Modelers of molecular signaling networks must cope with the combinatorial explosion of protein states generated by posttranslational modifications and complex formation. Rule-based models provide a powerful alternative to approaches that require explicit enumeration of all possible molecular species of a system. Such models consist of formal rules stipulating the (partial) contexts wherein spec...

Cytokines and their receptors are involved in the pathophysiology of many diseases. Here we present a detailed review on cytokines, receptors and signalling routes, and show that one important lesson from cytokine biology is the complex and diverse regulation of cytokine activity. The activity of cytokines is controlled at the level of transcription, translation, storage, processing, posttransl...

Directionality in protein signalling networks is due to modulated protein-protein interactions and is fundamental for proper signal progression and response to external and internal cues. This property is in part enabled by linear motifs embedding post-translational modification sites. These serve as recognition sites, guiding phosphorylation by kinases and subsequent binding of modular domains...

The understanding of cellular processes and their pathophysiological alterations requires comprehensive data on the abundance, distribution, modification, and interaction of all cellular components. On the one hand, artificially introduced fluorescent fusion proteins provide information about their distribution and dynamics in living cells but not about endogenous factors. On the other hand, an...

Availability of computational methods that predict disorder from protein sequences fuels rapid advancements in the protein disorder field. The most accurate predictions are usually obtained with consensus-based approaches. However, their design is performed in an ad hoc manner. We perform first-of-its-kind rational design where we empirically search for an optimal mixture of base methods, selec...

In recent years, the number of recombinant proteins used for therapeutic applications and industry has increased dramatically. Recombinant proteins are produced in many host organisms (microbial, insect, plant and mammalian cells). There are many factors to consider when choosing the optimal system for protein expression and purification including the mass, purity or solubility of the recombina...

Enduring modification of synapses is central to long-lasting neural circuit plasticity. Such adaptations include rapid posttranslational modification of existing synaptic proteins over periods of minutes and persisting changes in the abundance of synaptic proteins over hours to days. Recently, ubiquitination and protein degradation have emerged as additional mechanisms for modifying the functio...

Protein functions in cells may be activated or modified by the attachment of several kinds of chemical groups. While protein phosphorylation, i.e. the attachment of a phosphoryl (PO−3 ) group, is the most studied form of protein modification, and is known to regulate the functions of many proteins, protein behavior can also be modified by nitrosylation, acetylation, methylation, etc. A protein ...