Exact rotamer optimization for protein design

Computational methods play a central role in the rational design of novel proteins. The present work describes a new hybrid exact rotamer optimization (HERO) method that builds on previous dead-end elimination algorithms to yield dramatic performance enhancements. Measured on experimentally validated physical models, these improvements make it possible to perform previously intractable designs of entire protein core, surface, or boundary regions. Computational demonstrations include a full core design of the variable domains of the light and heavy chains of catalytic antibody 48G7 FAB with 74 residues and 10(128) conformations, a full core/boundary design of the beta1 domain of protein G with 25 residues and 10(53) conformations, and a full surface design of the beta1 domain of protein G with 27 residues and 10(60) conformations. In addition, a full sequence design of the beta1 domain of protein G is used to demonstrate the strong dependence of algorithm performance on the exact form of the potential function and the fidelity of the rotamer library. These results emphasize that search algorithm performance for protein design can only be meaningfully evaluated on physical models that have been subjected to experimental scrutiny. The new algorithm greatly facilitates ongoing efforts to engineer increasingly complex protein features.     

Sensitivity in Supramolecular Architectures of Polyaromatic Salts Containing Two Singly‐Pimerized Bipyridines

Three novel supramolecular arrays of zigzag polyaromatic salts are reported. Both the conformation and disposition of the dications are subjected to various noncovalent interactions. Thus, the presence or absence of the π‐π interacting enclathrated molecules, the efficient packing and the involved hydrogen bonding interactions of anions, as well as the increased hydrophobic property of the dications themselves exert influence.     

Resistance to Surfactant and Protein Fouling Effects at Conducting Diamond Electrodes

Boron‐doped diamond thin‐film electrodes display negligible fouling effects in the presence of high levels of surface‐active materials, including proteins. Dramatic improvements in the stability of the analyte response (compared to common glassy carbon and carbon paste electrodes) are illustrated using bovine serum albumin (BSA), gelatin, and Triton X‐100 in connection with repetitive square‐wave voltammetric (SWV) measurements. The voltammetric response of ascorbic acid at the diamond electrode exhibits negligible shifts in peak potentials and minimal depressions of current signals over a wide range of surfactant concentrations (0–750 ppm). For example, the diamond electrode exhibited 70, 50 and 60 mV potential shifts for 10 repetitive voltammetric scans in the presence of 100 ppm BSA, gelatin and Triton X‐100, respectively, compared to 120, 190, and 280 mV shifts observed at the glassy carbon electrode. Furthermore, only 4.3 and 6.2% of the initial current decays were observed in the presence of 100 ppm Triton X‐100 and gelatin, respectively (compared to 45.2 and 34.4% diminutions at the glassy carbon electrode). Such improved performance was also confirmed from the SWV measurements of uric acid, dihydroxyphenylacetic acid, and catechol. The greatly improved resistance to surfactant interference reflects the fact that the as‐grown diamond thin film, composed of oxide‐free and hydrogen‐terminated surface, has a relatively lower surface energy and minimal electrostatic attributes, either specific or general, so that little adsorption of surface‐active agents occurs. The topographic AFM images of the diamond electrode surface confirm a negligible BSA fouling effect after repetitive SWV measurements. Such enhanced antifouling features make diamond electrodes very attractive for numerous real‐life electroanalytical applications.     

A new algorithm to evaluate bielectronic integrals with 1s Slater‐type orbitals obtained by the integral transforms

This article presents a variation of the integral transform method to evaluate multicenter bielectronic integrals (12|34), with 1s Slater‐type orbitals. It is proved that it is possible to define, out of the expression of (12|34) given by the integral transform method, a function F(q) that has the property of having a unique Q, such that F(Q) = (12|34). Therefore, F(q) may be used to calculate (12|34). It is shown that the evaluation of F(Q) turns out to be simpler than the three‐dimensional integral involved in the calculation of (12|34), and an algorithm is presented to calculate Q. The results show that relative errors on the order of 10^?3 or lower are obtained very efficiently. In addition, it is shown that the proposed algorithm is very stable. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Structure determination of homoleptic AuI, AgI, and CuI aryl/alkylethynyl coordination polymers by X-ray powder diffraction

This article describes the structure determination of five homoleptic d(10) metal-aryl/alkylacetylides [RC triple bond CM] (M=Cu, R=tBu 1, nPr 2, Ph 3; R=Ph, M=Ag 4; Au 5) by using X-ray single-crystal and powder diffraction. Complex 1.C6H6 reveals an unusual Cu20 catenane cluster structure that has various types of tBuC triple bond C-->Cu coordination modes. By using this single-crystal structure as a starting model for subsequent Rietveld refinement of X-ray powder diffraction data, the structure of the powder synthesized from CuI and tBuC triple bond CH was found to have the same structure as 1. Complex 2 has an extended sheet structure consisting of discrete zig-zag Cu4 subunits connected through bridging nPrC triple bond C groups. Complex 3 forms an infinite chain structure with extended Cu-Cu ladders (Cu-Cu=2.49(4)-2.83(2) A). The silver(I) congener 4 is iso-structural to 3 (average Ag-Ag distance 3.11 A), whereas the gold(I) analogue 5 forms a Au...Au honeycomb network with PhC triple bond C pillars (Au-Au=2.98(1)-3.26(1) A). Solid-state properties including photoluminescence, nu(C triple bond C) stretching frequencies and thermal stability of these polymeric systems are discussed in the context of the determined structures.     

Simultaneous quantitative analysis of ketanserin and ketanserinol in plasma by RP-HPLC with fluorescence detection

A sensitive and selective high-performance liquid chromatographic assay for the quantification of ketanserin and ketanserinol in human plasma was developed and validated. The procedure involves extraction of ketanserin and ketanserinol from plasma using an Extrelut NT-1 solid-phase extraction column. The chromatograph was equipped with a Hypersil BDS column (100 x 4.5 mm, 3 micro m particle size). Separation was performed with a mixture of acetate buffer 0.01 M, pH 4.9-methanol-acetonitrile (52:40:8, v/v/v). Detection was performed with fluorescence detection (lambda(ex) = 332 nm and lambda(em) = 410 nm). Calibration curves were linear (r(2) = 0.999) in the range 0-400 ng/mL for both ketanserin and ketanserinol. The repeatability coefficient for ketanserin and ketanserinol was 3.1 and 3.0%, respectively. The reproducibility coefficient for ketanserin and ketanserinol was 10.5 and 9.1%, respectively. The limit of quantification for both ketanserin and ketanserinol was 2.0 ng/mL. The mean recovery yield for both ketanserin and ketanserinol was 60%. In an 8 h work day approximately 60 samples, including calibration and reference standards, could be processed.     

A liquid chromatography-mass spectrometry method for the quantification of both etoricoxib and valdecoxib in human plasma

A practicable and selective liquid chromatography-mass spectrometry assay for the determination of two cyclooxygenase-2 inhibitors, etoricoxib and valdecoxib, in human plasma is presented. The analytical technique is based on reversed-phase high-performance liquid chromatography (HPLC) coupled to atmospheric pressure chemical ionisation (APCI) mass spectrometry (Finnigan Mat LCQ ion trap). Mass analysis was performed in the positive ion mode. The ion trap was operated in the tandem MS mode (MS2) and the transitions of etoricoxib (m/z 359.2 --> 280.3) and valdecoxib (m/z 315.1 --> 235.1) were followed by selected reaction monitoring. Retention times of etoricoxib and valdecoxib were 1.05 and 1.08 min, respectively. The method was validated over a linear range 10-2500 and 5-1000 microg/L using the other substrate as internal standard. After validation, the method was used to study the pharmacokinetic pro fi le of etoricoxib or valdecoxib in a healthy volunteer after administration of a single oral dose (valdecoxib, 20 mg; etoricoxib, 90 mg). The presented method was suf fi cient to cover more than 90% of the area under the plasma concentration time curve.     

Organosoluble and transparent polyimides derived from alicyclic dianhydride and aromatic diamines

Organosoluble polyimides were synthesized with the alicyclic dianhydride 1,8‐dimethylbicyclo[2,2,2]oct‐7‐ene‐2,3,5,6‐tetracarboxylic dianhydride and aromatic diamines. The polyimides possessed good solubility both in strong dipolar solvents and in common solvents; the thermal decomposition temperature of the polyimides exceeded 420 °C. Strong and flexible films of the polyimides, with the cutoff of ultraviolet–visible absorption lower than 310–320 nm, exhibited good features as the alignment layers for nematic liquid crystals with pretilt angles of 1.5–2.9°. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 40: 110–119, 2002     

Photoinitiators with functional groups. V. New water‐soluble photoinitiators containing carbohydrate residues and copolymerizable derivatives thereof

The synthesis of new water‐soluble photoinitiators (PIs) based on hydroxyalkylphenones, benzophenones, and thioxanthones with carbohydrate residues such as glucose, cellobiose, and 1‐amino‐1‐deoxy‐D ‐glucitol (glucamine) is described. In addition, selected initiators were reacted with methacryloyl chloride to obtain copolymerizable initiators with improved migration stability. Results from photo differential scanning calorimetry and gel‐content measurements in commercially available water‐thinnable and emulsion‐type resins as well as 2‐hydroxyethyl acrylate are included. Glucose‐modified PIs gave the best results with respect to compatibility with the resin, reactivity, and gel content. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 1504–1518, 2002     

Effect of Pluronic F127 on the pore structure of macrocellular biodegradable polylactide foams

Thermally induced phase separation technique was utilized to fabricate biodegradable poly(l ‐lactic acid) (PLLA) macrocellular foams which were capable of being applied in tissue engineering. The block copolymer Pluronic F127 composed of (polyethyleneoxide)‐(polypropyleneoxide)‐(polyethyleneoxide) [(PEO)‐(PPO)‐(PEO)] was used as a porogen. Water/dioxane mixtures with different volume ratios were used as solvents. The addition of Pluronic F127 could induce an appearance of large pores (50–200 μm) besides small pores (10–20 μm) or a change from a solid–liquid phase separation to a liquid–liquid phase separation. The role of Pluronic F127 depends on the water/dioxane ratios in the PLLA/dioxane/water system. The X‐ray diffraction patterns and porosity measurement results showed that Pluronic F127 was crystallized and existed on the pore wall. The effect of Pluronic F127 on changing pore structure is attributed to the occurrence of the interaction of the lipophilic PPO blocks in Pluronic F127 with PLLA clews, consequently, this results in PLLA aggregation and early phase separation on cooling. Copyright © 2004 John Wiley & Sons, Ltd.