Preprocessing of rotamers for protein design calculations

We have developed a process that significantly reduces the number of rotamers in computational protein design calculations. This process, which we call Vegas, results in dramatic computational performance increases when used with algorithms based on the dead-end elimination (DEE) theorem. Vegas estimates the energy of each rotamer at each position by fixing each rotamer in turn and utilizing various search algorithms to optimize the remaining positions. Algorithms used for this context specific optimization can include Monte Carlo, self-consistent mean field, and the evaluation of an expression that generates a lower bound energy for the fixed rotamer. Rotamers with energies above a user-defined cutoff value are eliminated. We found that using Vegas to preprocess rotamers significantly reduced the calculation time of subsequent DEE-based algorithms while retaining the global minimum energy conformation. For a full boundary design of a 51 amino acid fragment of engrailed homeodomain, the total calculation time was reduced by 12-fold.     

The stereochemistry of the hydroboration rearrangement.

Hydroboration of 1,2-dimethylcyclopentene with BH₃·THF affords a product in which boron migrates $\text{stereospecifically}$ at low temperature into the cyclopentane ring. At higher temperatures subsequent (non-stereospecific) isomerisation occurs via a competing reaction mechanism.     

Cyclic ketones and substituted α-keto acids as alternative substrates for novel Biginelli-like scaffold syntheses

The reactions of benzocyclic ketones and α-ketoacids as carbonyl components in the Biginelli reaction were investigated. These unusual Biginelli substrates furnished novel drug-like dihydropyrimidinone scaffolds suitable for further elaboration.     

Electrospray tandem mass spectrometric analysis of zeaxanthin and its oxidation products

Carotenoids have been implicated in protection of the eye from light-mediated photo-toxicity caused by free radicals. Under conditions of normal oxidative stress the carotenoids serve as protective antioxidants; however, when the oxidative stress exceeds the antioxidant capacity, carotenoids can be oxidized into numerous cleavage products. The determination and identification of oxidized carotenoids in biological samples remains a major challenge due to the small sample size and low stability of these compounds. We investigated the reaction of various zeaxanthin cleavage products with O-ethyl hydroxylamine to evaluate their levels in a biological sample. For this, a sensitive and specific electrospray tandem mass spectrometry (ESI-MS/MS) was developed, avoiding the classical lower sensitive and specific HPLC-UV and fluorescence absorption methods. Protonated molecules [M + H](+) of carotenoids upon collision-induced dissociation produced a number of structurally characteristic product ions. A series of complicated clusters of product ions differing in 14 (CH(2))and 26 (C(2)H(2))Da was characteristic of the polyene chain of intact carotenoids. All carotenoid ethyl oximes of zeaxanthin cleavage products were characterized by the losses of 60 and 61 Da in their MS/MS spectra. Through the application of the LC/MS/MS method, we identified two oxime derivatives of 3-hydroxy-beta-ionone and 3-hydroxy-14'-apocarotenal with protonated molecules at m/z 252 and m/z 370 respectively, in a human eye sample.     

Intramolecular photochemical [2+2] cycloadditions. Regiochemistry of the photocyclizations of some oxygen-substituted 6-allylcyclohexenones.

The regioselectivity of the intramolecular [2+2] photocycloaddition of certain 6-allylcyclohexenones appears to be largely independent of the substituent (H,OR) on the dital terminus of the isolated double bond.     

2,8'-disubstituted-1,1'-binaphthyls: a new pattern in chiral ligands

The title binaphthyls 19 and 26, which are the positional isomers of 2-methoxy-2'-(diphenylphosphino)-1,1'-binaphthyl (MOP, 19) and 2-amino-2'-hydroxy-1,1'-binaphthyl (NOBIN, 26), have been synthesized by Suzuki coupling as the key step (10 + 15-->18), followed by functional group transformations, involving C-P and C-N bond formation (18-->19 and 18-->23). Racemic intermediate 22 was resolved by co-crystallization with N-benzylcinchonidinium chloride and the absolute configuration determined by X-ray crystallography. These novel binaphthyls are configurationally stable and, as such, potentially usable as chiral ligands in asymmetric reactions. Michael addition of the glycine-derived enolate 40 to methyl acrylate, carried out in the presence of (R)-(-)-27 as the chiral phase-transfer catalyst, afforded L-glutamic acid (S)-(+)-43 of 92% ee (after hydrolysis of the primary product).     

Liquid chromatographic separation of the thyroid hormones

The liquid Chromatographic separation of 3,3',5-triiodothyronine, 3,3',5'-triiodothyronine, and thyroxine with a nonpolar stationary phase was studied as a function of pH, temperature, organic content of the mobile phase, and ionic strength using aqueous phosphate—acetonitrile, aqueous phosphate—methanol, and aqueous phosphate— n-propanol mobile phase systems. It was demonstrated that the quality of the thyroid hormone separations, as determined by normalized peak capacity values, was unchanged with temperature, remained relatively constant with increasing ionic strength, and was affected to the greatest extent by changes in pH and organic modifier content of the mobile phase. Chromatographic behavior of the compounds studied as a function of these variables was found to be consistent with existing Chromatographic theory and/or empirical observations. Recommended conditions are aqueous phosphate—methanol mobile phase, pH 2–5 (aqueous portion), and high temperature (60–70°C).     

A new expression for the direct quantum mechanical evaluation of the thermal rate constant

Based on the formalism of Miller, Schwartz, and Tromp [J. Chem. Phys. 79, 4889(1983)], we derive a new expression for the thermal rate constant for a chemical reaction. The expression involves an unperturbed, i.e., reactant or product channel Boltzmann operator for the imaginary time propagation, making it possible to compute efficiently the rate constant for a range of temperatures. We illustrate numerical aspects with an extensive study of the one-dimensional Eckart barrier problem, as well as a study of the three-dimensional (J = 0) D + H2 problem.     

Tandem (quadrupole-time-of-flight) electrospray mass spectrometry of oligo(vinyl acetates) with isopropylol or (1-hydroxyethyl)-2-oxyisopropanyl end groups

Poly(vinyl acetates) with either isopropylol or (1-hydroxyethyl)-2-oxyisopropanyl end groups were analysed by tandem mass spectrometry using a quadrupole-time-of-flight (Q-TOF) instrument. Random scission along the polymer backbone was not observed. Instead the initial scissions were derived from the cleavage of end-group species. The resultant macrocations were subject to further elimination reactions that eventually produced polyene macrocations. A smaller fraction of the initial macrocations also reacted by loss of ketene and this reaction produced macrocations containing vinyl alcohol units.     

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.