A theoretical study of the copper–cysteine bond in blue copper proteins

 The accuracy of theoretical calculations on models of the blue copper proteins is investigated using density functional theory (DFT) Becke's three-parameter hybrid method with the Lee–Yang–Parr correlation functional (B3LYP) and medium-sized basis sets. Increasing the basis set to triple-zeta quality with f-type functions on all heavy atoms and enlarging the model [up to Cu(imidazole-CH₃)₂(SC₂H₅) (CH₃SC₂H₅)^0/+] has only a limited influence on geometries and relative energies. Comparative calculations with more accurate wave-function–based methods (second-order M?ller–Plesset perturbation theory, complete-active-space second-order perturbation theory, coupled-cluster method, including single and double replacement amplitudes and in addition triple replacement perturbatively) and a variety of basis sets on smaller models indicate that the DFT/B3LYP approach gives reliable results with only a small basis set dependence, whereas the former methods strongly depend on the size of the basis sets. The effect of performing the geometry optimizations in a continuum solvent is quite small, except for the flexible Cu-S_Met bond. The results of this study confirm the earlier results that neither the oxidized nor the reduced copper site in the blue proteins is strained to any significant degree (in energy terms) by the protein surrounding. Received: 7 July 2000 / Accepted: 17 November 2000 / Published online: 21 March 2001     

Residue currents and ideals of holomorphic functions

We define a residue current of a holomorphic mapping, or more generally of a holomorphic section of a holomorphic vector bundle, by means of Cauchy-Fantappie-Leray type formulas, and prove that a holomorphic function that annihilates this current belongs to the corresponding ideal locally. We also prove that the residue current coincides with the Coleff-Herrera current in the case of a complete intersection. The residue current is globally defined and this is used in some geometric applications. By means of the residue current we also construct, for an arbitrary ideal, an integral formula for interpolation and division.     

A division problem for\bar \partial _b - CLOSED forms

LetG ₁,…,G_m be bounded holomorphic functions in a strictly pseudoconvex domainD such that . We prove that for each (0,q)-form ϕ inL ^p(∂D), 1<p<∞, there are formsu ₁, …,u _m inL ^p(∂D) such that ΣG _ju_j=ϕ. This generalizes previous results forq=0. The proof consists in delicate estimates of integral representation formulas of solutions and relies on a certainT1 theorem due to Christ and Journé. For (0,n−1)-forms there is a simpler proof that also gives the result forp=∞. Restricted to one variable this is precisely the corona theorem. The author was partially supported by the Swedish Natural Research Council.     

Optimization of steam pretreatment of SO2-impregnated corn stover for fuel ethanol production

In this study, corn stover with a dry matter content of 20% was impregnated with SO₂ and then steam pretreated for various times at various temperatures. The pretreatment was evaluated by enzymatic hydrolysis of the solid material and analysis of the sugar content in the liquid. The maximum overall yield of glucose, 89% of the theoretical based on the glucan in the raw material, was achieved when the corn stover was pretreated at 200°C for 10 min. The maximum overall yield of xylose, 78%, was obtained with pretreatment at 190°C for 5 min.     

Production of milligram quantities of affinity tagged-proteins using automated multistep chromatographic purification

A new chromatography system, AKTAxpress (GE Healthcare, Amersham Biosciences, Uppsala, Sweden) has been designed to meet the demand for high-throughput purification of proteins in structural genomics and drug discovery. The system offers a number of automated multistep purification protocols for affinity-tagged proteins. All protocols start with affinity chromatography followed by combinations of desalting, ion exchange chromatography and gel filtration. As an option, tag removal can be included in the purification protocols. Up to 16 proteins can be purified per day and the yield can be as high as 50 mg of each protein at > 90% purity. To highlight the versatility of the system, this paper presents several case studies; purifications of hexahistidine- and glutathione S-transferase-tagged proteins using different protocols, automated on-column tag cleavage and optimization studies for a hexahistidine-tagged kinase.     

Assessment of docking poses: interactions-based accuracy classification (IBAC) versus crystal structure deviations

Six docking programs (FlexX, GOLD, ICM, LigandFit, the Northwestern University version of DOCK, and QXP) were evaluated in terms of their ability to reproduce experimentally observed binding modes (poses) of small-molecule ligands to macromolecular targets. The accuracy of a pose was assessed in two ways: First, the RMS deviation of the predicted pose from the crystal structure was calculated. Second, the predicted pose was compared to the experimentally observed one regarding the presence of key interactions with the protein. The latter assessment is referred to as interactions-based accuracy classification (IBAC). In a number of cases significant discrepancies were found between IBAC and RMSD-based classifications. Despite being more subjective, the IBAC proved to be a more meaningful measure of docking accuracy in all these cases.     

Easy-to-execute carbonylations: microwave synthesis of acyl sulfonamides using Mo(CO)(6) as a solid carbon monoxide source

The development of a robust palladium-catalyzed amidocarbonylation protocol for the preparation of aromatic acyl sulfonamides utilizing high-density microwave heating is described. This synthetic approach employs Mo(CO)(6) as a convenient CO-releasing reagent and allows for the direct preparation of acyl sulfonamides from both aryl iodides and aryl bromides. The reactions can be performed under air, employing only 15 min of microwave irradiation, to produce acyl sulfonamide derivatives in good to excellent yields. To illustrate the usefulness of this method, we reported the synthesis of a novel hepatitis C virus NS3 protease inhibitor.     

Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase

Elucidating the role of nuclear quantum mechanical (NQM) effects in enzyme catalysis is a topic of significant current interest. Despite the great experimental progress in this field it is important to have theoretical approaches capable of evaluating and analyzing nuclear quantum mechanical contributions to catalysis. In this study, we use the catalytic reaction of lipoxygenase, which is characterized by an extremely large kinetic isotope effect, as a challenging test case for our simulation approach. This is done by applying the quantum classical path (QCP) method with an empirical valence bond potential energy surface. Our computational strategy evaluates the relevant NQM corrections and reproduces the large observed kinetic isotope effect and the temperature dependence of the H atom transfer reaction while being less successful with the D atom transfer reaction. However, the main point of our study is not so much to explore the temperature dependence of the isotope effect but rather to develop and validate an approach for calculations of nuclear quantum mechanical contributions to activation free energies. Here, we find that the deviation between the calculated and observed activation free energies is small for both H and D at all investigated temperatures. The present study also explores the nature of the reorganization energy in the enzyme and solution reactions. It is found that the outer-sphere reorganization energy is extremely small. This reflects the fact that the considered reaction involves a very small charge transfer. The implication of this finding is discussed in the framework of the qualitative vibronic model. The main point of the present study is, however, that the rigorous QCP approach provides a reliable computational tool for evaluating NQM contributions to catalysis even when the given reaction includes large tunneling contributions. Interestingly, our results indicate that the NQM effects in the lipoxygenase reaction are similar in the enzyme and in the reference solution reactions, and thus do not contribute to catalysis. We also reached similar conclusions in studies of other enzymes.     

Zinc selenium oxochloride, β‐Zn2(SeO3)Cl2, a synthetic polymorph of the mineral sophiite

Dizinc selenium dichloride trioxide, β‐Zn₂(SeO₃)Cl₂, a monoclinic polymorph of the orthorhombic mineral sophiite, has a structure built of distorted ZnO₄Cl₂ octahedra, ZnO₂Cl₂ tetrahedra and SeO₃E tetrahedra (E being the 4s² lone pair of the Se^IV ion), joined through shared edges and corners to form charge‐neutral layers. The Cl atoms and the Se lone pairs protrude from each layer towards adjacent layers. The main structural difference between the mineral and synthetic polymorphs lies in the packing of the layers.