Rational design of a (S)-selective-transaminase for asymmetric synthesis of (1S)-1-(1,1′-biphenyl-2-yl)ethanamine

Amine transaminases offer an environmentally sustainable synthesis route for the production of pure chiral amines. However, their catalytic efficiency toward bulky ketone substrates is greatly limited by steric hindrance and therefore presents a great challenge for industrial synthetic applications. We hereby report an example of rational transaminase enzyme design to help alleviate these challenges. Starting from the Vibrio fluvialis amine transaminase that has no detectable catalytic activity toward the bulky aromatic ketone 2-acetylbiphenyl, we employed a rational design strategy combining in silico and in vitro studies to engineer the transaminase enzyme with a minimal number of mutations, achieving an high catalytic activity and high enantioselectivity. We found that, by introducing two mutations W57G/R415A, detectable enzyme activity was achieved. The rationally designed variant, W57F/R88H/V153S/K163F/I259M/R415A/V422A, showed an improvement in reaction rate by more than 1716-fold toward the bulky ketone under study, producing the corresponding enantiomeric pure (S)-amine (enantiomeric excess (ee) value of >99%)

Further improvement of the implementation of the Aarhus convention in Malta : a review

Chapter 2Th e Twinning project MT/06/IB/EN/01 “Further Institution Building in the Environment Sector” aimed at supporting the Maltese Government in improving the implementation of the Aarhus Convention on public access to environmental information, public participation in environmental decision making and access to justice in environmental matters. Th e project was carried out by MEPA as Benefi ciary Institution and the Austrian Environment Agency as Lead Member State Partner. Th e project duration was 15 months as from 16th April 2008. Th e project was co-funded by the European Union and the Maltese Government under the 2006 Transition Facility Programme for Malta. Th e project consisted of four components: • Component 1: Assessment of the current situation and development of recommendations, • Component 2: Implementation of recommendations, • Component 3: Development of guidance documents, • Component 4: Training and awareness-raising. In Component 1, the legal instruments and institutional arrangements in place for the implementation of the Aarhus Convention in Malta were assessed, and recommendations were drawn up on how to improve the existing situation with regard to public access to environmental information, public participation in environmental decision-making and access to justice in environmental matters. In Component 2, the recommendations were discussed with a wide range of stakeholders, and consequently applied in the practice, establishing an effi cient and eff ective administrative system to implement the Aarhus Convention. Amongst other measures, its implementation formulated a series of agreements between the benefi ciary and key holders of environmental information in Malta, with the aim of securing the availability, timeliness and quality of environmental data, supported by effi cient information management systems. In Component 3, guidelines were produced addressing the public authorities, the industry and the general public in Malta. Component 4 provided training for public offi cers and awareness-raising for key stakeholders and the general public. The most relevant project results are summarised in this chapter, as achieved under each Component.peer-reviewe

Editorial overview: Folding and binding: In silico, in vitro and in cellula

The essence of any biological processes relies on the conformational states of macromolecules and their interactions. It comes therefore with no surprises that the study of folding and binding has been centre stage since the birth of structural biology. In this context, the collaborative efforts of experimen- talists and theoreticians have tremendously increased our current knowl- edge on macromolecular structure and recognition. Nevertheless, several challenges and open questions are still present and a multidisciplinary approach would appear the most appropriate means to shed light onto the mechanisms of folding and binding to the highest level of detail. This thematic issue brings together a collection of reviews describing our current understanding of folding and binding, looking at these fundamental pro- blems from a wide perspective ranging from the single molecule to the complexity of the living cell, drawing on approaches that span from compu- tational (in silico), to the test tube (in vitro) and cell cultures (in cellula)

The EU Emissions Trading System and Climate Policy towards 2050: Real incentives to reduce emissions and drive innovation? CEPS Special Reports, 12 January 2011

With the EU Emissions Trading System (ETS) now entering in its seventh year of operation, this report takes stock of the largest multi-sector greenhouse gas trading scheme in the world. It reviews the experiences of the pilot phase from 2005-07, assesses the adjustments introduced in the second phase (2008-12) and looks ahead to the radical changes that will come into effect in the third phase starting in 2013. The assessment is based on a literature review of recently published ex-post analyses and ex-ante studies and draws as well on our own calculations. It investigates the main controversies surrounding the EU ETS, such as its environmental effectiveness, economic rents, windfall profits and fairness, the role of CDM and JI and its impact of on industrial competitiveness. It also evaluates the scheme’s ability to promote innovation and low-carbon technology deployment. Finally, the study addresses the fundamental question of whether the ETS has lived up to its promise to “promote reductions of greenhouse gas emissions in a cost-effective and economically efficient manner”, and if not, what are the prospects of its doing so in the future and what additional changes will be required

Consensus virtual screening approaches to predict protein ligands

In order to exploit the advantages of receptor-based virtual screening, namely time/cost saving and specificity, it is important to rely on algorithms that predict a high number of active ligands at the top ranks of a small molecule database. Towards that goal consensus methods combining the results of several docking algorithms were developed and compared against the individual algorithms. Furthermore, a recently proposed rescoring method based on drug efficiency indices was evaluated. Among AutoDock Vina 1.0, AutoDock 4.2 and GemDock, AutoDock Vina was the best performing single method in predicting high affinity ligands from a database of known ligands and decoys. The rescoring of predicted binding energies with the water/butanol partition coeffcient did not lead to an improvement averaged over all receptor targets. Various consensus algorithms were investigated and a simple combination of AutoDock and AutoDock Vina results gave the most consistent performance that showed early enrichment of known ligands for all receptor targets investigated. In case a number ligands is known for a specific target, every method proposed in this study should be evaluated

Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes

We propose a novel stochastic global optimization algorithm with applications to the refinement stage of protein docking prediction methods. Our approach can process conformations sampled from multiple clusters, each roughly corresponding to a different binding energy funnel. These clusters are obtained using a density-based clustering method. In each cluster, we identify a smooth “permissive” subspace which avoids high-energy barriers and then underestimate the binding energy function using general convex polynomials in this subspace. We use the underestimator to bias sampling towards its global minimum. Sampling and subspace underestimation are repeated several times and the conformations sampled at the last iteration form a refined ensemble. We report computational results on a comprehensive benchmark of 224 protein complexes, establishing that our refined ensemble significantly improves the quality of the conformations of the original set given to the algorithm. We also devise a method to enhance the ensemble from which near-native models are selected.Published versio

Salary-Setting Mechanisms Across the EU

Eurofound has a considerable body of research findings looking at how salary levels are set in EU Member States. This report looks at the mechanisms used to determine statutory minimum wages, the use of variable pay schemes in companies in the EU, and national systems of supplementary pay. The analysis finds that variable pay usually represents a fairly significant percentage of total salary levels, ranging from 5% to 11% in most of the countries where information is available. This ad hoc report was drawn up in response to a request from the Bulgarian EU Presidency to provide information on current debates in the country

Computational structure‐based drug design: Predicting target flexibility

The role of molecular modeling in drug design has experienced a significant revamp in the last decade. The increase in computational resources and molecular models, along with software developments, is finally introducing a competitive advantage in early phases of drug discovery. Medium and small companies with strong focus on computational chemistry are being created, some of them having introduced important leads in drug design pipelines. An important source for this success is the extraordinary development of faster and more efficient techniques for describing flexibility in three‐dimensional structural molecular modeling. At different levels, from docking techniques to atomistic molecular dynamics, conformational sampling between receptor and drug results in improved predictions, such as screening enrichment, discovery of transient cavities, etc. In this review article we perform an extensive analysis of these modeling techniques, dividing them into high and low throughput, and emphasizing in their application to drug design studies. We finalize the review with a section describing our Monte Carlo method, PELE, recently highlighted as an outstanding advance in an international blind competition and industrial benchmarks.We acknowledge the BSC-CRG-IRB Joint Research Program in Computational Biology. This work was supported by a grant from the Spanish Government CTQ2016-79138-R.J.I. acknowledges support from SVP-2014-068797, awarded by the Spanish Government.Peer ReviewedPostprint (author's final draft