed into two parts: DNA and copper ions, and the rate of formation of DNA should be faster than that of copper ions; the mechanism of transformation may be bimolecular, but further investigation is necessary to confirm this.     

Osmotic stress alters the balance between organic and inorganic solutes in flax (Linum usitatissimum)

Flax (Linum usitatissimum) is grown for its oil and its fiber. This crop, cultivated in temperate regions, has seen a renewed interest due to the presence of abundant molecules of interest for many applications. Little information is available about the behavior of flax during osmotic stress; yet this is considered a major stress that causes significant yield losses in most crops. To control the presence of this stress better, flax behavior was investigated following the application of osmotic stress and the response was examined by applying increasing concentrations of PEG 8000. This resulted in the reorganization of 32 metabolites and 6 mineral ions in the leaves. The analysis of these two types of solute highlighted the contrasting behavior between a higher metabolite content (particularly fructose, glucose and proline) and a decrease in mineral ions (especially nitrate and potassium) following PEG treatment. However, this reorganization did not lead to a greater accumulation of solutes, with the total amount remaining unchanged in leaves during osmotic stress.     

Conductance behavior of symmetrical tetraalkylammonium halides in aqueous sucrose solutions

The conductance behavior of some tetraalkylammonium halides (R₄NX) in saturated, aqueous solutions of sucrose has been investigated, and data on the conductance of these salts in water saturated by sucrose at 50° are reported at several temperatures within the range 25 to 70°. In these homogeneous, ternary systems, plots of —log K versus 1/T show a break at the saturation temperature, where two straight lines intersect one another. Divergence of the pair of straight lines has been found to decrease with increasing chain-length of the R₄N⁺ ions, in contrast to the structural behavior of common, alkali-metal ions. The results are interpreted in terms of the hydrophobic nature of the tetraalkylammonium halides, as well as the salting-in behavior of these salts towards sucrose molecules.     

头部位移检测法动物悬尾实验仪的研制

采用红外传感、激光定位、51系列单片微机控制和记忆等技术,研制一种检测动物悬尾特性的仪器,用于药物研究中的动物悬尾实验。经30例小鼠实验证明,效果良好,该仪器为动物悬尾实验提供了一种全新的先进方法。     

Transducin-activated cGMP-specific phosphodiesterase of external segments of bovine retinal rods: The influence of magnesium ions

The kinetic behavior of phosphodiesterase activated by transducin in a complex with a non-hydrolyzable GTP analogue (guanosine-5′-O-thiotriphosphate) was studied by the pH-metric method in preparations of light-adapted external segments of bovine retinal rods in a range of magnesium ion concentrations from 0.4 to 20 mM. These results indicate that when using the reaction media containing 10–15 mM Mg²⁺ ions, introduction of 2–4 mM ethylene glycol tetraacetic acid (a chelator of calcium ions) in the reaction medium induces only relatively small changes in the concentration of free magnesium ions that are not able to significantly influence the phosphodiesterase activity.     

Molecular Dynamics Simulation Studies of the Limiting Conductances of CaCl2 using Extended Simple Point Charge and Revised Polarizable Models

We have carried out molecular dynamics (MD) simulations of the limiting conductances of CaCl₂ in ambient and supercritical states as a function of water density using extended simple point charge (SPC/E) and revised polarizable (RPOL) models for ions and water molecules. Both models predict the limiting conductances of CaCl₂ in supercritical water that are a linear dependence on water density. The effect of the electronic polarization on the limiting conductances is too small to cause a deduction in the lower water density of 0.6?～?0.7?g/cc in this study. The most significant effect of the electronic polarization is appeared in a decrease in the ion–water potential energy and, as a result, an increase in the limiting conductances for both ions. Different charge distributions of water molecules in the first hydration shell around the ions lead the opposite behavior of the induced dipole moment with water density for a positive and a negative ion in supercritical water; the induced dipole moment of Ca²⁺ decreases with increasing water density but for Cl^-, the opposite is observed. The same kind of opposite behavior due to the structure of water molecules around the ions is also found in hydrogen-bond correlations of water around the ions and of bulk water; hydrogen bonding around Ca²⁺ persists longer than in bulk water whereas the opposite is observed for Cl^-.     

Metal ion and DNA binding by single-chain <Emphasis Type="Italic">Pvu</Emphasis>II endonuclease: lessons from the linker

Understanding the roles of metal ions in restriction enzymes has been complicated by both the presence of two metal ions in many active sites and their homodimeric structure. Using a single-chain form of the wild-type restriction enzyme PvuII (scWT) in which subunits are fused with a short polypeptide linker (Simoncsits et al. in J. Mol. Biol. 309:89–97, 2001), we have characterized metal ion and DNA binding behavior in one subunit and examined the effects of the linker on dimer behavior. scWT exhibits heteronuclear single quantum coherence NMR spectra similar to those of native wild-type PvuII (WT). For scWT, isothermal titration calorimetry data fit to two Ca(II) sites per subunit with low-millimolar K _ds. The variant scWT|E68A, in which metal ion binding in one subunit is abolished by mutation, also binds two Ca(II) ions in the WT subunit with low-millimolar K _ds. When there are no added metal ions, DNA binding affinity for scWT is tenfold stronger than that of the native WT, but tenfold weaker at saturating Ca(II) concentration. In the presence of Ca(II), scWT|E68A binds target DNA similarly to scWT, indicating that high-affinity substrate binding can be carried energetically by one metal-ion-binding subunit. Global analysis of DNA binding data for scWT|E68A suggests that the metal-ion-dependent behaviors observed for WT are reflective of independent subunit behavior. This characterization provides an understanding of subunit contributions in a homodimeric context.     

Solution structure of copper ion-induced molecular aggregates of tyrosine melanin.

Melanin, the ubiquitous biological pigment, provides photoprotection by efficient filtration of light and also by its antioxidant behavior. In solutions of synthetic melanin, both optical and antioxidant behavior are affected by the aggregation states of melanin. We have utilized small-angle x-ray and neutron scattering to determine the molecular dimensions of synthetic tyrosine melanin in its unaggregated state in D(2)O and H(2)O to study the structure of melanin aggregates formed in the presence of copper ions at various copper-to-melanin molar ratios. In the absence of copper ions, or at low copper ion concentrations, tyrosine melanin is present in solution as a sheet-like particle with a mean thickness of 12.5 A and a lateral extent of approximately 54 A. At a copper-to-melanin molar ratio of 0.6, melanin aggregates to form long, rod-like structures with a radius of 32 A. At a higher copper ion concentration, with a copper-to-melanin ratio of 1.0, these rod-like structures further aggregate, forming sheet-like structures with a mean thickness of 51 A. A change in the charge of the ionizable groups induced by the addition of copper ions is proposed to account for part of the aggregation. The data also support a model for the copper-induced aggregation of melanin driven by pi stacking assisted by peripheral Cu(2+) complexation. The relationship between our results and a previous hypothesis for reduced cellular damage from bound-to-melanin redox metal ions is also discussed.     

Eu3+ luminescence studies of oncomodulin. The origin of the pH-dependent behavior

The Eu3+ 7F0----5D0 excitation spectra of parvalbumin and oncomodulin are pH-dependent. Until now, it had been assumed that both the CD and EF ion-binding sites shared this property and that deprotonation of water molecules coordinated to the bound Eu3+ ions might be responsible for the pH dependence. Results obtained with the site-specific variant of oncomodulin known as D59E, in which glutamate replaces the aspartate naturally present at position 59, have necessitated substantial revision of these ideas. It now appears that the pH-dependent behavior is confined to the CD site. Moreover, we observe no corresponding change in the number of O-H oscillators coordinated to the bound Eu3+ ions in the pH range over which we observe the spectroscopic alteration. It is likely that the behavior results from deprotonation of one or more carboxyl groups clustered at the COOH-terminal end of the CD domain.     

The effect of laser radiations on human ceruloplasmin. Absorption, circular dichroism and electron paramagnetic resonance study.

Laser radiations at wavelengths ranging from 514.5 to 360.0 nm decolorize human ceruloplasmin. Kinetic behavior of the two chromophores absorbing at 610 nm, as measured by absorption and circular dichroism data, indicate different quantum yields of the two type I copper ions, whose maximum lies approximatively at 400 nm. Furthermore, as Electron Paramagnetic Resonance measurements demonstrate, the photochemical process involves reduction of the two type I copper ions leaving type II copper unchanged.     

Negative ion ammonia chemical ionization and electron impact ionization mass spectrometric analysis of steryl fatty acyl esters

Synthesis of steryl palmitates, varied in the nature of the steryl moiety, provided model compounds for investigation of the mass spectrometric behavior of steryl long-chain fatty acyl esters. The structure of the steryl moiety was varied according to: (i) position and degree of unsaturation in the steroid nucleus and C-17 side-chain, (ii) position and degree of methylation, (iii) presence or absence of a 9 beta, 19-cyclopropane ring. Compounds were chosen so as to be representative of biochemically important steryl esters. Electron impact (EI) behavior of steryl palmitate esters closely resembles that of their short-chain (e.g. acetate) counterparts. M+.ions were generally weak or absent and the major high mass ions arose from characteristic fragmentations of the steroid nucleus following loss of the acyl moiety ([M-RCO2H]+.). Fragment ions characteristic of the acyl moiety were lacking. Negative ion chemical ionization (NICI) using ammonia as reagent gas, on the other hand, afforded spectra containing characteristic fragment ions [RCO2]-, [RCO2-18]-, and [RCO2-19]- from which the nature of the fatty acyl moiety can be readily deduced. Hence, NICI and EI provide complementary means of ionization for the mass spectrometric determination of structures of steryl esters.     

The Behaviour of Ions in Narrow Water-Filled Pores

Today, the equilibrium behavior of ions in solution may be predicted with some confidence, essentially because rapid ionic diffusion over small distances ensures homogeneity throughout the solution. Equilibrium concepts such as ionic strength and pH apply. However, when attempting to understand the behavior of ions passing rapidly through narrow pores such as ion channels, no such equilibrium state may be assumed. The passing solution may have been in equilibrium with conditions at the mouth of the pore but will not be in equilibrium with charged molecules on the pore wall. In addition, the water in narrow pores will be partially ordered by contact with the pore walls and will not behave like bulk water.To illustrate this difference, a simple equilibrium calculation of the ion concentrations near a plastic sheet penetrated by narrow pores and containing in its surface partially ionized carboxyl groups is shown to be in good agreement with experiment. However, to predict the non-equilibrium behavior within the narrow pores is much more difficult. To illustrate the difficulty, a Monte Carlo computer model is described which attempts to predict the rapid switching of ion current observed experimentally with these narrow pores.