PRO-Simat: Protein network simulation and design tool.

PRO-Simat is a simulation tool for analysing protein interaction networks, their dynamic change and pathway engineering. It provides GO enrichment, KEGG pathway analyses, and network visualisation from an integrated database of more than 8 million protein-protein interactions across 32 model organisms and the human proteome. We integrated dynamical network simulation using the Jimena framework, which quickly and efficiently simulates Boolean genetic regulatory networks.

Controlling Supramolecular Structures of Drugs by Light.

Controlling physicochemical properties of light-unresponsive drugs, by light, prima facie, a paradox approach. We expanded light control by ion pairing light-unresponsive salicylate or ibuprofen to photoswitchable azobenzene counterions, thereby reversibly controlling supramolecular structures, hence the drugs' physicochemical and kinetic properties. The resulting ion pairs photoliquefied into room-temperature ionic liquids under ultraviolet light.

Bioinspired Ion Pairs Transforming Papaverine into a Protic Ionic Liquid and Salts.

Microbial, mammalian, and plant cells produce and contain secondary metabolites, which typically are soluble in water to prevent cell damage by crystallization. The formation of ion pairs, for example, with carboxylic acids or mineral acids, is a natural blueprint to maintain basic metabolites in solution. Here, we aim at showing whether the mostly large carboxylates form soluble protic ionic liquids (PILs) with the basic natural product papaverine resulting in enhanced aqueous solubility.

Impurity profiling of l-aspartic acid and glycine using high-performance liquid chromatography coupled with charged aerosol and ultraviolet detection.

For the compendial related substances test of l-aspartic acid (Asp) and glycine (Gly), two separate reversed-phase ion-pair high-performance liquid chromatography methods coupled with charged aerosol and ultraviolet detection were developed. Separation of all putative impurities, in particular of the related carboxylic and amino acids, was achieved using volatile perfluorocarboxylic acids as ion-pairing reagents on a polar embedded C18 stationary phase. It was shown that an adjustment of the evaporation temperature of the charged aerosol detector (CAD) was an efficient strategy for meeting the required quantitation limits, when dealing with non-volatile analytes.

Recent applications of the Charged Aerosol Detector for liquid chromatography in drug quality control.

High performance liquid chromatography (HPLC) methods with UV/vis detection are the most widespread analytical procedures in modern pharmaceutical applications, but reach their limitations when it comes to non-chromophore molecules. Hence, instead of using tiresome derivatization procedures, many liquid chromatography methods make use of the so-called aerosol-based universal detectors, namely the evaporative light scattering detector (ELSD), the condensation nucleation light scattering detector (CNLSD) and the charged aerosol detector (CAD). Amongst these, the CAD, being the youngest (introduced in 2005) of these three options, is often described as the most easy-to-use detector and is stated to exhibit sufficient sensitivity and good linearity of signal in a dedicated range of concentration.

Comparing Human Factors for Augmented Reality Supported Single-User and Collaborative Repair Operations of Industrial Robots.

In order to support the decision-making process of industry on how to implement Augmented Reality (AR) in production, this article wants to provide guidance through a set of comparative user studies. The results are obtained from the feedback of 160 participants who performed the same repair task on a switch cabinet of an industrial robot. The studies compare several AR instruction applications on different display devices (head-mounted display, handheld tablet PC and projection-based spatial AR) with baseline conditions (paper instructions and phone support), both in a single-user and a collaborative setting.

Quantitative structure-property relationship modeling of polar analytes lacking UV chromophores to charged aerosol detector response.

In this study, a quantitative structure-property relationship model was built in order to link molecular descriptors and chromatographic parameters as inputs towards CAD responsiveness. Aminoglycoside antibiotics, sugars, and acetylated amino sugars, which all lack a UV/vis chromophore, were selected as model substances due to their polar nature that represents a challenge in generating a CAD response. Acetone, PFPA, flow rate, data rate, filter constant, SM5_B(s), ATS7s, SpMin1_Bh(v), Mor09e, Mor22e, E1u, R7v+, and VP as the most influential inputs were correlated with the CAD response by virtue of ANN applying a backpropagation learning rule.

Influence of charged aerosol detector instrument settings on the ultra-high-performance liquid chromatography analysis of fatty acids in polysorbate 80.

The analysis of polysorbate 80 is a challenge because all components lack a chromophore. Here, an ultra-high-performance liquid chromatography system equipped with a charged aerosol detector (UHPLC-CAD) was used to study the effect of systematic variation of the CAD settings, namely evaporation temperature, filter constant and power function value (PFV), on the detector response of fatty acid standards and manufacturing batches of polysorbate. Evaporation temperature and filter constant strongly affect the detection limits described by signal-to-noise (S/N) ratios.

Impurity profiling of l-asparagine monohydrate by ion pair chromatography applying low wavelength UV detection.

l-asparagine is a non-essential amino acid being used for a variety of pharmaceutical applications. The compound may be produced following synthetic or fermentative pathways leading to the formation of distinct impurities such as organic acids, other amino acids, dipeptides, or cyclic amino acid derivatives. Analysis of the respective analytes is challenging due to the lack of a chromophore, thus the monograph of the European Pharmacopoeia describes a thin layer chromatographic test for detection of other amino acids.

Control of a HexaPOD treatment couch for robot-assisted radiotherapy.

Moving tumors, for example in the vicinity of the lungs, pose a challenging problem in radiotherapy, as healthy tissue should not be irradiated. Apart from gating approaches, one standard method is to irradiate the complete volume within which a tumor moves plus a safety margin containing a considerable volume of healthy tissue. This work deals with a system for tumor motion compensation using the HexaPOD® robotic treatment couch (Medical Intelligence GmbH, Schwabmünchen, Germany).

Selectivity of propeptide-enzyme interaction in cathepsin L-like cysteine proteases.

Cathepsin L-like endopeptidases of the papain family are synthesized as proenzymes. N-terminal proregions are essential for folding and latency of the enzyme unit. While selectivity has been reported for the inhibitory function of papain-family propeptides, there is no systematic investigation of the selectivity of their chaperone-like function to date.

Tumor tracking and motion compensation with an adaptive tumor tracking system (ATTS): system description and prototype testing.

A novel system for real-time tumor tracking and motion compensation with a robotic HexaPOD treatment couch is described. The approach is based on continuous tracking of the tumor motion in portal images without implanted fiducial markers, using the therapeutic megavoltage beam, and tracking of abdominal breathing motion with optical markers. Based on the two independently acquired data sets the table movements for motion compensation are calculated.

Optimized folding and activation of recombinant procathepsin L and S produced in Escherichia coli.

Large scale production of the recombinant human cathepsins L and S was optimized. Final purity was nearly 100%, yield 65% and 41%, respectively. Cost-effective expression in Escherichia coli, inclusion body purification and solubilization followed modified standard protocols.

Specificity of human cathepsin S determined by processing of peptide substrates and MHC class II-associated invariant chain.

Cathepsin S (CatS) is a lysosomal cysteine protease of the papain family, the members of which possess relatively broad substrate specificities. It has distinct roles in major histocompatibility complex (MHC) class II-associated peptide loading and in antigen processing in both the MHC class I and class II pathways. It may therefore represent a target for interference with antigen presentation, which could be of value in the therapy of (auto)immune diseases.

The crystal structure of a Cys25 -> Ala mutant of human procathepsin S elucidates enzyme-prosequence interactions.

The crystal structure of the active-site mutant Cys25 --> Ala of glycosylated human procathepsin S is reported. It was determined by molecular replacement and refined to 2.1 Angstrom resolution, with an R-factor of 0.

Interaction of papain-like cysteine proteases with dipeptide-derived nitriles.

A series of 44 dipeptide nitriles with various amino acids at the P2 position and glycine nitrile at position P1 were prepared and evaluated as inhibitors of cysteine proteinases. With respect to the important contribution of the P2-S2 interaction to the formation of enzyme-inhibitor complexes, it was focused to introduce structural diversity into the P2 side chain. Nonproteinogenic amino acids were introduced, and systematic fluorine, bromine, and phenyl scans for phenylalanine in the P2 position were performed.

Functions of propeptide parts in cysteine proteases.

Regulation of proteolytic enzyme activity is an essential requirement for cells and tissues because proteolysis at the wrong time and location may be lethal. Two principal mechanisms to control the activity of proteases have been developed during evolution. The first is the co-evolution of endogenous inhibitors, typically occurring in cellular compartments separated from those containing active enzymes.

An unfolding/refolding step helps in the crystallization of a poorly soluble protein.

Proteins that are unstable or poorly soluble often elude crystallization. Here, a novel strategy is presented that leads to the crystallization of the isolated N-terminal propeptide of human procathepsin S, a proteinase belonging to the cathepsin L-like endopeptidases of the clan CA1 cysteine peptidases. Being very hydrophobic, the propeptide is extremely poorly soluble in aqueous solvents at neutral pH.

Parasite-specific immunomodulatory functions of filarial cystatin.

Cystatins of parasitic nematodes are well-described pathogenicity factors which contribute to downregulation of T-cell proliferation of their hosts and induce anti-inflammatory cytokine responses. We compared the immunomodulatory effects of two cystatins of the filarial nematodes Onchocerca volvulus and Acanthocheilonema viteae with two homologous proteins of the free-living nematode Caenorhabditis elegans. Like filarial cystatins, the C.

Foldase function of the cathepsin S proregion is strictly based upon its domain structure.

Folding of cathepsin S, like other cathepsin L-like proteases, depends on its proregion. The major part of the proregion forms a small domain distal from the catalytic centre, suggesting function(s) beyond active-site shielding. Using an optimised in vitro trans-refolding assay, we compared reactivation of denatured cathepsin S by the genuine propeptide, wild-type and ten selected mutants.

Defective oligomerization of arylsulfatase a as a cause of its instability in lysosomes and metachromatic leukodystrophy.

In one of the most common mutations causing metachromatic leukodystrophy, the P426L-allele of arylsulfatase A (ASA), the deficiency of ASA results from its instability in lysosomes. Inhibition of lysosomal cysteine proteinases protects the P426L-ASA and restores the sulfatide catabolism in fibroblasts of the patients. P426L-ASA, but not wild type ASA, was cleaved by purified cathepsin L at threonine 421 yielding 54- and 9-kDa fragments.