Uncovering the rules for protein-protein interactions from yeast genomic data

Identifying protein-protein interactions is crucial for understanding cellular functions. Genomic data provides opportunities and challenges in identifying these interactions. We uncover the rules for predicting protein-protein interactions using a frequent pattern tree (FPT) approach modified to generate a minimum set of rules (mFPT), with rule attributes constructed from the interaction features of the yeast genomic data. The mFPT prediction accuracy is benchmarked against other commonly used methods such as Bayesian networks and logistic regressions under various statistical measures. Our study indicates that mFPT outranks other methods in predicting the protein-protein interactions for the database used. We predict a new protein-protein interaction complex whose biological function is related to premRNA splicing and new protein-protein interactions within existing complexes based on the rules generated.

Anticancer Drug-DNA Interactions Measured Using a Photoinduced Electron-Transfer Mechanism Based on Luminescent Quantum Dots

A sensing system based on the photoinduced electron transfer of quantum dots (QDs) was designed to measure the interaction of anticancer drug and DNA, taking mitoxantrone (MTX) as a model drug. MTX adsorbed on the surface of QDs can quench the photoluminescence (PL) of QDs through the photoinduced electron-transfer process; and then the addition of DNA will bring the restoration of QDs PL intensity, as DNA can bind with MTX and remove it from QDs. Sensitive detection of MTX with the detection limit of 10 nmol L-1 and a linear detection range from 10 nmol L-1 to 4.5 mu mol L-1 was achieved. The dependence of PL intensity on DNA amount was successfully utilized to investigate the interactions between MTX and DNA. Both the binding constants and the sizes of binding site of MTX-DNA interactions were calculated based on the equations deduced for the PL recovery process. The binding constant obtained in our experiment was generally consistent with previous reports. The sensitive and speedy detection of MTX as well as the avoidance of modification or immobilization process made this system suitable and promising in the drug-DNA interaction studies.

Affinity and Specificity of Levamlodipine-Human Serum Albumin Interactions: Insights into Its Carrier Function

The affinity and specificity of drugs with human serum albumin (HSA) are crucial factors influencing the bioactivity of drugs. To gain insight into the carrier function of HSA, the binding of levamlodipine with HSA has been investigated as a model system by a combined experimental and theoretical/computational approach. The fluorescence properties of HSA and the binding parameters of levamlodipine indicate that the binding is characterized by one binding site with static quenching mechanism, which is related to the energy transfer. As indicated by the thermodynamic analysis, hydrophobic interaction is the predominant force in levamiodipine-HSA complex, which is in agreement with the computational results. And the hydrogen bonds can be confirmed by computational approach between levamlodipine and HSA. Compared to predicted binding energies and binding energy spectra at seven sites on HSA, levamlodipine binding HSA at site I has a high affinity regime and the highest specificity characterized by the largest intrinsic specificity ratio (ISR). The binding characteristics at site I guarantee that drugs can be carried and released from HSA to carry out their specific bioactivity.

Selective hydrogenation of nitrobenzene to aniline in dense phase carbon dioxide over Ni/gamma-Al2O3: Significance of molecular interactions

The selective hydrogenation of nitrobenzene (NB) over Ni/gamma-Al2O3 Catalysts Was investigated using different media of dense phase CO2, ethanol, and n-hexane. In dense phase CO2, the total rate of NB hydrogenation was larger than that in organic solvents under similar reaction conditions; the selectivity to the desired product, aniline, was almost 100% over the whole conversion range of 0-100%. The phase behavior of the reactant mixture in/under dense phase CO2 was examined at reaction conditions. In situ high-pressure Fourier transform infrared measurements were made to study the molecular interactions Of CO2 with the following reactant and reaction intermediates: NB, nitrosobenzene (NSB), and N-phenylhydroxylamine (PHA). Dense phase CO2 strongly interacts with NB, NSB, and PHA, modifying the reactivity of each species and contributing to positive effects on the reaction rate and the selectivity to aniline. A possible reaction pathway for the hydrogenation of NB in/under dense phase CO2 over Ni/gamma-Al2O3 is also proposed.

The adsorption of dopamine on gold and its interactions with iron(III) ions studied by microcantilevers

The adsorption of dopamine (DA) molecules on gold and their interactions with Fe3+ were studied by a microcantilever in a flow cell. The microcantilever bent toward the Au side with the adsorption of DA due to the change Of Surface stress induced by the intermolecular hydrogen bonds of DA or the charge transfer effect between adsorbates and the Substrate. The interaction process between DA adsorbates and Fe3+ was revealed by the deflection curves of microcantilever. As indicated by the appearance of a variation during the decline of curves, two steps were observed in the curve at relative high concentrations of Fe3+. In this case, Fe3+ reacted with DA molecules only in the outer layers and the complexes removed with solution. Then Fe3+ reacted further with DA molecules forming the surface complex in the first layer next to the gold. At this stage, the stability Of Surface complexes was time dependent, i.e., unstable initially and stable finally. This may be due to the surface complexes change from mono-dentate to bi-dentate complexes. In another case, i.e., at relative low concentration of Fe3+, only the first step was observed as indicated by the absence of a variation.

Why [6,6]- and 1,2-Benzal-3-N-4-O-Cyclic Phenylimidate C-60 Undergo Electrochemically Induced Retro-Addition Reactions while 1,4-Dibenzyl-2,3-Cyclic Phenylimidate C-60 Does Not? C-H center dot center dot center dot X (X = N, O) Intramolecular Interactions in Organofullerenes

The electrochemical properties of a series of structurally related fullerooxazoles, [6,6] cyclic phenylimidate C-60 (1), 1,2-benzal-3-N-4-O-cyclic phenylimidate C-60 (2), and 1,4-dibenzyl-2,3-cyclic phenylimidate C-60 (3), are described, and the spectroscopic characterizations of their anionic species are reported. The results show that compounds I and 2 undergo retro-cycloaddition reactions that lead to the formation of C-60 and C61HPh, respectively, upon two-electron-transfer reduction. However, compound 3 demonstrates much more electrochemical stability as no retro-cycloaddition reaction occurs under similar conditions. Natural bond orbital (NBO) calculations on charge distribution show there is no significant difference among the dianions of 1, 2, and 3, indicating that the electrochemical stability of 3 is unlikely to be caused by the charge distribution difference of the dianions of three compounds. Examination on the crystal structure of compound 3 reveals close contacts of the C-H group with the heteroatoms (N and O) of cyclic phenylimidate, suggesting the existence of C-H center dot center dot center dot X (X = N, O) intramolecular hydrogen bonding among the addends, which is further confirmed by NBO analysis.

Interactions of Rare Earth-Amino Acid Complexes with Nucleic Acids

A number of metal-based anticancer drugs are designed to target nucleic acids. Therefore, the elucidation of their interactions with nucleic acids is important for rational design of new anticancer agents with high selectivity and low toxicity, which has been received much attention in this field. Lanthanide complexes have the potential to be therapeutic agents due to their unique magnetic, optical, electronic, and coordinate characteristics. However, lanthanide ions are easy to hydrolysis under physiological pH, which makes it difficult to study rare earth complexes nucleic acids selectivity. Recent studies have shown that natural amino acids can form stable complexes with rare earth ions under near physiological condition and the complexes have high solubility. This review summarizes the current progress in rare earth-amino acid complexes binding to nuclelic acids and their selectivity.

Tight intermolecular packing through supramolecular interactions in crystals of cyano substituted oligo(para-phenylene vinylene): a key factor for aggregation-induced emission

Strong supramolecular interactions, which induced tight packing and rigid molecules in crystals of cyano substituent oligo(para-phenylene vinylene) (CN-DPDSB), are the key factor for the high luminescence efficiency of its crystals; opposite to its isolated molecules in solution which have very low luminescence efficiency.

Physical and spectral characterization of the human cyclin A gene and its interactions with anthracycline anticancer drugs

Over expression of cyclin A in human tumors has been linked to cancer by various experimental lines of evidence. However, physical and spectral characterization of the human cyclin A gene and its interactions with anticancer drugs have not been reported. Our gene sequence analysis, singular value decomposition method and melting studies in the presence of antitumor agents, daunomycin, doxorubicin and Hoechst 33258 showed that cyclin A gene had both AT-rich and GC-rich domains. For a ligand with unknown DNA binding specificity, this gene sequence can be used to differentiate its DNA binding preference.

Daunomycin binding to detergent micelles: A model system for evaluating the hydrophobic contribution to drug-DNA interactions

The interaction of daunomycin with sodium dodecyl sulfate and Triton X-100 micelles was investigated as a model for the hydrophobic contribution to the free energy of DNA intercalation reactions. Measurements of visible absorbance, fluorescence lifetime, steady-state fluorescence emission intensity, and fluorescence anisotropy indicate that the anthraquinone ring partitions into the hydrophobic micelle interior. Fluorescence quenching experiments using both steady-state and lifetime measurements demonstrate reduced accessibility of daunomycin in sodium dodecyl sulfate micelles to the anionic quencher iodide and to the neutral quencher acrylamide. Quenching of daunomycin fluorescence by iodide in Triton X-100 micelles was similar to that seen with free daunomycin. Studies of the energetics of the interaction of daunomycin with micelles by fluorescence and absorbance titration methods and by isothermal titration calorimetry in the presence of excess micelles revealed that association with sodium dodecyl sulfate and Triton X-100 micelles is driven by a large negative enthalpy. Association of the drug with both types of micelles also has a favorable entropic contribution, which is larger in magnitude for Triton X-100 micelles than for sodium dodecyl sulfate micelles.

Water-resistant conducting hybrids from electrostatic interactions

Conductive hybrids were prepared in a water/ethanol solution via the Solgel process from an inorganic sol containing carboxyl groups and water-borne conductive polyaniline (cPANI). The inorganic sol was prepared by the hydrolysis and condensation of methyltriethoxysilane with the condensed product of maleic anhydride and aminopropyltriethoxysilane as a catalyst, for which the carboxyl counterion along the cPANI backbone acted as an electrostatic-interaction moiety. The existence of this electrostatic interaction could improve the compatibility of the two components and contribute to the homogeneous dispersion of cPANI in the silica phase. The electrostaticinteraction hybrids displayed a conductivity percolation threshold as low as 1.1 wt % polyaniline in an emeraldine base, showing 2 orders of magnitude higher electrical conductivity than that without electrostatic interactions. The electrostatic-interaction hybrids also showed good water resistance; the electrical conductivity with a cPANI loading of 16 wt % underwent a slight change after 14 days of soaking in water.

Surface morphology evolution of a thin polymeric supramolecular film by tuning interactions

A polymeric supramolecule consisting of symmetric polystyrene-block-poly(4-vinylpytidine) (PS-b-P4VP), dodecylbenzenesulfonic acid (DBSA), and 3-pentadecylphenol (PDP) was formed by proton transfer and hydrogen bonding. The surface morphology,of a thin film of the polymeric supramolecule has been investigated. The spherical PS microdomains embedded in a P4VP(DBSA)(1.0)(PDP)(1.0) matrix are observed for the as-cast film because the weight fraction, f(comb), of the P4VP(DBSA) (1.0)(PDP)(1.0) blocks is much higher than that of PS as a result of the non-covalent interactions of P4VP and DBSA and DBSA and PDR Upon annealing the PS-b-P4VP(1:1)(DBSA)(1.0)(PDP)(1.0) film at high temperatures, the hydrogen bonding between the DBSA and PDP diminishes, which leads to a change of overall morphology from an ordered sphere to a pitted structure.

Interactions of the human telomeric DNA with terbium-amino acid complexes

The human telomeric DNA can form four-stranded structures: the G-rich strand adopts a G-quadruplex conformation stabilized by G-quartets and the C-rich strand may fold into an I-motif based on intercalated C (.) C+ base pairs. There is intense interests in the design and synthesis of compounds which can target telomeric DNA and inhibit the telomerase activity. Here we report the thermodynamic studies of the two newly synthesized terbium-amino acid complexes bound to the human telomeric G-quadruplex and I-motif DNA which were studied by means of UV-Visible, DNA meltings, fluorescence and circular dichroism. These two complexes can bind to the human telomeric DNA and have shown different features on DNA stability, binding stoichiometry, and sequence-dependent fluorescence enhancement. To our knowledge, this is the first report to show terbium-amino acid complexes can interact with the human telomeric DNA.