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Výzkumné skupiny

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The Center for Nanobiology and Structural Biology has its roots in the year 2002, when the laboratory of high performance computing was established in Nove Hrady (R. Ettrich, M. Kuty) and started to cooperate with the also newly established laboratory of crystallogenesis (I. Kuta Smatanova). The research groups grew quickly and the demands for molecular biology on a high level lead to engagement of E. Csefalvay in 2005. In the following years the strength of the department fomed by the two goups was in the close collaboration of the two laboratories that allow a very complex research approach using a broad range of methods with a synthesis of theoretical and experimental protein research.

The research topics at the department focused mainly at the elucidation of the relationships between structure and function of proteins, dynamic changes related to functional processes on the level of proteins and the mutual interaction of cofactors and subunits in protein complexes. Also, processes and structures on the level of large molecular complexes, cells and tissues are investigated. The collected empirical evidence provides insights into the molecular structural elements of the systems, their metabolic and regulative pathways, their interactions, and serves to describe the structure-function relationships of the biological systems on the aforementioned scales of complexity. The research approach is very complex using various methods of protein research with a synthesis of theoretical and experimental methods.  Molecular dynamics calculations, quantum chemical and semiempiric calculations of optical spectra, charge localisation or energy transfer and molecular modelling methods are combined with mostly spectroscopic and crystallographic methods of protein structure determination. In January 2011, the two groups were joined by the laboratory of cell biology lead by Josef Lazar to form the newly founded Center for Nanobiology and Strutural Biology. In March 2011 David Reha from Essex University joined the new center to establish a new group of computational biology. The center has highly ambitious aims with regard to the development of new methods in molecular systems biology and its application to systems of a common interest and/or hot topic systems.

Grant Support:

  • 2012-2016, GAČR GAP207/12/2323 (Ettrich): Cleavage and translocation by Type I restriction-modification complexes

  • 2011-2014, GAČR GAP207/11/0629 (Ettrich): Thiazolinové inhibitory ß-N-acetylhexosaminidas založené na nových, nepřirozených substrátech

  • 2010-2014, GAČR GAP207/10/1934 (Ettrich): Structural insight into E. coli protein WrbA, the founding member of a family of proteins implicated in defense of cells against oxidative stress

  • 2007-2012, European UnionFP6-2005-Life Sciences, Genomics and Biotechnology for Health / Specific Targeted Research Project (Lazar): AUTOSCREEN for cell based high-throughput and high-contentgene function analysis and drug discovery screens.

  • 2008-20012, GAČR GA203/08/0114 (Ettrich): Specific ion effects for proteins in solutions and related biologically relevant systems.

  • 2009-20012, MSMT ME09016 (Kuta): The role of WrbA protein in vivo.

  • 2005-2007, GAČR GA203/05/0172 (Ettrich): a-N-Acetylgalactosaminidase and a-galactosidase-structural and functional characterisation, use in synthesis of biologically important glycoconjugates

  • 2007-2008, GAAV KJB500870701 (Csefalvay): Purification and structure determination of rpaC gene product regulates phycobilisome-photosystems II interaction in cyanobacteria

  • 2006-2011, MSMT LC 06010 (Ettrich, PI in USBE AVCR, Kuta Smatanova PI in UFB JU,) Center of Biocatalysis and Biotransformation

  • 2005-2010, výzkumný záměr (institutional research concept) ÚSBE AV0Z60870520

  • 2005-2011, výzkumný záměr (institutional research concept) ÚFB JcU MSM6007665808

  • 2011-2013, GAČR GAP503/11/2263 (Safarikova): Magnetické nano- a mikročástice pro pokročilou membránovou úpravu vody

  • 2010-2014, ESFCOST TD1003: Bio-inspired nanotechnologies: from concepts to applications (Safarikova): Smart biomaterials for bioapplications.

  • 2010-2014, ESFCOST TFA0907: Yeast flavour production - New biocatalysts and novel molecular mechanisms (BIOFLAVOUR) (Safarikova): Magnetic materials for innovative bioprocesses for natural flavour bioproduction.

  • 2010-2013,MSMT, ESFCOST FA0901: Putting halophytes to work – from genes to ecosystems (Sera): Okraje silnic a kontaminovaná pole jako sekundární halofytní habitaty.

  • 2009-2012, CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nivel Superior) CON-NANO - Research, Development & Innovation and Graduation Network on Nanobiotechnology. (Safarikova): Spolupráce s Institute of Biological Sciences, University of Brasilia, Brasil

  • 2009-2012, MSMT, ESFCOST MP0701: Composites with Novel Functional and Structural Properties by Nanoscale Materials (Safarikova): Magnetické kompozitní materiály pro bioaplikace.

  • 2006-2011, Ministerstvo průmyslu a obchodu (Trvalá prosperita, 2A-1TP1/094) (Safarikova): Magnetické kompozitní materiály.

Protein Structures deposited in the PDB-database

2W74 MUTANT (K220R) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP, Authors: Lapkouski, M., Csefalvay, E., Shevelev, I., Janscak, P., Kuta-Smatanova, I., Carey, J., Ettrich, R.

2VU4 Structure of PsbP protein from Spinacia oleracea at 1.98 A resolution, Authors: Lapkouski, M., Ristvejova, R., Arellano, J.B., Revuelta, J.L., Kuta Smatanova, I., Ettrich, R.

3FBW Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA mutant C176Y, Authors:  Dohnalek, J., Stsiapanava, A., Gavira, J.A., Kuta Smatanova, I., Kuty, M.

2R96   Crystal structure of E. coli WrbA in complex with oxidised FMN, Authors: Kuta Smatanova, I., Wolfova, J., Brynda, J., Lapkouski, M., Ettrich, R.H., Palencar, P., Kuty, M., Mesters, J.R., Grandori, R., Carey, J.

2R97 Crystal structure of E. coli WrbA in complex with FMN, Authors: Kuta Smatanova, I., Wolfova, J., Brynda, J., Lapkouski, M., Ettrich, R.H., Palencar, P., Kuty, M., Mesters, J.R., Grandori, R., Carey, J.

2RG1 Crystal structure of E. coli WrbA in Apoprotein, Authors: Kuta Smatanova, I., Wolfova, J., Brynda, J., Lapkouski, M., Ettrich, R.H., Palencar, P., Kuty, M., Mesters, J.R., Grandori, R., Carey, J.

2W00 Crystal structure of the HsdR subunit of the EcoR124I restriction enzyme in complex with ATP, Authors: Lapkouski, M., Panjikar, S., Janscak, P., Ettrich, R., Kuta Smatanova, I., Csefalvay, E.

2V9Z Structure of the Rhodococcus haloalkane dehalogenase mutant with enhanced enantioselectivity, Authors: Koudelakova, T., Prokop, Z., Sato, Y., Lapkouski, M., Chovancova, E., Monincova, M., Jesenska, A., Emmer, J., Senda, T., Nagata, Y., Kuta Smatanova, I., Damborsky, J.

2Q8W Crystal structure of PAP-S1aci, a pokeweed antiviral protein from seeds of Phytolacca acinosa, Authors: Hogg, T., Bezouska, K., Ulbrich, N., Kuta Smatanova, I., Hilgenfeld, R.

The Center for Nanobiology and Structural Biology has its roots in the year 2002, when the laboratory of high performance computing was established in Nove Hrady (R. Ettrich, M. Kuty) and started to cooperate with the also newly established laboratory of crystallogenesis (I. Kuta Smatanova). The research groups grew quickly and the demands for molecular biology on a high level lead to engagement of E. Csefalvay in 2005. In the following years the strength of the department fomed by the two goups was in the close collaboration of the two laboratories that allow a very complex research approach using a broad range of methods with a synthesis of theoretical and experimental protein research.

The research topics at the department focused mainly at the elucidation of the relationships between structure and function of proteins, dynamic changes related to functional processes on the level of proteins and the mutual interaction of cofactors and subunits in protein complexes. Also, processes and structures on the level of large molecular complexes, cells and tissues are investigated. The collected empirical evidence provides insights into the molecular structural elements of the systems, their metabolic and regulative pathways, their interactions, and serves to describe the structure-function relationships of the biological systems on the aforementioned scales of complexity. The research approach is very complex using various methods of protein research with a synthesis of theoretical and experimental methods.  Molecular dynamics calculations, quantum chemical and semiempiric calculations of optical spectra, charge localisation or energy transfer and molecular modelling methods are combined with mostly spectroscopic and crystallographic methods of protein structure determination. In January 2011, the two groups were joined by the laboratory of cell biology lead by Josef Lazar to form the newly founded Center for Nanobiology and Strutural Biology. In March 2011 David Reha from Essex University joined the new center to establish a new group of computational biology. The center has highly ambitious aims with regard to the development of new methods in molecular systems biology and its application to systems of a common interest and/or hot topic systems.

The most important recent publication in 2009 in Nature Structural & Molecular Biology:

Structure of the motor subunit of type I restriction-modification complex EcoR124I conventional adenine methylases on hemimethylated DNAs, but unmethylated recognition targets induce them to translocate thousands of base pairs before cleaving distant sites nonspecifically. The first crystal structure of a type I motor subunit responsible for translocation and cleavage suggests how the pentameric translocating complex is assembled and provides a structural framework for translocation of duplex DNA by RecA-like ATPase motors. M. Lapkouski , S. Panjikar , P. Janscak , I. Kuta Smatanova , J. Carey, R. Ettrich , E. Csefalvay, Nature Structural & Molecular Biology, 2009 Jan16(1):94-5.

Grant Support:

  • 2012-2016, GAČR GAP207/12/2323 (Ettrich): Cleavage and translocation by Type I restriction-modification complexes

  • 2011-2014, GAČR GAP207/11/0629 (Ettrich): Thiazolinové inhibitory ß-N-acetylhexosaminidas založené na nových, nepřirozených substrátech

  • 2010-2014, GAČR GAP207/10/1934 (Ettrich): Structural insight into E. coli protein WrbA, the founding member of a family of proteins implicated in defense of cells against oxidative stress

  • 2007-2012, European UnionFP6-2005-Life Sciences, Genomics and Biotechnology for Health / Specific Targeted Research Project (Lazar): AUTOSCREEN for cell based high-throughput and high-contentgene function analysis and drug discovery screens.

  • 2008-20012, GAČR GA203/08/0114 (Ettrich): Specific ion effects for proteins in solutions and related biologically relevant systems.

  • 2009-20012, MSMT ME09016 (Kuta): The role of WrbA protein in vivo.

  • 2005-2007, GAČR GA203/05/0172 (Ettrich): a-N-Acetylgalactosaminidase and a-galactosidase-structural and functional characterisation, use in synthesis of biologically important glycoconjugates

  • 2007-2008, GAAV KJB500870701 (Csefalvay): Purification and structure determination of rpaC gene product regulates phycobilisome-photosystems II interaction in cyanobacteria

  • 2006-2011, MSMT LC 06010 (Ettrich, PI in USBE AVCR, Kuta Smatanova PI in UFB JU,) Center of Biocatalysis and Biotransformation

  • 2005-2010, výzkumný záměr (institutional research concept) ÚSBE AV0Z60870520

  • 2005-2011, výzkumný záměr (institutional research concept) ÚFB JcU MSM6007665808

  • 2011-2013, GAČR GAP503/11/2263 (Safarikova): Magnetické nano- a mikročástice pro pokročilou membránovou úpravu vody

  • 2010-2014, ESFCOST TD1003: Bio-inspired nanotechnologies: from concepts to applications (Safarikova): Smart biomaterials for bioapplications.

  • 2010-2014, ESFCOST TFA0907: Yeast flavour production - New biocatalysts and novel molecular mechanisms (BIOFLAVOUR) (Safarikova): Magnetic materials for innovative bioprocesses for natural flavour bioproduction.

  • 2010-2013,MSMT, ESFCOST FA0901: Putting halophytes to work – from genes to ecosystems (Sera): Okraje silnic a kontaminovaná pole jako sekundární halofytní habitaty.

  • 2009-2012, CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nivel Superior) CON-NANO - Research, Development & Innovation and Graduation Network on Nanobiotechnology. (Safarikova): Spolupráce s Institute of Biological Sciences, University of Brasilia, Brasil

  • 2009-2012, MSMT, ESFCOST MP0701: Composites with Novel Functional and Structural Properties by Nanoscale Materials (Safarikova): Magnetické kompozitní materiály pro bioaplikace.

  • 2006-2011, Ministerstvo průmyslu a obchodu (Trvalá prosperita, 2A-1TP1/094) (Safarikova): Magnetické kompozitní materiály.

Protein Structures deposited in the PDB-database

2W74 MUTANT (K220R) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP, Authors: Lapkouski, M., Csefalvay, E., Shevelev, I., Janscak, P., Kuta-Smatanova, I., Carey, J., Ettrich, R.

2VU4 Structure of PsbP protein from Spinacia oleracea at 1.98 A resolution, Authors: Lapkouski, M., Ristvejova, R., Arellano, J.B., Revuelta, J.L., Kuta Smatanova, I., Ettrich, R.

3FBW Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA mutant C176Y, Authors:  Dohnalek, J., Stsiapanava, A., Gavira, J.A., Kuta Smatanova, I., Kuty, M.

2R96   Crystal structure of E. coli WrbA in complex with oxidised FMN, Authors: Kuta Smatanova, I., Wolfova, J., Brynda, J., Lapkouski, M., Ettrich, R.H., Palencar, P., Kuty, M., Mesters, J.R., Grandori, R., Carey, J.

2R97 Crystal structure of E. coli WrbA in complex with FMN, Authors: Kuta Smatanova, I., Wolfova, J., Brynda, J., Lapkouski, M., Ettrich, R.H., Palencar, P., Kuty, M., Mesters, J.R., Grandori, R., Carey, J.

2RG1 Crystal structure of E. coli WrbA in Apoprotein, Authors: Kuta Smatanova, I., Wolfova, J., Brynda, J., Lapkouski, M., Ettrich, R.H., Palencar, P., Kuty, M., Mesters, J.R., Grandori, R., Carey, J.

2W00 Crystal structure of the HsdR subunit of the EcoR124I restriction enzyme in complex with ATP, Authors: Lapkouski, M., Panjikar, S., Janscak, P., Ettrich, R., Kuta Smatanova, I., Csefalvay, E.

2V9Z Structure of the Rhodococcus haloalkane dehalogenase mutant with enhanced enantioselectivity, Authors: Koudelakova, T., Prokop, Z., Sato, Y., Lapkouski, M., Chovancova, E., Monincova, M., Jesenska, A., Emmer, J., Senda, T., Nagata, Y., Kuta Smatanova, I., Damborsky, J.

2Q8W Crystal structure of PAP-S1aci, a pokeweed antiviral protein from seeds of Phytolacca acinosa, Authors: Hogg, T., Bezouska, K., Ulbrich, N., Kuta Smatanova, I., Hilgenfeld, R.