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Oddělení struktury a funkce proteinů
Podřízená oddělení
Laboratoř strukturní biologieLaboratoř krystalogeneze a biomolekularni krystalografie
Doc. RNDr. Rüdiger Ettrich, PhD.
Tel.: +420 386361297
Fax: +420 386361279
ettrich@nh.usbe.cas.cz
Adresa
Zámek 136, CZ-37333 Nové Hrady
Výzkum
The Department of structure and function of proteins 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 department grew quickly and the demands for molecular biology on a high level lead to engagement of E. Csefalvay in 2005. Today the strength of the department is 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 focus 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. The department 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.
The department consists of two closely cooperating laboratories:
Laboratory of Structural Biology (head: Rudiger H. Ettrich)
email: ettrich@nh.usbe.cas.cz, tel. +420 386 361 297
Laboratory of Crystallogenesis and Biomolecular Crystallography (head: Ivana Kutá Smatanová)
email: ivas@nh.usbe.cas.cz, tel. +4203 8903 7517
Both laboratories are part of the Center of Biocatalysis and Biotransformation and have a close collaboration with the Institute of Physical Biology of the University of South Bohemia.
Current Research Projects:
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2008-20012, GAČR GA203/08/0114 (Ettrich): Specific ion effects for proteins in solutions and related biologically relevant systems.
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2009-20012, MSMT ME09016 (Kuta): The role of WrbA protein in vivo.
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2005-2007, GAČR GA203/05/0172 (Ettrich): a-N-Acetylgalactosaminidase and a-galactosidase-structural and functional characterisation, use in synthesis of biologically important glycoconjugates
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2007-2008, GAAV KJB500870701 (Csefalvay): Purification and structure determination of rpaC gene product regulates phycobilisome-photosystems II interaction in cyanobacteria
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2006-2010, MSMT LC 06010 (Ettrich, PI in USBE AVCR, Kuta Smatanova PI in UFB JU,) Center of Biocatalysis and Biotransformation
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2005-2010, výzkumný záměr (institutional research concept) ÚSBE AV0Z60870520
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2005-2011, výzkumný záměr (institutional research concept) ÚFB JcU MSM6007665808
Successfully Finished Research Projects:
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2000-2003, GAČR GA206/00/D007 (Kuta) Biocrystallogenesis of photosystem II
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2003-2006, GAČR GP206/03/D061 (Kuta) Crystallization and structural studies of photosynthetic proteins from higher plants
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2002-2005, GAČR GP206/02/D177 (Kuty) Photosynthetic reaction centres studied by means of molecular modelling methods
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2003-2006, GAČR GP206/03/D082 (Ettrich) Proteins of oxygen evolving complexes of Photosystem II studied by means of molecular modelling and vibrational spectroscopy
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2003-2006, MSMT ME 640 (Kuta) Stuctural study of new type of protein (WrbA),which is like flavodoxin.
Department seminars (spring 2009)
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9/2/2009; 9 AM - Natalia, Abdul
- 23/2/2009; 9 AM – Morteza, Martina
- 2/3/2009; 9 AM - Zofie, Vasilina
- 9/3/2009; 9 AM - Oxana, Jaroslava
- 16/3/2009; 9 AM - BRNO
- 23/3/2009; 9 AM – Iryna, Tanya
- 30/3/2009; 9 AM - Katja, Vitali
- 6/4/2009; 9 AM - Alex, Martin
- 20/4/2009; 9 AM - Elena, Tatyana
References 2005-2008
Mikalai Lapkouski, Santosh Panjikar, Pavel Janscak, Ivana Kuta Smatanova, Jannette Carey, Rüdiger Ettrich, Eva Csefalvay (2009) Structure of the motor subunit of type I restriction-modification complex EcoR124I. Nat Struct Mol Biol 16: 1. 94-95 Jan
J Kohoutová, I Kutá Smatanová, J Brynda, M Lapkouski, J L Revuelta, J B Arellano, R Ettrich (2009) Crystallization and preliminary crystallographic characterization of the extrinsic PsbP protein of photosystem II from Spinacia oleracea. Acta Crystallogr Sect F Struct Biol Cryst Commun 65: Pt 2. 111-115 Feb
Peter Palencar, Tatyana Prudnikova, Frantisek Vacha,Michal Kuty, 2008: The effects of light induced reduction of the Photosystem II reaction center, Journal of Molecular Modeling, online publication, 27.1.2009, DOI: 10.1007/s00894-008-0448-z
Eva Csefalvay, Mikalai Lapkouski, Ondrej Komarek, Expression, purification and preliminary crystallization study of RpaC protein from Synechocystis sp. PCC6803, Photosynthetica, Vol. 47, 2009.
Alena Stsiapanava, Tana Koudelakova, Mikalai Lapkouski, Martina Pavlova, Jiri Damborsky and Ivana Kuta Smatanova,:Crystals of DhaA mutants from Rhodococcus rhodochrous NCIMB 13064 diffracted to ultra high resolution: crystallization and preliminary diffraction analysis. Acta Cryst. F64, 137-140 (2008)
Susankova K., Ettrich R., Vyklicky L., Teisinger J., Vlachova V.: Contribution of the putative inner-pore region to the gating of the transient receptor potential vanilloid subtype 1 channel (TRPV1). Journal of Neuroscience (2007), 27 (28), 7578-75850.
Ristvejova J, Kopecky V, Sovova Z, Balsera M, Arrelano JB, Green M. and Ettrich R: Structure and Dynamics of the N-terminal Loop Region of PsbQ from Photosystem II of Spinacia oleracea. Biochem.Biophys.Res.Commun. 345 (2006) 287-291.
Ettrich R, Kopecky V, Hofbauerova K, et al.: Structure of the dimeric N-glycosylated form of fungal beta-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies. BMC Structural Biology 7 (2007): Art. No. 32
Carey J, Brynda J, Wolfova J, Grandori R, Gustavsson T, Ettrich R, Smatanova IK.: WrbA bridges bacterial flavodoxins and eukaryotic NAD(P)H:quinone oxidoreductases.
Protein Sci. 2007 (10):2301-5.
Shlyk-Kerner O, Samish I, Kaftan D, et al.
Protein flexibility acclimatizes photosynthetic energy conversion to the ambient temperature NATURE 442 (7104): 827-830 AUG 17 2006
Novakova-Tousova K, Vyklicky L, Susankova K, Benedikt J, Samad A, Teisinger J, Vlachova V. Functional changes in the vanilloid receptor subtype 1 channel during and after acute desensitization. Neuroscience. 2007 Oct 12;149(1):144-54.
Wolfova J, Grandori R, Kozma E, et al.
Crystallization of the flavoprotein WrbA optimized by using additives and gels
JOURNAL OF CRYSTAL GROWTH 284 (3-4): 502-505 NOV 1 2005
Tomcova I, Branca RMM, Bodo G, et al.
Cross-crystallization method used for the crystallization and preliminary diffraction analysis of a novel di-haem cytochrome c(4)
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS 62: 820-824 Part 8 AUG 2006
Smatanova IK, Gavira JA, Rezacova P, et al.
New techniques for membrane protein crystallization tested on photosystem II core complex of Pisum sativum
PHOTOSYNTHESIS RESEARCH 90 (3): 255-259 DEC 2006
Lapkouski M, Panjikar S, Smatanova IK, et al.
Purification, crystallization and preliminary X-ray analysis of the HsdR subunit of the EcoR124I endonuclease from Escherichia coli
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS 63: 582-585 Part 7 JUL 2007
Wolfova J, Mesters JR, Brynda J, et al.
Crystallization and preliminary diffraction analysis of Escherichia coli WrbA in complex with its cofactor flavin mononucleotide
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS 63: 571-575 Part 7 JUL 2007
Carmona AT, Fialova P, Kren V, et al.
Cyanodeoxy-glycosyl derivatives as substrates for enzymatic reactions
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY (8): 1876-1885 APR 10 2006
Vacha F, Psencik J, Kuty M, et al.
Evidence for localisation of accumulated chlorophyll cation on the D1-accessory chlorophyll in the reaction centre of Photosystem II
PHOTOSYNTHESIS RESEARCH 84 (1-3): 297-302 JUN 2005
Palencar P, Vacha F, Kuty M
Force field development on pigments of photosystem 2 reaction centre
PHOTOSYNTHETICA 43 (3): 417-420 2005
Fialova P, Carmona AT, Robina I, Ettrich R, Sedmera P, Prikrylova V, Petraskova-Husakova L, Kren V
Glycosyl azide - a novel substrate for enzymatic transglycosylations
TETRAHEDRON LETTERS 46 (50): 8715-8718 DEC 12 2005
Fialova P, Namdjou DJ, Ettrich R, et al.
Combined application of galactose oxidase and beta-N-acetylhexosaminidase in the synthesis of complex immunoactive N-acetyl-D-galactosaminides
ADVANCED SYNTHESIS & CATALYSIS 347 (7-8): 997-1006 JUN 2005
Stys D, Schoefberger W, Halbhuber Z, Ristvejova J, Muller N, Ettrich R
Secondary structure estimation of recombinant psbH, encoding a photosynthetic membrane protein of cyanobacterium Synechocystis sp PCC 6803
PHOTOSYNTHETICA 43 (3): 421-424 2005
Adamec F, Kaftan D, Nedbal L
Stress-induced filament fragmentation of Calothrix elenkinii (Cyanobacteria) is facilitated by death of high-fluorescence cells
JOURNAL OF PHYCOLOGY 41 (4): 835-839 AUG 2005
Vacha F, Bumba L, Kaftan D, et al.
Microscopy and single molecule detection in photosynthesis
MICRON 36 (6): 483-502 2005
Jindrova E, Schmid-Nuoffer S, Hamburger F, et al.
On the DNA cleavage mechanism of Type I restriction enzymes
NUCLEIC ACIDS RESEARCH 33 (6): 1760-1766 2005
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.
