Thermodynamic functions characterizing intermolecular interactions

It is shown that the Gibbs vaporization potential G^* is additive with respect to molecular groups at all temperatures and it most completely characterizes the intermolecular interactions. The excess entropy of vaporization is identical for all spherical molecules (30 J/mole·K and does not depend on the size of the molecule or the temperature. In long-chain molecules it is additive with respect to the number of links in the chain, varies with temperature, and is equal to the difference between the heat capacities of the gas and liquid and exceeds 30 J/mole·K.Leningrad State Scientific Institute of Industrial Chemistry. Translated from Teoreticheskaya i Éksperimental'naya Khimiya, No. 1, pp. 66–70, January–February, 1991. Original article submitted April 27, 1988.     

Photoactivable peptides for identifying enzyme-substrate and protein-protein interactions

Photoactivated cross-linking of peptides to proteins is a useful strategy for identifying enzyme-substrate and protein-protein interactions in cell lysates as demonstrated by studies on the human hypoxia inducible factor system.     

HolT Hunter: Software for identifying and characterizing low‐strain DNA holliday triangles

Synthetic DNA nanostructures are most commonly held together via Holliday junctions. These junctions allow for a wide variety of different angles between the double helices they connect. Nevertheless, only constructs with a very limited selection of angles have been built, to date, because of the computational complexity of identifying structures that fit together with low strain at odd angles. I have developed an algorithm that finds over 95% of the possible solutions by breaking the problem down into two portions. First, there is a problem of how smooth rods can form triangles by lying across one another. This problem is easily handled by numerical computation. Second, there is the question of how distorted DNA double helices would need to be to fit onto the rod structure. This strain is calculated directly. The algorithm has been implemented in a Mathematica 8 notebook called Holliday Triangle Hunter. A large database of solutions has been identified. Additional interface software is available to facilitate drawing and viewing models. © 2012 Wiley Periodicals, Inc.     

Novel features for identifying A-minors in three-dimensional RNA molecules

RNA tertiary interactions or tertiary motifs are conserved structural patterns formed by pairwise interactions between nucleotides. They include base-pairing, base-stacking, and base-phosphate interactions. A-minor motifs are the most common tertiary interactions in the large ribosomal subunit. The A-minor motif is a nucleotide triple in which minor groove edges of an adenine base are inserted into the minor groove of neighboring helices, leading to interaction with a stabilizing base pair. We propose here novel features for identifying and predicting A-minor motifs in a given three-dimensional RNA molecule. By utilizing the features together with machine learning algorithms including random forests and support vector machines, we show experimentally that our approach is capable of predicting A-minor motifs in the given RNA molecule effectively, demonstrating the usefulness of the proposed approach. The techniques developed from this work will be useful for molecular biologists and biochemists to analyze RNA tertiary motifs, specifically A-minor interactions.     

Nondiagonal second order intermolecular forces for interactions involving molecules

Very often only “diagonal” second order energies, varying as an even power of R^?1, occur in the multipole expansion of the interaction energy. However for many molecular interactions important “nondiagonal” second order energies, varying as an odd or even power of R^?1 can arise. This point is emphasized by a general discussion and by a detailed specific example, the interaction of an ionized dipolar molecule with a nondegenerate atom. Also some useful theorems, on the orientation average of various types of second order energies, are derived.     

Retarded intermolecular interactions involving diamagnetic molecules

Second‐ and third‐order time‐dependent perturbation theory within the multipolar framework of nonrelativistic quantum electrodynamics is used to calculate the retarded dispersion interaction between two diamagnetic molecules, a diamagnetic molecule and a magnetic‐dipole susceptible molecule, and a diamagnetic molecule and an electric‐quadrupole polarizable molecule. New expressions for the energy shift valid for all intermolecular separation distances, R, beyond the region of overlap of molecular electronic wave functions and applicable to a pair of randomly oriented molecules in the ground electronic state are given. The R‐dependent behavior of the far‐zone limit of the interaction energies is also examined. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 437–442, 2000     

Characterization of polyplexes involving small RNA

The purpose of the present study is to provide a tool for an efficient design and synthesis of non-viral vectors for small RNA delivery. The effects of properties of the polycation, such as molecular weight, charge density and backbone structure, to polyplex structure and physicochemical behavior were systematically evaluated. The condensing agents, polyethylenimine (PEI), chitosan (CS) and poly(allylamine) (PAA) were added to sRNA molecules at different N/P ratio. The efficiency of encapsulation and protection of sRNA, as well as polyplex size, zeta potential and morphology were followed and compared. The results show that PEI/sRNA polyplexes display a small size and positive zeta potential. However, for low molecular weights, this polycation is unable to protect sRNA in the presence of a decompacting agent. With chitosan, sRNA is efficiently compacted at high N/P ratios. The CS/sRNA complexes display small sizes, ca. 200 nm, positive surface charge and also good stability. Finally, the PAA/sRNA polyplexes were found to be the smallest at low N/P ratios, displaying a good encapsulation efficiency and high stability. A rationale for the experimental observations is provided using Monte Carlo simulation for systems with polycations of different length and charge density. The simulations showed that there is an interplay between the size of polycation chains and its charge density that define the degree of condensation for sRNA.     

A model for the interactions involving hydrophilic structure maker solutes

Enthalpies of dilution of ternary aqueous solutions containing glucose and alkan-1-ols, alkan-1,2-diols and alkan-m,n-diols were determined at 298.15 K by flow microcalorimetry. The pair-wise cross interaction coefficients of the virial expansion of the excess enthalpies were evaluated: they are positive and depend in a complex manner on the length of the alkyl chain of the alkanols. The behaviour of these systems is interpreted in terms of preferential interactions between the hydrophilic groups of the alkanols and the destructured domain present on glucose.     

Contact ion-exchange interactions in systems involving zeolites

Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1505–1506, August, 1994.     

Fluorescence-based approach for detecting and characterizing antibiotic-induced conformational changes in ribosomal RNA: comparing aminoglycoside binding to prokaryotic and eukaryotic ribosomal RNA sequences

Aminoglycoside antibiotics bind specifically to a conserved sequence of the 16S ribosomal RNA (rRNA) A site and interfere with protein synthesis. One model for the mechanism underlying the deleterious effects of aminoglycosides on protein synthesis invokes a drug-induced conformational change in the rRNA that involves the destacking of two adenine residues (A1492 and A1493 in Escherichia coli) at the A site. We describe here a fluorescence-based approach for detecting and characterizing this drug-induced conformational change in the target rRNA. In this approach, we insert the fluorescent base analogue 2-aminopurine in place of A1492 in an E. coli 16S rRNA A-site model oligonucleotide (EcWT) as well as in a mutant form of this oligomer (A1408G) in which A1408 has been replaced with a guanine. The presence of guanine at 1408 instead of adenine represents one of the major sequence differences between prokaryotic and eukaryotic A sites, with the latter A sites being resistant to the deleterious effects of aminoglycosides. Binding of the aminoglycoside paromomycin to the 2AP-substituted forms of EcWT and A1408G induced changes in fluorescence quantum yield consistent with drug-induced base destacking in EcWT but not A1408G. Isothermal titration calorimetry studies reveal that paromomycin binds to the EcWT duplex with a 31-fold higher affinity than the A1408G duplex, with this differential affinity being enthalpic in origin. In the aggregate, these observations are consistent with both rRNA binding affinity and drug-induced base destacking being important determinants in the prokaryotic specificity of aminoglycosides. Combining fluorescence quantum yield and lifetime data allows for quantification of the extent of drug-induced base destacking, thereby providing a convenient tool for evaluating the relative impacts of both novel and existing A-site targeting ligands on rRNA conformation and potentially for predicting relative antibiotic activities and specificities.     

Intermacromolecular interactions involving linear and network polyacids and nonionic polymers

Interactions between linear and network polymers are studied in the case when one component is a polyacid and the other component is an uncharged polymer. It is shown that, under different reaction conditions, swelling or contraction of the polymer network can be observed for the same pair of reagents. It is found that, during consideration of the formation of an interpolymer complex between network and linear polymers, a distinction should be made between a semi-interpenetrating network and a hydrogel with a modified surface. The latter forms under conditions when the linear polymer practically does not penetrate the network and the complexation occurs predominantly on the sample surface.     

Methods for investigating G-quadruplex DNA/ligand interactions

DNA is considered an important target for drug design and development. Until recently, the focus was on double-stranded (duplex) DNA structures. However, it has now been shown that single stranded DNA can fold into hairpin, triplex, i-motif and G-quadruplex structures. The more interesting G-quadruplex DNA structures comprise four strands of stacked guanine (G)-tetrads formed by the coplanar arrangement of four guanines, held together by Hoogsteen bonds. The DNA sequences with potential to form G-quadruplex structures are found at the chromosomal extremities (i.e. the telomeres) and also at the intra-chromosomal region (i.e. oncogenic promoters) in several important oncogenes. The formation of G-quadruplex structures is considered to have important consequences at the cellular level and such structures have been evoked in the control of expression of certain genes involved in carcinogenesis (c-myc, c-kit, K-ras etc.) as well as in the perturbation of telomeric organization. It has been shown that the formation of quadruplexes inhibits the telomere extension by the telomerase enzyme, which is up-regulated in cancer cells. Therefore, G-quadruplex structures are an important target for drug design and development and there is a huge interest in design and development of small molecules (ligands) to target these structures. A large number of so-called G-quadruplex ligands, displaying varying degrees of affinity and more importantly selectivity (i.e. the ability to interact only with quadruplex-DNA and not duplex-DNA), have been reported. Access to efficient and robust in vitro assays is needed to effectively monitor and quantify the G-quadruplex DNA/ligand interactions. This tutorial review provides an overview of G-quadruplex ligands and biophysical techniques available to monitor such interactions.     

Methods for modified nucleotide identification in ribosomal RNA

Modified nucleotides are ubiquitous in all functional RNA, such as ribosomal RNA. The identification of modified nucleotides is essential for understanding the functional role of RNA in living cells. This review is devoted to methods used to identify modified nucleotides in ribosomal RNA.     

Electronic structure of carbon trioxide and vibronic interactions involving Jahn-Teller states

The electronic structure of CO3 is characterized by equation-of-motion and coupled-cluster methods. C(2v) and D(3h) isomers are considered. Vertical excitation energies, transition dipoles, and the molecular orbital character of the excited states are presented for singlet and triplet manifolds. Ground-state equilibrium structures and frequencies are strongly affected by vibronic interactions with low-lying excited states. At D(3h) geometries, the vibronic interactions are enhanced by the Jahn-Teller character of the excited states. The curvature of the potential energy surface and the existence of the D(3h) minimum are very sensitive to the correlation treatment and the basis set. The correlation effects are stronger at D(3h), in agreement with a smaller HOMO-LUMO gap.     

Calculation of van der Waals interactions involving lipid vesicles

Van der Waals energies of interaction involving vesicles and lipid layers are calculated for different geometries. Results from exact and approximate calculations are compared with some existing experimental data. It is shown that sufficient accuracy can be obtained using relatively simple ‘additivity’ approximations for the contribution of dispersion interactions. A set of calculated results is presented for a small unilamellar vesicle interacting with coated and uncoated metal and polymer surfaces. A lipid coating lowers magnitude of the interaction energy approximately two-fold. The procedure gives a simple possibility to estimate Hamaker constants (and ‘Hamaker functions’) from handbook data taking into account the existing uncertainity in the materials constants of the interacting substances.     

Comprehensive chemical characterization of complexes involving lead-amino acid interactions

Complexes of lead with L-phenylalanine, L-isoleucine, L-valine, or L-arginine have been isolated from reaction mixtures containing lead nitrate and the respective amino acid in acidic aqueous solution. The compounds have been comprehensively characterized using X-ray crystallography, solid state NMR spectroscopy and solution state NMR spectroscopy, IR and Raman spectroscopies, and electrospray ionization mass-spectrometry. The solid state structures of lead-phenylalanine, lead-valine, and lead-valine-isoleucine complexes show a lead center coordinated by two amino acid ligands, while the lead-arginine complex is a cluster involving two lead centers and three arginine molecules. The structural, spectroscopic, and spectrometric characterization of the complexes provides a basis to establish a fundamental understanding of heavy metal-amino acid interactions.