Observed interactions of thermal-energy helium and argon atoms with vapor-deposited, single- crystal silver surfaces

Electron diffraction in scattering of rare gases from vacuum-deposited silver crystal

X-Ray Crystallographic Studies of DNA-Drug and DNA-Protein Interactions

I. Cisplatin-12mer Cisplatin (cis-diamminodichloroplatinum[II]) is a widely used antineoplastic agent, which is believed to work by means of covalent interaction with DNA. Complexes of this compound were made with the B-DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G by diffusion of the drug into pregrown DNA crystals, and a structure determined to 2.6 Angstrom resolution by molecular replacement. Cisplatin was found to bind with partial occupancy at three discrete sites: G16 (61%), G4 (30%) and G10 (22%), in each case by means of a single covalent bond from the metal to guanine N7 in the major groove. The square plane of the metal complex ligands is rotated out of the plane of the guanine base, with one of the ligands that is cis to the guanine N7, presumably an amine, in a position to make a hydrogen bond with guanine 06; the long metal-06 distance precludes the possiblilty of a direct metal-06 bond. The DNA structure itself is essentially undisturbed by the metal binding; the only change is a slight notion of the bound guanines outward into the major groove toward the metals, resulting in a slight opening up of the groove but without pulling the base-pairs out of the helix stack. The structure shows that it is not possible for a direct N7-to-N7 crosslink between two adjacent bases by the metal to exist in an intact B-DNA double-helix. It is suggested that the observed structure is a primary mode of binding of the drug, which then could become this postulated active form upon disruption of the DNA duplex. II. Lac headpiece-operator complex The lac repressor protein of E. coli controls expression of the genes necessary for lactose utilization by the organism. It is a tetramer of four identical subunits of 355 amino acids each, each of which is divided into a 51 amino acid N-terminal DNA-binding, or "headpiece" domain and a 300 residue C-terminal regulatory region, or "core." In the presence of 1M Tris.HCl pH 7.5 and 30% glycerol, the headpiece can be isolated intact by proteolytic digestion and is believed to retain its specific DNA binding properties for the lac operator site. A large-scale purification scheme for the headpiece protein has been developed, using a specific protease-affinity column to eliminate all residual proteolytic activity from the prep, thus making it possible to isolate large quantities of the protease-sensitive fragment in stable form for crystallization trials. Attempts to crystallize the protein by itself resulted only in fibrous microcrystals. But cocrystallization trials with a 21 base-pair lac operator DNA oligomer yielded what appear to be small cocrystals, too small to characterize, under conditions in which neither the protein nor the DNA by themselves would crystallize. III. Hoechst 33258-Complex with DNA 12mer Hoechst 33258 is a widely used histological stain that forms a fluorescent complex with DNA, showing strong preference for AT-rich regions. Crystals were grown of a 1:1 complex of the dye with the B-DNA 12rner C-G-C-G-A-A-T-T-C-G-C-G, and a structure was determined to 2.2 Angstrom resolution. The compound was found to bind noncovalently in the minor groove, with its aromatic phenol and two benzimidazole rings spanning three bases of the A-A-T-T region, and its aliphatic piperazine ring binding in the adjacent C-G-C-G region. Three hydrogen bond contacts were found to bridge between adjacent base-pairs, the bridging resembling that by water molecules in the native structure. This bridging of base pairs was achieved via three amine groups on the dye. These all undoubtedly help to stabilize the interaction, but the shape of the compound allows a good hydrogen bonding interaction of normal length through only one of these contacts. The piperazine ring, because of its orientation perpendicular to the other rings, is unable to bind into the narrower minor groove of the AT region and must bind in the wider CG minor groove. In a second conformation of the dye, also seen in the structure, the piperazine ring points out of the minor groove because of a rotation of the benzimidazole ring to which it is attached around its bond to the other benzimidazole. In this orientation, the piperazine ring no longer makes contact with the DNA, and therefore the drug is not restricted to binding at a site containing GC base-pairs. As a result, it could bind within a region of contiguous AT base-pairs without the problem of steric clash due to the piperazine ring.</p

Dissociation of minor groove binders from DNA: insights from metadynamics simulations

We have used metadynamics to investigate the mechanism of noncovalent dissociation from DNA by two representatives of alkylating and noncovalent minor groove (MG) binders. The compounds are anthramycin in its anhydrous form (IMI) and distamycin A (DST), which differ in mode of binding, size, flexibility and net charge. This choice enables to evaluate the influence of such factors on the mechanism of dissociation. Dissociation of IMI requires an activation free energy of ∼12 kcal/mol and occurs via local widening of the MG and loss of contacts between the drug and one DNA strand, along with the insertion of waters in between. The detachment of DST occurs at a larger free energy cost, ∼16.5 or ∼18 kcal/mol depending on the binding mode. These values compare well with that of 16.6 kcal/mol extracted from stopped-flow experiments. In contrast to IMI, an intermediate is found in which the ligand is anchored to the DNA through its amidinium tail. From this conformation, binding and unbinding occur almost at the same rate. Comparison between DST and with kinetic models for the dissociation of Hoechst 33258 from DNA uncovers common characteristics across different classes of noncovalent MG ligands

Interatomic potentials and solvation parameters from protein engineering data for buried residues

Van der Waals (vdW) interaction energies between different atom types, energies of hydrogen bonds (H‐bonds), and atomic solvation parameters (ASPs) have been derived from the published thermodynamic stabilities of 106 mutants with available crystal structures by use of an originally designed model for the calculation of free‐energy differences. The set of mutants included substitutions of uncharged, inflexible, water‐inaccessible residues in α‐helices and β‐sheets of T4, human, and hen lysozymes and HI ribonuclease. The determined energies of vdW interactions and H‐bonds were smaller than in molecular mechanics and followed the “like dissolves like” rule, as expected in condensed media but not in vacuum. The depths of modified Lennard‐Jones potentials were −0.34, −0.12, and −0.06 kcal/mole for similar atom types (polar–polar, aromatic–aromatic, and aliphatic–aliphatic interactions, respectively) and −0.10, −0.08, −0.06, −0.02, and nearly 0 kcal/mole for different types (sulfur–polar, sulfur–aromatic, sulfur–aliphatic, aliphatic–aromatic, and carbon–polar, respectively), whereas the depths of H‐bond potentials were −1.5 to −1.8 kcal/mole. The obtained solvation parameters, that is, transfer energies from water to the protein interior, were 19, 7, −1, −21, and −66 cal/moleÅ 2 for aliphatic carbon, aromatic carbon, sulfur, nitrogen, and oxygen, respectively, which is close to the cyclohexane scale for aliphatic and aromatic groups but intermediate between octanol and cyclohexane for others. An analysis of additional replacements at the water–protein interface indicates that vdW interactions between protein atoms are reduced when they occur across water.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106915/1/111984_ftp.pd

Polyamide-Scorpion Cyclam Lexitropsins Selectively Bind AT-Rich DNA Independently of the Nature of the Coordinated Metal

Cyclam was attached to 1-, 2- and 3-pyrrole lexitropsins for the first time through a synthetically facile copper-catalyzed “click” reaction. The corresponding copper and zinc complexes were synthesized and characterized. The ligand and its complexes bound AT-rich DNA selectively over GC-rich DNA, and the thermodynamic profile of the binding was evaluated by isothermal titration calorimetry. The metal, encapsulated in a scorpion azamacrocyclic complex, did not affect the binding, which was dominated by the organic tail

Solid municipal waste

Import 06/06/2008Prezenční546 - Institut environmentálního inženýrstvíNeuveden

Monitoring of Polycyclic Aromatic Hydrocarbons in Selected Locations of Sokolov Brown Coal Basin

Import 29/09/2010Diplomová práce je zaměřena na studium polycyklických aromatických uhlovodíků (PAHs) v hnědouhelné sokolovské pánvi, které patří mezi persistentní organické polutanty s karcinogenním potenciálem, jako např. dobře známý benzo[a]pyren. Vybrané polycyklické aromatické uhlovodíky jmenovitě [nafthalene (NAP), fenanthrene (FEN), anthracene (ANT), fluoranthene (FLA), pyrene (PYR), benzo[a]anthracene (BaA), Chrysene (CHR), benzo[b]fluoranthene (BbF), benzo[k]fluoranthene (BkF), benzo[a]pyrene (BaP),benzo[g,h,i]perylene (BGP), indeno[1,2,3-cd]pyren (INP) a jejich suma (∑PAHs)] jsem analyzoval v půdě vybraných lokalit na Sokolovsku, konkrétně se jednalo o následující lokality: Nejdek - skládka komunálního odpadu, Karlovy Vary - Skalníkovy sady a Hoštěc - železniční průjezd. Laboratorní analýza vybraných zástupců PAHs byla po úpravě vzorků provedena metodou vysokoúčinné kapalinové chromatografie (HPLC) s fluorescenčním detektorem (FLD). Zjištěné hodnoty sledovaných PAHs byly porovnány s legislativou České republiky.This diploma thesis focuses on polycyclic aromatic hydrocarbons (PAHs) in Sokolov brown coal basin, that belong to the group of persistent organic pollutants with a carcinogenic potential, such as the well known benzo[a]pyrene. I analyse the selected polycyclic aromatic hydrocarbons [naphthalene (NAP), fenantrene (FEN), anthracene (ANT), fluoranthene (FLA), pyrene (PYR), benzo[a]anthracene (BaA), Chrysene (CHR), Benzo[b]fluoranthene (BbF), Benzo[k]fluoranthene (BkF), Benzo[a]pyrene (BaP), Benzo[g,h,i]perylene (BGP), indeno[1,2,3-cd]pyren (INP) and the total sum of PAHs (∑PAHs)] in soil from the following areas of Sokolov region: Nejdek - dump, Karlovy Vary - Skalníkovy sady and Hoštěc - train crossover. High performance chromatography (HPLC) with a fluorescence detector (FLD) was applied for the laboratory analysis. The obtained values of PAHs were compared to legislation limits of Czech Republic.Prezenční546 - Institut environmentálního inženýrstvívýborn