Quantum-mechanical studies of environmental effects on biomolecules VI.Ab initio Studies on the hydration scheme of the phosphate group

Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks

Water plays an important role in stabilizing the structure of DNA and mediating its interactions. Here, the hydration of DNA was analyzed in terms of dinucleotide fragments from an ensemble of 2727 nonredundant DNA chains containing 41 853 dinucleotides and 316 265 associated first-shell water molecules. The dinucleotides were classified into categories based on their 16 sequences and the previously determined structural classes known as nucleotide conformers (NtCs). The construction of hydrated dinucleotide building blocks allowed dinucleotide hydration to be calculated as the probability of water density distributions. Peaks in the water densities, known as hydration sites (HSs), uncovered the interplay between base and sugar-phosphate hydration in the context of sequence and structure. To demonstrate the predictive power of hydrated DNA building blocks, they were then used to predict hydration in an independent set of crystal and NMR structures. In ten tested crystal structures, the positions of predicted HSs and experimental waters were in good agreement (more than 40% were within 0.5 Å) and correctly reproduced the known features of DNA hydration, for example the `spine of hydration' in B-DNA. Therefore, it is proposed that hydrated building blocks can be used to predict DNA hydration in structures solved by NMR and cryo-EM, thus providing a guide to the interpretation of experimental data and computer models. The data for the hydrated building blocks and the predictions are available for browsing and visualization at the website https://watlas.datmos.org/watna/.

Multimolecular complexes of the phosphodiester anion with Zn(II) or Mg(II) and water molecules-Preliminary validations of a polarizable potential by ab initio quantum chemistry

Dimethyl phosphate (DMP^- ) is a model for the phosphodiester backbone of DNA, RNA, and phospholipids. It is central for the binding of divalent cations and water along the backbone of nucleic acids. Significant polarization and charge-transfer contributions and nonadditivity come into play in the multimolecular complexes organized around phosphate. Prior to large-scale molecular dynamics (MD) with advanced polarizable potentials, it is essential to evaluate how well the values and trends of intermolecular interaction energies (ΔE) from ab initio quantum chemistry (QC) and their individual contributions are reproduced in a diversity of such complexes. These differ by the starting binding modes of a divalent cation, Zn(II), namely direct, bi- or mono-dentate to anionic and/or ester oxygens, versus through-water binding. We present first the results from automated refinements of the individual contributions of the SIBFA potential with respect to their QC counterparts using a Zn(II) or a water probe. This is followed by validations on eight relaxed multimolecular complexes of DMP^- with Zn(II) or Mg(II) and seven waters, then on sixteen complexes of DMP^- with Zn(II) and eight waters in arrangements extracted from MD or energy-minimization on a droplet of sixty-four waters. This monitors the compared evolutions of SIBFA and QC ΔE and their individual contributions in the competing arrangements. Some waters, bridging Zn(II) and DMP^- , were found to have exceptionally large dipole moments, of up to 3.8 Debye. The perspectives of extension to a flexible phosphodiester backbone are discussed in the context of the SIBFA potential for DNA and RNA.

Low-energy electron attachment to 5'-thymidine monophosphate: modeling single strand breaks through dissociative electron attachment

Mechanisms of low-energy electron (LEE) attachment and subsequent single-strand break (SSB) formation are investigated by density functional theory treatment of a simple model for DNA, i.e., the nucleotide, 5'-thymidine monophosphate (5'-dTMPH). In the present study, the C5'-O5' bond dissociation due to LEE attachment has been followed along the adiabatic as well as on the vertical (electron attached to the optimized geometry of the neutral molecule) anionic surfaces using B3LYP functional and 6-31G* and 6-31++G** basis sets. Surprisingly, it is found that the PES of C5'-O5' bond dissociation in the anion radicals have approximately the same barrier for both adiabatic and vertical pathways. These results provide support for the hypothesis that transiently bound electrons (shape resonances) to the virtual molecular orbitals of the neutral molecule likely play a key role in the cleavage of the sugar-phosphate C5'-O5' bond in DNA resulting in the direct formation of single strand breaks without significant molecular relaxation. To take into account the solvation effects, we considered the neutral and anion radical of 5'-dTMP surrounded by 5 or 11 water molecules with Na+ as a counterion. These structures were optimized using the B3LYP/6-31G** level of theory. We find the barrier height for adiabatic C5'-O5' bond dissociation of 5'-dTMP anion radical in aqueous environment is so substantially higher than in the gas phase that the adiabatic route will not contribute to DNA strand cleavage in aqueous systems. This result is in agreement with experiment.

Relationships between 31P chemical shift tensors and conformation of nucleic acid backbone: a DFT study

Density functional theory (DFT) has been applied to study the conformational dependence of 31P chemical shift tensors in B-DNA. The gg and gt conformations of backbone phosphate groups representing BI- and BII-DNA have been examined. Calculations have been carried out on static models of dimethyl phosphate (dmp) and dinucleoside-3',5'-monophosphate with bases replaced by hydrogen atoms in vacuo as well as in an explicit solvent. Trends in 31P chemical shift anisotropy (CSA) tensors with respect to the backbone torsion angles alpha, zeta, beta, and epsilon are presented. Although these trends do not change qualitatively upon solvation, quantitative changes result in the reduction of the chemical shift anisotropy. For alpha and zeta in the range from 270 degrees to 330 degrees and from 240 degrees to 300 degrees , respectively, the delta22 and delta33 principal components vary within as much as 30 ppm, showing a marked dependence on backbone conformation. The calculated 31P chemical shift tensor principal axes deviate from the axes of O-P-O bond angles by at most 5 degrees . For solvent models, our results are in a good agreement with experimental estimates of relative gg and gt isotropic chemical shifts. Solvation also brings the theoretical deltaiso of the gg conformation closer to the experimental gg data of barium diethyl phosphate.

Hydration of the phosphate group in double-helical DNA

Water distributions around phosphate groups in 59 B-, A-, and Z-DNA crystal structures were analyzed. It is shown that the waters are concentrated in six hydration sites per phosphate and that the positions and occupancies of these sites are dependent on the conformation and type of nucleotide. The patterns of hydration that are characteristic of the backbone of the three DNA helical types can be attributed in part to the interactions of these hydration sites.

Probing DNA-cationic lipid interactions with the fluorophore trimethylammonium diphenyl-hexatriene (TMADPH)

The aim of this study is to get a better understanding of DNA-cationic lipid complex formation and its characterization through the properties of the lipid assembly, using fluorescent probes known to have different locations in the vesicle bilayer, 1,6-diphenylhexa-1,3,5-triene (DPH) and 1-(4-trimethylammoniumphenyl)-6-phenyl-1,3,5-hexatriene (TMADPH). The location of these two fluorescent probes in the membrane differs; the positive charge of TMADPH is localized close to the water/lipid interface and its fluorophore is present in the upper part of the acyl chain region while DPH (lacking polar group) is embedded deeper in the hydrophobic part of the bilayer. Unilamellar vesicles ( approximately 100 nm size) composed of N-(1-(2, 3-dioleoyloxy)-propyl)-N,N,N-trimethylammonium chloride (DOTAP) and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) as a helper lipid (at 1 : 1 mole ratio) were used as a model of cationic liposomes. Both linear and circular DNA gave almost identical results. DNA-/L+ (mole charge ratio of DNA negatively-charged phosphate to positively-charged lipid) ratios have large effects on the measured parameters. The effects monitored through TMADPH are much more striking than those obtained through the use of DPH, suggesting that the major DNA-lipid interaction occurs at the lipid/water interface. The fact that DNA induced much larger changes in TMADPH fluorescence intensity in H2O than in D2O suggests that the changes in the exposure of TMADPH to water and solvent relaxation effects are involved in the interaction. At DNA-/L+>/=1, fluorescence intensity increased concomitantly with a small increase in TMADPH fluorescence anisotropy without much affect in the size of the complex. At DNA-/L+<0.6, fluorescence quenching proportional to DNA-/L+ occurred, as well as a large increase in TMADPH fluorescence anisotropy and in complex size. These results suggest that at low DNA-/L+, negatively-charged DNA condenses positively-charged lipid headgroups, thereby inducing formation of lipid-ordered domains. This phase separation results in membrane defects at the lipid/water interface and increased exposure of the hydrophobic upper parts of the acyl chains to water, as indicated by the quenching of TMADPH. This leads to instability and aggregation/fusion of the DNA-lipid complexes. On the other hand, at DNA-/L+>/=1, the condensing effect is smaller, involving homogeneous lateral condensation of all the lipids, leading to a reduction in water content near the probe, and the DNA-lipid complexes are relatively small and stable.

Membrane electrostatics

In conclusion, charged membrane together with their adjacent electrolyte solution form a thermodynamic and physico-chemical entity. Their surfaces represent an exceptionally complicated interfacial system owing to intrinsic membrane complexity, as well as to the polarity and often large thickness of the interfacial region. Despite this, charged membranes can be described reasonably accurately within the framework of available theoretical models, provided that the latter are chosen on the basis of suitable criteria, which are briefly discussed in Section A. Interion correlations are likely to be important for the regular and/or rigid, thin membrane-solution interfaces. Lateral distribution of the structural membrane charge is seldom and charge distribution perpendicular to the membranes is nearly always electrostatically important. So is the interfacial hydration, which to a large extent determines the properties of the innermost part of the interfacial region, with a thickness of 2-3 nm. Fine structure of the ion double-layer and the interfacial smearing of the structural membrane charge decrease whilst the surface hydration increases the calculated value of the electrostatic membrane potential relative to the result of common Gouy-Chapman approximation. In some cases these effects partly cancel-out; simple electrostatic models are then fairly accurate. Notwithstanding this, it is at present difficult to draw detailed molecular conclusions from a large part of the published data, mainly owing to the lack of really stringent controls or calibrations. Ion binding to the membrane surface is a complicated process which involves charge-charge as well as charge-solvent interactions. Its efficiency normally increases with the ion valency and with the membrane charge density, but it is also strongly dependent on the physico-chemical and thermodynamic state of the membrane. Except in the case of the stereospecific ion binding to a membrane, the relatively easily accessible phosphate and carboxylic groups on lipids and integral membrane proteins are the main cation binding sites. Anions bind preferentially to the amine groups, even on zwitterionic molecules. Membrane structure is apt to change upon ion binding but not always in the same direction: membranes with bound ions can either expand or become more condensed, depending on the final hydrophilicity (polarity) of the membrane surface. The more polar membranes, as a rule, are less tightly packed and more fluid. Diffusive ion flow across a membrane depends on the transmembrane potential and concentration gradients, but also on the coulombic and hydration potentials at the membrane surface.(ABSTRACT TRUNCATED AT 400 WORDS)

A theoretical study of the aqueous hydration of canonical B d(CGCGAATTCGCG): Monte Carlo simulation and comparison with crystallographic ordered water sites

Monte Carlo computer simulation is described for the dodecamer d(CGCGAATTCGCG) together with 1777 water molecules at an environmental density of 1 gm/cc in a cubic cell under periodic boundary conditions. Water-water interactions were treated using the TIP4P potential and the solute water interactions by TIP4P spliced with the non-bonded interactions from the AMBER 3.0 force field. The stimulation was subjected to proximity analysis to obtain solute coordination numbers and pair interaction energies for each solute atom. Hydration density distributions partitioned into contributions from the major groove side, the minor groove side and the sugar-phosphate backbone were examined, and the probabilities of occurence for one- and two-water bridges in the simulation were enumerated. The results were compared with observations of crystallographic ordered water sites from x-ray diffraction studies on the native dodecamer by Dickerson and coworkers.

Theoretical conformational analysis of phospholipids. II. Role of hydration in the gel to liquid crystal transition of phospholipids

To obtain a satisfactory agreement between computed transition temperatures and those determined experimentally, we introduce explicitly water molecules which hydrate the polar headgroup of dipalmitoylphosphatidylethanolamine molecules. The calculated free energy curves as a function of the intermolecular interchain distance and the degree of hydration of the polar groups permit the determination of the transition of the phospholipid system from the gel to the liquid crystalline phase. The detailed structure of the hydration shell is defined using the supermolecular approach.

The docking manoeuvre at a drug receptor: a quantum mechanical study of intercalative attack of ethidium and its carboxylated derivative on a DNA fragment

Various semi-empirical quantum mechanical methods have been used to investigate the docking manoeuvre of ethidium and of its carboxylated derivative at the (dC-dG) • (dC-dG) receptor. The objective of the work was to determine whether the drug attacks the receptor in a random orientation or is pre-aligned for effective docking. An analogy was made between the interaction and two docking space vehicles. Charge distributions were computed for the intercalative site and the drug molecules; from these distributions it was possible to map, in three-dimensional space, the molecular electrostatic potential surrounding the receptor. Perturbation of the receptor fields by an approaching drug molecule showed field neutralization and a shifting local minimum as docking proceeds. Most of the electrostatic potential surrounding the receptor was shown to be derived from the two ionized phosphate groups. The orientation of the drug molecule was studied in a simplified anionic field constructed to reproduce that of the receptor phosphates. Rotation of ethidium and p -carboxyphenylethidium round the Eulerian axes in this simulated anionic field showed up distinct preferences for orientation of drug molecules in the vicinity of the receptor. Probability distributions for rotational populations demonstrated clearly that the receptor induces an orientation in the approaching ligand. The energy involved in modification of the alignment could be attributed to electrostatic interactions over large separation distances and to induced electron delocalization as the drug approaches closer to the receptor. This partition of the energy was considered further by monitoring electron migration in the drug molecules and analysis of dipole moment fluctuations. Orientation restrictions reflect entropy changes in the association reaction; these are discussed with respect to their importance in determination of reaction kinetics, and in two established models for drug- receptor interaction, namely, the ‘lock and key’ and ‘zipper’ mechanisms.