Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).     

Cationic complexes of Eu(III) and Sr(II) with diphosphine dioxides in organic extracts

IR spectroscopy was used to study the structure and composition of Eu(III) and Sr(II) complexes formed by cation-exchange extraction of these metals from their aqueous nitrate solutions with dichlorethane solutions of mixtures of chlorinated cobalt(III) dicarbollide (CCD) as a superacid with diphenyldiphosphine dioxides containing a methyl (Me-DPDO), ethyl (Et-DPDO), or polyoxyethylene bridge between two phosphorus atoms of phosphine oxide groups. At molar ratios DPDO/CCD ≤ 1, [Eu(H₂O)_nL₄]³⁺ complexes are formed in organic phases, whereas with an excess of DPDO relative to CCD, Eu(NO₃)L ₄ ²⁺ complexes are formed, where L = Me-or Et-DPDO. Polyoxyethylenediphosphine dioxide forms anhydrous complexes of composition Eu:L = 1:1 and 1:2 with Eu(III) and outer-spheric complexes of composition Sr:L = 1:1 and 1:2 with Sr(II), where the organic ligand molecules envelop the hydrated Sr(H₂O) _n ²⁺ cation. The peculiarities of extraction of the complexes are explained based on data about their composition and structure.     

Molecular caps for full quantum mechanical computation of peptide-water interaction energy

We present a systematic study of numerical accuracy of various forms of molecular caps that are employed in a recently developed molecular fractionation scheme for full quantum mechanical computation of protein-molecule interaction energy. A previously studied pentapeptide (Gly-Ser-Ala-Asp-Val) or P5 interacting with a water molecule is used as a benchmark system for numerical testing. One-dimensional potential energy curves are generated for a number of peptide-water interaction pathways. Our study shows that various forms of caps all give consistently accurate energies compared to the corresponding full system calculation with only small deviations. We also tested the accuracy of cutting peptide backbone at different positions and comparisons of results are presented.     

Electronically-coupled MM quadruply-bonded complexes of molybdenum and tungsten

The reaction of M2(O2CBu(t))4 (M = Mo, W) with a dicarboxylic acid in toluene yields compounds of general formula [M2]-O2C-X-CO2-[M2] ([M2] = M2(O2CBu(t))3; X = conjugated spacer). The M2 units are electronically coupled via interactions between the M2 delta and dicarboxylate pi* orbitals, and the magnitude of this coupling is revealed by electronic structure calculations and spectroscopic data. These compounds show intense metal to ligand charge transfer (MLCT) absorptions in the visible region of the electronic spectrum that are temperature and solvent dependent. Evidence of electronic coupling is seen in their cyclic voltammograms, which show two successive one-electron oxidations. The extent of electronic coupling in the mixed valence radical cations [M2]-O2C-X-CO2-[M2]+, generated by oxidation with one equivalent of AgPF6 or FeCp2PF6, is evaluated by EPR and UV-vis-NIR spectroscopic data, and delocalized behavior is observed in compounds with W2 units separated by up to 13.6 angstroms. The simplicity of the frontier M2 orbital interactions with the bridge pi orbitals provides a convenient system with which to study electron transfer in mixed valence systems, as compared to the extensively studied, but more complicated, dinuclear t(2g)6/t(2g)5 mixed valence compounds. Oligomeric and polymeric compounds incorporating M2 units have also been synthesized, having general formula [M2(O2CR)2(O2C-Thio-CO2)]n (Thio = n-hexyl substituted ter- and quinque-thiophenes). They can be deposited as thin films by spin coating, and show photoluminescence and electroluminescence. These metallo-polythiophenes show potential for application in electronic materials. (     

Own N-layered integrated molecular orbital and molecular mechanics study of the reaction of OH<Superscript>−</Superscript> with polychlorinated hydrocarbons CH<Subscript>(4−n)</Subscript>Cl<Subscript>n</Subscript> (n=2–4)

The reliability of the two-layer own N-layered integrated molecular orbital and molecular mechanics (ONIOM) method was examined for the S_N2 reaction CH_(4–n)Cl_n+OH^–. In the ONIOM calculation, only the methyl chloride and OH^–were treated at a high level and the effect of polychlorination was taken into account only at a low level. The ONIOM results were compared with the target CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ results obtained by Borisov etal. [(2001) J. Phys. Chem. A 105:7724]. The ONIOM[MP2/aug-cc-pVDZ:B3LYP/6-31+G(d)] was found to reproduce well the target geometry and energy at the MP2/aug-cc-pVDZ level. The single-point improved energetics at the ONIOM[CCSD(T)/aug-cc-pVDZ:MP2/6-31+G(d)] is found to give results nearly as accurate as the target CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ results. The substantially reduced cost, 20% for optimization and 5% for single-point improved energy of the target cost for n=4, as well as small errors suggest that ONIOM is a powerful tool for accurate potential-energy surfaces of the reaction of large polyhalohydrocarbons.     

A computational model of the nicotinic acetylcholine binding site

We have derived a model of the nicotinic acetylcholine binding site. This was accomplished by using three known agonists (acetylcholine, nicotine and epibatidine) as templates around which polypeptide side chains, found to be part of the receptor cavity from published molecular biology studies, are allowed to flow freely in molecular dynamics simulations and mold themselves around these templates. The resulting supramolecular complex should thus be a complement, both in terms of steric effects as well as electronic effects, to the agonists and it should be a good estimation of the true receptor cavity structure. The shapes of those minireceptor cavities equilibrated rapidly on the simulation time scale and their structural congruence is very high, implying that a satisfactory model of the nicotinic acetylcholine binding site has been achieved. The computational methodology was internally tested against two rigid and specific antagonists (dihydro--erytroidine and erysoidine), that are expected to give rise to a somewhat differently shaped binding site compared to that derived from the agonists. Using these antagonists as templates there were structural reorganizations of the initial receptor cavities leading to distinctly different cavities compared to agonists. This indicates that adequate times and temperatures were used in our computational protocols to achieve equilibrium structures for the agonists. Overall, both minireceptor geometries for agonists and antagonists are similar with the exception of one amino acid (ARG209).     

Sol-gel polyimide-silica composite membrane: gas transport properties

The effect of introduction of silica particles prepared by the sol-gel technique on the gas transport properties of a polyimide film was studied. The sorption and permeation of N₂, O₂, CO₂, H₂ and CH₄ were studied and correlated with morphological changes in the polymer structure. From sorption isotherms, we observed that the composite membrane presents higher solubility coefficients than the polyimide one. The solubility coefficient ratio between the composite and the polyimide is about 1.5–2.0. The isotherms were analyzed in terms of the dual mode sorption. The Henry's coefficient and the Langmuir's affinity and saturation constants were obtained allowing to calculate the Langmuir to Henry concentration ratios as function of the gas pressure. These ratios decrease until zero within a certain pressure range as long as the Langmuir's mode is acting and they are higher for the polyimide membrane when compared with the composite one. This study was completed with calorimetric measurements during the sorption. The gas interaction energy in kJ/mol decreases within the same pressure range as previously described. The measured energies are higher for the polyimide film when compared with the composite one because the polyimide membrane presents a stronger energetic effect caused by a higher Langmuir's contribution. From permeation studies at 3.15⁵ Pa, the composite membrane showed higher permeability coefficients and permselectivities than the polyimide one. All these results were explained, taking into account the difference on the imidization degree of both membranes and the morphological changes which may be induced by the silica nodules in the organic/inorganic interphases.     

On the calculation of expectation values and transition matrix elements by coupled cluster method

Summary Finite order expressions are derived for expectation values and transition matrix elements within the framework of the coupled cluster method.     

First radical cation salts of 2,5-bis(1,3-dithian-2-ylidene)-1,3,4,6-tetrathiapentalene (BDA-TTP) with copper(II) metal complex anions: β-(BDA-TTP)4Cu2Cl6 and (BDA-TTP)2CuCl4

New radical cation salts based on 2,5-bis(1,3-dithian-2-ylidene)-1,3,4,6-tetrathiapentalene (BDA-TTP) with copper(II) metal complex anions, β-(BDA-TTP)₄Cu₂Cl₆ and (BDA-TTP)₂CuCl₄, were synthesized and structurally characterized. Single crystals were prepared by electrochemical oxidation of BDA-TTP under galvanostatic conditions. X-ray diffraction study demonstrated that the salts have a layered structure, in which the conducting BDA-TTP layers alternate with the [Cu₂Cl₆]²⁻ or [CuCl₄]²⁻ anions. Both salts show the semiconductor-type temperature dependence of the conductivity. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 48–54, January, 2007.     

Occurrence and distribution of metals and porphyrins in Nigerian coal minerals

The metal contents of Nigerian coal minerals were analyzed using an atomic absorption spectrophotometer. Calcium, Na, and Fe occurred as the major elements with concentrations ranging from 9 782 μg/g for Ca to 432 μg/g for Na whereas K, Mg, Mn, Ni, Cr, Zn, Pb, and Cu, which occurred at trace levels ranged from 673.73 μg/g for Mg to 2.97 μg/g for Mn. The results of the quantitative analysis of porphyrins extracted from the coal minerals showed that Onyeama coal has the highest amount of porphyrins (ca～0.96 μg/g) while Okpara has the lowest (ca～0.30 μg/g). The porphyrins were qualitatively characterized by a combination of thin layer chromatography (TLC), infrared, and ultraviolet-visible spectrophotometers. The results of the mid infrared analysis (MIR) showed the presence of absorption bands at 3 440 cm～1～3 450 cm-1 and 1 640 cm-1～1 680 cm-1 , which are owing to the stretching vibrations of N - H and C = C of aromatics, with C- H out of plane (oop) bending vibrations at wavenumbers less than 900 cm-1, all of which are characteristic absorptions of porphyrin free base. The ultraviolet-visible data showed prominent peaks at ～400 nm(Soret band) and at wavelength ranges of 535 nm～550 nm(β-band) and 565 nm～ 600 nm (α-band) for the coal porphyrins analyzed. The geochemical significance of the metals and porphyrins in coal minerals are discussed.