Improved interaction potentials for charged residues in proteins

Electrostatic interactions dominate the structure and free energy of biomolecules. To obtain accurate free energies involving charged groups from molecular simulations, OPLS-AA parameters have been reoptimized using Monte Carlo free energy perturbation. New parameters fit a self-consistent, experimental set of hydration free energies for acetate (Asp), propionate (Glu), 4-methylimidazolium (Hip), n-butylammonium (Lys), and n-propylguanidinium (Arg), all resembling charged residue side chains, including beta-carbons. It is shown that OPLS-AA free energies depend critically on the type of water model, TIP4P or TIP3P; i.e., each water model requires specific water-charged molecule interaction potentials. New models (models 1 and 3) are thus described for both water models. Uncertainties in relative free energies of charged residues are approximately 2 kcal/mol with the new parameters, due to variations in system setup (MAEs of ca. 1 kcal/mol) and noise from simulations (ca. 1 kcal/mol). The latter error of approximately 1 kcal/mol contrasts MAEs from standard OPLS-AA of up to 13 kcal/mol for the entire series of charged residues or up to 5 kcal/mol for the cationic series Lys, Arg, and Hip. The new parameters can be used directly in molecular simulations with no modification of neutral residues needed and are envisioned to be particular important in simulations where charged residues change environment.     

Electron-intramolecular-vibration interactions in positively charged phenanthrene-edge-type hydrocarbons

Electron-phonon interactions in positively charged phenanthrene-edge-type hydrocarbons such as phenanthrene, chrysene, and picene are studied. The C-C stretching modes around 1500 cm(-1) and the low-frequency modes around 500 cm(-1) strongly couple to the highest occupied molecular orbitals (HOMO) in phenanthrene-edge-type hydrocarbons. The total electron-phonon coupling constants for the monocations (lHOMO) of 0.251, 0.135, and 0.149 eV for phenanthrene, chrysene, and picene, respectively, are estimated to be larger than those of 0.130, 0.107, and 0.094 eV for anthracene, tetracene, and pentacene, respectively. The phase patterns difference between the HOMO localized on carbon atoms which are located at the molecular edge in acene-edge-type hydrocarbons and the delocalized HOMO in phenanthrene-edge-type hydrocarbons is the main reason for the result. Strengths of orbital interactions between two neighboring carbon atoms in the HOMO become weaker with an increase in molecular size because the electron density on each carbon atom in the HOMO becomes smaller with an increase in molecular size in phenanthrene-edge-type hydrocarbons. On the other hand, the frontier orbitals of acene-edge-type hydrocarbons have somewhat nonbonding characters and thus cannot strongly couple to the totally symmetric vibrational modes compared with the frontier orbitals of phenanthrene-edge-type hydrocarbons. This is the reason why the lHOMO value for phenanthrene-edge-type hydrocarbons decreases with an increase in molecular size more significantly than that for acene-edge-type hydrocarbons, and the reason why the lHOMO value for polyphenanthrene with C2v geometry (0.033 eV) is estimated to be similar to that for polyacene (0.036 eV). The reorganization energies between the neutral molecules and the corresponding monocations for phenanthrene-edge-type hydrocarbons with large molecular size are estimated to be larger than those for acene-edge-type hydrocarbons with large molecular size.     

Interactions between chlorinated dioxins and a positively charged molecular probe: New molecular interaction potential

Interaction with the ligand binding domain of receptors for natural chemicals present one potential mechanism for the biological effects of environmental chemicals. Evidence suggests that the electrostatic interaction between the ligand and the receptor is an important component for binding to some of the relevant receptors. The presence of charged residues near the binding site suggests that the charge distribution of the free ligand may be different from the charge distribution of the ligand as it approaches the binding domain of the protein. In this study a new type of potential is computed for a series of dibenzo-p-dioxin (dioxin) ligands. This quantum mechanically computed potential results from interaction between the ligand and a trimethyl ammonium probe at a set of grid points. This interaction potential is compared with the molecular electrostatic potential computed from the wave function of the isolated ligands. Three types of local minima are found: (1) above the oxygen; (2) above the conjugated ring; and (3) above the chlorine(s). The molecular electrostatic potential emphasizes the minima associated with the chlorine atoms and, in that potential, the minima associated with the oxygen atoms disappear with chlorination. In the new potential, the minima over the oxygen atoms are maintained even in tetrachlorodioxin. As chlorination is increased the differences between the two potentials increases. The new potential shows the influence of the π-cation interaction, which is largest when there is little substitution on the ring. The presence of the probe induces a dipole component of 1 debye perpendicular to the plane of the ligand. Local minima in the interaction potential are then used as starting structures for the determination of the most stable ligand–probe complexes. The most stable structures are obtained from the minima associated with the oxygen atoms. These structures are stabilized by a hydrogen bond formation between the probe and the oxygen and the molecule is bent by 30° about the O(SINGLE BOND)O axis. For this series of molecules, the new potential retains some of the features that determine the hydrogen bond whereas the molecular electrostatic potential does not. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 673–684, 1998     

A new radon monitor with a positively charged aluminum disk

A new air radon monitor is proposed based on the combination of an aluminum disk and an electric multilevel clearance system (EMCS). The positively charged, small aluminum disk has a high collection ability to radon with a collection efficiency of about 60%. The old radon progenies were eliminated by the EMCS in the air entrance of the monitor with an efficiency of about 99%. The monitor was calibrated in the national standard radon chamber in Hengyang, China. Compared to the radon double-filter equipment, the results, gained by both apparatus, coincide with each other.     

Molecular structure of single DNA complexes with positively charged dendronized polymers

Positively charged dendronized polymers with protonated amine groups at the periphery and different dendron generations are cylindrically shaped nanoobjects whose radii and linear charge densities can be varied systematically. These polyelectrolytes have been complexed with DNA and subsequently adsorbed on precoated mica substrates. The analysis of scanning force microscopy data indicates that DNA wraps around the dendronized polymers. The calculated pitch is 2.30 +/- 0.27 and 2.16 +/- 0.27 nm for DNA wrapped around dendronized polymers of generation two and four, respectively. The complex with the second generation has been shown to be negatively charged, which is consistent with the theory of spontaneous overcharging of macro-ion complexes, when the electrostatic contribution to the free energy dominates over the elastic energy. The complexes may be of interest for the development of nonviral gene delivery systems.     

Induced polymersome formation from a diblock PS-b-PAA polymer via encapsulation of positively charged proteins and peptides

In contrast to simple salts or negatively charged macromolecules, positively charged proteins and peptides including cytochrome c (yeast) and poly-L-lysine are efficiently encapsulated while inducing the formation of polymersomes from polystyrene(140)-b-poly(acrylic acid)(48) (PS(140)-b-PAA(48)).     

Coarse-graining intermolecular interactions in dispersions of highly charged colloids

Effective pair potentials between charged colloids, obtained from Monte Carlo simulations of two single colloids in a closed cell at the primitive model level, are shown to reproduce accurately the structure of aqueous salt-free colloidal dispersions, as determined from full primitive model simulations by Linse et al. (Linse, P.; Lobaskin, V. Electrostatic Attraction and Phase Separation in Solutions of Like-Charged Colloidal Particles. Phys. Rev. Lett.1999, 83, 4208). Excellent agreement is obtained even when ion-ion correlations are important and is in principle not limited to spherical particles, providing a potential route to coarse-grained colloidal interactions in more complex systems.     

Photobiological properties of positively charged methylene violet analogs

O-Methyl methylene violet (OMeMV), O-methyl bromomethylene violet (OMeBrMV) and O-methyl iodomethylene violet (OMeIMV) have been prepared in order to test their potential utility as anti-viral and anti-tumor phototoxic dyes. Rates of photosensitized toxicity of KB cells with 633 nm irradiation are (x 10(-19) photon-1): 2.4, 2.2, 1.9 and 0.17 for OMeIMV, OMeBrMV, methylene violet (MV) and OMeMV, respectively. Rates of photosensitized inactivation of Sindbis virus in phosphate-buffered saline with 633 nm irradiation are (x 10(-18) photon-1): 3.3, 1.8, 0.99, 0.15 for MV, OMeIMV, OMeBrMV and OMeMV, respectively. Quantum efficiencies for singlet oxygen formation were determined as OMeIMV, 0.64; OMeBrMV, 0.40; OMeMV, 0.054. Titration of the dyes with double-stranded (ds)DNA resulted in bathochromic shifts and hypochromic effects in the visible absorption spectra. Association constants for interaction of the methylated dyes with dsDNA of approximately 1 x 10(5) M-1 were determined by Scatchard analysis of equilibrium dialysis and UV absorption titration data. Photolysis of the halogenated dyes with DNA under argon led to covalent bond formation with the nucleic acid; there was no evidence of covalent binding in the dark.     

Preparation and characterization of positively charged ruthenium nanoparticles

Positively charged ruthenium nanoparticles were prepared by NaBH(4) reduction at room temperature and at pH values lower than 4.9. The ruthenium nanoparticles were characterized by zeta potential measurement, TEM, XPS, and XRD. Particles with a mean diameter of 1.8 nm and a standard deviation of 0.40 nm could be obtained under the experimental conditions. The surface charge on the particles is believed to originate from hydrated proton adsorption. The positively charged ruthenium nanoparticles could be used as the starting material for further functionalization by PVP, ethylenediamine, and dodecylamine.     

Preparation of positively charged oil/water nano-emulsions with a sub-PIT method

The phase inversion temperature (PIT) method is generally used to prepare nonionic surfactant stabilized nano-emulsions because of its low energy and surfactant consumption. The emulsion droplets are usually negatively charged because of the selective adsorption of OH(-) onto the droplet surfaces. In this work, positively charged oil/water nano-emulsions were prepared by adding a cationic surfactant to the system. The cationic molecules change the spontaneous curvature of the surfactant layers and raise the PIT above 100 °C. The PIT can be depressed by addition of NaBr, as shown by conductivity measurements and equilibrium phase behavior. Therefore, these nano-emulsions can be prepared by the PIT method. We found that the formation of the nano-emulsions did not require a cross-PIT cycle. The mechanism of the emulsification is the formation of mixed swollen micelles that can solubilize all the oil above a "clearing boundary", followed by a stir-quench to a temperature where these droplets become metastable emulsions. The zeta potential of the emulsion droplets can be easily tuned by varying the cationic surfactant concentrations. Due to electrosteric stabilization, the resulting nano-emulsions are highly stable, thus could find significant applications in areas such as pharmaceuticals, cosmetics and food industries.     

Interaction of dextran sulfates with positively and negatively charged silver bromide hydrosols

Summary The effects of dextran sulfates of different molecular weights and charge densities on the stability of positively and negatively charged silver bromide solsin statu nascendi have been studied by means of light scattering.The plots of scattering intensities of a positively charged sol against the concentration of the added dextran sulfates show one pronounced maximum, the position which is independent on the molecular weight of the polyelectrolyte used. The maximum shifts to lower polyion concentrations with dilution of the sol.The effect of polyanions on the stability of silver bromide sols of the same sign of charge were investigated as a function of molecular weight of the polymers, the sol concentration, the charge and the concentration of counterions, and the addition of methanol. Destabilization only occurred if sufficient amount of indifferent electrolyte was present in the system. However, the concentration of counterions necessary to produce a flocculation maximum was lower in the presence of the polyelectrolytes than in their absence. The results obtained were compared with the data on sols containing nonionic dextrans reported earlier.

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Zusammenfassung Der Einfluß der Dextransulfate von verschiedenen Molekulargewichten und Ladungsdichten auf die Stabilität der positiv und negativ geladenen Silberbromid-Solein statu nascendi wurden durch Lichtstreuung untersucht. Wenn die Intensitäten der Lichtstreuung eines positiv geladenen Silberbromid-Sols gegen die Konzentration der zugesetzten DextranSulfate aufgetragen werden, tritt ein ausgeprägtes Maximum auf, dessen Lage von dem Molekulargewicht des angewandten Polyelektrolyten unabhängig ist. Bei Verdünnung des Sols wird das Maximum zur niedrigeren Konzentration des Polyanions verschoben.Der Einfluß der Polyanionen auf die Stabilität der Silberbromid-Sole mit gleichem Ladungsvorzeichen wurde in Abhängigkeit von dem Molekulargewicht des zugesetzten Dextransulfats, der Solkonzentration, der Ladung und Konzentration der Gegenionen und dem Zusatz von Methylalkohol untersucht. Destabilisierung wird nur in Anwesenheit einer genügenden Menge von Neutralelektrolyten in den untersuchten Systemen beobachtet. Die Konzentration der Gegenionen, die ein Flockungsmaximum verursachen, ist immer niedriger als die kritische Koagulationsmenge derselben Ionen für das gleiche Sol in Abwesenheit von Makroionen. Die Resultate wurden mit den Wechselwirkungen der Silberbromid-Sole mit nichtionogenen Dextranen verglichen, und der Mechanismus der Flockung durch Polyelektrolyte wurde diskutiert.

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5 figures and 1 table

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Supported by the NSF Grant GP 42331 X.

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A part of the Ph.D. Thesis by David Lindsay.     

Solvent-induced effects: self-association of positively charged pi systems

Antimalarial cationic drugs, such as chloroquine (CQ) and ferroquine (FQ), form stable dimer structures not only in the solid state but also in solution. The short distances (3.3-3.5 A) observed between the positively charged quinolinium rings suggest that this self-association process is driven by pi/pi stacking interactions. Nevertheless, the strength of these dispersive forces is likely not sufficient to overcome the strong repulsive +/+ electrostatic effects. The question of the exact role of the environment, particularly the solvent, is clearly raised here. Characterization of these unconventional stabilizing nonbonding interactions which we have named +-pi/+-pi is therefore of great importance. In the present work, we describe theoretical calculations and NMR experiments undertaken to probe the nature and the strength of +-pi/+-pi interactions occurring upon self-association of FQ and CQ molecules in water.     

Vibronic interactions and possible electron pairing in positively charged cyanodienes

The conditions under which the attractive electron-electron interactions are realized in the monocations of sigma-conjugated cyanodienes such as C(6)N(4)H(4), C(8)N(6)H(4), and C(10)N(8)H(4) and of pi-conjugated acenes are discussed. The total electron-phonon coupling constants for the monocations l(HOMO) of cyanodienes are much larger than those for the monocations of acenes. The strong sigma orbital interactions between two neighboring atoms in the highest occupied molecular orbitals (HOMO) of sigma-conjugated cyanodienes are the main reason for the calculated results. Furthermore, we discuss how the conditions under which the monocation crystals become good conductor are related to the molecular size. Both the l(HOMO) values and the reorganization energies between the neutral molecules and the monocations decrease with an increase in molecular size in cyanodienes. The calculated results for the sigma-conjugated cyanodienes are compared with those for the pi-conjugated acenes in order to investigate how the CH-N substitutions in cyanodienes are closely related to the l(HOMO) values and the reorganization energies. Both the l(HOMO) and the reorganization energies in the positively charged sigma-conjugated cyanodienes are much larger than those in the positively charged pi-conjugated acenes. This means that in order to become good conductors, the positively charged sigma-conjugated cyanodienes need larger overlap integral between two adjacent molecules than the positively charged pi-conjugated acenes. On the other hand, since the l(HOMO) values for cyanodienes are much larger than those for acenes, the condition of attractive electron-electron interactions is more easily to be realized in the monocations of cyanodienes than in the monocations of acenes. It is suggested that the positively charged sigma-conjugated cyanodienes cannot easily become good conductors, but the conditions under which the electron-electron interactions become attractive are realized more easily in the positively charged sigma-conjugated cyanodienes than in the positively charged pi-conjugated acenes.     

Charge distributions in polyacetylene chains containing a positively charged defect

We present a comparative study of the AIM, CHELPG, GAPT, MK, Mulliken, NPA, and RESP charge distributions associated with a positively charged soliton on increasingly large trans‐polyacetylene chains, at HF, MP2, and DFT levels of theory. The charge storage in the soliton‐bearing systems is explored in detail, including charge magnitude, charge separation, charge alternation, and chain length effects. The grouping of the charge distributions at a given level of theory, as well as the sensitivity of a given charge distribution to the inclusion of electron correlation in its computation, are investigated using similarity analysis. Several of the charge definitions have been applied for the first time for charged soliton‐bearing systems, and there are substantial differences between the charge distributions for the charged and neutral systems. Thus, AIM charges are no longer one of the largest charge values, the AIM charges can be in counterphase with other definitions, and the GAPT charges for neutral systems are quite different from the GAPT charges for charged systems, e.g., the magnitudes of the GAPT charges are anomalously large and increase with the size of the charged system. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Inhibition of the binding of low-density lipoprotein to its cell surface receptor in human fibroblasts by positively charged proteins.

A group of proteins and polyamino acids with positively charged domains were shown to inhibit the binding of 125I-LDL to its receptor on the surface of human fibroblasts. The list of inhibitory proteins included platelet factor 4 (which has a cluster of lysine residues at its carboxyl terminus), two lysine-rich histones, poly-L-lysines of chain length greater than 4, and protamine. These proteins were effective in the concentration range of 5--10 microgram/ml. Two other positively charged proteins, lysozyme and avidin, did not inhibit 125I-LDL binding. Kinetic studies suggested that protamine was not acting simply as a competitive inhibitor with regard to the LDL receptor. In light of previous data showing that polyanions such as heparin and polyphosphates also inhibit 125-I-LDL binding to its cell surface receptor, the current findings suggest that charge interactions are important in this binding reaction. In a related series of studies, a number of glycoproteins and their asialo derivatives as well as a number of sugar phosphates failed to inhibit 125I-LDL binding to its receptor in fibroblasts.     

Formation of positively charged poly(butyl cyanoacrylate) nanoparticles stabilized with chitosan

To investigate the formation of positively charged nanoparticles (NP) stabilized with chitosan, positively charged poly(butyl cyanoacrylate) (PBCA) NP were prepared by emulsion polymerization in the presence of chitosan as a polymeric stabilizer at low pH. The effect of physicochemical factors such as the pH, the concentration and the volume of the chitosan solution, the chitosan molecular weight and the temperature on the mean particle size and the turbidity of PBCA-NP was investigated. Particle size was determined using a transmission electron microscope. The chemical interaction between chitosan and PBCA was identified by Fourier transform infrared (FT-IR) spectroscopy and the grafting percentage at various pH values was determined. The zeta potential of PBCA-NP coated with chitosan was determined from the electrophoretic mobility in 10 mM NaCl. The pH, the concentration and the volume of the chitosan solution and the molecular weight of chitosan were shown to be important factors in controlling the mean particle size of NP in the range 10–100 nm. FT-IR spectra indicated that chitosan was covalently linked to PBCA and the maximum grafting percentage reached about 120% w/w at pH 2.0. Nimodipine as a model drug was successfully incorporated into chitosan-stabilized PBCA-NP with a mean particle diameter of 31.6 nm. PBCA-NP coated with chitosan carried a positive charge. The results indicate that positively charged NP may be produced in the presence of cationic polysaccharide chitosan and might increase their potential use as a targeting drug delivery system. Received: 17 March 1999/Accepted in revised form: 4 October 1999     

Spectroscopic studies of nanostructures of negatively charged free base porphyrin and positively charged tin porphyrins

Spectroscopic studies were carried out on the homoaggregates of negatively charged free base meso-tetraphenylsulfonated porphyrin ([H₂TPPS₄]⁴⁻) and heteroaggregates of a mixture of protonated ([H₄TPPS₄]²⁻) and tin meso-tetra (N-methyl-4-pyridyl) porphyrin ([SnTMPyP]⁴⁺). The spectroscopic studies were done to determine the optimal conditions required for the fabrication of porphyrin nanorods by ionic self assembly of two oppositely charged porphyrins. In addition, the various spectral changes of [H₄TPPS₄]²⁻ with concurrent change in pH and concentration are also investigated. In acid media at pH <3, and at concentrations >1 × 10⁻⁵ M, [H₄TPPS₄]²⁻ molecules form J aggregates. A mixture of [H₄TPPS₄]²⁻ and [SnTMPyP]⁴⁺ forms heteroaggregates of the J type in acid media. At pH’s 2 to 3, the optimum ratio for the formation of J aggregates is 3:1 and for pH 1, the optimum ratio is 2:1. Transmission electron microscope images of the nanostructures formed show that they are of cylindrical shape.     

Modern state of intermolecular interaction theory

The concept of potential surfaces and classification of various types of intermolecular forces are given. The possibilities and the criteria of applicability of modern methods for potential surface calculation at short, intermediate, and long distances are discussed. Special attention is paid to the methods for calculating interactions between large molecules.     

Enhancement of nitrogen physisorption in coadsorption with oxygen on free, positively charged silver clusters

The coadsorption of molecular nitrogen and oxygen on small cationic silver clusters in the gas phase is experimentally studied. The presence of oxygen enhances the adsorption probabilities of N2. This indicates a partial charge transfer out of the finite free electron reservoir of the small silver particles into the chemisorbed oxygen molecule.