The Carbazymes project will be present this Saturday, June 10th at the 2016 Biocatalysis Gordon Research Conference (GRC) that is taking place at the University of New England (Biddeford, ME).

The 2016 GRC will focus on creativity, expanding both the underlying scientific developments as well as new process concepts for industrial implementation. Such creativity is also opening whole new fields such as biocatalytic retrosynthesis, enzyme cascades and systems biocatalysis. The 2016 GRC will again enable the very latest developments in biocatalysis to be discussed in depth, with a view to defining the future of this expanding field and identifying new applications.

During this meeting, Carbazymes partners involved will perform relevant oral presentations.

  • June 11th,  Monday, 11:00 am - Gerrit Poelarends (University of Groningen, RUG): "Exploiting Catalytic Promiscuity: Design of Novel Biocatalysts for Carbon-Carbon Bond Formation"
  • June 12th, Tuesday, 9:00h am - Wolf-Dieter Fessner (Technical University of Darmstadt, TUDA): "Systems Biocatalysis: Back to the Future"

Other Carbazymes partners will be directly involved in the conference, such as Anett Schallmey from Technische Universitaet Braunschweig, TUBS, which is presenting a poster, and Gerrit Poelarends (University of Groningen, RUG) that will be the discussion leader of “Industrial Processes” section.

Finally the partner Enzymicals AGENZ will have an important role as contributor to the event.

Dr. habil. Pablo Domínguez de María, CEO of Sustainable Momentum SL (SUSMOM) visits the Chemical Engineering group (led by Prof. Carlos Carlesi) at the Chemical Engineering Faculty at Pontificia Universidad Católica de Valparaiso, Chile, to explore synergies between Sustainable Momentum SL and the academic and spin-off activities of the Prof. Carlesi group. Several fruitful discussion meetings with active partners (at Valparaiso and Santiago´s campuses) were held. Moreover, Dr. habil. Domínguez de María lectured on some scientific activities related to ionic liquids, deep-eutectic-solvents and biorefineries. In the course of the lecture the CarbaZymes project was presented and at the end informative flyers were handed out to the participants.

More information (in Spanish) can be found on: http://bit.ly/29m07Am

Bio-Prodict has recently released a novel tool for automatic design of enzyme panels using protein family data. This tool ensures that the enzymes in a panel have maximum specificity diversity. This allows for rapid screening for enzymes that can convert (novel) substrates.  

How it works
First hotspots related to specificity are defined using different parameters such as, structural distance to the substrate cave, availability of literature describing relations to specificity, correlated mutation data, etc. Than the tool divides a protein family into groups based on the different sequence motifs that are present at these specificity hotspots. Next, the user can select the number and the type of sequences (e.g. a published sequence, or a swiss-prot sequence, see fig 1) which are preferred in the panel from each group. The result is plotted on a phylogenic tree of the enzyme family to analyze how the groups are divided over the phylogenetic tree (see figure 2).

Fig 1. Panel design tool. At the top five selected hotspots are shown, (here based on correlating positions) which are used for generating motif groups (45 groups). In this example published sequences and sequences from the Swiss-prot and the TrEMBL databases are preferred in the panel. The bottom shows the different sequence motifs detected at the five hotspots.

 

Fig 2. Phylogenetic tree tool. The resulting sequence selection (fig 1) is plotted on a phylogenetic tree of the protein family. This enables the user to analyze the coverage and spread of sequences over the protein family. The colored sequences are the sequences selected for the enzyme panel. 

In the summer of 2015, the project partners gathered in Nijmegen, the Netherlands for a three day course given by Bio-Prodict on 3DM protein super-family information systems. In this course the participants were taught to use 3DM for the design of smart but small mutant libraries to optimize enzymes. This course covered the use of protein structure visualization tools, the use of protein sequence alignments to discover evolutionary patterns and automated literature mining tools to assign function to protein residues.

The 3DM course will gave an overview of what 3DM information systems can and cannot do when applied to problems in Protein Engineering, Homology Modeling and Drug Design. The participants explored different kinds of protein super-family data and learned how to use and extract relations from the data. The structure visualization tool YASARA was used to deal with the data from a structural perspective, whereas Utopia Documents showed them how the data in the 3DM systems is integrated with full-text literature. The course contained a large practical component in which the participants learned to work with the tools using real-life protein engineering and drug design examples.

If you want to know more about 3DM technology  visit BIOP website or watch the following video:

https://www.youtube.com/watch?v=CAcWOxJ-D4M&feature=youtu.be

SUSMOM is a project partner specialized in Intellectual Property and in Industrial Sustainable Chemistry. A new product of the firm is being commercialized: a Competitive Intelligence analysis of Ezetimibe.

Ezetimibe is a commercially available anti-cholesterolemic drug whose IP rights will expire shortly. Tthis Competitive Intelligence dossier includes a patent analysis on Ezetimibe, in particular about its synthesis and pharmaceutical formulations.

See Dr. Pablo Domíngez and his team’s work and request  a copy: http://sustainable-momentum.net/uploads/File/Ezetimibe_Patent_Analysis_Flyer.pdf

For more information about their expertise, services and products visit the Sustainable Momentum page.

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