PocketOptimizer 2.0: A modular framework for computer-aided ligand-binding design

The ability to design customized proteins to perform specific tasks is of great interest. We are particularly interested in the design of sensitive and specific small molecule ligand-binding proteins for biotechnological or biomedical applications. Computational methods can narrow down the immense combinatorial space to find the best solution and thus provide starting points for experimental procedures. However, success rates strongly depend on accurate modeling and energetic evaluation. Not only intra- but also intermolecular interactions have to be considered. To address this problem, we developed PocketOptimizer, a modular computational protein design pipeline, that predicts mutations in the binding pockets of proteins to increase affinity for a specific ligand. Its modularity enables users to compare different combinations of force fields, rotamer libraries, and scoring functions. Here, we present a much-improved version––PocketOptimizer 2.0. We implemented a cleaner user interface, an extended architecture with more supported tools, such as force fields and scoring functions, a backbone-dependent rotamer library, as well as different improvements in the underlying algorithms. Version 2.0 was tested against a benchmark of design cases and assessed in comparison to the first version. Our results show how newly implemented features such as the new rotamer library can lead to improved prediction accuracy. Therefore, we believe that PocketOptimizer 2.0, with its many new and improved functionalities, provides a robust and versatile environment for the design of small molecule-binding pockets in proteins. It is widely applicable and extendible due to its modular framework. PocketOptimizer 2.0 can be downloaded at https://github.com/Hoecker-Lab/pocketoptimizer .     

A competition smFRET assay to study ligand-induced conformational changes of the dengue virus protease

Ligand binding to proteins often is accompanied by conformational transitions. Here, we describe a competition assay based on single molecule Förster resonance energy transfer (smFRET) to investigate the ligand-induced conformational changes of the dengue virus (DENV) NS2B-NS3 protease, which can adopt at least two different conformations. First, a competitive ligand was used to stabilize the closed conformation of the protease. Subsequent addition of the allosteric inhibitor reduced the fraction of the closed conformation and simultaneously increased the fraction of the open conformation, demonstrating that the allosteric inhibitor stabilizes the open conformation. In addition, the proportions of open and closed conformations at different concentrations of the allosteric inhibitor were used to determine its binding affinity to the protease. The K_D value observed is in accordance with the IC₅₀ determined in the fluorometric assay. Our novel approach appears to be a valuable tool to study conformational transitions of other proteases and enzymes.     

The role of phosphorylation of HPr,a phosphocarrier protein of the phosphotransferase system,in the regulation of carbon metabolism in gram-positive bacteria

HPr of the Gram-positive bacterial phosphotransferase system (PTS) can be phosphorylated by an ATP-dependent protein kinase on a serine residue or by PEP-dependent Enzyme I on a histidyl residue. Both phosphorylation events appear to influence the metabolism of non-PTS carbon sources. Catabolite repression of the gluconate (gnt) operon of B. subtilis appears to be regulated by the former phosphorylation event, while glycerol kinase appears to be regulated by the latter phosphorylation reaction. The extent of our understanding of these processes will be described. © 1993 Wiley-Liss, Inc.     

Physical map of the bacteriophage L (Salmonella typhimurium)

Abstract A circular restriction map of the genome of the phage L ( Salmonella typhimurium ) has been constructed with five restriction endonucleases, Eca I, Eco RI, Bam HI, Bgl I, and Pst I. The Eco RI fragments of phage-L DNA were cloned into pACYC184, and the resulting recombinant plasmids pL1, pL2,…,pL7 were introduced into Salmonella typhimurium . The genes present on the fragments cloned were identified by the marker rescue experiments with the L-phage amber mutants. A physical gene map of the L genome obtained in this way was compared with that of P22.     

Topo-optische Färbung der Erythrocytenmembran mit Thiazin- und Chinolinfarbstoffen

Zusammenfassung Die Untersuchungen erwiesen, daß die Farbstoffe 1:9-Dimethyl-Methylenblau, Azur A und N,N-Diäthylpseudoisozyaninchlorid für topo-optische Reaktionen an der Membran von Erythrocyten geeignet sind. Die Farbstoffmoleküle werden an der Membran orientiert gebunden. Ihre Bindung kann durch Behandlung mit Präzipitationslösungen stabilisiert werden, und zugleich wird die Anisotropie verstärkt. Die optische Analyse ergab, daß 1:9-Dimethyl-Methylenblau und Azur A radiär zur Membran ausgerichtet sind, während sich N,N-Diäthylpseudoisozyaninchlorid membranparallel anlagert.

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Tope-optical staining with thiazin and quinolin dyestuffs of the erythrocyte membrane

Summary The present studies prove the dyestuffs 1.9-dimethyl methyleneblue, azure A and N,N-diethylpseudoisocyanine chloride suitable for topo-optical reactions with the membrane of the red blood cell. The dye molecules are bound in orientated fashion. Treatment with precipitants stabilizes the binding of dye molecules and, in addition, it enhances the birefringence. Optical analysis revealed 1.9-dimethyl methyleneblue and azure A bound in radial position, however, N,N-diethylpseudoisocyanine chloride was bound parallel to the membrane's plane.

     

Arthopyrenia endobrya,spec. nov., eine hepaticole Flechte mit intrazellulärem Thallus aus Brasilien

Arthopyrenia endobrya from Southern Brazil is illustrated and described as a new species of lichens. The thallus is composed of filamentous green algae loosely surrounded by fungal hyphae. Both symbionts grow endophytically within the leaf cells of two species ofLejeuneaceae (Hepaticae). The algae and hyphae penetrate the cell walls of the host by means of fine perforations. The ascocarps develop between the leaves and perforate them with their apical region. The classification as a member of the genusArthopyrenia is preliminary.

     

Cell division and sister chromatid exchanges in 45,X/46,X,i(Xq) mosaicism

Summary The kinetics of cell division and sister chromatid exchanges were studied in PHA-stimulated short-term cultivations of peripheral blood by means of the BUDR/FPG technique in controls and in five patients with 45,X/46,X,i(Xq) mosaicism. No significant differences in the length of the cell cycle were observed between 45,X/46,X,i(Xq) and control 46,XX cells. The number of SCE on late i(Xq) was only nonsignificantly elevated (0.6 per i(Xq)) against the value expected on the basis of its relative length.