How does modification of adenine by hydroxyl radical influence the stability and the nature of stacking interactions in adenine-cytosine complex?

This study reports on ab initio calculations of adenine - cytosine complexes in two different context alignments appearing in B-DNA. The influence of adenine modification by hydroxyl radical on the stability of the complexes is also discussed. The analysis was performed on over 40 crystallographic structures for each of the sequence contexts. In most cases, modification of adenine by hydroxyl radical leads to less negative intermolecular interaction energies. The issue of the influence of alteration of structural base step parameters on the stability of modified and unmodified adenine - cytosine complexes is also addressed. Analysis of the dependence of intermolecular interaction energy on base step parameters reveals that for twist and shift modification of adenine by hydroxyl radical leads to quite different interaction energy profiles in comparison with unmodified complexes. In order to elucidate the physical origins of this phenomenon, i.e. to analyze how the modification of adenine by hydroxyl radical is reflected in the change of intermolecular interaction energy components, a variational-perturbational decomposition scheme was applied at the MP2/aug-cc-pVDZ level of theory.     

Interaction of caffeine with basic nucleic acids my a molecular mechanic method

To understand some aspects of the biological action of caffeine (CAF), the interaction energies for various mutual positions of CAF and DNA bases or basepairs were calculated. Three types of mutual CAF-base (CAF-basepair) arrangements corresponding to the minima of interaction energy were revealed. One type of minima correspond to the stacking arrangement of molecules. This type is important for interactions of CAF with DNA monomers and single-stranded fragments. The other two types of minima correspond to the formation of intermolecular hydrogen bonds. Some of these minima may occur during the interaction of CAF with the double helix. One of these types corresponds to the nearly in-plane position of molecules. The other type of minima correspond to the nearly perpendicular arrangement of molecule planes. The minima of the last type are supposed to be the most important for the interaction of CAF with the DNA duplex, and interaction energies for this type of minima have the most negative values.     

Interactions between nucleic acid bases. New parameters of potential functions and energy minima

The parameters of atom-atom potential functions suggested by one of the authors in 1979-1986 were slightly changed. The changes were performed to achieve a better agreement with experimental data of interaction energy values in global minima and hydrogen bond lengths. These changes resulted in better accord with experimental values of distances between the layers in DNA monomer crystals and between the base pairs in oligonucleotide duplexes. The refined potential functions were used to calculate the energy of interactions between nucleic acid bases in various mutual positions. The calculations revealed a few types of mutual base arrangements in minima of interaction energy for each pairwise base combination. A new type of minima was found, which correspond to a nearly perpendicular arrangement of base rings and the formation of the intermolecular hydrogen bond.     

Insight on the interaction of polychlorobiphenyl with nucleic acid–base

The interaction between one polychlorobiphenyl (3,3′,4,4′,-tetrachlorobiphenyl, coded PCB77) and the four DNA nucleic acid–base is studied by means of quantum mechanics calculations in stacked conformations. It is shown that even if the intermolecular dispersion energy is the largest component of the total interaction energy, some other contributions play a non negligible role. In particular the electrostatic dipole-dipole interaction and the charge transfer from the nucleobase to the PCB are responsible for the relative orientation of the monomers in the complexes. In addition, the charge transfer tends to flatten the PCB, which could therefore intercalate more easily between DNA base pairs. From these seminal results, we predict that PCB could intercalate completely between two base pairs, preferably between Guanine:Cytosine pairs.

Possible configuration of dimers of Gua-Cyt bases. Computation by molecular mechanic models and density functional theory

The energies of interactions between guanine and cytosine in various mutual positions were calculated by the methods of molecular mechanics with refined atom-atom potential functions and the quantum mechanics theory of density functional. Both methods indicate three types of mutual positions of bases in local energy minima. These types correspond to (1) nearly coplanar base positions with intermolecular hydrogen bond formation (base pairing); (2) arrangements of two bases in nearly parallel planes one above another (base stacking); and (3) nearly perpendicular positions of base planes. According to the calculations, the global energy minimum corresponds to the Watson-Crick base pair with three hydrogen bonds. A specific feature of the pair is a transition from many positions of type (2) to positions of type (1) without any energy barrier. This feature is revealed by both methods. Another special feature of this pair is a deviation, for most of mutual base positions, of the amine group atoms from the ring plane, the deviation being more pronounced for Gua. These features are important for understanding the conformational behavior of DNA fragments and the RNA structure.     

Monitoring the Activity of Single Translocons

Recent studies introduced a novel view that the SecYEG translocon functions as a monomer and interacts with the dimeric SecA ATPase, which fuels the preprotein translocation reaction. Here, we used nanodisc-reconstituted SecYEG to characterize the functional properties of single copies of the translocon. Using a method based on intermolecular Förster resonance energy transfer, we show for the first time that isolated nanodisc-reconstituted SecYEG monomers support preprotein translocation. When several copies of SecYEG were co-reconstituted within a nanodisc, no change in translocation kinetics was observed, suggesting that SecYEG oligomers do not facilitate enhanced translocation. In contrast, nanodisc-reconstituted monomers of the PrlA4 variant of SecYEG showed increased translocation rates. Experiments based on intramolecular Förster resonance energy transfer within the nanodisc-isolated monomeric SecYEG demonstrated a nucleotide-dependent opening of the channel upon interaction with SecA. In conclusion, the nanodisc-reconstituted SecYEG monomers are functional for preprotein translocation and provide a new prospect for single-molecule analysis of dynamic aspects of protein translocation.     

Strong interaction between disulfide derivatives and aromatic groups in peptides and proteins

The intermolecular interaction energy of complexes of dimethyldisulfide with benzene and cyclohexane, respectively, was computed as function of the relative distance and orientation within each pair of molecules. The energy of the most stable orientation of the dimethyldisulfide-cyclohexane complex is ?2.57 kcal/mol, while that of the most stable orientation of the dimethyldisulfide-benzene complex is ?3.33 kcal/mol. The energy difference of ～0.8 kcal/mol is due to favorable specific nonbonded interactions between the sulfur atoms and the atoms of the aromatic ring. Proper parameterization of empirical interatomic energies, used in computations in this laboratory, accounts for these interactions without the need for a $\text{special}$ sulfur-aromatic potential energy function.     

The Spherical Expansion of H2 Dimer Interaction Energy by Double Symmetry-Adapted Perturbation Theory

Abstract

The weak interaction energy of H₂ dimer is studied by double symmetry-adapted perturbation theory (SAPT) within second-order of intermolecular and intramonomer perturbation for molecular simulations. The assumed orientations of H₂ dimer are linear, parallel, T type and X type. Among four orientations T orientation is the most stable, while linear orientation is the most repulsive. The second-order dispersion energy E _disp ⁽²⁾ is the most attractive contribution in all orientations. The interaction energy has the anisotropy, so we expressed our total interaction energy by the spherical expansion to compare with the experimental value. The isotropic interaction energy is about 85% of the experimental value.     

Computer simulation of the association of caffeine and actinocin derivatives in aqueous solutions

The association of caffeine and actinocin derivatives (ActII), analogs of the antitumor antibiotic actinomycin D, was studied by molecular dynamics simulation in explicit solvent (water and Na⁺ and Cl^? ions). Information was obtained describing in detail the association of caffeine and ActII in water and water-salt solution and the interaction of monomers and their associates with the ionic hydrate environment. The schemes of hydration of monomers of actinocin derivatives and caffeine and their self-and heteroassociates are determined. The calculated energies of monomer interaction in associates indicate that dimerization of these compounds in aqueous solutions is advantageous in energy. Both self-and heteroassociates are stabilized by van der Waals, electrostatic, and hydrophobic interactions, as well as intermolecular hydrogen bonds. The rearrangement of the hydration shells of monomers during their association in water is energy-unfavorable and destabilizes the associates. In water-salt solutions, it is energy-favorable for the systems containing associates of the singly charged ActII⁺ and caffeine-ActII⁺. The formation of caffeine-actinocin heterodimers is preferable in energy to the formation of self-associates. In this way caffeine can decrease the concentration of the actinocin derivatives in solution and thereby decrease their biological activity.     

Quantum mechanical study of bases interactions in various associates in atomic dipole approximation

Expressions for the various components of the long-range interaction energy of any number of molecules are obtained by the perturbation theory method in atomic dipole approximation. These expressions are used for the study of base interaction nature in coplanar pairs and stacked dimers formed of neighbouring Watson-Crick pairs. Bases wave functions are computed by the CNDO-CI method. The in-plane interactions are shown to give the dominant contribution into the DNA stabilization energy in vacuum. The estimations performed for the solvent effect on intermolecular interaction energy allowed one to draw a conclusion about the decisive role of hydrophobic interactions in a base stacking.     

Synthesis and properties of DNA-PNA chimeric oligomers.

Adenine, thymine and cytosine PNA monomers have been prepared using 3-amino-1,2-propanediol as a starting material. The benzoyl group was used to protect the exocyclic amines of the heterocyclic bases of A and C PNA monomers and the backbone primary amine was protected with the monomethoxytrityl group. The thymine and cytosine PNA monomers were used in conjunction with standard DNA synthesis monomers to produce chimeric PNA DNA (PDC) oligomers. Ultraviolet melting studies confirmed that these oligomers form stable hybrids with complementary DNA strands and that mismatches in the DNA but more so in the PNA sections lead to duplex destabilisation.     

Energy migration as related to the mutual position and orientation of donor and acceptor molecules in LH1 and LH2 antenna complexes of purple bacteria

Many approaches to discovering the interaction energy of molecular transition dipoles use the well-known coefficient xi(phi, psi (1) psi (2)) = (cos phi - 3 cos psi (1) cos psi (2))(2), where phi, Psi (1), and Psi (2) are inter-dipole angles. Unfortunately, this formula often yields rather approximate results, in particular, when it is applied to closely positioned molecules. This problem is of great importance when dealing with energy migration in photosynthetic organisms, because the major part of excitation transfers in their chlorophyllous antenna proceed between closely positioned molecules. In this paper, the authors introduce corrected values of the orientation factor for several types of mutual orientation of molecules exchanging with electronic excitations for realistic ratios of dipole lengths and spacing. The corrected magnitudes of interaction energies of neighboring bacteriochlorophyll molecules in LH2 and LH1 light-absorbing complexes are calculated for the class of photosynthetic purple bacteria. Some advantageous factors are revealed in their mutual positions and orientations in vivo.     

Molecular dynamics simulations of the auxin‐binding protein 1 in complex with indole‐3‐acetic acid and naphthalen‐1‐acetic acid

Auxin‐binding protein 1 (ABP1) is suggested to be an auxin receptor which plays an important role in several processes in green plants. Maize ABP1 was simulated with the natural auxin indole‐3‐acetic acid (IAA) and the synthetic analog naphthalen‐1‐acetic acid (NAA), to elucidate the role of the KDEL sequence and the helix at the C‐terminus. The KDEL sequence weakens the intermolecular interactions between the monomers but stabilizes the C‐terminal helix. Conformational changes at the C‐terminus occur within the KDEL sequence and are influenced by the binding of the simulated ligands. This observation helps to explain experimental findings on ABP1 interactions with antibodies that are modulated by the presence of auxin, and supports the hypothesis that ABP1 acts as an auxin receptor. Stable hydrogen bonds between the monomers are formed between Glu40 and Glu62, Arg10 and Thr97, Lys39, and Glu62 in all simulations. The amino acids Ile22, Leu25, Trp44, Pro55, Ile130, and Phe149 are located in the binding pocket and are involved in hydrophobic interactions with the ring system of the ligand. Trp151 is stably involved in a face to end interaction with the ligand. The calculated free energy of binding using the linear interaction energy approach showed a higher binding affinity for NAA as compared to IAA. Our simulations confirm the asymmetric behavior of the two monomers, the stronger interaction of NAA than IAA and offers insight into the possible mechanism of ABP1 as an auxin receptor. Proteins 2014; 82:2744–2755. © 2014 Wiley Periodicals, Inc.     

On the nature of stability of the nucleotide base associates in water solution

Expression for the long-range intermolecular interaction energy obtained by the perturbation theory method in atomic dipole approximation are used for the study of the nature of base interaction in stacked dimers formed of two neighbouring DNA base pairs. Base wave functions are computed by the CNDO-CI method. The inplane interactions are shown to give the dominant contribution into the DNA stabilization energy in vacuum. The estimations performed for the solvent effect on intermolecular interaction energy allowed us to draw conclusions about the decisive role of hydrophobic interactions in a base stacking.     

Towards an understanding of the arginine-aspartate interaction.

We have made a comparison of the geometries of intra- and intermolecular arginine-aspartate interactions by extracting orientation information from protein co-ordinate data. The results show a pronounced difference, with both types of interaction preferring to form twin N-H . . . O = C hydrogen bonds, but involving different nitrogen atoms. In intramolecular interactions, the aspartate favours a "side on" geometry, forming hydrogen bonds with N epsilon and N eta 2; in the intermolecular case, however, "end on" contacts involving N eta 1 and N eta 2 of the arginine are preferred. We have used Distributed Multipole Analysis of the methylguanidinium-acetate system to model the electrostatic component of the arginine-aspartate ion pair interaction in vacuo. We find, in agreement with the experimental arginine-aspartate distribution, that side on and end on doubly N-H . . . O = C hydrogen-bonded configurations are clearly the most favourable, with the side on being marginally lower in energy. Thus, despite the many competing side-chain interactions in proteins, many arginine-aspartate pairs adopt one of the minimum electrostatic energy conformations, or one close to a minimum. Within each of the two regions (side on and end on) we find only a small energy gap between the "symmetric" doubly hydrogen-bonded and slightly displaced "staggered" structures, again in agreement with the crystal structure data. Further calculations of the total ab initio interaction energy show that this follows the electrostatic term in its orientational variation, this phenomenon of "electrostatic domination" being well known in hydrogen-bonded systems. The end on arginine nitrogen atoms are observed to be more surface-exposed than N epsilon, as demonstrated by their greater accessibilities over a large sample of proteins. This helps explain the side on and end on preferences of intra- and intermolecular interactions, respectively. We also note the effect of short sequence intervals, particularly i in equilibrium with i + 2 relationships, in forcing many intramolecular contacts to be side on.     

Study of the interaction of DNA and acridine orange by various optical methods

The degree of binding of acridine orange to DNA, native or denatured, has been determined by equilibrium dialysis in 0.1M and 0.001M NaCl at 20°. The nature of the binding process has been investigated by studying various optical properties of the dye–DNA complexes and by relating them to the binding ratio. All these properties were found to vary quantitatively and qualitatively according to the successive stages of the process. These stages were assumed to be a strong binding of intercalated monomers followed by formation of bound dimers and finally by external binding of aggregates of native DNA. Absorption spectra of the complexes could be interpreted on that basis. Circular dichroism spectra were resolved into components: one band for intercalated monomers without interactions, two excition splittings for interacting monomers and bound dimers, respectively, weak bands and exciton splitting for external aggregates. The fluorescence intensity was greatly enhanced in intercallated monomers; its quenching at higher binding ratio was quantitatively related to dimer fixation. The value of the anisotropy of fluorescence at low binding ratio suggested a limited mobility of intercalated monomers; the decrease of polarization at higher binding was attributed to energy transfer between monomers. Electric dichroism displayed by the complexes in the dye absorption bands indicated an orientation of the bound molecules quite parallel to the base rings at low binding. In the range of fixation of dimers and external molecules, the dichroism was lower but still indicated an important degree of ordering.     

Analysis of intermolecular interaction energy inputs in benzene-imidazole and imidazole-imidazole systems in parallel displaced and T-configuration

Intermolecular interactions in several dimer aromatic systems were analyzed to determine how various energy contributions (electrostatic, exchange, repulsion, and polarization) change depending on the value of monomers separation. Different contributions to the intermolecular energy interactions between imidazole-imidazole and benzene-imidazole dimers are studied using the aug-cc-pVDZ basis set in the framework of ab initio Hartree-Fock and second-order Møller-Plesset perturbation theory methods. Special attention is paid to the exchange and dispersion energy binding contributions.     

Interactions Between Amino Groups in DNA. An Ab Initio Study and a Comparison with Empirical Potentials

Abstract

An ab initio quantum chemical analysis of the close amino group contacts, existing in many DNA crystal structures, is presented. The calculations are made at the Hartree-Fock (HF) level with medium 6–31G* and 6–31 G(NH₂*) basis sets as well as with inclusion of correlation energy using the second order Møller-Plesset theory (MP2) with the 6–31G* basis set. We demonstrate that the model system (methylamine dimer, cytosine dimer) amino groups are forced to adopt significantly non-planar geometry to stabilize their mutual interaction. Comparison is made with a representative set of empirical potentials including AMBER, CHARMM and GROMOS. The empirical potentials are not reliable enough to analyze the amino group contacts occurring in the DNA double helices. We propose that the mutual amino group interactions contribute to the conformational variability of the CpG and ApT B-DNA steps.     

Computer simulation of the association of caffeine and actinocin derivatives in aqueous solutions

The association of caffeine and actinocin derivatives (ActII), the analogues of anticancer antibiotic actinomycin D, was studied by molecular dynamics simulation. The simulation was carried out with consideration of solvent molecules, water and Na+ and Cl- ions. The information was obtained which describes in detail the association of caffeine and ActII in water and aqueous-salt solutions and interaction of monomers and dimers with water-ion environment. The hydration schemes for monomers and associated forms of caffeine and ActII were determined. The calculated values of interaction energies of monomers in dimers show that the aggregation of these compounds in aqueous solutions is an energetically favorable process. The self- and heteroassociates were stabilized by van-der-Waals, electrostatic, and hydrophobic interactions and also due to the formation of intermolecular hydrogen bonds. The reconstruction of hydration shells of monomers after their association in water is energetically unfavorable and destabilizes the dimer formation. The reconfiguration of hydration shell of monomers after their association in the presence of Na+ and Cl- ions is energetically favorable for dimer of singly charged ActII+ and heteroassociates Cf-ActII+. The formation of heterodimers Cf-ActII is energetically more favorable than the formation of self-associates of caffeine. Therefore, caffeine can decrease the concentration of aromatic biologically active compounds, actinocin derivatives, in solution through the formation of heteroassociates and hence lead to a decrease in the pharmacological activity of the analogues of anticancer antibiotic acting as an interceptor.     

Modeling interactions between a β‐O‐4 type lignin model compound and 1‐allyl‐3‐methylimidazolium chloride ionic liquid

Aiming at understanding the molecular mechanism of the lignin dissolution in imidazolium‐based ionic liquids (ILs), this work presents a combined quantum chemistry (QC) calculation and molecular dynamics (MD) simulation study on the interaction of the lignin model compound, veratrylglycerol‐β‐guaiacyl ether (VG) with 1‐allyl‐3‐methylimidazolium chloride ([Amim]Cl). The monomer of VG is shown to feature a strong intramolecular hydrogen bond, and its dimer is indicated to present important π‐π stacking and intermolecular hydrogen bonding interactions. The interactions of both the cation and anion of [Amim]Cl with VG are shown to be stronger than that between the two monomers, indicating that [Amim]Cl is capable of dissolving lignin. While Cl^– anion forms a hydrogen‐bonded complex with VG, the imidazolium cation interacts with VG via both the π‐π stacking and intermolecular hydrogen bonding. The calculated interaction energies between VG and the IL or its components (the cation, anion, and ion pair) indicate the anion plays a more important role than the cation for the dissolution of lignin in the IL. Theoretical results provide help for understanding the molecular mechanism of lignin dissolution in imidazolium‐based IL. The theoretical calculations on the interaction between the lignin model compound and [Amim]Cl ionic liquid indicate that the anion of [Amim]Cl plays a more important role for lignin dissolution although the cation also makes a substantial contribution.