How do size-expanded DNA nucleobases enhance duplex stability? Computational analysis of the hydrogen-bonding and stacking ability of xDNA bases

Computational chemistry (B3LYP, MP2) is used to study the properties of size-expanded DNA nucleobases generated by inserting a benzene spacer into the natural nucleobases. Although the addition of the spacer does not significantly affect the hydrogen-bonding properties of natural nucleobases, the orientation of the base about the glycosidic bond necessary for Watson-Crick binding is destabilized, which could have implications for the selectivity of expanded bases, as well as the stability of expanded duplexes. Consideration of the (stacked) binding energies in the preferred relative orientation of natural and expanded nucleobases aligned according to their centers of mass reveals that the stacking within natural dimers can be increased by up to 50% upon expansion of one nucleobase and up to 90% upon expansion of two nucleobases. The implications of these findings to the stability of expanded duplexes were revealed by considering simplified models of natural and mixed duplexes composed of four nucleobases. Although intra- and interstrand interactions within double helices are typically less than those predicted when nucleobases are stacked according to their centers of mass, some nucleobases utilize their full stacking potential within double helices, where both intra- and interstrand interactions can be significant. Most importantly, increasing the size of nucleobases within the duplex significantly increases both intra- and interstrand stacking interactions. Specifically, some interactions are double the magnitude of the corresponding intrastrand interactions in natural helices, and even greater increases in interstrand interactions are sometimes found. Thus, our work suggests that mixed duplexes composed of natural bases hydrogen bound to expanded bases may exploit the increase in the inherent stacking ability of the expanded bases in more than one way and thereby afford duplexes with greater stability than natural DNA.     

A study of Src SH2 domain protein-phosphopeptide binding interactions by electrospray ionization mass spectrometry

The noncovalent binding of various peptide ligands to pp60^src (Src) SH2 (Src homology 2) domain protein (12.9 ku) has been used as a model system for development of electrospray ionization mass spectrometry (ESI-MS) as a tool to study noncovalently bound complexes. SH2 motifs in proteins are critical in the signal transduction pathways of the tyrosine kinase growth factor receptors and recognize phosphotyrosine-containing proteins and peptides. ESI-MS with a magnetic sector instrument and array detection has been used to detect the protein-peptide complex with low-picomole sensitivity. The relative abundances of the multiply charged ions for the complex formed between Src SH2 protein and several nonphosphorylated and phosphorylated peptides have been compared. The mass spectrometry data correlate well to the measured binding constants derived from solution-based methods, indicating that the mass spectrometry-based method can be used to assess the affinity of such interactions. Solution-phase equilibrium constants may be determined by measuring the amount of bound and unbound species as a function of concentration for construction of a Scatchard graph. ESI-MS of a solution containing Src SH2 with a mixture of phosphopeptides showed the expected protein-phosphopeptide complex as the dominant species in the mass spectrum, demonstrating the method’s potential for screening mixtures from peptide libraries.     

A designed glycoprotein analogue of Gc-MAF exhibits native-like phagocytic activity

Rational protein design has been successfully used to create mimics of natural proteins that retain native activity. In the present work, de novo protein engineering is explored to develop a mini-protein analogue of Gc-MAF, a glycoprotein involved in the immune system activation that has shown anticancer activity in mice. Gc-MAF is derived in vivo from vitamin D binding protein (VDBP) via enzymatic processing of its glycosaccharide to leave a single GalNAc residue located on an exposed loop. We used molecular modeling tools in conjunction with structural analysis to splice the glycosylated loop onto a stable three-helix bundle (alpha3W, PDB entry 1LQ7). The resulting 69-residue model peptide, MM1, has been successfully synthesized by solid-phase synthesis both in the aglycosylated and the glycosylated (GalNAc-MM1) form. Circular dichroism spectroscopy confirmed the expected alpha-helical secondary structure. The thermodynamic stability as evaluated from chemical and thermal denaturation is comparable with that of the scaffold protein, alpha3W, indicating that the insertion of the exogenous loop of Gc-MAF did not significantly perturb the overall structure. GalNAc-MM1 retains the macrophage stimulation activity of natural Gc-MAF; in vitro tests show an identical enhancement of Fc-receptor-mediated phagocytosis in primary macrophages. GalNAc-MM1 provides a framework for the development of mutants with increased activity that could be used in place of Gc-MAF as an immunomodulatory agent in therapy.     

Geometry of simple molecules: nonbonded interactions, not bonding orbitals, and primarily determine observed geometries.

The forces responsible for the observed geometries of the YX(3) (Y = N or P; X = H, F, or Cl) molecules were studied through ab initio computations at the HF-SCF/6-31G level. The calculated molecular orbitals were grouped as contributing primarily to (a) the covalent bonds, (b) the terminal atom nonbonding electrons (for X = F or Cl), and (c) the central atom nonbonding electrons. This grouping was accomplished through 3-D plotting and an atomic population analysis of the molecular orbitals. The molecules were then moved through a X-Y-X angular range from 90 degrees to 119 degrees, in four or five degree increments. Single-point calculations were done at each increment, so as to quantify the energy changes in the molecular orbital groups as a function of geometry. These calculations show that the nonbonding electrons are much more sensitive to geometry change than are the bonding orbitals, particularly in the trihalide compounds. The molecular orbitals representing the nonbonding electrons on the terminal atoms (both valence and core electrons) contribute to the spreading forces, as they favor a wider X-Y-X angle. The contracting forces, which favor a smaller X-Y-X angle, consist of the orbitals comprising the nonbonding electrons on the central atom (again, both valence and core electrons). The observed geometry is seen as the balance point between these two sets of forces. A simple interaction-distance model of spreading and contracting forces supports this hypothesis. Highly linear trends are obtained for both the nitrogen trihalides (R(2) = 0.981) and phosphorus trihalides (R(2) = 0.992) when the opposing forces are plotted against each other. These results suggest that a revision of the popular conceptual models (hybridization and VSEPR) of molecular geometry might be appropriate.     

Efficient and Practical Algorithms for Sequential Modular Decomposition

A module of an undirected graph G = (V, E) is a set X of vertices that have the same set of neighbors in V\X. The modular decomposition is a unique decomposition of the vertices into nested modules. We give a practical algorithm with an O(n + mα(m, n)) time bound and a variant with a linear time bound.     

Colonic drug delivery using amylose films: the role of aqueous ethylcellulose dispersions in controlling drug release

Amylose, a plant polysaccharide from starch, can be combined with ethylcellulose to produce a film coating capable of effecting colon specific drug release from a dosage form through bacterial fermentation of the amylose component. Ethylcellulose is present in the system as a structuring agent in the form of the aqueous dispersion Surelease^® grade EA-7100. There are, however, two other grades of Surelease^® (E-7-7050 and E-7-19010), which vary slightly in terms of their composition. The aim of the study was to establish whether these grades differ in their drug release profiles, when used as a film coat, either as one-component coatings, or in combination with amylose. The dissolution profiles of Surelease^® coated pellets were investigated and it was found that there was no difference between the grades when used as coating materials on their own. However, when used in combination with amylose, it was found that grade EA-7100 showed retardation of drug release in simulated upper gastro-intestinal (GI) conditions, whereas grades E-7-7050 and E-7-19010 did not limit the release to the same extent. E-7-19010 showed very poor controlled release properties when combined with amylose. These differences could not be attributed to the minimum film forming temperature (MFT) of the coating formulation, which was found to be independent of the grade of Surelease^®. It was also confirmed that the film coated pellets prepared from amylose and EA-7100 showed good release in human faecal slurry, i.e. simulated colonic conditions. It was concluded that the grades of Surelease^®, when combined with amylose, are not interchangeable.     

The synthesis, characterisation and reactivity of 2-phosphanylethylcyclopentadienyl complexes of cobalt, rhodium and iridium

2-Phosphanylethylcyclopentadienyl lithium compounds, Li[C(5)R'(4)(CH(2))(2)PR(2)] (R = Et, R' = H or Me, R = Ph, R' = Me), have been prepared from the reaction of spirohydrocarbons C(5)R'(4)(C(2)H(4)) with LiPR(2). C(5)Et(4)HSiMe(2)CH(2)PMe(2), was prepared from reaction of Li[C(5)Et(4)] with Me(2)SiCl(2) followed by Me(2)PCH(2)Li. The lithium salts were reacted with [RhCl(CO)(2)](2), [IrCl(CO)(3)] or [Co(2)(CO)(8)] to give [M(C(5)R'(4)(CH(2))(2)PR(2))(CO)] (M = Rh, R = Et, R' = H or Me, R = Ph, R' = Me; M = Ir or Co, R = Et, R' = Me), which have been fully characterised, in many cases crystallographically as monomers with coordination of the phosphorus atom and the cyclopentadienyl ring. The values of nu(CO) for these complexes are usually lower than those for the analogous complexes without the bridge between the cyclopentadienyl ring and the phosphine, the exception being [Rh(Cp'(CH(2))(2)PEt(2))(CO)] (Cp' = C(5)Me(4)), the most electron rich of the complexes. [Rh(C(5)Et(4)SiMe(2)CH(2)PMe(2))(CO)] may be a dimer. [Co(2)(CO)(8)] reacts with C(5)H(5)(CH(2))(2)PEt(2) or C(5)Et(4)HSiMe(2)CH(2)PMe(2) (L) to give binuclear complexes of the form [Co(2)(CO)(6)L(2)] with almost linear PCoCoP skeletons. [Rh(Cp'(CH(2))(2)PEt(2))(CO)] and [Rh(Cp'(CH(2))(2)PPh(2))(CO)] are active for methanol carbonylation at 150 degrees C and 27 bar CO, with the rate using [Rh(Cp'(CH(2))(2)PPh(2))(CO)] (0.81 mol dm(-3) h(-1)) being higher than that for [RhI(2)(CO)(2)](-) (0.64 mol dm(-3) h(-1)). The most electron rich complex, [Rh(Cp'(CH(2))(2)PEt(2))(CO)] (0.38 mol dm(-3) h(-1)) gave a comparable rate to [Cp*Rh(PEt(3))(CO)] (0.30 mol dm(-3) h(-1)), which was unstable towards oxidation of the phosphine. [Rh(Cp'(CH(2))(2)PEt(2))I(2)], which is inactive for methanol carbonylation, was isolated after the methanol carbonylation reaction using [Rh(Cp'(CH(2))(2)PEt(2))(CO)]. Neither of [M(Cp'(CH(2))(2)PEt(2))(CO)] (M = Co or Ir) was active for methanol carbonylation under these conditions, nor under many other conditions investigated, except that [Ir(Cp'(CH(2))(2)PEt(2))(CO)] showed some activity at higher temperature (190 degrees C), probably as a result of degradation to [IrI(2)(CO)(2)](-). [M(Cp'(CH(2))(2)PEt(2))(CO)] react with MeI to give [M(Cp'(CH(2))(2)PEt(2))(C(O)Me)I] (M = Co or Rh) or [Ir(Cp'(CH(2))(2)PEt(2))Me(CO)]I. The rates of oxidative addition of MeI to [Rh(C(5)H(4)(CH(2))(2)PEt(2))(CO)] and [Rh(Cp'(CH(2))(2)PPh(2))(CO)] are 62 and 1770 times faster than to [Cp*Rh(CO)(2)]. Methyl migration is slower, however. High pressure NMR studies show that [Co(Cp'(CH(2))(2)PEt(2))(CO)] and [Cp*Rh(PEt(3))(CO)] are unstable towards phosphine oxidation and/or quaternisation under methanol carbonylation conditions, but that [Rh(Cp'(CH(2))(2)PEt(2))(CO)] does not exhibit phosphine degradation, eventually producing inactive [Rh(Cp'(CH(2))(2)PEt(2))I(2)] at least under conditions of poor gas mixing. The observation of [Rh(Cp'(CH(2))(2)PEt(2))(C(O)Me)I] under methanol carbonylation conditions suggests that the rhodium centre has become so electron rich that reductive elimination of ethanoyl iodide has become rate determining for methanol carbonylation. In addition to the high electron density at rhodium.     

Analysis of a compliantly suspended acoustic velocity sensor

The dynamics of a compliantly suspended acoustic velocity sensor having a spherical geometry are analyzed using theory and experiment. The analysis starts with a review of the motion associated with an unconstrained solid sphere when subjected to an acoustic plane wave in an unbounded inviscid fluid medium. The theory is then modified to account for the inclusion of an inertial sensor and an external suspension system. Accordingly, the open-circuit receiving response of a geophone-based and accelerometer-based device is derived. Density variations associated with the sphere and the surrounding fluid medium are assessed along with the effects fluid viscosity. Wave effects in the sphere and the suspension system are also analyzed.