Biomedical subjects

Andriy Kovalenko

Publications and source records attributed to Andriy Kovalenko.

14 recordsLinked to original sources

PubMed2007

Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation.

Water molecules confined in protein cavities are of great importance in understanding the protein structure and functions. However, it is a nontrivial task to locate such water molecules in protein by the ordinary molecular simulation and modeling techniques as well as experimental methods. The present study proves that the three-dimensional reference interaction site model (3D-RISM) theory, a recently developed statistical-mechanical theory of molecular solvation, has an outstanding advantage in locating such water molecules. In this paper, we demonstrate that the 3D-RISM theory is able to reproduce the structure and the number of water molecules in cavities of hen egg-white lysozyme observed commonly in the X-ray structures of different resolutions and conditions. Furthermore, we show that the theory successfully identified a water molecule in a cavity, the existence of which has been ambiguous even from the X-ray results. In contrast, we confirmed that molecular dynamics simulation is helpless at present to find such water molecules because the results substantially depend on the initial coordinates of water molecules. Possible applications of the theory to problems in the fields of biochemistry and biophysics are also discussed.

Computational Biology↗

PubMed2006

Microtubule stability studied by three-dimensional molecular theory of solvation.

We study microtubular supramolecular architectures of tubulin dimers self-assembling into linear protofilaments, in turn forming a closed tube, which is an important component of the cytoskeleton. We identify the protofilament arrangements with the lowest free energy using molecular dynamics to optimize tubulin conformations. We then use the three-dimensional molecular theory of solvation to obtain the hydration structure of protofilaments built of optimized tubulins and the solvent-mediated effective potential between them. The latter theoretical method, based on first principles of statistical mechanics, is capable of predicting the structure and thermodynamics of solvation of supramolecular architectures. We obtained a set of profiles of the potential of mean force between protofilaments in a periodic two-dimensional sheet in aqueous solution. The profiles were calculated for a number of amino acid sequences, tubulin conformations, and spatial arrangements of protofilaments. The results indicate that the effective interaction between protofilaments in aqueous solution depends little on the isotypes studied; however, it strongly depends on the M loop conformation of beta-tubulin. Based on the analysis of the potential of mean force between adjacent protofilaments, we found the optimal arrangement of protofilaments, which is in good agreement with other studies. We also decomposed the potential of mean force into its energetic and entropic components, and found that both are considerable in the free-energy balance for the stabilized protofilament arrangements.

Computer Simulation↗

PubMed2006

The role of capillary and surface forces in the crossover behavior of solid nanoparticles at liquid interfaces.

We investigate the interaction between a nanoparticle and an oil-water interface with particular emphasis on the particle crossing through the interface. The formation of a three-phase contact line is investigated in two cases, namely in the presence and in the absence of surface forces. We carefully examine the interplay between capillary and surface forces in such systems. Two instabilities of the interface (snap-in/snap-out) as the particle is moved through the interface are identified and quantitatively described. While the snap-in instability was observed in some AFM studies, the precise interface position and configuration relative to the particle at the instability depends on the nature of the surface forces present in the system. After the snap-in, the particle is adsorbed and must overcome an energy barrier due to the interface deformation in order to cross-over to the other liquid. We make quantitative predictions on the interface configuration at the instabilities and the free energy barrier height. The roles of particle size and different interaction parameters characterizing the system in determining the magnitude of the energy barrier for crossing and in the formation of a three-phase contact line are discussed. Ultimately, this study will enable us to make quantitative predictions on capillary effects in nanoparticle-microemulsions mixtures and other colloidal systems. For particles in the micrometer range and larger the capillary forces dominate over the surface forces and dictate how the snap-in occurs. However, the situation becomes different for particle sizes smaller than about 100 nm. The presence of surface forces modifies the interface configuration and the free energy jump at the snap-in instability.

Journal Article↗

PubMed2006

A theoretical analysis on hydration thermodynamics of proteins.

The hydration free energy (HFE) of several proteins modeled using the all-atom force field is calculated by employing the three-dimensional reference interaction site model theory, a recently developed integral equation theory of molecular solvation. The HFE is decomposed into the energetic and entropic components under the isochoric condition. The former comprises the protein-water interaction energy and the water reorganization energy arising from the structural changes induced in water. Each component is further decomposed into the nonelectrostatic and electrostatic contributions. It is found that the HFE is governed by the nonelectrostatic hydration entropy and the electrostatic hydration energy. The nonelectrostatic hydration entropy is almost exclusively ascribed to the translational entropy loss of water upon the protein insertion. It asymptotically becomes proportional to the excluded volume (EV) for water molecules as the protein size increases. The hydration energy is determined by the protein-water interaction energy which is half compensated by the water reorganization energy. These energy terms are approximately proportional to the water-accessible surface area (ASA). The energetic and entropic contributions are balanced with each other and the HFE has no apparent linear relation with the EV and ASA.

Biophysics↗

PubMed2006

Theoretical study of volume changes accompanying xenon-lysozyme binding: implications for the molecular mechanism of pressure reversal of anesthesia.

The change in partial molar volume (PMV) accompanying the xenon-lysozyme binding was investigated for elucidating the molecular mechanism of the pressure reversal of general anesthesia, using the three-dimensional reference interaction site model theory of molecular solvation. An increase of the PMV from xenon binding to the substrate binding site of lysozyme was found, and the binding is suppressed by pressure, while the internal site binding did not change the PMV. The PMV change was analyzed by decomposing it into several contributions from geometry and hydration. We also analyzed the hydration change due to the binding. From the results, we draw a molecular picture of the PMV change accompanying xenon-lysozyme binding, which gives a possible mechanism of pressure reversal of anesthesia.

Anesthesia, General↗

PubMed2006

Self-consistent combination of the three-dimensional RISM theory of molecular solvation with analytical gradients and the Amsterdam density functional package.

The three-dimensional reference interaction site model with the closure relation by Kovalenko and Hirata (3D-RISM-KH) in combination with the density functional theory (DFT) method has been implemented in the Amsterdam density functional (ADF) software package. The analytical first derivatives of the free energy with respect to displacements of the solute nuclear coordinates have also been developed. This enables study of chemical reactions, including reaction coordinates and transition state search, with the molecular solvation described from the first principles. The method yields all of the features available by using other solvation approaches, for instance infrared spectra of solvated molecules. To evaluate the accuracy of the present method, test calculations have been carried out for a number of small molecules, including four glycine conformers, a set of small organic compounds, and carbon nanotubes of various lengths in aqueous solution. Our predictions for the solvation free energy agree well with other approaches as well as experiment. This new development makes it possible to calculate at modest computational cost the electronic properties and molecular solvation structure of a solute molecule in a given molecular liquid or mixture from the first principles.

Algorithms↗

PubMed2006

Fundamental mechanism of translocation across liquidlike membranes: toward control over nanoparticle behavior.

We envision and theoretically investigate a novel behavior of a functionalized nanoparticle designed to translocate through a liquidlike membrane. We develop a statistical-mechanical approach to such a system. We predict a new mechanism for the opening of a circular energy-dominated pore on the membrane by a nanoparticle functionalized with a peptide aggregate. Following fluctuations in the position and orientation of the nanoparticle, the peptide aggregate incorporates into the membrane and locally destabilizes it. The nucleation of a pore centered at the peptide aggregate attached to the particle is a precursor to particle translocation. The subsequent opening of the pore is assisted by adhesion of the membrane to the particle. We determine the conditions in which thermal fluctuations in the membrane shape and the pore size can induce translocation of the particle. For different system parameters quantities such as the free energy, entropy, pore size, degree of particle wrapping, and the probability of spontaneous translocation are obtained.

Membrane Fluidity↗

PubMed2005

Water molecules in a protein cavity detected by a statistical-mechanical theory.

Four water molecules confined in a small cavity of hen egg-white lysozyme were detected by means of the three-dimensional (3D) RISM theory, a statistical-mechanical theory of molecular solutions. This is the first theoretical realization of confined molecules in a protein without making nonsense tricks, such as placing the molecules in the space a priori. Possible impacts which the result may have on biochemistry and biophysics, including the molecular recognition, enzymatic reactions, etc., are discussed.

Animals↗

PubMed2005

Theoretical study of volume changes associated with the helix-coil transition of an alanine-rich peptide in aqueous solution.

The changes in the partial molar volume (PMV) associated with the conformational transition of an alanine-rich peptide AK16 from the alpha-helix structure to various random coil structures are calculated by the three-dimensional interaction site model (3D-RISM) theory coupled with the Kirkwood-Buff theory. The volume change is analyzed by decomposing it into contributions from geometry and hydration: the changes in the van der Waals, void, thermal, and interaction volume. The total change in the PMV is positive. This is primarily due to the growth of void space within the peptide, which is canceled in part by the volume reduction resulting from the increase in the electrostatic interaction between the peptide and water molecules. The changes in the void and thermal volume of the coil structures are widely distributed and tend to compensate each other. Additionally, the relations between the hydration volume components and the surface properties are investigated. We categorize coil structures into extended coils with the PMV smaller than helix and general coils with the PMV larger than helix. The pressure therefore can both stabilize and destabilize the coil structures. The latter seems to be a more proper model of random coil structures of the peptide.

Alanine↗

PubMed2005

Criticality of a liquid-vapor interface from an inhomogeneous integral equation theory.

A microscopic theory is developed to study the liquid-vapor interfacial properties of simple fluids with ab initio treatment of the inhomogeneous two-body correlation functions, without any interpolation. It consists of the inhomogeneous Ornstein-Zernike equation coupled with the Duh-Henderson-Verlet closure and the Lovett-Mou-Buff-Wertheim equation. For the liquid-vapor interface of the Lennard-Jones fluid, we obtained the density profile and the surface tension, as well as their critical behaviour. In particular, we identified non-classical critical exponents. The theory accurately predicts the phase diagram and the interfacial properties in a very good agreement with simulations. We also showed that the method leads to true capillary-wave asymptotics in the macroscopic limit.

Computer Simulation↗

PubMed2005

Helical rosette nanotubes with tunable stability and hierarchy.

The design of nanostructured materials with tunable dimensions and properties that maintain their structural integrity under physiological conditions is a major challenge in biomedical engineering and nanomedicine. Helical rosette nanotubes (HRN) are a new class of materials produced through a hierarchical self-assembly process of low molecular weight synthetic organic modules in water. Here, we describe a synthetic strategy to tune their stability and hierarchy by preorganization of the self-assembling units, control of net charge per unit of nanotube surface area, amphiphilicity, and number of H-bonds per self-assembling module, and through peripheral steric (de)compression. Using these criteria, HRNs with tunable stability and hierarchical architecture were produced from self-assembling modules that (a) persist as individual molecules in solution, (b) self-assemble into HRN but denature at high temperature (<85 degrees C), (c) self-assemble into HRN whose structural integrity persists even in boiling water (>95 degrees C), and (d) self-assemble into well-dispersed short nanotubes, long nanotubes, ribbons, or superhelices. Given the biocompatibility, synthetic accessibility, and chemical and physical tunability of these materials, numerous applications in biomedical engineering, materials science, and nanoscience and technology are envisioned.

Journal Article↗

PubMed2005

Self-consistent molecular theory of polymers in melts and solutions.

We propose a self-consistent molecular theory of conformational properties of flexible polymers in melts and solutions. The method employs the polymer reference interaction site model for the intermolecular correlations and the Green function technique for the intramolecular correlations. We demonstrate this method on n-alkane molecules in different environments: water, hexane, and in melt, corresponding to poor, good, and theta condition, respectively. The numerical results of the intramolecular correlation function, the radius of gyration, and the characteristic ratio of a polymer chain are indicative of conformational changes from one environment to another and are in agreement with other findings in the literature. Scaling laws for the chain size with respect to the number of monomers are discussed. We show results for the intra- and intermolecular correlation functions and the medium-induced potential. We also extract the Kuhn length and the characteristic ratio for the infinite chain limit for melts. The latter is compared to the experimental results and computer simulation. The conformational free energy per monomer in different solvents is calculated. Our treatment can be generalized readily to other polymer-solvent systems, for example, those containing branched copolymers and polar solvents.

Journal Article↗

PubMed2005

Partial molar volume of proteins studied by the three-dimensional reference interaction site model theory.

The three-dimensional reference interaction site model (3D-RISM) theory is applied to the analysis of hydration effects on the partial molar volume of proteins. For the native structure of some proteins, the partial molar volume is decomposed into geometric and hydration contributions using the 3D-RISM theory combined with the geometric volume calculation. The hydration contributions are correlated with the surface properties of the protein. The thermal volume, which is the volume of voids around the protein induced by the thermal fluctuation of water molecules, is directly proportional to the accessible surface area of the protein. The interaction volume, which is the contribution of electrostatic interactions between the protein and water molecules, is apparently governed by the charged atomic groups on the protein surface. The polar atomic groups do not make any contribution to the interaction volume. The volume differences between low- and high-pressure structures of lysozyme are also analyzed by the present method.

Binding Sites↗

PubMed2004

Molecular description of the collapse of hydrophobic polymer chains in water.

We propose a self-consistent molecular theory of conformational properties of flexible polymers in solution. It is applied to the collapse of a hydrophobic polymer chain in water, and can be readily generalized to any polymer-solvent system (e.g., copolymers with high complexity). We stress the potential of this method for a variety of problems, such as protein folding.

Journal Article↗