Catalytic protein modification with dirhodium metallopeptides: specificity in designed and natural systems

In this study, we present advances in the use of rhodium(II) metallopeptides for protein modification. Site-specific, proximity-driven modification is enabled by the unique combination of peptide-based molecular recognition and a rhodium catalyst capable of modifying a wide range of amino-acid side chains. We explore catalysis based on coiled-coil recognition in detail, providing an understanding of the determinants of specificity and culminating in the demonstration of orthogonal modification of separate proteins in cell lysate. In addition, the concepts of proximity-driven catalysis are extended to include modification of the natural Fyn SH3 domain with metallopeptides based on a known proline-rich peptide ligand. The development of orthogonal catalyst-substrate pairs for modification in lysate, and the extension of these methods to new natural protein domains, highlight the capabilities for new reaction design possible in chemical approaches to site-specific protein modification.     

A negative stain for electron microscopic tomography

While negative staining can provide detailed, two-dimensional images of biological structures, the potential of combining tomography with negative staining to provide three-dimensional views has yet to be fully realized. Basic requirements of a negative stain for tomography are that the density and atomic number of the stain are optimal, and that the stain does not degrade or rearrange with the intensive electron dose (~10? e/nm2) needed to collect a full set of tomographic images. A commercially available, tungsten-based stain appears to satisfy these prerequisites. Comparison of the surface structure of negatively stained influenza A virus with previous structural results served to evaluate this negative stain. The combination of many projections of the same structure yielded detailed images of single proteins on the viral surface. Corresponding surface renderings are a good fit to images of the viral surface derived from cryomicroscopy as well as to the shapes of crystallized surface proteins. Negative stain tomography with the appropriate stain yields detailed images of individual molecules in their normal setting on the surface of the influenza A virus.     

Catenated PS–PMMA Block Copolymers via Supramolecularly Templated ATRP Initiator Approach

A novel route to synthesize catenated macrocyclic PS–PMMA block copolymers is demonstrated via combination of supramolecular chemistry and controlled radical polymerization (CRP). Polymerization of styrene with bromopropionate ester initiator coupled with phenanthroline Cu(I) complex affords a four arm PS macroinitiator, which upon further chain extension by polymerization of MMA generates a four arm PS–PMMA block copolymer. Intramolecular coupling of PS–PMMA–Br arms via low temperature styrene‐assisted atom transfer radical coupling (ATRC) leads to the formation of PS–PMMA catenand, which generates the metal‐free catenated macrocyclic PS–PMMA block copolymer after removal of Cu metal. The interlocked structures of catenated block copolymers are confirmed by GPC, NMR, and AFM image analysis.     

Hydrogenation and Fluorination of Graphene Models: Analysis via the Average Local Ionization Energy

We have investigated the use of the average local ionization energy, I?(S)(r), as a means for rapidly predicting the relative reactivities of different sites on two model graphene surfaces toward the successive addition of one, two, and three hydrogen or fluorine atoms. The I?(S)(r) results were compared with directly computed interaction energies, at the B3LYP/6-311G(d,p) level. I?(S)(r) correctly predicts that the edges of graphene sheets are more reactive than the interior portions. It shows that added hydrogens activate the adjoining (ortho) sites and deactivate those that are separated by one site (meta). Overall, I?(S)(r) is effective for rapidly (single calculations) estimating the relative site reactivities of these large systems, although it reflects only the system prior to an interaction and cannot take into account postinteraction factors, e.g., structural distortion.     

A designer bleomycin with significantly improved DNA cleavage activity

The bleomycins (BLMs) are used clinically in combination with a number of other agents for the treatment of several types of tumors, and the BLM, etoposide, and cisplatin treatment regimen cures 90-95% of metastatic testicular cancer patients. BLM-induced pneumonitis is the most feared, dose-limiting side effect of BLM in chemotherapy, which can progress into lung fibrosis and affect up to 46% of the total patient population. There have been continued efforts to develop new BLM analogues in the search for anticancer drugs with better clinical efficacy and lower lung toxicity. We have previously cloned and characterized the biosynthetic gene clusters for BLMs from Streptomyces verticillus ATCC15003, tallysomycins from Streptoalloteichus hindustanus E465-94 ATCC31158, and zorbamycin (ZBM) from Streptomyces flavoviridis SB9001. Comparative analysis of the three biosynthetic machineries provided the molecular basis for the formulation of hypotheses to engineer novel analogues. We now report engineered production of three new analogues, 6'-hydroxy-ZBM, BLM Z, and 6'-deoxy-BLM Z and the evaluation of their DNA cleavage activities as a measurement for their potential anticancer activity. Our findings unveiled: (i) the disaccharide moiety plays an important role in the DNA cleavage activity of BLMs and ZBMs, (ii) the ZBM disaccharide significantly enhances the potency of BLM, and (iii) 6'-deoxy-BLM Z represents the most potent BLM analogue known to date. The fact that 6'-deoxy-BLM Z can be produced in reasonable quantities by microbial fermentation should greatly facilitate follow-up mechanistic and preclinical studies to potentially advance this analogue into a clinical drug.     

Compatible relations on Heyting chains

We give a sufficient condition for a finite algebra to admit only finitely many compatible relations (modulo a natural equivalence) and show that every finite Heyting chain satisfies this condition, thereby confirming a conjecture of Davey and Pitkethly.     

Heteroaromatic alkaloids,nakijinamines, from a sponge Suberites sp.

The structures of seven new secondary metabolites isolated from an Okinawan marine sponge Suberites sp., nakijinamines A (1), B (2), and F–I (3–6) and 6-bromoconicamin (7), have been elucidated on the basis of spectroscopic analysis, chemical conversion, and conformational analysis. These analyses disclosed that 1–6 were heteroaromatic alkaloids having the hybrid structures of an aaptamine-type alkaloid and an indole alkaloid, while 7 was a bromoindole alkaloid. Nakijinamine I (6) is the first example of an aaptamine-type alkaloid possessing a 1,4-dioxane ring. Antimicrobial activities of 1–7 were evaluated.     

Arene cis-dihydrodiols—useful precursors for the preparation of antimetabolites of the shikimic acid pathway: application to the synthesis of 6,6-difluoroshikimic acid and (6S)-6-fluoroshikimic acid

The synthesis of 6,6-difluoroshikimic acid (11) has been achieved in ten steps from the enantiopure diol 16, which is derived from enzymatic cis-dihydroxylation of iodobenzene. The versatility of the synthetic strategy has been demonstrated by the preparation of the known antimicrobial agent, (6S)-6-fluoroshikimic acid (5).     

Atomically flat gold on elastomeric substrate

We present a procedure to fabricate extremely smooth Au films supported on thin elastomeric (PDMS) substrates. Minimum rms roughness and largest grain size are obtained using Si wafers, coated with native oxide and release layers, as templates for the growth of thermally evaporated Au films. The wafers are held at a temperature of 300 degrees C during deposition. The Au films, up to 200 nm thick, are then transferred onto poly(dimethylsiloxane) substrates which have been previously surface-functionalized with a (3-mercaptopropyl)trimethoxysilane adhesion layer. The resulting Au films have been found by AFM to be extremely smooth with rms-roughness 2.5-4 angstroms and to exhibit a crystalline morphology with flat grains >500 nm in size. Thinner films, down to 20 nm, are grown at lower temperature and are comparably smooth, but with a loss in crystalline morphology. We compare the results of this optimized procedure with other gold films grown on mica sheets as templates and to those produced using Ti-O-Si interfacial chemistry.     

Nitroprusside-PEO enthalpic interaction as a driving force for partitioning of the [Fe(CN)(5)NO](2-) anion in aqueous two-phase systems formed by poly(ethylene oxide) and sulfate salts

Ions are known to concentrate in the salt-enriched phase of aqueous two-phase systems, with the only known exception being the pertechnetate anion, TcO(4)(-). We have discovered a second ion, nitroprusside anion (NP), which is markedly transferred from the salt phase to the polymer phase. The partitioning behavior of [Fe(CN)(5)NO](2-) anion was investigated in ATPS formed by poly(ethylene oxide) of molar mass 3350 and 35000 g mol(-1), and different sulfate salts (Na(2)SO(4), Li(2)SO(4), and MgSO(4)). On the basis of a model, the nitroprusside high affinity for the macromolecular phase was attributed to an enthalpic specific interaction between the anion and ethylene oxide unit. Partition coefficients increased exponentially with tie-line length increase, reaching values as high as 1000 and showing a relationship very dependent on the salt nature, but independent of the polymer molar mass.