Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide-Activated Sirtuin 7**

The sirtuins are NAD⁺-dependent lysine deacylases, comprising seven isoforms (SIRT1–7) in humans, which are involved in the regulation of a plethora of biological processes, including gene expression and metabolism. The sirtuins share a common hydrolytic mechanism but display preferences for different ϵ-N-acyllysine substrates. SIRT7 deacetylates targets in nuclei and nucleoli but remains one of the lesser studied of the seven isoforms, in part due to a lack of chemical tools to specifically probe SIRT7 activity. Here we expressed SIRT7 and, using small-angle X-ray scattering, reveal SIRT7 to be a monomeric enzyme with a low degree of globular flexibility in solution. We developed a fluorogenic assay for investigation of the substrate preferences of SIRT7 and to evaluate compounds that modulate its activity. We report several mechanism-based SIRT7 inhibitors as well as de novo cyclic peptide inhibitors selected from mRNA-display library screening that exhibit selectivity for SIRT7 over other sirtuin isoforms, stabilize SIRT7 in cells, and cause an increase in the acetylation of H3 K18.     

Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents

The self-assembly of cyclic D,L-alpha-peptides into hollow nanotubes is a crucial mechanistic step in their application as antibacterial and drug-delivery agents. To understand this process, molecular dynamics (MD) simulations were performed on dimers of cyclic peptides formed from cyclo [(-L-Trp-D-N-MeLeu-)4-]2 and cyclo [(-L-Trp-D-Leu-)4-]2 subunits in nonpolar (nonane) and polar (water) solvent. The dimers were observed to be stable only in nonpolar solvent over the full 10 ns length of the MD trajectory. The behavior of the dimers in different solvents is rationalized in terms of the intersubunit hydrogen bonding, hydrogen bonding with the solvent, and planarity of the rings. It is shown that the phi and psi dihedral angles of a single uncapped ring in nonane lie in the beta-sheet region of the Ramachandran plot, and the ring stays in a flat conformation. Steered MD (SMD) simulations based on Jarzynski's equality were performed to obtain the potential of mean force as a function of the distance between the two rings of the capped dimer in nonane. It is also shown that a single peptide subunit prefers to reside close to the nonane/water interface rather than in bulk solvent because of the amphiphilic character of the peptide ring. The present MD results build the foundation for using MD simulations to study the mechanism of the formation of cyclic peptide nanotubes in lipid bilayers.     

Origin of Stability in Branched Alkanes

The potential origins of stability in branched alkanes are investigated, paying close attention to two recent hypotheses: geminal steric repulsion and protobranching. All alkane isomers through C₆H₁₄ along with heptane and octane were investigated at the MPW1B95/6‐311++G(d,p) level. Their geminal steric repulsion, total steric repulsion, and orbital interactions were evaluated by using natural bond orbital analysis. All measures of steric repulsion fail to explain the stability of branched alkanes. The extra stability of branched alkanes and protobranching, in general, is tied to stabilizing geminal σ→σ* delocalization, particularly of the type that involves adjacent C? C bonds and, thus, preferentially stabilizes branched alkanes. This picture is corroborated by valence bond calculations that attribute the effect to additional ionic structures (e.g., CH₃⁺ :CH₂ :CH₃^? and CH₃:^? CH₂: CH₃⁺ for propane) that are not possible without protobranching.     

Random benzotrithiophene-based donor-acceptor copolymers for efficient organic photovoltaic devices

A series of benzotrithiophene-containing random terpolymers for polymer solar cells is reported. Through variations of the two other components in the terpolymers, the absorption profile and the frontier energy levels are optimized and maximum power conversion efficiencies are nearly doubled (5.14%) relative to the parent alternating copolymer.     

Effect of glycation on the heterogeneity of human serum albumin analysed by reversed-phase high-performance liquid chromatography in a solvent containing formic acid.

Non-enzymic glycation of human serum albumin (HSA) induces a change in its charge heterogeneity that may account for its particular renal clearance in patients with early diabetic nephropathy. A new high-performance liquid chromatographic analysis for the study of HSA heterogeneity is described based on a high content of formic acid in the mobile phase combined with a concave gradient of isopropanol. Under these conditions, native HSA was separated into three individual components (I, II and III). When glycated HSA was analysed, it was found that although the present method is not suitable for the separation of glycated from non-glycated HSA, it shows the effect of glycation in producing changes in HSA heterogeneity that are different from those reported on surface change. This finding suggests an additional factor (probably conformational changes) that is contributing to the heterogeneity of glycated HSA.     

Single crystal Raman study of potassium oxalate monohydrate,K2C2O4. H2O,and potassium oxalate monodeuterate,K2C2O4. D2O

Raman spectra of poly crystalline and single crystal K₂C₂O₄. H₂O and K₂C₂O₄. D₂O have been recorded at room temperature. From an earlier neutron diffraction study it is known that the space group is C⁶₂h. The water molecule occupies a C₂ site and the oxalate ion a C₁ site. The assigned water vibrations show small factor group splitting between g modes (Raman active) and u modes (IR active). The internal oxalate vibrations are found to have wavenumbers in good agreement with those reported from Raman studies of other oxalates.     

Substituted 1,8-naphthyridin-2(1H)-ones are superior to thymine in the recognition of adenine in duplex as well as triplex structures

The synthesis and evaluation of a series of novel nucleobases based on substituted 1,8-naphthyridin-2(1H)-ones are reported. The nucleobases were designed to meet the requirements for incorporation into peptide nucleic acids (PNAs) and were evaluated as part of PNA duplex and triplex nucleic acid recognition systems. Of the various nucleobases tested, only the 7-chloro-1,8-naphthyridin-2(1H)-one (7-Cl-bT) nucleobase led to consistently increased affinity in all recognition systems, duplex (Watson-Crick) as well as triplex (Hoogsteen). For multiply modified systems, the increase in thermal stability per modification was dependent on the sequence context, ranging from 2.0 degrees C (in separate positions) to 3.5 degrees C (in adjacent positions) in PNA-DNA duplexes and from 1.2 degrees C (in separate positions) to 3.2 degrees C (in adjacent positions) in PNA-RNA duplexes. Singly mismatched oligonucleotide targets were employed to demonstrate uncompromised sequence discrimination. When part of multiply modified triplex (Hoogsteen) recognition systems, the 7-Cl-bT unit gave rise to increases in the thermal stability ranging from 2.7 to 3.5 degrees C when incorporated into separated and adjacent positions, respectively. Our results furthermore indicate that the duplex stabilization is predominantly enthalpic and therefore most likely not a consequence of single-strand preorganization. Finally, and most surprisingly, we find no direct correlation between the end-stacking efficiency of this type of nucleobase and its helix stabilization when involved in Watson-Crick base pairing within a helix.     

Local-in-time adjoint-based method for design optimization of unsteady flows

We present a new local-in-time discrete adjoint-based methodology for solving design optimization problems arising in unsteady aerodynamic applications. The new methodology circumvents storage requirements associated with the straightforward implementation of a global adjoint-based optimization method that stores the entire flow solution history for all time levels. This storage cost may quickly become prohibitive for large-scale applications. The key idea of the local-in-time method is to divide the entire time interval into several subintervals and to approximate the solution of the unsteady adjoint equations and the sensitivity derivative as a combination of the corresponding local quantities computed on each time subinterval. Since each subinterval contains relatively few time levels, the storage cost of the local-in-time method is much lower than that of the global methods, thus making the time-dependent adjoint optimization feasible for practical applications. Another attractive feature of the new technique is that the converged solution obtained with the local-in-time method is a local extremum of the original optimization problem. The new method carries no computational overhead as compared with the global implementation of adjoint-based methods. The paper presents a detailed comparison of the global- and local-in-time adjoint-based methods for design optimization problems governed by the unsteady compressible 2-D Euler equations.