Ettrich lab

Prof. RNDr. Rüdiger Ettrich, PhD.
Tel.: +420 386361297
Fax: +420 386361279
Zámek 136, CZ-373 33 Nové Hrady


The Laboratory of Structure and Function of Proteins was founded in 2002 as a joint laboratory of the Institute of Systems Biology and Ecology of the Academy of Sciences and the Institute of Physical Biology of the University of South Bohemia named Laboratory of High Performance Computing . The fundamental methods were the demanding computational techniques that cover a range of processes involving solving structure, interactions and dynamics of proteins and membranes up to the conformational changes of small molecules such as nucleic acids and carbohydrates. The relationship between the structure and function of the proteins and their complexes became a central research issue. Continuesly growing, the laboratory today combines methods ranging from computational and spectroscopic, to molecular biological, biochemical, and in collaboration with the Kuta Smatanova lab protein crystallisation. With its focus on molecular systems biology, the relationship 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 the laboratory is an integral part of the new research concept of the Institute. The research approach is very complex using various methods of protein research with a synthesis of theoretical and experimental methods. Molecular dynamics, 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 and methods of protein structure determination. The laboratory 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, hot topic systems.

Current research topics:

Structure and function of Type I restriction-modification complexes, translocation model for recA-like translocases

Molecular dynamics analysis of E. coli arginine repressor

Structure and function of WrbA, bridging bacterial flavodoxins and eukaryotic NAD(P)H:quinone oxidoreductases.

Structure and function of the oxygen-evolving complex of higher plants

Membrane-protein interactions, TRP-ion channels, Orai channel simulation, Modeling of TrK quarterny structure and PsbI simulations in lipid bilayers

Coarse-graining molecular dynamics simulations of proteins

Influence of organic solvents on enzyme functions

Homology modeling and substrate prediction for hexosaminidases, galactosaminidases and galactosidases 

Homology modeling of TRPA1

Molecular dynamics of lectin-like NKrp1 receptors on NK cells

Localisation of accumulated chlorophyll cation on the D1-accessory chlorophysll in the reaction center of photosystem II

Former PhD students:

Katsiarina Shamayeva (PhD., 2015), now post-doc in our group

Vasilina Zayats (PhD., 2014), now post-doc in our group

Iryna Kishko (PhD., 2013)

Morteza Khabiri (PhD., 2011), now University of Michigan, Ann Arbor

Natalia Kulik (PhD., 2011), now staff scientist in our group

Abdul Samad (PhD., 2010), Institute of Microbiology, Prague

Jaroslava Kohoutova (PhD., 2010), now University of South Bohemia

Mikalai Lapkouski (PhD., 2008), now Karolinska Institute 

Peter Palencar (PhD., 2007), now Slovak Academy of Sciences


Recent international collaborations:

Dr. Alex de Vries, Groningen University, Netherlands

Dr. Christoph Romanin, Johanner Kepler University, LInz, Austria

Dr. Jost Ludwig, Bonn University, Germany

Prof. Stephan Grissmer, Ulm University, Germany

Dr. Thomas Stockner, Vienna Medical University, Austria

Prof. Jannette Carey, Chemistry Department, Princeton University, NJ, USA

Dr. Santosh Panjikar, EMBL outstation, DESY, Hamburg, Germany

Dr. Juan B. Arellano, Instituto de Recursos Naturales y Agrobiologia de Salamanca (IRNASA–CSIC), Salamanca, Spain

Dr. Pavel Janscak, Institute of Molecular Cancer Research, University of Zürich, Zürich, Switzerland

Prof. Norbert Mueller, Johannes Kepler University, Linz, Austria