Nonexistence of local maxima in molecular electrostatic potential maps

It has been rigorously established by means of classical electrostatic arguments, that molecular electrostatic potential maps are devoid of local maxima. This forms a generalization of the earlier works of Politzer and co-workers which were restricted to the case of atoms.     

Molecular dynamics simulation of clustered DNA damage sites containing 8-oxoguanine and abasic site

Clustered DNA damage sites induced by ionizing radiation have been suggested to have serious consequences to organisms, such as cancer, due to their reduced probability to be repaired by the enzymatic repair machinery of the cell. Although experimental results have revealed that clustered DNA damage sites effectively retard the efficient function of repair enzymes, it remains unclear as to what particular factors influence this retardation. In this study, approaches based on molecular dynamics (MD) simulation have been applied to examine conformational changes and energetic properties of DNA molecules containing clustered damage sites consisting of two lesioned sites, namely 7,8-dihydro-8-oxoguanine (8-oxoG) and apurinic/apyrimidinic (AP) site, located within a few base pairs of each other. After 1 ns of MD simulation, one of the six DNA molecules containing a clustered damage site develops specific characteristic features: sharp bending at the lesioned site and weakening or complete loss of electrostatic interaction energy between 8-oxoG and bases located on the complementary strand. From these results it is suggested that these changes would make it difficult for the repair enzyme to bind to the lesions within the clustered damage site and thereby result in a reduction of its repair capacity.     

The electrostatical molecular potential — A tool for the prediction of electrostatic molecular interaction properties

Starting from the molecular potential we get, by using elementary electrostatics, information about energetically favoured regions for interaction with ions and dipoles around H₂O and H₂CO. The molecule-dipole interaction is represented by the electric field patterns.     

Electrostatic energy analysis of 8-oxoguanine DNA lesion—molecular dynamics study

One nanosecond molecular dynamics (MD) simulation was performed for two DNA segments each composed of 30 base pairs. In one DNA segment the native guanines at nucleotides positions 17 and 19 were replaced with two 8-oxoguanines (8-oxoG) (8-oxoG is mutagenic DNA oxo-lesion). The analysis of results was focused on the electrostatic energy that is supposed to be significant factor causing the disruption of DNA base stacking in DNA duplex and may also serve as a signal toward the repair enzyme informing the presence of the lesion. The repulsive interaction between 8-oxoG and the entire DNA molecule was observed, which caused the extrahelical position of 8-oxoG (position 19). The repulsive electrostatic interaction between both 8-oxoG lesions contributed to the flipping out of one 8-oxoG and to the local instability of the lesioned DNA region. The electrostatic potential at the surface of DNA close to the lesions has more negative value than the same region on the native DNA. This electrostatic potential may signal presence of the lesion to the repair enzyme. In the simulation of native DNA segment, no significant structural changes were observed and B-DNA structure was well preserved throughout the MD simulation.     

Approximation of the molecular electrostatic potential in a gaussian density functional method

The recently developed Asymptotic Density Model (ADM) [6, 9] is here implemented in the density functional framework using the program deMon-KS [13]. While the original implementation divided the atoms into a core shell and a valence shell, the present version allows for an arbitrary number of shells making it therefore more flexible and, as shown with benzene, potentially more accurate. Moreover, since this method is derived through Poisson's equation, an expression for the electronic charge density is also obtained. However, the present discussion will restrict itself to the electrostatic potential. Finally, even though this method requires parametrization, it is shown that the parameters obtained for homonuclear diatomic species, and used as is in molecular calculations, yield satisfactory results. Indeed, the ADM reproduces almost all basic features of the MEP for all molecules presented here, (water, ammonia, ethylene, acetylene, hydrogen cyanide, carbon monoxide, benzene, nitrous acid). Received: 5 July 1996 / Accepted: 12 November, 1996     

Near-infrared induced membrane surface electrostatic potential, fluorescent measurements

The change of the electrostatic surface potential induced by near-infrared radiation was monitored by the fluorescence probe technique. Fluorescence intensity of 1-anilinonaphtalene-8-sulfate (ANS) was studied in the pH range 4.8–9.5 before and after exposition to NIR (700–2000 nm). The intensity of fluorescence changed (decreased after exposition on radiation) only at pH 7.4. The effect is due to decreasing concentration of ANS in liposome membrane after irradiation. The modified distribution of ANS in liposome membrane upon irradiation is attributed to the dehydration of membrane surface. Dehydratation diminishes the electrostatic surface potential about 36±15 mV.     

The effect of screening the electrostatic potentials of reactive sites within B-DNA by metal cations

The effect of screening the backbone phosphates by Mg²⁺ ions, in various ways, on the negative electrostatic potential minima associated with the nucleic acid bases in B-DNA is investigated. The results are compared to screening by Na⁺ ions and to the corresponding potential minima in unscreened B-DNA.     

8-oxoguanine and 8-oxodeoxyguanosine Biomarkers of Oxidative DNA Damage: A Review on HPLC–ECD Determination

Reactive oxygen species (ROS) are continuously produced in living cells due to metabolic and biochemical reactions and due to exposure to physical, chemical and biological agents. Excessive ROS cause oxidative stress and lead to oxidative DNA damage. Within ROS-mediated DNA lesions, 8-oxoguanine (8-oxoG) and its nucleotide 8-oxo-2′-deoxyguanosine (8-oxodG)—the guanine and deoxyguanosine oxidation products, respectively, are regarded as the most significant biomarkers for oxidative DNA damage. The quantification of 8-oxoG and 8-oxodG in urine, blood, tissue and saliva is essential, being employed to determine the overall effects of oxidative stress and to assess the risk, diagnose, and evaluate the treatment of autoimmune, inflammatory, neurodegenerative and cardiovascular diseases, diabetes, cancer and other age-related diseases. High-performance liquid chromatography with electrochemical detection (HPLC–ECD) is largely employed for 8-oxoG and 8-oxodG determination in biological samples due to its high selectivity and sensitivity, down to the femtomolar range. This review seeks to provide an exhaustive analysis of the most recent reports on the HPLC–ECD determination of 8-oxoG and 8-oxodG in cellular DNA and body fluids, which is relevant for health research.     

The electrostatic molecular potential of yeast tRNAPhe. III. The molecular potential and the steric acessibility associated with the phosphate groups

The molecular electrostatic potential of yeast tRNA^Phe is calculated at sites bridging the anionic oxygens of each of the 76 phosphate groups of the molecule. A quantitative measure of the steric accessibility of the anionic oxygens of the phosphates toward a spherical cation is presented. Both the resulting potentials and accessibilities are discussed in terms of the molecular and electronic structure of tRNA.     

Modeling the folding and hydrogen production of Clostridium acetobutylicum and Clostridium saccharobutylium mutants using electrostatic potential surfaces and molecular dynamics

Electrostatic potential surfaces (EPS) were used with molecular dynamics to model the folding mechanisms and kinetics of hydrogenase mutants from wild types Clostridium acetobutylicum and Clostridium saccharobutylium. The purpose of the EPS approach was to incorporate long range electrostatic forces between widely separated regions of the mutants which contain 575 amino acids. Also, it was demonstrated that the ratio of positive to negative EPS of unfolded mutants could be used to predict the production of molecular hydrogen from the folded mutants. Using the prediction model, mutant compositions were determined that should yield hydrogen of up to 40 times that obtainable from the wild type C. acetobutylicum. It is expected that the developed EPS techniques can be used to study the folding of other proteins and to predict the reactivity of the folded protein structures.     

Atomic and molecular energies as functionals of the electrostatic potential

Starting from the Hohenberg–Kohn theorem, atomic and molecular energies have been expressed rigorously as functionals of the electronic electrostatic potential, V_elec(r). Explicit formulations have been derived for the functionals representing the kinetic energy and electronic interaction contributions to the total energies.Acknowledgements. The assistance of Dr. Jane S. Murray is greatly appreciated.Contribution to the Jacopo Tomasi Honorary Issue     

A new method to determine electrostatic potential around a macromolecule in solution from molecular wave functions

The three-dimensional reference interaction site model integral equation theory (3D-RISM) combined with the ab initio molecular orbital method (3D-RISM-SCF) is applied to a solvated macromolecular system. The solvation structure around a solute molecule is obtained from the 3D-RISM integral equation under the electrostatic potential of the solute molecule, calculated by the ab initio molecular orbital theory. The electrostatic potential should be calculated on each grid point in the three-dimensional real space. Therefore, the calculation of the electrostatic potential is the most time consuming part in this method. In this article, we propose a new procedure to save the computational cost for calculating the electrostatic potential and the solvated fock matrix. The strategy of this procedure is to evaluate the electrostatic potential and the solvated fock matrix in different ways, depending on the distance between solute and solvent. Inside the repulsive cores of solute atoms, it is possible to avoid the calculation of electrostatic potential and solvated Fock matrix by assuming the potential to be infinity. In the region sufficiently far from solute, they are evaluated classically by putting the effective point charge on each atom. In the intermediate region, the electrostatic potential is evaluated directly by integrating the molecular orbitals of the solute molecule. The electronic structure and the energy gradient of Methionine-Enkephalin and solvation structure are estimated by using this procedure in aqueous solution, and are compared with the results from other procedures. The results are compared also with those from the continuum model.     

Poisson-Boltzmann calculations versus molecular dynamics simulations for calculating the electrostatic potential of a solvated peptide

We performed a very long molecular dynamics simulation of a peptide in explicit water molecules and ions and averaged the electrostatic potential caused by peptide, water and ions at eight points in the vicinity of the peptide. These electrostatic potential values were directly compared to the potential calculated by solving the non-linear Poisson-Boltzmann equation for the system, which describes the solvent using continuum electrostatics. We analyze the contribution of dielectric constant, conformational flexibility and solvation effects on the electrostatic potential at these eight points. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 23 November 1998     

An ab initio SCF study on the tautomerisation of the 8-oxo-guanine and xanthine

All possible H₉-tautomers of 8-oxo-guanine and xanthine were studied by means of PM3 semiempirical and DFT (density functional theory) quantum chemistry methods. Additionally, the five most stable tautomers of both guanine derivatives were estimated on 3-21G, 6-31G, 6-31G^** and MP2 (6-31G^**) ab initio levels. The impact of the environment polarity on the tautomeric equilibrium was also taken into account. Among the variety of tautomeric isomers most probable are diketo forms of both studied derivatives in non-polar and polar surroundings.

The tautomeric equilibrium was unchanged after connection of the sugar backbone. The most preferred diketo forms of 8-oxo-guanosine and xanthidine are in syn conformations both in polar and non-polar environments. The increase of the syn conformations over anti ones may have the source in the formation of the internal hydrogen bonds between H′5 and N₃ atoms. The calculated values of the pseudorotation phase angle were between 144 and 180° in all cases. This corresponds to C′2-endo conformations of all optimised structures.

The N-glycosidic bond stability of most stable tautomers was compared to standard guanosine. Most tautomers of 8-oxo-guanosine and xanthidine are characterised by more stable C₁′-N₉ bond. This indicates that both these derivatives are hardly susceptible to spontaneous depurination and its removal from the DNA will depend mostly on the activity of DNA repair enzymes.     

Monte Carlo study of three-dimensional organization of water molecules around DNA fragments

Interactions with water molecules are important for the stabilization of three-dimensional structures of nucleic acids and for their functioning. The first hydration shells of macromolecules can be considered as structural parts of nucleic acid. We performed a Monte Carlo study of systems containing a nucleic acid base or base pair with water molecules using improved potential functions. These potential functions enable experimental data on both single base–single water interaction energies and enthalpies of base hydration to be reproduced. Hydration shell structures of base pairs are dependent on the pair geometry. Structural elements of hydration shells can contribute to the pair stability and hence to the probability of mispair formation during nucleic acid biosynthesis. The distribution of water molecules around bases and base pairs is essentially nonhomogeneous.From the Proceedings of the 28th Congreso de Químicos Teóricos de Expresión Latina (QUITEL 2002).     

DNA strand break: structural and electrostatic properties studied by molecular dynamics simulation

Due to their lethal consequences and a relatively high probability of introduction of repair errors and mutations, single and double strand breaks are among the most important and dangerous DNA lesions. However, the mechanisms of their recognition and repair processes are only poorly known at present. This work defines and analyzes a DNA with single strand break as a template study for future complex analyses of biologically serious double strand break damage and its enzymatic repair mechanisms. Besides a non-damaged DNA serving as a reference system with no surprising results, system with open valences of the atoms at the strand break ends as well as a system with filled valences were simulated. In both cases during the first few nanoseconds the broken ends of strand breaks are significantly exposed to the outside of the molecule. However, with increasing time, the system with single strand break with open valences is partially disrupted. On the contrary, the system with filled valences shows stable conformation with newly created hydrogen bond between the two strand break endings. Moreover, these endings are steadily situated in the inner part of the molecule, thus making the recognition and docking process of a repair enzyme more complicated in the case of filled valences.     

Mechanisms of oxidation of guanine in DNA by carbonate radical anion, a decomposition product of nitrosoperoxycarbonate

Peroxynitrite is produced during inflammation and combines rapidly with carbon dioxide to yield the unstable nitrosoperoxycarbonate, which decomposes (in part) to CO(3) (.-) and (.)NO(2) radicals. The CO(3) (.-) radicals oxidize guanine bases in DNA through a one-electron transfer reaction process that ultimately results in the formation of stable guanine oxidation products. Here we have explored these mechanisms, starting with a spectroscopic study of the kinetics of electron transfer from 20-22mer double-stranded oligonucleotides to CO(3) (.-) radicals, together with the effects of base sequence on the formation of the end-products in runs of one, two, or three contiguous guanines. The distributions of these alkali-labile lesions were determined by gel electrophoresis methods. The cascade of events was initiated through the use of 308 nm XeCl excimer laser pulses to generate CO(3) (.-) radicals by an established method based on the photodissociation of persulfate to sulfate radicals and the oxidation of bicarbonate. Although the Saito model (Saito et al., J. Am. Chem. Soc. 1995, 117, 6406-6407) predicts relative ease of one-electron oxidations in DNA, following the trend 5'-GGG > 5'-GG > 5'-G, we found that the rate constants for CO(3) (.-)-mediated oxidation of guanines in these sequence contexts (k(5)) showed only small variation within a narrow range [(1.5-3.0)x10(7) M(-1) s(-1)]. In contrast, the distributions of the end-products are dependent on the base sequence context and are higher at the 5'-G in 5'-GG sequences and at the first two 5'-guanines in the 5'-GGG sequences. These effects are attributed to a combination of initial hole distributions among the contiguous guanines and the subsequent differences in chemical reaction yields at each guanine. The lack of dependence of k(5) on sequence context indicates that the one-electron oxidation of guanine in DNA by CO(3) (.-) radicals occurs by an inner-sphere mechanism.     

Formation of 8-nitroguanine and 8-oxoguanine due to reactions of peroxynitrite with guanine

Reactions of peroxynitrite with guanine were investigated using density functional theory (B3LYP) employing 6-31G** and AUG-cc-pVDZ basis sets. Single point energy calculations were performed at the MP2/AUG-cc-pVDZ level. Genuineness of the calculated transition states (TS) was tested by visually examining the vibrational modes corresponding to the imaginary vibrational frequencies and applying the criterion that the TS properly connected the reactant and product complexes (PC). Genuineness of all the calculated TS was further ensured by intrinsic reaction coordinate (IRC) calculations. Effects of aqueous media were investigated by solvating all the species involved in the reactions using the polarizable continuum model (PCM). The calculations reveal that the most stable nitro-product complex involving the anion of 8-nitroguanine and a water molecule i.e. 8NO(2)G(-) + H(2)O can be formed according to one reaction mechanism while there are two possible reaction mechanisms for the formation of the oxo-product complex involving 8-oxoguanine and anion of the NO(2) group i.e. 8OG + NO(2)(-). The calculated relative stabilities of the PC, barrier energies of the reactions and the corresponding enthalpy changes suggest that formation of the complex 8OG + NO(2)(-) would be somewhat preferred over that of the complex 8NO(2)G(-) + H(2)O. The possible biological implications of this result are discussed.