The statistical significance of selected sense–antisense peptide interactions

Sense and antisense peptides, encoded by sense and corresponding antisense DNA strands, are capable of specific interactions that could be a driving force to mediate protein–protein or protein–peptide binding associations. The complementary residue hypothesis suggests that these interactions are founded upon the sum of pairwise interactions between amino acids encoded by corresponding sense and antisense codons. Despite many successful experimental results obtained with the hypothesis, however, the physicochemical basis for these interactions is poorly understood. We examined the potential of the hypothesis for general identification of protein–protein interaction sites, and the possible role of the hypothesis in determining folding in a broad set of protein structures. In addition, we performed a structural study to investigate the binding of a complementary peptide to IL‐1F2. Our results suggest that complementary residue pairs are no more frequent or conserved than average in protein–protein interfaces, and are statistically under‐represented amongst contacting residue pairs in folded protein structures. Although our structural results matched experimental observations of binding between the peptide and IL‐1F2, complementary residue interactions do not appear to be dominant in the bound structure. Overall, our data do not allow us to conclude that the complementary residue hypothesis accounts for specific sense–antisense peptide interactions. © 2012 Wiley Periodicals, Inc.     

Synthesis of 2,2′-bipyrrole-5-carboxaldehydes and their application in the synthesis of B-ring functionalized prodiginines and tambjamines

Facile, versatile, and cost-effective synthetic routes for the preparation of a range of new 3-alkyl-, 4-alkyl-, 3,4-dialkyl-, and 3-halo-4-alkyl-2,2′-bipyrrole-5-carboxaldehydes have been developed. These 2,2′-bipyrrole-5-carboxaldehydes offer interesting potential as building blocks for making bioactive natural and unnatural products, as demonstrated by the synthesis of B-ring functionalized prodiginines (PGs) and tambjamines.     

Characterization of inclusion complexes of betamethasone-related steroids with cyclodextrins using high-performance liquid chromatography

HPLC was used to study the inclusion complexes formed between various beta- and gamma-cyclodextrins and a series of corticosteroids related to betamethasone. Apparent association constants were measured in acetonitrile-water for a set of 13 steroids. An increase in the stability of the steroid-cyclodextrin complex is observed at lower concentrations of acetonitrile. The effects of the nature of the halide at the 9-position, the location of a double bond within the C-ring, substitution at the 9- and 11-positions, and modification of the D-ring of the steroid backbone were studied. The 11- and 17-positions were found to be critically involved in the inclusion process. Larger apparent association constants were obtained with gamma-cyclodextrin (gamma-CD) than with beta-cyclodextrin (beta-CD) due to the increased diameter of the gamma-CD cavity. Van't Hoff plots were constructed to examine the thermodynamic properties of the inclusion process. Plots constructed using retention factors were found to be nonlinear when gamma-CD was present in the mobile phase. This is due to an increase in the strength of the inclusion complex as temperature decreases. Plots constructed using apparent association constants were linear, indicating that the mechanism of inclusion does not change over the range of temperatures studied (10 to 80 degrees C). Enthalpy-entropy compensation was observed for 11 of the 13 steroids studied. The usefulness of cyclodextrins to achieve the separation of steroids in HPLC is discussed and a practical application for the analysis of a steroid and three potential impurities is described.     

Monte Carlo Model of Stricture Formation in Photodynamic Therapy of Normal Pig Esophagus

Photodynamic therapy (PDT) is FDA-approved for use in patients with Barrett's esophagus using porfimer sodium (2 mg per kg) and a recommended light dose of 130 J cm⁻¹ for high grade dysplasia. Despite uniform drug and light doses, the clinical outcome of PDT is variable. A significant number of PDT cases result in esophageal strictures, a side effect related to excessive energy absorption. The purpose of this project was to model esophageal stricture formation with a Monte Carlo simulation. An original multilayer Monte Carlo computer simulation was developed for esophageal PDT. Optical absorption and scattering coefficients were derived for mucosal and muscle layers of normal porcine esophagus. Porfimer sodium was added to each layer by increasing the absorption coefficient by the appropriate amount. A threshold-absorbed light dose was assumed to be required for stricture formation and ablation. The simulation predicted irreversible damage to the mucosa with a 160 J cm⁻¹ light dose and damage to the muscle layer with an additional 160 J cm⁻¹ light dose for a tissue porfimer sodium content of 3.5 mg kg⁻¹. The simulation accurately modeled photodynamic stricture formation in normal pig in vivo esophageal tissue. This preliminary work suggests that the absorbed light threshold for stricture formation may be between 2 and 4 J per gram of tissue.     

Directed formation of micro- and nanoscale patterns of functional light-harvesting LH2 complexes

The precision placement of the desired protein components on a suitable substrate is an essential prelude to any hybrid "biochip" device, but a second and equally important condition must also be met: the retention of full biological activity. Here we demonstrate the selective binding of an optically active membrane protein, the light-harvesting LH2 complex from Rhodobacter sphaeroides, to patterned self-assembled monolayers at the micron scale and the fabrication of nanometer-scale patterns of these molecules using near-field photolithographic methods. In contrast to plasma proteins, which are reversibly adsorbed on many surfaces, the LH2 complex is readily patterned simply by spatial control of surface polarity. Near-field photolithography has yielded rows of light-harvesting complexes only 98 nm wide. Retention of the native optical properties of patterned LH2 molecules was demonstrated using in situ fluorescence emission spectroscopy.     

Thermodynamic evaluation of a partial charge model assumptionfor the dissolved silica system

The Partial Charge Model was developed to predict the hydroxylation, polymerization, and precipitation of ions. The purpose of this study is to evaluate the Partial Charge Model for describing the polymerization of silica in aqueous solutions. The Partial Charge Model predicts the stability of ions and complexes based on the assumption that the stable species will have the same electronegativity as the mean electronegativity of the solution. The silica system was chosen for model validation because of the rare availability of self-consistent thermodynamic data on many dissolved but polymerized silicate anions, including both linear and cyclical species. The electronegativity of each species was calculated using the Partial Charge Model and the results were plotted against the stability constants for the ions. The silicate anions segregated into groups on the plot based on the number of charges per silicon atom in the polymer. Plots of the log of the stability constant versus the change in electronegativity produced a linear relationship for the silica polymers containing one negative charge per silicon atom, which resulted in an r ² of 0.9978. Thus, the Partial Charge Model successfully describes the thermodynamics of silica polymerization in aqueous solution for species that are sufficiently alike, but was not accurate for all silica species.     

Deprotonation-electrophile trapping of terminal epoxides

Organolithium-induced deprotonation of terminal epoxides in the presence of appropriate diamine ligands allows trapping with a range of electrophiles, yielding functionalised di- and tri-substituted epoxides in good yields and with control of stereochemistry at the epoxide.     

Adsorption and reversed-phase high-performance liquid chromatography of p-nitrobenzyl esters of monohydroxy fatty acids

To enhance the UV detectability of hydroxy fatty acids, p-nitrobenzyl (PNB) esters of twenty-two different monohydroxy fatty acids of various chain-lengths (C16-C22) and differing positional isomers were formed using O-(p-nitrobenzyl)-N,N-(diisopropyl)-isourea (PNBDI) as alkylating agent. Reversed-phase and adsorption high-performance liquid chromatography (HPLC) of the twenty-two monohydroxy fatty acid PNB esters were studied. The PNB group did not dominate the chromatographic properties of monohydroxy fatty acids and it did not interfere with the HPLC separation of positional isomers. PNBDI was, however, found to be less than ideal for formation of PNB derivatives of monohydroxy fatty acids because UV absorbing contaminants of PNBDI interfered with the HPLC analyses.