…excellent young Polish scientists. The results of our work are worldwide innovative technological and biomedical solutions. Some of them are converted into commercial projects that can be disseminated across the…
Enzymes are extremely powerful natural catalysts able to perform almost any type of chemical reaction while being mild by nature and highly specific. In fact, the delicate functioning of enzymes forms the basis of every living creature. The catalytic potential of enzymes is more and more appreciated by the industry as many industrial processes rely on these sophisticated catalysts. However, the number of reactions catalyzed by enzymes is restricted as enzymes only have evolved to catalyze reactions that are physiologically relevant. Furthermore, enzymes have adapted to the direct (cellular) environment in which they have to function (e.g. operative at ambient temperature, resilient towards proteolysis, catalytic turnover rate should fit with metabolic enzyme partners). This excludes the existence of enzymes that do not fit within boundaries set by nature. It is a great challenge to go beyond these natural boundaries and develop methodologies to design ‘unnatural’ tailor-made enzymes. Ideally it should become possible to (re)design enzymes to convert pre-defined substrates. Such designer enzymes could theoretically exhibit unsurpassed catalytic properties and, obviously, will be of significant interest for industrial biotechnology. The OXYGREEN project aims at the design and construction of novel oxygenating enzymes (designer oxygenases) for the production of compounds that can be used in medicine, food and agriculture and the development of novel powerful and generic enzyme redesign tools for this purpose. The enzymes and whole-cell biocatalysts that will be developed should catalyze the specific incorporation of oxygen to afford synthesis of bioactive compounds in a selective and clean way, with minimal side products and with no use of toxic materials. For this, generic platform technologies (novel high-throughput methodology and methods for engineering dedicated host cells) will be developed that allow effective structure-inspired directed evolution of enzyme.
The four principal objectives of the ELM consortium are to (1) design, (2) develop, (3) maintain and (4) apply, a novel infrastructure resource devoted to the prediction of functional motifs in protein sequences. ELM (short for Eukaryotic Linear Motif) will be both “virtual” – provided electronically – and “distributed” – provided by a network of sites. Effective prediction of short motifs will require the implementation of hitherto unique context-dependent filtering software. The ELM resource will be made available to researchers as WWW servers and as a package for local installation.
The four principle objectives correspond approximately to overlapping phases of the ELM project:
Design: The initial design requirements are to integrate: (I) a relational database; (II) data input requirements; (III) new application software; (IV) private consortium web servers; and (V) public web servers. The partners will collectively contribute both the inferred biological needs and the underlying technical specifications. A document will be prepared that describes the internal ELM architecture. Subsequent revisions to the document will be ratified by all ELM partners. A web-based input form will ensure that data input meets the internal specification.
Develop: An extensive development phase is needed to create the software needed to effectively query ELM and to generate useful predictions. Various context filters will be developed as separate modules. The easiest filter modules will be completed first, and the more complex filters later in the project. As the modules are completed, they will be integrated into the ELM resource as serial filters. For optimal performance, the fastest executing filters will be accessed first, so that only the surviving motif candidates are passed on to the slower filters.
Maintain: The ELM servers will be continually maintained and extended as the project matures. Data will be continually added into the ELM resource and older data will be revised as new biological findings are published in the literature. While many motifs are already known, during the project there will be a steady stream of new motif publications. In the mature phase of ELM, releases will be scheduled at 6 month intervals.
Apply: As the ELM resource matures, it will become increasingly powerful and useful to experimentalists. Predicted motifs will suggest unexpected functional interactions or help to confirm suspected but poorly characterised ones. The consortium partners, and their close collaborators in the host institutes, will investigate predicted motifs relevant to their research interests. Verification (and to an extent exclusion) of predicted linear motifs will lead to enhanced understanding of multifunctional multidomain proteins, many of which assemble (via linear motifs) into huge complexes whose aggregate functions are hard to investigate with current experimental approaches.
The new partner will develop an additional ab-initio filter to estimate the conformational preferences of parts of proteins. The main objective of the task proposed by the new partner is to provide a reliable tool for detection of protease target sites. This new objective represents an expansion of the ongoing work complementary to the objectives outlined in WP2 and W3.