BioInfoBank Institute

Poznań, Poland

BioInfoBank Institute

Poznań, Poland
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Riebel A.,University of Groningen | Dudek H.M.,University of Groningen | De Gonzalo G.,University of Groningen | Stepniak P.,Bioinfobank Institute | And 2 more authors.
Applied Microbiology and Biotechnology | Year: 2012

To expand the available set of Baeyer-Villiger monooxygenases (BVMOs), we have created expression constructs for producing 22 Type I BVMOs that are present in the genome of Rhodococcus jostii RHA1. Each BVMO has been probed with a large panel of potential substrates. Except for testing their substrate acceptance, also the enantioselectivity of some selected BVMOs was studied. The results provide insight into the biocatalytic potential of this collection of BVMOs and expand the biocatalytic repertoire known for BVMOs. This study also sheds light on the catalytic capacity of this large set of BVMOs that is present in this specific actinomycete. Furthermore, a comparative sequence analysis revealed a new BVMO-typifying sequence motif. This motif represents a useful tool for effective future genome mining efforts. © 2012 The Author(s).


Grant
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: KBBE-2007-3-2-03 | Award Amount: 7.44M | Year: 2008

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.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-TP | Phase: KBBE.2011.3.3-02 | Award Amount: 7.77M | Year: 2011

The objective of KYROBIO project is to broaden the toolbox of single enantiomer chiral chemicals that are produced by industry in Europe using biotechnological routes. The main target is applications of lyase enzymes to selectively synthesize molecules with multiple chiral centres applying enzymatic carbon-carbon and carbon-nitrogen bond formation as the key technical platforms. We will then apply synthetic biology to improve fermentation processes in order to generate better enzymes. Chiral compounds are an important class of chemicals that biocatalytic transformation has already demonstrated great potential to compete with chemocatalysts in their production with associated benefits that come from reductions in use of organic solvents, toxic metals and energy but application has been relatively limited. KYROBIO will address the main challenges with moving forward to the next generation of added value industrial applications of white biotechnology for high value chemical synthesis. Using a supradisciplinary approach ranging from enzyme development, chemistry, molecular biology, fermentation and innovative isolation techniques the bottlenecks to applying this new technology will be overcome. It is expected that promising candidate chemicals will be commercialised within three years of completion and so scale up with economic and feasibility studies that are also key technology developments. The consortium includes a strong presence of SMEs including SME leadership and also a large multinational company which ensures multiple routes to market for the outcomes of this project. We will also have economic and life cycle analysis coupled with significant dissemination plans to ensure wider understanding of this technology that will lead to increased acceptance and uptake. The use of this environmentally beneficial technology will help to keep the European chemicals industry at the forefront of white biotechnology and increase opportunities in economic and employment.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-TP | Phase: HEALTH-2007-1.1-4 | Award Amount: 4.03M | Year: 2009

Our particle-based method allows us to synthesise high complexity peptide arrays by combinatorial synthesis and for an unrivalled prize. We plan to further develop this new technology up to the level of robust prototype machines, and mate it to bioinformatics and readout tools. Together, our procedure(s) should boost the field of proteomics in a similar way as the lithographic technologies did with the field of genomics. Central to our novel method are the activated chemical building blocks that are frozen within solid amino acid particles. Thereby, we can use a colour laser printer to send them to defined addresses on a 2D support, where the particles are simply melted to induce a spatially defined coupling reaction of now freed amino acid derivatives. By repeated printing and melting cycles this simple trick yields high complexity peptide arrays. Based on existing pre-prototypes, we will develop a user-friendly peptide laser printer that spatially defined addresses our 20 different amino acid toners in high resolution to a support (WP1), and a scanner that especially fast and sensitive reads out the large formats delivered by the peptide laser printer (WP2). The increased production of amino acid toners and array supports are other bottlenecks in the output of peptide arrays that are tackled in WP3. This should allow us to increase the output of individual peptide spots from currently 0,5 Million to >10 Million peptides per month. Finally, to foster a market for high complexity peptide arrays, we will work out paradigmatic application examples in WP4. These aim to directly screen for antibiotic or apoptosis inducing D-peptides, and for the comprehensive readout of the different antibodies that patrol the serum of autoimmune patients. Based on user-friendly prototype machines, on first paradigmatic application examples for high complexity peptide arrays, and shielded by a strong patent, the participating SMEs will commercialise this new technology.


Malkowska M.,Center of Oncology of Poland | Kokoszynska K.,Center of Oncology of Poland | Rychlewski L.,BioInfoBank Institute | Wyrwicz L.,Center of Oncology of Poland
Biochimie | Year: 2013

The Transcription Factor IID is a large macromolecular complex composed of the TATA-box binding protein (TBP) and a group of 13-14 conserved TBP-associated factors (TAFs). TAFs are known to regulate transcription at various levels-mediating transcription via interaction with activators, histone modifications; recognition and binding to promoters; acting as a platform for other Transcription Factors and RNA polymerase II. Despite numerous previous studies of the TFIID complex, the knowledge concerning the structure of its components, and thus the exact mechanism of its function, remains undetermined. To carry out an in-depth analysis of TFIID we performed the structural bioinformatic analysis of the TFIID complex. The sequence identity and similarity of 13.74% and 37.56%, respectively (calculated with PAM250 matrix) between M1 aminopeptidase protein and TAF2 and the high similarity of their putative secondary structures allowed us to model a large part of the TAF2 structure. The sequence analysis enabled the mapping of previously not fully characterized structural domains in well-studied TAF proteins (including the full histone domains of TAF4 and 12 or TAF3 and 8). In this study we provided detailed structural models for all the elements of human analyzed in the context of TFIID activity, along with indications of structural alterations within TFIID in various animal model species. © 2012 Elsevier Masson SAS. All rights reserved.


Steczkiewicz K.,University of Warsaw | Muszewska A.,University of Warsaw | Knizewski L.,University of Warsaw | Rychlewski L.,BioInfoBank Institute | Ginalski K.,University of Warsaw
Nucleic Acids Research | Year: 2012

Proteins belonging to PD-(D/E)XK phosphodiesterases constitute a functionally diverse superfamily with representatives involved in replication, restriction, DNA repair and tRNA-intron splicing. Their malfunction in humans triggers severe diseases, such as Fanconi anemia and Xeroderma pigmentosum. To date there have been several attempts to identify and classify new PD-(D/E)KK phosphodiesterases using remote homology detection methods. Such efforts are complicated, because the superfamily exhibits extreme sequence and structural divergence. Using advanced homology detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses, we provide a comprehensive reclassification of proteins containing a PD-(D/E)XK domain. The PD-(D/E)XK phosphodiesterases span over 21 900 proteins, which can be classified into 121 groups of various families. Eleven of them, including DUF4420, DUF3883, DUF4263, COG5482, COG1395, Tsp45I, HaeII, Eco47II, ScaI, HpaII and Replic-Relax, are newly assigned to the PD-(D/E)XK superfamily. Some groups of PD-(D/E)XK proteins are present in all domains of life, whereas others occur within small numbers of organisms. We observed multiple horizontal gene transfers even between human pathogenic bacteria or from Prokaryota to Eukaryota. Uncommon domain arrangements greatly elaborate the PD-(D/E)XK world. These include domain architectures suggesting regulatory roles in Eukaryotes, like stress sensing and cellcycle regulation. Our results may inspire further experimental studies aimed at identification of exact biological functions, specific substrates and molecular mechanisms of reactions performed by these highly diverse proteins. © The Author(s) 2012.


Jankowski W.,Adam Mickiewicz University | Jankowski W.,BioInfoBank Institute | Hoffmann M.,Adam Mickiewicz University
Journal of Medical Internet Research | Year: 2016

Background: Predicting the popularity of and harm caused by psychoactive agents is a serious problem that would be difficult to do by a single simple method. However, because of the growing number of drugs it is very important to provide a simple and fast tool for predicting some characteristics of these substances. We were inspired by the Google Flu Trends study on the activity of the influenza virus, which showed that influenza virus activity worldwide can be monitored based on queries entered into the Google search engine. Objective: Our aim was to propose a fast method for ranking the most popular and most harmful drugs based on easily available data gathered from the Internet. Methods: We used the Google search engine to acquire data for the ranking lists. Subsequently, using the resulting list and the frequency of hits for the respective psychoactive drugs combined with the word "harm" or "harmful", we estimated quickly how much harm is associated with each drug. Results: We ranked the most popular and harmful psychoactive drugs. As we conducted the research over a period of several months, we noted that the relative popularity indexes tended to change depending on when we obtained them. This suggests that the data may be useful in monitoring changes over time in the use of each of these psychoactive agents. Conclusions: Our data correlate well with the results from a multicriteria decision analysis of drug harms in the United Kingdom. We showed that Google search data can be a valuable source of information to assess the popularity of and harm caused by psychoactive agents and may help in monitoring drug use trends.


Kurzynski M.,Adam Mickiewicz University | Torchala M.,Adam Mickiewicz University | Torchala M.,BioInfoBank Institute | Chelminiak P.,Adam Mickiewicz University
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2014

Biological molecular machines are proteins that operate under isothermal conditions and hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free energy-donating (input) reaction and the free energy-accepting (output) one. Most if not all biologically active proteins display a slow stochastic dynamics of transitions between a variety of conformational substates composing their native state. This makes the description of the enzymatic reaction kinetics in terms of conventional rate constants insufficient. In the steady state, upon taking advantage of the assumption that each reaction proceeds through a single pair (the gate) of transition conformational substates of the enzyme-substrates complex, the degree of coupling between the output and the input reaction fluxes has been expressed in terms of the mean first-passage times on a conformational transition network between the distinguished substates. The theory is confronted with the results of random-walk simulations on the five-dimensional hypercube. The formal proof is given that, for single input and output gates, the output-input degree of coupling cannot exceed unity. As some experiments suggest such exceeding, looking for the conditions for increasing the degree of coupling value over unity challenges the theory. Performed simulations of random walks on several model networks involving more extended gates indicate that the case of the degree of coupling value higher than 1 is realized in a natural way on critical branching trees extended by long-range shortcuts. Such networks are scale-free and display the property of the small world. For short-range shortcuts, the networks are scale-free and fractal, representing a reasonable model for biomolecular machines displaying tight coupling, i.e., the degree of coupling equal exactly to unity. A hypothesis is stated that the protein conformational transition networks, as just as higher-level biological networks, the protein interaction network, and the metabolic network, have evolved in the process of self-organized criticality. © 2014 American Physical Society.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ERG | Phase: FP7-PEOPLE-2009-RG | Award Amount: 30.00K | Year: 2010

Beside these well-known molecules there is a vast unknown world of tiny RNAs (RiboNucleic Acids) that might play a crucial role in a number of cellular processes. Those elements are named noncoding RNAs (ncRNA) and they play their function without transcription to the protein product. Here is proposed development of integrated bioinformatics platform that is specifically addressed for detecting, verifying, and classifying of noncoding RNAs. This complex approach to Computational RNomics will provide the pipeline which will be capable of detecting RNA motifs with low sequence conservation. It will also integrate RNA motif prediction which should significantly improve the quality of the RNA homolog search. The first commercial application is the integrated system for detection of new regulatory elements located in the non coding genome parts. Up to now numerous human disorders have been found to be related to some of the noncoding RNAs The second application of the project is so called RNA nanotechnology. It is designing of artificial nanoparticles, which are assembled mainly from ribonucleic acid which possess both the right size and ability to gain entry into cells and halt viral growth or cancers progress or deliver drugs. The project will benefit from latest achievements in High Performance Computing and General-Purpose computing on Graphics Processing Units and Graph theory.


Grant
Agency: European Commission | Branch: FP7 | Program: ERC-SG | Phase: ERC-SG-PE5 | Award Amount: 872.55K | Year: 2008

This project is about the design of cryptographic schemes that are secure even if implemented on not-secure devices. The motivation for this problem comes from an observation that most of the real-life attacks on cryptographic devices do not break their mathematical foundations, but exploit vulnerabilities of their implementations. This concerns both the cryptographic software executed on PCs (that can be attacked by viruses), and the implementations on hardware (that can be subject to the side-channel attacks). Traditionally fixing this problem was left to the practitioners, since it was a common belief that theory cannot be of any help here. However, new exciting results in cryptography suggest that this view was too pessimistic: there exist methods to design cryptographic protocols in such a way that they are secure even if the hardware on which they are executed cannot be fully trusted. The goal of this project is to investigate these methods further, unify them in a solid mathematical theory (many of them were developed independently), and propose new ideas in this area. The project will be mostly theoretical (although some practical experiments may be performed). Our main interest lies within the theory of private circuits, bounded-retrieval model, physically-observable cryptography, and human-assisted cryptography. We view these theories just as the departing points, since the area is very fresh and we expect to soon witness completely new ideas in this field.

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