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.     

Tetraethyl 4-(3-nitrophenyl)-2,3,5,6-pyridinetetracarboxylate

Reaction of 3-nitrobenzaldehyde with diethyl oxalacetate in the presence of piperidine acetate and then ammonium acetate/acetic acid gave a moderate yield of tetraethyl 1,4-dihydro-4-(3-nitrophenyl)-2,3,5,6-pyridinetetracarboxylate. This was oxidized with nitric acid to tetraethyl 4-(3-nitrophenyl)-2,3,5,6-pyridinetetracarhoxylate which was hydrolyzed and decarboxylated to give 4-(3-nitrophenyl)pyridine.     

The loop expansion for the effective potential in theP(φ)2 quantum field theory

We study the loop expansion for the effective potential, defined as the Fenchel transform (convex conjugate) of the pressure in an external field, in theP()₂ quantum field theory. For values of the classical fielda for which the classical potentialU ₀(a)=P(a)+1/2m ² a ² equals its convex hull and has nonvanishing curvature we prove that the 1-PI loop expansion is asymptotic as 0. We also give an example of a double well classical potential for which the 1-PI loop expansion fails to be asymptotic, and find the true asymptotics.This paper is a condensed version of the author's Ph.D. thesis for the Department of Mathematics, University of British Columbia, Vancouver, B.C., Canada V6T 1Y4     

Improvements in the N,N-diethyl-p-phenylenediamine method for the determination of free and combined residual chlorine through the use of FIA

In the determination of free and combined chlorine, the reaction of permanganate standards with N,N-diethyl-p-phenylenediamine (DPD) exhibits nonlinearity presumably because both the colored semiquinoid product and the colorless quinoid product are both formed. The titrimetric DPD method titrates both of the products while the colorimetric method monitors only the colored semiquinoid products. This results in a nonlinear response for the colorimetric method above 1.0 mg/l. as Cl(2). Under FIA conditions, the nonlinearity of the DPD colorimetric method is eliminated in the 0.1-5.0 mg/l. (as Cl(2)) range and the linear range is expanded to 0.1-8.0 mg/l. as Cl(2). Also, relative standard deviations are improved by 0.5-11% relative to the colorimetric method and 1.5-4.0% relative to the titrimetric method. The FIA method was developed further to sequentially determine both free and combined chlorine, since chloramine was found to have a negligible interference in the free chlorine determination.     

Oxazoline chemistry. Part 12: A metal-mediated synthesis of DMU-212; X-ray diffraction studies of an important anti-cancer agent

An improved synthesis of the anti-cancer agent DMU-212 (trans-3,4,5,4′-tetramethoxystilbene) is described. The methodology involves the use of a Pd-oxazoline catalyst as a mediator of a regio-selective (Heck) C-C bond formation reaction. A simple isolation step is then used to obtain the title material. The compound has been further characterised in the solid-state by X-ray diffraction methods.     

Determination of total dietary fiber in selected foods containing resistant maltodextrin by enzymatic-gravimetric method and liquid chromatography: collaborative study

A method was developed for determination of total dietary fiber (TDF) in foods containing resistant maltodextrin (RMD) which includes nondigestible carbohydrates that are not fully recovered as dietary fiber by conventional TDF methods such as AOAC 985.29 or 991.43. Because the average molecular weight (MW) of RMD is 2000 daltons, lower MW soluble dietary fiber components do not precipitate in 78% ethanol; therefore, RMD is not completely quantitated as dietary fiber by current AOAC methods. The accuracy and precision of the method was evaluated through an AOAC collaborative study. Ten laboratories participated and assayed 12 test portions (6 blind duplicates) containing RMD. The 6 test pairs ranged from 1.5 to 100% RMD. The method consisted of the following steps: (1) The insoluble dietary fiber (IDF) and high MW soluble dietary fiber (HMWSDF) were determined by AOAC 985.29. (2) Ion exchange resins were used to remove salts and proteins contained in the AOAC 985.29 filtrates (including ethanol and acetone). (3) The amount of low MWRMD (LMWRMD) in the filtrates were determined by liquid chromatography. (4) The TDF was calculated by summation of the IDF, HMWSDF, and LMWRMD fractions having nondigestible carbohydrates with a degree of polymerization of 3 and higher. Repeatability standard deviations (RSDr) were 1.33-7.46%, calculated by including outliers, and 1.33-6.10%, calculated by not including outliers. Reproducibility standard deviations (RSDR) were 2.48-9.39%, calculated by including outliers, and 1.79-9.39%, calculated by not including outliers. This method is recommended for adoption as Official First Action.     

Searching of chemical structure data bases with parallel computer hardware

The use of two types of parallel computer hardware for increasing the efficiency of processing in chemical structure data bases is discussed. The distributed array processor can be used for the clustering of 2-D chemical structure data bases by using the Jarvis—Patrick clustering method and for the ranking of output in an experimental system for substructure searching in the 3-D macromolecules in the Protein Data Bank. The Inmos transputer can be used in the construction of PC-based systems for 2-D substructure searching and in the identification of the maximal substructures common to pairs of 3-D molecules.     

Monitoring of sources of clinical exposure to nickel

Due to the widespread uses of Ni and Ni alloys, patients undergoing medical treatments can experience inadvertent exposure to the metal, present as a contaminant in fluids for intravenous administration or released from surgical implants and other medical devices. Because of the risk of acute allergic reactions in Ni-sensitive subjects, sources of metal exposure within medical care and its concentrations in biological fluids of potentially exposed patients should be periodically monitored, using reliable analytical procedures, which include strict measures of contamination control. The results of a recent survey on the concentrations of Ni and other potentially toxic metals in human albumin solutions are reported.     

Asymmetric induction in mixed [2 + 2] photoadditions employing a chiral auxiliary in the alkene component

Asymmetric induction was achieved in the photoaddition of 3-methyl-2-cyclohexenone to optically active enoates 1a–c and the absolute configuration of the major adduct was determined.     

Splicing I: Using mixed basis sets in ab initio calculations

The effect of mixing (or “splicing”) extended and minimal basis sets on molecular properties such as geometries, Mulliken charges, dipoles, and internal rotation barriers was studied for several test molecules. The effect is gauged by comparison with full extended basis set calculations. It is found that splicing improves most properties relative to full minimal basis set calculations, and little accuracy is lost if the splicing is done in a judicious manner.