Monte Carlo simulations of nucleotide crystal hydrates and their counter-ions

A knowledge of structural and energetic aspects of water- and ion-nucleic acid interactions is essential for the understanding of the role of solvent and counterions in stabilising the various helical forms of nucleic acids. In this study, Monte Carlo computer simulation techniques have been used to predict structural properties of solvent networks in small nucleic acid crystal hydrates containing the ions sodium, ammonium and calcium. Appropriate parameters to describe the interaction potentials of the ions are added to those previously developed for water and nucleic acid atoms. A comparison is made between the predicted and experimental results and it is concluded that the potential functions used lead to simulated solvent structure in reasonable agreement with experimental data, at least in the cases of sodium and calcium. It is now feasible to use these functions in studies of hydration of larger helical fragments of nucleic acids of more direct biological interest.     

The electrostatic potential for the phosphodiester group determined from X-ray diffraction.

The charge density distribution in the crystal structure of ammonium dimethylphosphate at 123 K has been determined from x-ray diffraction data (MoK alpha) using 8437 reflections with sin theta/lambda less than 1.33 A-1 [NH4+.(CH3)2PO4-, M(r) = 143.08, monoclinic, P2(1)/c, a = 10.007(1), b = 6.926(1), c = 9.599(2) A, beta = 105.40(1) degrees, V = 641.4(3) A3, Z = 4, F000 = 304, Dx = 1.4815 g.cm-3, mu = 3.726 cm-1]. Least-squares structure refinement assuming Stewart's rigid pseudoatom model (variables including Slater-type radial exponents and electron populations for multipole terms extending to octapoles for C, N, O, and P, and dipoles for H) gave R(F2) = 0.039 for all reflections. The dimethylphosphate anion is in the gauche-gauche conformation and has approximate twofold symmetry. One phosphoryl O atom forms three hydrogen bonds and the other forms one. Neither of the ester O atoms is hydrogen bonded. For the dimethylphosphate anion isolated from the crystal structure, a map of the electrostatic potential obtained using the pseudoatom charge parameters shows that the phosphoryl O atoms are considerably more electronegative than the ester O atoms. The electrostatic potential distribution obtained in this way has been fitted by least squares to a system of atom-centered point charges. The potential calculated from these point charges agrees with the experimental result. It also agrees reasonably well with potentials obtained from three other systems of point charges that are widely used as part of the semiempirical force field for molecular mechanics and molecular dynamics calculations involving nucleic acids.     

Effect of ion collisions on the parameters of dust-plasma structures

A study is made of how collisions of ions with gas atoms affect the parameters of an ion flow and the interaction between dust grains, as well as their interaction with the flow. The ion velocity distribution in a gas discharge is analyzed with allowance for both resonant charge exchange of the ions with parent gas atoms and polarizing collisions. The interaction forces between a dust grain and an ion flow and among the grains due to the charge exchange of ions with gas atoms near the grain are examined.     

Models of interaction between nucleic acids and proteins. Hydrogen bonding of arginine with nucleic acid bases, phosphate groups and carboxylic acids.

Complex formation between the side chain of arginine and nucleic acid bases has been investigated by proton magnetic resonance in dimethylsulfoxide. Simultaneous formation of two hydrogen bonds leads to a selectivity of arginine interaction towards cytosine and guanine. A comparison is made of the interaction of arginine side chain with nucleic acid bases, phosphate and carboxylate anions. It is shown that interaction between carboxylate and arginine is stronger than between phosphate and arginine. These results are discussed with respect to the selective recognition of nucleic acid bases by arginine side chains and by the arginyl-glutamyl ion pair which could form in proteins interacting with nucleic acids.     

Ions from the Hofmeister series and osmolytes: effects on proteins in solution and in the crystallization process

Sephadex G-10 gel sieving chromatography, Jones-Dole viscosity B coefficients, and solution neutron and X-ray diffraction are used to show that small ions of high charge density (e.g., sulfate, phosphate, the carboxylate, sodium, and fluoride) are strongly hydrated (kosmotropes) whereas large monovalent ions of low charge density (e.g., ammonium, chloride, potassium, and the positively charged amino acid side chains) are weakly hydrated (chaotropes). The heats of solution of the crystalline alkali halides are then used to show that only oppositely charged ions of equal water affinity spontaneously form inner sphere ion pairs, and that this controls ion binding to proteins. The net charge on a protein is a major determinant of its solubility. Finally, the surface potential difference and surface tension at an air-salt solution interface are used to generate a simple model for how ions affect protein stability and solubility through indirect interactions at the protein-solution interface. A few comments about small neutral osmolytes are also included.     

Molecular-dynamic simulation of phospholipid bilayers: Ion distribution at the surface of neutral and charged bilayer in the liquid crystalline state

The electric field and ion distribution at the surface of neutral and charged lipid bilayers (BeCl₂ and dipalmitoyl phosphatidylcholine/dipalmitoyl phosphatidylserine (DPPC/DPPS) + KCl) were studied with molecular dynamic (MD) methods. It is shown that the contributions of lipid molecules, water and ions to the electric potential compensate each other in the region of the diffuse double layer and decrease the potential value close to zero. It is also demonstrated that the ion distribution at the charged surface is determined not only by the electrostatic ion-medium interaction. The total energy of this interaction was compared with the potential of mean ion force. It was shown that cations and anions have a different effect on the state of water molecules at the surface. The order parameter of water in the system DPPC + BeCl₂ and the Clion distribution have the extremum at the distance of 10 α atoms of the phospholipid glycerol. This position was chosen as the “electrical” interface of the electrical double layer (EDL) for all lipid systems studied. The potential of mean force of counter ions in EDL allows us to obtain the value of potential at the lipid surface suitable for experimental test of the MD data. This surface potential and surface charge density was found from MD simulation different electrolyte concentrations and DPPS content of 20, 40 and 60% in the mixture with DPPC and was shown to be in a good agreement with the Gouy-Chapman-Stern model upon fitting parameters close to their experimental values.     

Competitive interaction of monovalent cations with DNA from 3D-RISM

The composition of the ion atmosphere surrounding nucleic acids affects their folding, condensation and binding to other molecules. It is thus of fundamental importance to gain predictive insight into the formation of the ion atmosphere and thermodynamic consequences when varying ionic conditions. An early step toward this goal is to benchmark computational models against quantitative experimental measurements. Herein, we test the ability of the three dimensional reference interaction site model (3D-RISM) to reproduce preferential interaction parameters determined from ion counting (IC) experiments for mixed alkali chlorides and dsDNA. Calculations agree well with experiment with slight deviations for salt concentrations >200 mM and capture the observed trend where the extent of cation accumulation around the DNA varies inversely with its ionic size. Ion distributions indicate that the smaller, more competitive cations accumulate to a greater extent near the phosphoryl groups, penetrating deeper into the grooves. In accord with experiment, calculated IC profiles do not vary with sequence, although the predicted ion distributions in the grooves are sequence and ion size dependent. Calculations on other nucleic acid conformations predict that the variation in linear charge density has a minor effect on the extent of cation competition.     

Solvent interactions in nucleic acid crystal hydrates

A detailed knowledge of structural and energetic aspects of water-nucleic acid interactions is essential for understanding the role of solvent in stabilizing the various helical forms of nucleic acids. In this study, computer simulation techniques have been used to predict structural properties of solvent networks in small nucleic acid crystal hydrates. A detailed comparison of predicted and experimental results on the structure of the solvent networks is presented and includes an analysis of both the local environment and hydrogen bond pattern of each water molecule. A correlation between the environment of each unique water molecule and its energetic properties (such a dipole moment and binding energy) is seen. As in the previous studies on small amino acid hydrate crystals, non-pair additive (cooperative) effects are found to be non-negligible. It is concluded that the potential functions used in this initial study lead to simulated solvent networks in reasonable agreement with experimental data. Thus, it is now feasible to use them in studies of hydration of larger helical fragments of nucleic acids of more direct biological interest.     

Simulation of interactions between nucleic acid bases by refined atom-atom potential functions

Energy of interaction between nitrogen bases of nucleic acid has been calculated as a function of parameters determining the mutual position of two bases. Refined atom-atom potential functions are suggested. These functions contain terms proportional to the first (electrostatics), sixth (or tenth for the atoms forming a hydrogen bond) and twelfth (repulsion of all atoms) powers of interatomic distance. Calculations have shown that there are two groups of minima of the base interaction energy. The minima of the first group correspond to coplanar arrangement of the base pairs and hydrogen bond formation. The minima of the second group correspond to the position of bases one above the other in almost parallel planes. There are 28 energy minima corresponding to the formation of coplanar pairs with two (three for the G:C pair) almost linear N-H . . . O and (or) N-H . . . N hydrogen bonds. The position of nitrogen bases paired by two such H-bonds in any crystal of nucleic acid component in polynucleotide complexes and in tRNA is close to the position in one of these minima. Besides, for each pair there are energy minima corresponding to the formation of a single N-H . . . O or N-H . . . N and one C-H . . . O or C-H . . . N hydrogen bond. The form of potential surface in the vicinity of minima has been characterized. The results of calculations agree with the experimental data and with more rigorous calculations based on quantum-mechanical approach.     

On the thermodynamics and kinetics of the cooperative binding of bacteriophage T4-coded gene 32 (helix destabilizing) protein to nucleic acid lattices.

In this paper we summarize a series of thermodynamic, and preliminary kinetic, studies on the molecular details and specificity of interaction of phage T4-coded gene 32-protein (GP32) with nucleic acid lattices. It is shown that the binding of GP32 to short (l = 2--8 residues) oligonucleotides is essentially independent of base composition and sugar-type, as well as of salt concentration. In contrast, cooperative (continuous) or isolated binding of GP32 to single-stranded polynucleotides is base and sugar composition-dependent (binding is tighter to DNA than to RNA) and highly dependent on salt concentrations. Binding constants (K), cooperativity parameters (w), and binding site sizes (n) are determined for binding to various nucleic acid lattices under a variety of environmental conditions. These results are used to show that GP32 can bind to nucleic acid lattices in two different conformations, and to characterize the molecular details of these binding species. Further insight into the molecular origins of binding cooperativity is obtained by determining these thermodynamic parameters also for the specifically proteolytically degraded GP32 fragments GP32 I (C-terminal peptide removed) and GP32 III (C- and N-terminal peptides removed). It is also shown that these GP32-nucleic acid binding measurements can be used to provide a quantitative molecular interpretation of the sequential (competitive) binding equilibria involved in the autogenous translational regulation of GP32 synthesis (Lemaire et al., 1978, J. Mol. Biol. 126:73, 1978), and to illustrate some general principles of the development of interactional specificity in cooperatively binding protein-nucleic acid complexes. Preliminary experiments have also been carried out on the kinetics of GP32 association to, and dissociation from, single-stranded nucleic acid lattices. In particular, fluorescence stopped-flow measurements of the dissociation of GP32 from such lattices as a function of lattice saturation (and protein cluster size) can be interpreted to suggest that the protein may translocate ("slide") on the lattice before dissociation, These studies permit an approach to possible rates and mechanisms of such translocation events.     

Correlation between structure of polyoxotungstates and their inhibitory activity on polymerases

The 21-tungsto-9-antimonate (TA, HPA 23), a polyoxotungstate, has shown a significant antiviral activity in vivo and in vitro. It inhibits viral and bacterial DNA polymerases. In this paper, several compounds of two polyoxotungstic families, tungstoantimonates and tungstoarsenates, have been used to specify the mechanism of polymerase inhibition. It has been demonstrated that the inhibitory activity of polyoxotungstates is not related to the occupation of their coordinative sites by cations, nor to the nature of these bound cations. Kinetic studies and binding assays have shown that polyoxotungstates bind to the polymerases in competition with the nucleic acid template. This result seems to be related to their polyanionic nature. Furthermore, the size and charge of these compounds may play a prominent part in their affinity for the polymerases.     

Amyloid-associated nucleic acid hybridisation

Nucleic acids promote amyloid formation in diseases including Alzheimer's and Creutzfeldt-Jakob disease. However, it remains unclear whether the close interactions between amyloid and nucleic acid allow nucleic acid secondary structure to play a role in modulating amyloid structure and function. Here we have used a simplified system of short basic peptides with alternating hydrophobic and hydrophilic amino acid residues to study nucleic acid - amyloid interactions. Employing biophysical techniques including X-ray fibre diffraction, circular dichroism spectroscopy and electron microscopy we show that the polymerized charges of nucleic acids concentrate and enhance the formation of amyloid from short basic peptides, many of which would not otherwise form fibres. In turn, the amyloid component binds nucleic acids and promotes their hybridisation at concentrations below their solution K(d), as shown by time-resolved FRET studies. The self-reinforcing interactions between peptides and nucleic acids lead to the formation of amyloid nucleic acid (ANA) fibres whose properties are distinct from their component polymers. In addition to their importance in disease and potential in engineering, ANA fibres formed from prebiotically-produced peptides and nucleic acids may have played a role in early evolution, constituting the first entities subject to Darwinian evolution.     

How are Nucleic Acids Released in Cells from Cationic Lipid-Nucleic Acid Complexes?

Abstract

Cationic lipid-nucleic acid complexes are widely used to deliver oligonucleotides, RNA and DNA into cells. Although much has been learned about the structure and forces that hold the complex together, an understanding of the mechanism of release of the nucleic acids from the complex into cells has been lacking. Recent studies have shown that anionic liposomes with compositions similar to the cytoplasmic face of the endosomal membrane are potent agents for inducing the rapid release of oligonucleotides and DNA from cationic lipid-nucleic acid complexes. Based upon these results, we propose that after the cationic lipid/nucleic complex is internalized by endocytosis it destabilizes the endosomal membrane. This destabilization induces flip-flop of anionic lipids from the cytoplasmic facing monolayer, which laterally diffuse into the complex and form a charge neutral ion-pair with the cationic lipids. This results in displacement of the nucleic acid from the cationic lipid and subsequent release of the nucleic acid into cytoplasm of the cell. We review the data that show the proposed mechanism accounts for a variety of observations on cationic lipid/nucleic acid complex-cell interactions.     

Conformational difference in cation complexes of tetranactin in solution

The conformational changes and binding behavior of tetranactin on complexation with sodium, potassium, rubidium, cesium, and ammonium ions were investigated by the measurements of proton magnetic resonance, ir, and Raman spectra. It has been clearly shown that alkali cations coordinate to the oxygen atoms of both the carbonyl group and the tetra-hydrofuran ring, but the ammonium ion coordinates only to the oxygen atom of the tetrahydrofuran. Among the alkali cations the potassium ion most strongly coordinates to the tetrahydrofuran oxygen atoms. The complexation with larger cations induces an expansion of the cavity of the macrocyclic ring of tetranactin and smaller cations contract the cavity. The evidence is revealed by the coupling constants of the methylene protons and the frequency separation between the carbonyl stretching vibrations of the ir- and Raman-active modes. The conformations of the cation complexes in the solid are maintained in solution but that of the cation free form is not.     

A biophysical investigation on the binding and controlled DNA release in a cetyltrimethylammonium bromide-sodium octyl sulfate cat-anionic vesicle system

The interactions between cat-anionic (an acronym indicating surfactant aggregates (micelles and vesicles) formed upon mixing cationic and anionic surfactants in nonstoichiometric amounts) vesicles and DNA have been the subject of intensive studies because of their potential applications in biomedicine. Here we report on the interactions between DNA and cetyltrimethylammonium bromide (CTAB)-sodium octyl sulfate (SOS) cat-anionic vesicles. The study was performed by combining dielectric relaxation spectroscopy, circular dichroism, dynamic light scattering, ion conductivity, and molecular biology techniques. DNA is added to positively charged vesicles until complete charge neutralization of the complex and formation of lipoplexes. This occurs when the mole ratio between the phosphate groups of DNA and positive charges on the vesicle is about 1.8. Above this threshold the nucleic acid in excess remains free in solution. This very interesting new result shows that anionic surfactants are not expelled upon saturation, and therefore, no formation of micelles occurs. Furthermore, vesicle-bound DNA can be released in its native form, as confirmed by dielectric spectroscopy and circular dichroism measurements. The nucleic acid is released upon addition of SOS, which competes with the phosphate groups of the DNA: this results in the demolition of the CTAB-SOS cat-anionic vesicles. These results indicate the possibility of a controlled DNA release and might be of interest in biomedicine.     

Hydration of nucleic acid bases studied using novel atom-atom potential functions

New simple atom-atom potential functions for simulating behavior of nucleic acids and their fragments in aqueous solutions are suggested. These functions contains terms which are inversely proportional to the first (electrostatics), sixth (or tenth for the atoms, forming hydrogen bonds) and twelfth (repulsion of all the atoms) powers of interatomic distance. For the refinement of the potential function parameters calculations of ice lattice energy, potential energy and configuration of small clusters consisting of water and nucleic acid base molecules as well as Monte Carlo simulation of liquid water were performed. Calculations using new potential functions give rise to more linear hydrogen bonds between water and base molecules than using other potentials. Sites of preferential hydration of five nucleic bases - uracil, thymine, cytosine, guanine and adenine as well as of 6,6,9-trimethyladenine were found. In the most energetically favourable sites water molecular interacts with two adjacent hydrophilic centres of the base. Studies of interaction of the bases with several water molecules showed that water-water interactions play an important role in the arrangement of the nearest to the base water molecules. Hydrophilic centres are connected by "bridges" formed by hydrogen bonded water molecules. The results obtained are consistent with crystallographic and mass-spectrometric data.     

Simulation of interactions in the co-planar nucleic acid base pairs using atom-atom potential functions

Calculations of the energy of nucleic acid base interactions as a function of parameters determining mutual position of two bases in a plane have been performed. Atom-atom potential functions used include terms proportional to the first (electrostatic), sixth (or tenth for the atoms of hydrogen bond) and 12th power of interatomic distance. The calculations have shown the existence of 27 energy minima which correspond to the formation of co-planar pairs with two (or three for G : C pair) almost linear N--H...O and N--H...N hydrogen bonds. The positions of nitrogen bases bound by two hydrogen bonds in every crystal of nucleic acid components, in the complexes of polynucleotides and in tRNA are near to the positions in one of these minima. In addition for every pair there exist energy minima which correspond to the formation of one N--H...O or N--H...N and one C--H...O or C--H...N hydrogen bond. Energy behavior near minima have been investigated. The results of our calculations are in agreement with experimental data and with the calculations which employ quantum mechanical results.     

Hydration of Nucleic Acid Bases Studied Using Novel Atom-Atom Potential Functions

Abstract

New simple atom-atom potential functions for simulating behavior of nucleic acids and their fragments in aqueous solutions are suggested. These functions contain terms which are inversely proportional to the first (electrostatics), sixth (or tenth for the atoms, forming hydrogen bonds) and twelfth (repulsion of all the atoms) powers of interatomic distance. For the refinement of the potential function parameters calculations of ice lattice energy, potential energy and configuration of small clusters consisting of water and nucleic acid base molecules as well as Monte Carlo simulation of liquid water were performed. Calculations using new potential functions give rise to more linear hydrogen bonds between water and base molecules than using other potentials. Sites of preferential hydration of five nucleic bases—uracil, thymine, cytosine, guanine and adenine as well as of 6,6,9-trimethyladenine were found. In the most energetically favourable sites water molecule interacts with two adjacent hydrophilic centres of the base. Studies of interaction of the bases with several water molecules showed that water-water interaction play an important role in the arrangement of the nearest to the base water molecules. Hydrophilic centres are connected by “bridges” formed by hydrogen bonded water molecules. The results obtained are consistent with crystallographic and mass-spectrometric data.