Statistical coupling analysis of aspartic proteinases based on crystal structures of the Trichoderma reesei enzyme and its complex with pepstatin A

The crystal structures of an aspartic proteinase from Trichoderma reesei (TrAsP) and of its complex with a competitive inhibitor, pepstatin A, were solved and refined to crystallographic R-factors of 17.9% (R(free)=21.2%) at 1.70 angstrom resolution and 15.81% (R(free) = 19.2%) at 1.85 angstrom resolution, respectively. The three-dimensional structure of TrAsP is similar to structures of other members of the pepsin-like family of aspartic proteinases. Each molecule is folded in a predominantly beta-sheet bilobal structure with the N-terminal and C-terminal domains of about the same size. Structural comparison of the native structure and the TrAsP-pepstatin complex reveals that the enzyme undergoes an induced-fit, rigid-body movement upon inhibitor binding, with the N-terminal and C-terminal lobes tightly enclosing the inhibitor. Upon recognition and binding of pepstatin A, amino acid residues of the enzyme active site form a number of short hydrogen bonds to the inhibitor that may play an important role in the mechanism of catalysis and inhibition. The structures of TrAsP were used as a template for performing statistical coupling analysis of the aspartic protease family. This approach permitted, for the first time, the identification of a network of structurally linked residues putatively mediating conformational changes relevant to the function of this family of enzymes. Statistical coupling analysis reveals coevolved continuous clusters of amino acid residues that extend from the active site into the hydrophobic cores of each of the two domains and include amino acid residues from the flap regions, highlighting the importance of these parts of the protein for its enzymatic activity. (C) 2008 Elsevier Ltd. All rights reserved.

Exact penalties for variational inequalities with applications to nonlinear complementarity problems

In this paper, we present a new reformulation of the KKT system associated to a variational inequality as a semismooth equation. The reformulation is derived from the concept of differentiable exact penalties for nonlinear programming. The best theoretical results are presented for nonlinear complementarity problems, where simple, verifiable, conditions ensure that the penalty is exact. We close the paper with some preliminary computational tests on the use of a semismooth Newton method to solve the equation derived from the new reformulation. We also compare its performance with the Newton method applied to classical reformulations based on the Fischer-Burmeister function and on the minimum. The new reformulation combines the best features of the classical ones, being as easy to solve as the reformulation that uses the Fischer-Burmeister function while requiring as few Newton steps as the one that is based on the minimum.

Regression analysis of mean quality-adjusted survival time based on pseudo-observations

Regression models for the mean quality-adjusted survival time are specified from hazard functions of transitions between two states and the mean quality-adjusted survival time may be a complex function of covariates. We discuss a regression model for the mean quality-adjusted survival (QAS) time based on pseudo-observations, which has the advantage of directly modeling the effect of covariates in the QAS time. Both Monte Carlo Simulations and a real data set are studied. Copyright (C) 2009 John Wiley & Sons, Ltd.

Agar-based films for application as polymer electrolytes

New types of polymer electrolytes based on agar have been prepared and characterized by impedance spectroscopy, X-ray diffraction measurements, UV-vis spectroscopy and scanning electronic microscopy (SEMI). The best ionic conductivity has been obtained for the samples containing a concentration of 50 wt.% of acetic acid. As a function of the temperature the ionic conductivity exhibits an Arrhenius behavior increasing from 1.1 x 10(-4) S/cm at room temperature to 9.6 x 10(-4) S/cm at 80 degrees C. All the samples showed more than 70% of transparency in the visible region of the electromagnetic spectrum, a very homogeneous surface and a predominantly amorphous structure. All these characteristics imply that these polymer electrolytes can be applied in electrochromic devices. (C) 2009 Elsevier Ltd. All rights reserved.

Optimization of performances of gelatin/LiBF(4)-based polymer electrolytes by plasticizing effects

Gelatin is a cheap and abundant natural product with very good biodegradation properties and can be used to obtain acetic acid or LiClO(4)-based gel polymer electrolytes (GPEs) with high ionic conductivity and good stability. This article presents results of GPEs obtained by the plasticization of gelatin and addition of LiBF(4), where the optimization of the system was achieved by using a factorial design type 22 with two variables: glycerol and LiBF(4). From this analysis it was stated that the effect of glycerol as a plasticizer on the ionic conductivity results is much more important than the effect obtained by varying the lithium salt content or the effect of the interaction of both variables. Also all the samples were characterized by X-ray diffraction measurements, UV-vis-NIR spectroscopy and scanning electron microscopy (SEM) and impedance spectroscopy. The ionic conductivity results of all analyzed samples as a function of temperature obey predominantly an Arrhenius relationship and the samples are stable up to 160 degrees C. Good conductivity results combined with transparency and good adhesion to the electrodes have shown that gelatin-based GPEs are very promising materials to be used as solid electrolytes in electrochromic devices. (C) 2009 Elsevier Ltd. All rights reserved.

Rule versus interaction function : evaluating regional aggregations of commuting flows in Sweden

The aim of this paper is to evaluate the performance of two divergent methods for delineating commuting regions, also called labour market areas, in a situation that the base spatial units differ largely in size as a result of an irregular population distribution. Commuting patterns in Sweden have been analyzed with geographical information system technology by delineating commuting regions using two regionalization methods. One, a rule-based method, uses one-way commuting flows to delineate local labour market areas in a top-down procedure based on the selection of predefined employment centres. The other method, the interaction-based Intramax analysis, uses two-way flows in a bottom-up procedure based on numerical taxonomy principles. A comparison of these methods will expose a number of strengths and weaknesses. For both methods, the same data source has been used. The performance of both methods has been evaluated for the country as a whole using resident employed population, self-containment levels and job ratios for criteria. A more detailed evaluation has been done in the Goteborg metropolitan area by comparing regional patterns with the commuting fields of a number of urban centres in this area. It is concluded that both methods could benefit from the inclusion of additional control measures to identify improper allocations of municipalities.

The Physiological, Enzymatic, and Genetic Characterization of Staphylococcus sp. Chromium (VI) Reductase Function

A strain of Staphylococcus isolated by Dr. Fekete at the Sandia National Laboratory toxic metal dumping site in Sandia, New Mexico. has been found to reduce toxic Cr(VI) to the less toxic Cr(IlI) state. We have ascertained the environmental parameters for optimal bacterial growth and Cr(VI) reduction. This knowledge may be employed in a comprehensive bioremediation scheme designed to accelerate natural reparation of that Sandia ecosystem. In addition we have investigated the genetic and enzymatic basis for this Cr(VI) reducing ability. This information may allow us to create more effective bioremediation schemes based on the comprehensive knowledge of enzyme and gene function. Preliminary investigations have been carried out toward this end which may serve as the basis for a more thorough investigation.