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Aktivitätsbasierte Sonden sind wertvolle Werkzeuge in der chemischen Biologie. Nach wie vor ist es jedoch eine Herausforderung, molekulare Sonden zu entwickeln, die spezifisch an das aktive Zentrum eines bestimmten Enzyms binden. Wir stellen hier eine Strategie zur Ligandenselektion vor, die es ermöglicht, rasch elektrophile Sonden auf ausgewählte Enzyme zuzuschneiden, und zeigen in einer Machbarkeitsstudie ihre Anwendung für die beiden Cysteinproteasen von SARS‐CoV‐2. Die resultierenden Sonden markieren spezifisch die aktiven Zentren von 3CLpro und PLpro mit hinreichender Selektivität sowohl in einem lebenden Zellmodell als auch vor dem Hintergrund eines nativen menschlichen Proteoms. Durch die Nutzung der Sonden als Werkzeuge für das kompetitive Screening einer Bibliothek von Naturstoffen wurden Salvianolsäurederivate als vielversprechende 3CLpro‐Inhibitoren identifiziert. Unsere Strategie zur Ligandenselektion wird für die schnelle Entwicklung von maßgeschneiderten Sonden von großem Nutzen sein und die Entdeckung von Inhibitoren für eine Vielzahl von Zielproteinen ermöglichen, die auch über Coronavirus‐Proteasen hinausgehen. published

Peptides are highly promising building blocks for design and development of novel materials with potential application areas ranging from drug design to biotechnology. The necessity to understand the structural and thermodynamic properties of these complex materials has led to a dramatic increase in the development of computational techniques geared specifically towards peptide-based systems. Both all-atom (AA) and coarse-grained (CG) simulations of such materials have become extremely important, where the latter is an indispensable tool for reaching the time and length scales relevant to the experiments. Here, we review different approaches and discuss the challenges in the development of CG models for peptides. In particular, we concentrate on the transferability of fragment-based CG models. We analyze the transferability of a solvent-free CG model developed to model hydrophobic phenylalanine dipeptides (FF) in water. Here, we employ the same CG strategy-with non-bonded potentials based on peptide fragments-to two other hydrophobic dipeptides, valine-phenylalanine (VF) and isoleucine-phenylalanine (IF). In line with the previously developed model, the dipeptides are described by seven beads and the potentials developed for FF (bonded and non-bonded) are directly applied to describe the phenylalanine and backbone atoms, while new potentials are developed to account for the valine and isoleucine sidechains. By comparing AA and CG intra and intermolecular samplings, we show the ability of the CG model to reproduce the conformational behavior and thermodynamic association properties of the corresponding atomistic systems.

We present the latest version of the Groningen Molecular Simulation program package, GROMOS05. It has been developed for the dynamical modelling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization. An overview of GROMOS05 is given, highlighting features not present in the last major release, GROMOS96. The organization of the program package is outlined and the included analysis package GROMOS++ is described. Finally, some applications illustrating the various available functionalities are presented. © 2005 Wiley Periodicals, Inc.

Accurate simulation at the atomic level of the folding process of a variety of peptides into different native folds (see picture) can be achieved with a general purpose force field and Newton's equations of motion. The key to understanding this peptide folding lies in the unexpectedly small size of the denatured state and an accurate description thereof. published

γ-Tubulin is a protein found in all eukaryotic cells, where it plays a key role in the nucleation of microtubules. In higher plant cells, γ-tubulin is localized at the nuclear surface, a known microtubule-organizing centre, and is codistributed with all microtubule arrays. Functions of plant γ-tubulin remain to be determined. This study describes some properties of higher plant γ-tubulin. The overall level of γ-tubulin was constant during the cell cycle in synchronized tobacco BY-2 cells. Biochemical analysis of the subcellular distribution of γ-tubulin in maize cells revealed that, in contrast with animal γ-tubulin, plant γ-tubulin is mainly associated with endomembranes. We showed for the first time that the pool of soluble cytosolic γ-tubulin contained two main γ-tubulin complexes. γ-tubulin, Hsp70 and TCP1-related proteins might interact in a small complex of 750 kDa. A second γ-tubulin complex, larger than 1500 kDa was purified. The protein profile of this large complex was very similar to animal γ-tubulin complexes. The putative functions of these two complexes in plant microtubule nucleation are discussed.

In higher-plant cells, the different cell-cycle-dependent microtubule arrays are involved in a wide range of activities including chromosome segregation, cell-plate formation and cellulose microfibril distribution and orientation. A wealth of data, obtained using animal cells, has indicated that the differential stability and function of microtubules during cell-cycle and/or differentiation could be primarily regulated by selective microtubule-associated proteins (MAP). Compared to animal MAP, our knowledge of plant MAP is so far very limited. In this study, we have identified a maize heat-stable protein with apparent molecular mass 100 kDa (P-100) which binds to taxol-stabilized neurotubules and copolymerizes in vitro with purified neural tubulin. Moreover, P-100 cross-reacts with affinity-purified tau antibodies like a maize 83-kDa putative MAP described previously [Vantard, M., Schellenbaum, P., Fellous, A. & Lambert, A. M. (1991) Biochemistry 30, 9334-9340]. Polyclonal antibodies directed against P-100 were obtained and indicated that this protein is found in diverse higher-plant cultured cells suggesting the ubiquitous nature of this protein. P-100 can be phosphorylated in vitro by protein kinases present in a maize cytosol extract. Together, our data suggest that P-100 could be a higher plant MAP.