Laboratory of Structural Biology and Bioinformatics


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 oftheoretical 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:
  • 2016-2019/MŠMT Grant no. LM2015055/(Ettrich, Lazar, Ludwig):C4Sys Centrum pro systémovou biologii
    as Main Hosting Institution
    Program: Large Research Infrastructure
    Name of RI: Center for Systems Biology
    Acronym of RI: C4SYS
    Research area: Biomedicine
    Partners insitutions: Global Change Research Institute of the Czech Academy of Sciences (GCRI)
    Masaryk University
    University of South Bohemia in České Budějovice

  • 2017-2019/EFRR Grant no. ATCZ14 - CAC-SuMeR/(Ettrich, Lazar, Ludwig): Interreg Czech-Austrian Center for Supracellular Medical Research
    jako Projektový partner
    Název projektu: Czech –Austrian Center for Supracellular Medical Research
    Zkratka projektu: CAC-SuMeR
    Číslo projektu: ATCZ14
    Výzva: Call Interreg V-A AT-CZ
    Priorita programu: Posilování výzkumu, technologického rozvoje a inovací
    Specifické cíle: 1a Zkvalitnění a rozšíření výzkumu a inovací
    Trvání projektu: 10/2016 – 09/2019
    Vedoucí partner: FH OÖ Forschungs und Entwicklung GmbH, Linz
    Další partneři: Biologické centrum AV ČR, v.v.i.

  • 2015-2017/GAČR Grant no.15-12816S/(Řeha): Theoretical Study of Photosyntetic Processes in Photosystem II

  • 2016-2018/GAČR Grant no.16-19221S/(Ludwig): Structural and functional analysis of the yeast K+ translocation system(s) encoded by TRK1 and TRK2 genes

  • 2017-2019/GAČR Grant no. 17-14413Y/(Bondar): Insights into mechanisms of G protein signaling by the β2-adrenergic receptor

  • 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.

  • 2017 Visegrad Fund´s Small Grant No. 21640383

  • 2016 Visegrad Fund´s Small Grant No. 11610084

  • 2015 Visegrad Fund´s Small Grant No. 11510292

  • 2014 Visegrad Fund´s Small Grant No. 11340074

  • 2013 Visegrad Fund´s Small Grant No. 11310052 Visegrad conferences

  • 2011 - Visegrad Fund´s Standard grant No. 21120132

  • 2014 - funded from the registration fees

  • FEBS Ligand binding course - 2012, 2014, 2018

  • FEBS Advanced methods in macromolecular crystallization - 2004, 2008, 2010, 2012, 2014, 201, 2018

    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.