Single-molecule observation of the catalytic subunit of cAMP-dependent protein kinase binding to an inhibitor peptide

An engineered version of the staphylococcal alpha-hemolysin protein pore, bearing a peptide inhibitor near the entrance to the beta barrel, interacts with the catalytic (C) subunit of cAMP-dependent protein kinase. By monitoring the ionic current through the pore, binding events are detected at the single-molecule level. The kinetic and thermodynamic constants governing the binding interaction and the synergistic effect of MgATP are comparable but not identical to the values in bulk solution. Further, the values are strongly dependent on the applied membrane potential. Additional exploration of these findings may lead to a better understanding of the properties of enzymes at the lipid/water interface. Despite the complications, we suggest that the engineered pore might be used as a sensor element to screen inhibitors that act at either the substrate or ATP binding sites of the C subunit.     

IMPAIRED REPAIR OF UVC-INDUCED DNA DAMAGE IN L5178Y-R CELLS: SEDIMENTATION STUDIES WITH THE USE OF 5''-BROMODEOXYURIDINE PHOTOLYSIS

Abstract Relative to their L5178Y-S counterparts, L5178Y-R cells have an impaired capacity to form patches in DNA after exposure to UVC radiation. The photolysis of 5'-bromodeoxyuridine (BrdUrd) incorporated into DNA was used to estimate the number of 'repair patches'formed in response to a 254 nm UV (UVC) exposure. L5178Y-S cells, typical of rodent cell lines, formed a small number of patches in exposed DNA (1-2 patches per 1 times 10⁸ dalton during a 6 h recovery after an exposure of 20 J/m²). In contrast, DNA extracted from L5178Y-R cells exposed to UVC and subsequently incubated with BrdUrd for 6 h showed no evidence of BrdUrd incorporation indicating no capacity to form sites of repair (fewer than 0.5 sites of BrdUrd incorporation per 1 times 10⁸ dalton). Moreover, in L5178Y-R cells high fluences of UVC caused an extensive DNA degradation. Such degradation was not observed in L5178Y-S cells during the 24-h post-exposure period. These results are consistent with the notion that L5178Y-R cells have a reduced capacity to repair DNA damage induced by UVC radiation.     

Single-molecule detection of nitrogen mustards by covalent reaction within a protein nanopore

Mustards, including sulfur mustards and nitrogen mustards, form a class of cytotoxic, vesicant chemical warfare agents. Mustards have also been used to treat cancer and played a vital role in the development of chemotherapy. Additionally, because of their destructive properties, ease of synthesis, and the lack of effective antidotes, mustards are unquestionably terrorist threats. Therefore, quick and convenient detection of mustards is a critical issue. In the present study, we achieved detection of various mustards on the basis of their chemical reactivity by using engineered alpha-hemolysin (alphaHL) protein pores as sensor elements. We describe four classes of reactions for detecting mustards. These reactions occur between mustards and thiol groups contributed by cysteine side-chains within the lumen of the alphaHL pore or on an internal molecular adapter. The approach is quick and straightforward. It can confirm the existence of mustards in as little as 10 min at 50 microM or lower.     

Mobile Molecules: Reactivity Profiling Guides Faster Movement on a Cysteine Track

We previously reported a molecular hopper, which makes sub-nanometer steps by thiol-disulfide interchange along a track with cysteine footholds within a protein nanopore. Here we optimize the hopping rate (ca. 0.1 s⁻¹ in the previous work) with a view towards rapid enzymeless biopolymer characterization during translocation within nanopores. We first took a single-molecule approach to obtain the reactivity profiles of individual footholds. The pK_a values of cysteine thiols within a pore ranged from 9.17 to 9.85, and the pH-independent rate constants of the thiolates with a small-molecule disulfide varied by up to 20-fold. Through site-specific mutagenesis and a pH increase from 8.5 to 9.5, the overall hopping rate of a DNA cargo along a five-cysteine track was accelerated 4-fold, and the rate-limiting step 21-fold.     

Adducts of thianthrene- and phenoxathiin cation radical salts with symmetrical alkynes. Structure and formation of cumulenes on alumina leading to alpha-diketones, alpha-hydroxyalkynes, and alpha-acetamidoalkynes

[reaction: see text] Thianthrene cation radical tetrafluoroborate (Th*+ BF4-) added to 2-butyne, 3-hexyne, 4-octyne, and 5-decyne in MeCN to form trans bisadducts R(Th+)C=C(Th+)R, where R = Me, Et, Pr, Bu (7a-d). Phenoxathiin cation radical tetrafluoroborate (PO*+ BF4-) added similarly to the last three alkynes to form adducts R(PO+)C=C(PO+)R, 8b-d. Cyclic monoadducts were not found. The trans structures of 7 and 8 were deduced with X-ray crystallography (7c) and NMR spectroscopy. When solutions of adducts in CHCl3 and MeCN were deposited on activated alumina, elimination of thianthrene (Th) and phenoxathiin (PO) occurred almost quantitatively. Detailed studies with (7b-d) indicated that a cumulene (15) was formed by the elimination of Th and that 15 was subsequently converted into small amounts of other products. In CHCl3, these products were the respective alkyne, thianthrene 5-oxide, an alpha-diketone (11), an alpha-hydroxyalkyne (12), and hydrogen. The same products were formed in MeCN along with an alpha-acetamidoalkyne (13). The formation of 15 and products derived from it is explained and was confirmed by preparation and reactions of 2,3,4-hexatriene.     

Fe-N-O structure and bonding in six-coordinate {FeNO}6 porphyrinates containing imidazole: implications for reactivity of coordinated NO

We report density functional theory calculations on six-coordinate ferric-NO ({FeNO}6) porphyrinates that contain either imidazole or imidazolate as the trans axial ligand. Our results show that the sensitivities of the Fe-NO and N-O stretching frequencies to cis and trans influences are directly correlated. In other words, as one decreases so does the other for both the imidazole and the imidazolate complexes. This correlation is opposite that of the isoelectronic ferrous-CO systems, whose Fe-CO and C-O frequencies are well-known to be inversely correlated. Based on the results of our calculations, the molecular origin of the direct correlation in {FeNO}6 porphyrinates can be explained by trends in the electron density distributions within the HOMO or HOMO-1, which exhibits Fe-NO and N-O pi-antibonding character. Variability in the Fe-N-O pi-antibonding character of the HOMO or the HOMO-1 modulates the angleFeNO as well as the Fe-NO and N-O bond strengths in concert. Orbital interactions in the six-coordinate FeIIINO porphyrin complexes are compared and contrasted with those of the isoelectronic FeIICO analogues, and an overall view of {FeNO}6 bonding in these complexes is set forth.