Żaneta Czyżnikowska

Structural variability and the nature of intermolecular interactions in Watson-Crick B-DNA base pairs.

A set of nearly 100 crystallographic structures was analyzed using ab initio methods in order to verify the effect of the conformational variability of Watson-Crick guanine-cytosine and adenine-thymine base pairs on the intermolecular interaction energy and its components. Furthermore, for the representative structures, a potential energy scan of the structural parameters describing mutual orientation of the base pairs was carried out. The results were obtained using the hybrid variational-perturbational interaction energy decomposition scheme. The electron correlation effects were estimated by means of the second-order Møller-Plesset perturbation theory and coupled clusters with singles and doubles method adopting AUG-cc-pVDZ basis set. Moreover, the characteristics of hydrogen bonds in complexes, mimicking those appearing in B-DNA, were evaluated using topological analysis of the electron density. Although the first-order electrostatic energy is usually the largest stabilizing component, it is canceled out by the associated exchange repulsion in majority of the studied crystallographic structures. Therefore, the analyzed complexes of the nucleic acid bases appeared to be stabilized mainly by the delocalization component of the intermolecular interaction energy which, in terms of symmetry adapted perturbation theory, encompasses the second- and higher-order induction and exchange-induction terms. Furthermore, it was found that the dispersion contribution, albeit much smaller in terms of magnitude, is also a vital stabilizing factor. It was also revealed that the intermolecular interaction energy and its components are strongly influenced by four (out of six) structural parameters describing mutual orientation of bases in Watson-Crick pairs, namely shear, stagger, stretch, and opening. Finally, as a part of a model study, much of the effort was devoted to an extensive testing of the UBDB databank. It was shown that the databank quite successfully reproduces the electrostatic energy determined with the aid of ab initio methods.

Long-range corrected DFT calculations of charge-transfer integrals in model metal-free phthalocyanine complexes

An assessment of several widely used exchange--correlation potentials in computing charge-transfer integrals is performed. In particular, we employ the recently proposed Coulomb-attenuated model which was proven by other authors to improve upon conventional functionals in the case of charge-transfer excitations. For further validation, two distinct approaches to compute the property in question are compared for a phthalocyanine dimer.

Theoretical insights into the nature of intermolecular interactions in cytosine dimer

In this study we discuss stacking interactions in cytosine dimer in conformations appearing in B-DNA crystals. The variational-perturbational scheme was applied for decomposition of the intermolecular interaction energy at the MP2 level of theory. The significant influence of the mutual orientation of cytosine monomers was observed not only on the total intermolecular interaction energy but also on its components: Different components of intermolecular interaction energy depend in different manner on parameters describing mutual orientation of cytosine monomers.

Computational Studies of Darunavir into HIV-1 Protease and DMPC Bilayer: Necessary Conditions for Effective Binding and the Role of the Flaps

Human immunodeficiency virus type 1 protease (HIV-1 PR) is one of the main targets toward AIDS therapy. We have selected the potent drug darunavir and a weak inhibitor (fullerene analog) as HIV-1 PR substrates to compare proteases conformational features upon binding. Molecular dynamics (MD), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and quantum-mechanical (QM) calculations indicated the importance of the stability of HIV-1 PR flaps toward effective binding: a weak inhibitor may induce flexibility to the flaps, which convert between closed and semiopen states. A water molecule in the darunavir-HIV-1 PR complex bridged the two flap tips of the protease through hydrogen bonding (HB) interactions in a stable structure, a feature that was not observed for the fullerene-HIV-1 PR complex. Additionally, despite that van der Waals interactions and nonpolar contribution to solvation favored permanent fullerene entrapment into the cavity, these interactions alone were not sufficient for effective binding; enhanced electrostatic interactions as observed in the darunavir-complex were the crucial component of the binding energy. An alternative pathway to the usual way of a ligand to access the cavity was also observed for both compounds. Each ligand entered the binding cavity through an opening between the one flap of the protease and a neighboring loop. This suggested that access to the cavity is not necessarily regulated by flap opening. Darunavir exerts its biological action inside the cell, after crossing the membrane barrier. Thus, we also initiated a study on the interactions between darunavir and the DMPC bilayer to reveal that the drug was accommodated inside the bilayer in conformations that resembled its structure into HIV-1 PR, being stabilized via HBs with the lipids and water molecules.

Structure and mode of action of cyclic lipopeptide pseudofactin II with divalent metal ions

The interaction of natural lipopeptide pseudofactin II with a series of doubly charged metal cations was examined by matrix-assisted laser-desorption ionization-time of flight (MALDI-TOF) mass spectrometry and molecular modelling. The molecular modelling for metal-pseudofactin II provides information on the metal-peptide binding sites. Overall, Mg(2+), Ca(2+) and Zn(2+) favor the association with oxygen atoms spanning the peptide backbone, whereas Cu(2+) is coordinated by three nitrogens. Circular dichroism (CD) results confirmed that Zn(2+) and Cu(2+) can disrupt the secondary structure of pseudofactin II at high concentrations, while Ca(2+) and Mg(2+) did not essentially affect the structure of the lipopeptide. Interestingly, our results showed that the addition of Zn(2+) and Cu(2+) helped smaller micelles to form larger micellar aggregates. Since pseudofactin II binds metals, we tested whether this phenomena was somehow related to its antimicrobial activity against Staphylococcus epidermidis and Proteus mirabilis. We found that the antimicrobial effect of pseudofactin II was increased by supplementation of culture media with all tested divalent metal ions. Finally, by using Gram-positive and Gram-negative bacteria we showed that the higher antimicrobial activity of metal complexes of pseudofactin II is attributed to the disruption of the cytoplasmic membrane.

Physical origins of the stability of aromatic amino acid core ring-polycyclic hydrocarbon complexes: a post-Hartree-Fock and density functional study.

Noncovalent interactions between four aromatic amino acid core rings and polycyclic hydrocarbons (up to 58 carbon atoms) were investigated at the post–Hartree–Fock level of theory and with the aid of the density functional theory. In particular, the intermolecular interaction energy was partitioned into physically meaningful contributions using the hybrid variational–perturbational decomposition scheme. It was found that electrostatic interactions are completely quenched by associated exchange repulsion. In terms of magnitude, the latter component is 2–3 times larger than the former one. As a result, the complexes are solely stabilized by attractive dispersion forces. Moreover, the SAPT–DFT framework was employed with an eye toward a comparison of various approaches used to compute the dispersion energy. As part of a model study, the impact of the correct representation of the electron density on the description of intermolecular interactions was analyzed as well. It was shown that in the case of the investigated complexes, it is sufficient to augment the basis set with diffuse functions only in the region of the mutual overlap of molecules in stacked alignment.

Physicochemical study of biomolecular interactions between lysosomotropic surfactants and bovine serum albumin

The interactions between two cationic lysosomotropic surfactants (2-dodecanoyloxyethyl)trimethylammonium bromide (DMM-11) and (2-dodecanoyloxypropyl)trimethylammonium bromide (DMPM-11) with bovine serum albumin (BSA) in Hepes buffer (pH=7.4) were systematically studied by surface tension, fluorescence and circular dichroism (CD) spectroscopy and isothermal titration calorimetry (ITC). Furthermore, the size of the micellar aggregates and the polydispersity indexes of both cationic surfactants were studied by dynamic light scattering technique (DLS). The hydrodynamic radii, micellar volumes and aggregation numbers were calculated using a method based on density functional theory (DFT). The results showed that, in both cases, the surface tension was modified upon addition of BSA, and the critical micelle concentration (CMC) values of DMM-11 and DMPM-11 were higher in the presence of BSA. The fluorescence intensity of BSA decreased significantly as the concentration of both cationic surfactants increased and this effect was attributed to the formation of surfactant-BSA complexes. Synchronous fluorescence spectrometry showed the binding-induced conformational changes in BSA. Finally, CD and DLS results revealed the occurrence of changes in the secondary structure of the protein in the presence of both surfactants. In conclusion, understanding the interactions between lysosomotropic surfactants and BSA is required to explore their potential applications in medicine.

The impact of two –GlyProGly– motifs on formation of di-copper complexes by His4-cyclopeptides

The interactions of copper(II) ions with the macrocyclic peptide, c(HKHGPG)2, were investigated in aqueous solution as a function of pH by potentiometric titration, spectroscopic (UV-Vis, CD, and EPR) and mass spectrometry (ESI-MS) measurements. The experiments were conducted for two different ligand to metal ratios: 1:1 and 1:2. The present study reveals that below pH 6 only mononuclear complexes exist in the case of both systems (L:Cu(II) = 1:1, L:Cu(II) = 1:2). However, in an alkaline medium dinuclear forms are preferred, which are dominant in the system containing two equiv. of copper(II). Under basic conditions the {2NIm, 2Nam−} coordination mode is favored. Furthermore, a molecular modeling study was performed in order to characterize structural aspects of the formation of di-copper(II) complexes by His4-cyclopeptides. The comparison of coordination properties of c(HKHP)2 and c(HKHGPG)2 allowed to characterize the impact of two –GlyProGly– motifs on formation of di-copper complexes by His4-cyclopeptides.

The B–H–B bridging interaction in B-substituted oxazaborolidine–borane complexes: a theoretical study

Ten oxazaborolidine–borane complexes, nine among them boron-substituted (B–R, R=CH3, CF3, and OCH3), are carefully analysed using quantum-chemistry methods to determine their equilibrium geometries and the corresponding oxazaborolidine–borane interaction energies. It is observed that in all B-trifluoromethyl substituted oxazaborolidine–borane complexes and in one B-methyl substituted complex the B–H–B bond is formed and the interaction energies are 1.5–2.5 times as large as in other investigated complexes. We believe that the presented results may be helpful in experimental recognition of oxazaborolidine–borane complexes which may appear, inter alia, as reaction intermediates.

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.