Annual SUMMER SCHOOL
IN MOLECULAR BIOPHYSICS
AND SYSTEMS BIOLOGY
11th
JULY – 6th
AUGUST 2016
NOVE HRADY
CZECH REPUBLIC
Annual SUMMER SCHOOL IN MOLECULAR BIOPHYSICS AND SYSTEMS BIOLOGY
The scientific and research Summer school in molecular biophysics and systems
biology is supported by the International Visegrad Fund, and jointly organized by the
University of South Bohemia and the Center for Nanobiology and Structural Biology of
the Institute of Microbiology, Academy of Sciences of the Czech Republic. In
partnership with the University of Miskolc, Hungary, the University of Warsaw, Poland
and Comenius University in Bratislava, Slovakia, the summer school gives the chance
to Czech and foreign university students to work for a month with experienced scientists
and tutors in internationally respected research teams. During their time in Nove Hrady
the students do not only research but also participate in an excellent lecture series that
gets them a broad view on cutting-edge methodologies and research.
The participating students had to pass a highly competitive selection procedure and got
the chance to work in excellent fully-equipped laboratories on topics related to systems
biology and molecular biophysics. At the end of summer school, the research teams
present their results in a student conference, where the best presentation get awarded
by the scientific committee. In the final ceremony awards and certificates are presented
to all participants.
The summer school 2016 is attended by 17 distinguished students from Poland, Czech
Republic, Hungary, Ukraine, Belarus, Bulgaria, and Russia. 10 students were sponsored
by the Visegrad Fund and the additional seven were funded by the University of South
Bohemia.
Sponsors and partners:
University partners:
Univerzita Komenského v Bratislavě (Comenius University in Bratislava)
Miskolci Egyetem (University of Miskolc)
Universytet Warszawski (University of Warsaw)
PROJECT held: 11
th July – 06
th August 2016
SUMMER SCHOOL IN MOLECULAR BIOPHYSICS AND SYSTEMS BIOLOGY
Ladies and gentlemen, dear friends, dear participants,
A warm welcome to Nové Hrady and the Annual Visegrad Summer School
in Molecular Biophysics and Systems Biology organized jointly by the South Bohemian
University, Warsaw University in Poland, Comenius University in Bratislava, Slovakia,
and this year for the first time also by the University of Miskolc in Hungary, and the
Center for Nanobiology and Structural Biology of the Institute of Microbiology,
Academy of Sciences of the Czech Republic, in Nove Hrady, Czechia.
The Visegrad Summer School builds on two traditions, the first is the close
collaboration of the five institutions in the field of computational simulations and
spectroscopy of biologically relevant systems, following the tradition of the well
established Visegrad Symposium on Structural Systems Biology, which were initiated
as a scientific meeting by Dr. Babak Minofar back in 2009 and are co-organized by the
four Visegrad countries annually in one of the
Visegrad countries (This year´s symposium was in
June in Warsaw). The second tradition is the long
history of summer schools in the Academy and
University Center in Nove Hrady, dating back to
the first "Schola Ludus" in Biophysics initiated by
Prof. Ladislav Nedbal in 2002. It is a great
pleasure for us to welcome this year's students
from the Visegrad countries as well as from
Bulgaria, Russia, Ukraine, Austria and especially
from the Biological Faculty of the Belarusian State
University in Minsk with whom we have signed a
memorandum of understanding between our
institutions and feel that this now already well
established link continues to be mutually fruitful
and represents an established part of the summer
school. This year's summer school was sponsored
again by the Visegrad fund, and is co-financed by
the University of South Bohemia, a fact which we greatly appreciate.
We believe that the wide range of topics, ranging from various
computational methods used in the study of biologically relevant
macromolecules up to microscopic methods in living cells offer the
students a unique opportunity to get in touch with "real" cutting-
edge science and experience how science works. The lecture series
held not only by our scientists but also by various internationally
well-recognized speakers complements the scientific work
and shall give a broader overview about molecular biophysics and
systems biology. We believe that the unique setting in the chateau
makes social contacts easier and helps to further emphasize the collaborative
atmosphere of the summer school. On behalf of the organizing team, I wish you an enjoyable and inspiring year!
Professor Rüdiger H. Ettrich, Ph.D.
SUPERVISORS
Professor RÜDIGER H. ETTRICH, Ph.D.
ACADEMY OF SCIENCES OF THE CZECH REPUBLIC, CNSB IM
PD Dr. JOST LUDWIG
ACADEMY OF SCIENCES OF THE CZECH REPUBLIC, CNSB IM
JOSEF LAZAR, Ph.D.
ACADEMY OF SCIENCES OF THE CZECH REPUBLIC, CNSB IM
BABAK MINOFAR, Ph.D.
ACADEMY OF SCIENCES OF THE CZECH REPUBLIC, CNSB IM
DAVID REHA, Ph.D.
ACADEMY OF SCIENCES OF THE CZECH REPUBLIC, CNSB IM
PROJECT LEADERS and TUTORS
PROF. RÜDIGER H. ETTRICH, Ph.D.
JOSEF LAZAR, Ph.D.
BABAK MINOFAR, Ph.D.
DAVID ŘEHA, Ph.D.
IEVGENIA IERMAK, Ph.D
ALEXEY BONDAR, Ph.D.
PD Dr. JOST LUDWIG
PRADEEP HIRYUR NAGARAJ, MSc.
DEEPIKA KALE, MSc.
OLGA RYBAKOVA, BSc.
Summer school preparation and meetings
SPEAKERS and LECTURES
Prof. Mgr. Pavel Jungwirth, CSc., Dsc., IOCB Prague, Academy of
Sciences of the Czech Republic – Interactions Between Ions and
Proteins/Peptides in Water
PD Dr. Martin Smiesko, Department of Pharamceutical Science,
University of Basel, Switzerland – Modelling Session (VirtualToxLab)
Prof. Rndr. Ondřej Prášil, PhD., Center Algatech, Academy of
Sciences of the Czech Republic, Trebon – Ocean Acidification
Peter Hinterdorfer, PhD., Institute of Biophysics, Johannes-Kepler
University, Linz, Austria – AFM (Atomic Force Microscopy)
Ing. Pavel Izák, PhD., Institute of Chemical Process Fundamentals,
Academy of Sciences of the Czech Republic – Separation of Gases and
Liquids by Nonporous Membranes
Dr. Wojciech Mrozik, School of Civil Engineering and Geosciences,
Newcastle University, UK – Micropollutants in the environment
PhDr. Ing. Ota Kéhar, PhD., Department of Physics, University of
West Bohemia, Plzen – Interactive Examples from Astronomy
PROJECTS
1. a) Computational modeling of Human 3’-phosphoadenosine 5’-
phosphosulfate Synthase PAPSS: Gene sequence variation among human
populations and its consequences on protein structure/functions
b) Homology modeling of yeast YCP4, a putative oxidoreductase anchored to
the cell membrane.
Project`s aim:
a) By computational modeling gain a better understanding of the structural and
functional consequences of DNA mutations in Human 3’-phosphoadenosine 5’-
phosphosulfate Synthase PAPSS among various human populations. The results will
greatly contribute to the molecular understanding of diseases caused by deficiency in
intracellular sulfate as is autosomal recessive disorder osteochondrodysplasiae.
b) YCP4 is the yeast homolog of the WrBA-class of oxidoreductases bridging bacterial
flavodoxins and eukaryotic NAD(P)H:quinone oxidoreductases and has been
experimentally shown to be anchored to the cell membrane by its long c-terminal tails.
Although benzoquinone is generally used in in vitro assays, the physiological substrate
is still unknown and long-tailed quinones coming from the membrane cannot be
excluded. A structural model of the yeast homolog will help to understand how YCP4 is
anchored at the membrane and thus might help to elucidate the potential of known
WrbAs to act at or close to the membrane as well.
Project leader: Prof. RNDr. Rüdiger Ettrich, [email protected]
2013 - full Professor in biophysics
2006 - associate Professor in biophysics
2002 - PhD. in physical chemistry, Faculty of Sciences, Charles
University, Prague
1993 - Undergraduate studies (Vordiplom) in Chemistry,
Eberhard-Karls-University, Tuebingen, Germany
Students:
Lucie Henrychová - Charles University in Prague, Faculty of Science
Valentina Zinchenko
– Taras Schevchenko National University of Kyiv, ESC,
Institute of Biology
2. Crystallographic studies of the HsdM subunit in type I restriction
modification system EcoR124I
Project’s Aim:
Type I restriction-modification enzymes in bacteria are multisubunit, multifunctional
molecular machines that recognize specific, typically asymmetric, DNA target
sequences of ~13 to 17 bp. Depending on the methylation status of adenine residues in
the target sequence, three enzyme (1 Hsd S and 2 Hsd M) subunits either acting together
as a typical methyltransferase or recruiting a pair of endonuclease motor subunits that
enzymatically initiates translocation of DNA and eventually cleave non-specifically at
apparently random sites. The type I RM system EcoR124I complex meets the sample
standard required for cryo-EM procedures and the 3D reconstructions by single particle
analysis and 3D reconstruction. It has a molecular mass of about 386 kDa with low
symmetry and most flexible in its open conformation. One of our goals to understand
each of the subunit interactions and with the DNA molecule during the cleavage activity
and the role of EcoR124I pentameric complex in horizontal gene transfer mechanism.
While the first crystal structure of the motor (Hsd R) subunit was solved by our group,
no crystal structure of the methyltransferase (MTase) subunit or the individual subunits
Hsd M and Hsd S have been reported till date.
The available structural information is based either on poor resolution (~35 Å) model by
a combination of negative staining cryo-EM and SAXS/SANS or computational
prediction by homology modeling. The interdisciplinary approach of cryo-EM and X-
ray crystallography caters perfectly to the objectives of the project. The aim is to solve
the atomic-scale structure of the trimeric MTase in complex with DNA using a
combination of X-ray crystallography, SAXS and computational modeling methods.
Besides, the cryo-EM experimental data has been obtained for the EcoR124I pentamer
in complex wth dsDNA using FEI’s Titan Krios. The crystal structure and cryo-EM
maps would enable us to understand the structural transition between the native
complex and its interaction with dsDNA. The aim is directed towards understanding
structural flexibility of the HsdS and HsdM subunits and the mechanism of MTase
interaction with the motor subunit. Also important is to comprehend the conformational
changes that occur upon DNA binding and the contact points involved. Furthermore, we
envisage to use computational methods to predict the trajectory of movements arising
from the conformational transition and the rotations within the inter-domain hinges.
Project leader: Pradeep Hiryur Nagaraj, [email protected]
Students:
Judit Matejka – Belarusian State University, Faculty of Biology,
Jeremi Kuklwicz - Intercollegiate Faculty of Biotechnology UG and MUG
2015 - current
2011 – 2013
PhD student in biophysics, Department of protein
structure and function, Center for Nanobiology and
Structural Biology, Institute of Microbiology of
the Academy of Sciences, Nove Hrady, Czech
Republic
MRes in protein structure and function studies,
Department of Biology and Biochemistry,
University of Bath,
Bath, UK
3. Modeling interactions in biomolecules using methods of quantum and
molecular mechanics
Project`s aim:
The study of interactions between proteins and several ligands (drugs) and other related
bimolecular processes by means of various computational methods, particularly
quantum mechanics (QM), hybrid QM/MM methods, molecular dynamics (MD)
simulations and molecular docking.
Project leader: David Řeha, Ph.D., [email protected]
2011 - current
Research group leader, Dpt. of
Computational Biology, INSB GCRC AS
CR
2009 - 2011 Post-doc fellowship, Deparment of
Biological Sciences, University of Essex,
Colchester, UK
2007 - 2009
Post-doc fellowship, School of Physics and
Astronomy, University of Leeds, UK
2005
2000
PhD. in physical chemistry, Faculty of
Sciences, Charles University, Prague
Master of sciences (Mgr.) in physical and
macromolecular chemistry, Faculty of
Sciences, Charles University, Prague
Students:
Hanna Dudko – The Faculty of Biology of Belarusian State University
Julia Brechka – State Institution of Education "Researchers Training Institute National
Academy of Sciences of Belarus" and working on a Master’s degree at
the Laboratory of Protein Engineering of the Institute of Bioorganic
Chemistry, National Academy of Sciences of Belarus.
4. Theoretical investigation of the interactions of hydrated ionic
liquids with membranes for bio-applications and drug delivery
Project`s aim:
The objective of this project is to study theoretically the interaction of aqueous solutions
of ionic liquids with biologically related compounds in order to understand their roles in
possible bio-applications such as drug delivery, protein folding and protein
crystallization.
Project leader: Babak Minofar, Ph.D., [email protected]
2012 - current
Research group leader, Department of
molecular liquids, INSB GCRC AS CR
2010 -2012
Post-doc fellowship, Japanese society of
science, Kyushu University and Niigata
University, Japan,
2007 -2010
Post-doc fellowship INSB GCRC AS CR
2007
1998
PhD. in physical chemistry, Faculty of
Sciences, Charles University, Prague
Master of sciences (Msc.) in applied
chemistry, Faculty of Sciences, Azad
University, Tehran
Students:
Katerina Serafimova - Sofia University “St. Kliment Ohridski”, Faculty of Biology
Mykhailo Tolkachov – Taras Shevchenko National University of Kyiv, Ukraine, ESC
Institute of Biology, Department of Biophysics
5. Molecular mechanisms of G protein signaling investigated by two-photon
polarization microscopy
Project`s aim:
The aim of the project is to determine whether cholesterol in plasma membrane affects
conformation and functional activity of heterotrimeric G proteins. In order to achieve
this aim, participants will learn and employ techniques of molecular biology,
mammalian cell culture and advanced optical microscopy.
Project leader: Josef Lazar, Ph.D. [email protected]
2006 – 2007 Columbia Science Fellow, Dept. of
Biological Sciences, Columbia
University, USA
2002 – 2005
Postdoctoral research fellow, Dept. of
Biological Sciences, Columbia
University, USA
2001
1996
Ph.D., Medicinal Chemistry, University
of Utah, Salt Lake City, USA
M.Sc., Organic Chemistry, Charles
University /Institute of Organic
Chemistry & Biochemistry AS CR, Prague, Czech Republic
Project leader: Alexey Bondar, Ph.D., [email protected]
Students:
Yuliia Didan - Radboud University Medical Center, Master's programme in Molecular
Mechanisms of Disease
Zuzzana Pakosz – Jagiellonian University, Cracow, Poland, Faculty of Biochemistry,
Biophysics and Biotechnology
2014 Postdoctoral Research Fellow, Institute
of Nanobiology and Structural Biology
2007 – 2014 Doctor of Philosophy (Ph.D.)
Biophysics, University of South
Bohemia in Czech Budweis
2001 – 2006 Master of Science, Biochemistry,
Belarusian State University
6. Development of fluorescent proteins sensitive to cell membrane voltage
Project`s aim:
To develop a fluorescent protein suitable for observing electrical signals in neurons.
Project leader: Josef Lazar, Ph.D. [email protected]
Project leader: Ievgenia Iermak, PhD, iermak @nh.cas.cz
2006 – 2007 Columbia Science Fellow, Dept. of
Biological Sciences, Columbia
University, USA
2002 – 2005
Postdoctoral research fellow, Dept. of
Biological Sciences, Columbia
University, USA
2001
1996
Ph.D., Medicinal Chemistry, University
of Utah, Salt Lake City, USA
M.Sc., Organic Chemistry, Charles
University /Institute of Organic
Chemistry & Biochemistry AS CR, Prague, Czech Republic
2013 Travel grant for Advanced
School On Modern Trends
Of Biophotonics For
Diagnosis And Treatment Of
Cancer And Microbial
Control, Sao Carlos, SP,
Brazil
2011 Travel grant for URSI GASS
2011, Istanbul, Turkey
2009 PhD in Biophysics
Students:
Mariia Zeziulia - Taras Shevchenko National University of Kyiv, Educational and
Scientific Centre "Institute of Biology”
Kajetan Sawa – Faculty of Biochemistry, Biophysics and Biotechnology, Master of
Science in Molecular Biotechnology
7. Development of optical microscopy into a structural biology technique
Project´s aim:
The aim of the project is to develop two-photon polarization microscopy into a novel
quantitative technique of structural biology. In order to achieve this aim, students will
apply techniques of molecular biology, protein purification and crystallization,
advanced optical microscopy and mathematical modeling.
Project leader: Josef Lazar, Ph.D. [email protected]
Project leader: Olga Rybakova, [email protected]
STILL STUDYING
2006 – 2007 Columbia Science Fellow, Dept. of
Biological Sciences, Columbia
University, USA
2002 – 2005
Postdoctoral research fellow, Dept. of
Biological Sciences, Columbia
University, USA
2001
1996
Ph.D., Medicinal Chemistry, University
of Utah, Salt Lake City, USA
M.Sc., Organic Chemistry, Charles
University /Institute of Organic
Chemistry & Biochemistry AS CR, Prague, Czech Republic
Students:
Yifan Mayr - University of South Bohemia, Faculty of Science
Erik Kot – Moscow Institute of Physics and Technology (State University), Dept. of
Biological and Medical Physics
8. Monitoring intracellular pH changes of yeast cells
Project`s aim:
Analysis of intracellular pH changes of yeast (Saccharomyces cerevisiae) cells upon
changes in extracellular pH and external K+ concentration. In the project we’ll generate
different yeast strains (carrying mutations in K+ translocation system genes) producing
the genetically encoded pH sensor pHluorin. These strains will be verified by
fluorescence microscopy. Eventually time resolved measurements of intracellular pH
will be carried out using a fluorescence microplate reader. Mainly the response of
intracellular pH upon changes of external pH and external K+ concentration will be
analyzed.
Project leader: PD Dr. Jost Ludwig, [email protected]
Leader of Department of membrane physiology and bioenergetics
INSB GCRC AS CR
Dr. Ludwig’s work and his group is best known for functional
analysis of ion channels and transporters, cation transport in yeast
(Saccharomyces cerevisiae), cation homeostasis in yeast (more
specifically: Localization of cation transport proteins and
regulatory proteins, cation flux measurements using ion selective
electrodes), and his research in multiple drug resistance with the
analysis of promoters involved in expression of MDR relevant
genes.
Project leader: Deepika Kale, [email protected]
2015-current PhD student, Department of Membrane
Physiology and Energetics, INSB GCRC
AS CR
2012-2014
Junior Research Fellow, National
chemical Laboratory, Pune
2010-2012
2007-2010
Master of Microbiology(M.Sc), M.E.S.
Abasaheb Garware College, University
of Pune
Bachelor of Microbiology
(B.Sc), M.E.S. Abasaheb Garware
College, University of Pune
Students:
Wiktor Tokarek - Jagiellonian University in Kraków, Faculty of Biochemistry,
Biophysics and Biotechnology
Mariia Borbuliak - Ivan Franko National University of Lviv, Faculty of Biology
Igor Khassanov - Belarussian State University, Faculty of Biology
PHOTO GALLERY
Conference Center
at Academy of Sciences
of the Czech Republic
Zamek 136, 373 33 Nove Hrady
www.chateau-novehrady.cz
Tel.: +420 389 033 804
Conference Center AS CR
Château Nové Hrady
The Conference Centre ASCR Nove Hrady - New Castle in the historical building of the
Empire Château offers modernly equipped conference facilities, comfortable
accommodation, gastronomic services, restaurant and finally a large park, which is due
to its location an ideal for exploring the beautiful surrounding countryside
Novohradske Mountains.
• Conferences • Summits • Training • Seminars • Workshops • Corporate Events • Teambuilding • Weddings • Social gatherings and events • Events • Romantic getaways for individual clients • Family weekends • Sporting Events • Garden Party under the open sky • Fun and accompanying program
CENTER FOR NANBIOLOGY AND STRUCTURAL BIOLOGY
The Center for Nanobiology and Structural Biology, (CNSB) in Nové Hrady is a
research unit of the Institute of Microbiology of the Academy of Sciences and carries
out research in the field of structural and systems biology on a molecular, cell, tissue,
and organism level. Hence it provides knowledge on the molecular structure of system
elements and their principal metabolic and control pathways, and identifies links
between these elements to describe the structure of biological systems. Methods are
implemented from bioinformatics, molecular biology, microscopy, molecular modeling,
and structure determination, mainly by X-ray diffraction.
The educational center and laboratories in Nové Hrady were established in 2002. The
center occupies a renovated nineteenth-centrury castle. The campus in Nove Hrady was,
from the very beginning, meant to serve not only for research but also as a scientific
training facility, and organizes a large number of courses, workshops, conferences, and
symposia.
Despite the short time of their existence, the CNSB research groups already achieved
excellent scientific results published in highly visible journals including Nature, Nature
Structural & Molecular Biology, Nature Methods, Nature Chemical Biology, Science
Signaling, PLOS Computational Biology, and others. Scientists from Nove Hrady are
regularly invited to speak at international conferences and symposia, get invitations to
contribute review papers, book chapters, and invited papers. CNSB is regularly visited
by foreign scientists and participants of international internship programs.
Although its roots date back until 2002, when the first scientists moved to Nove Hrady,
the Center for Nanobiology and Structural Biology (CNSB) was established as an
independent research unit 1.1.2011 and joined the Institute of Microbiology of the
Academy of Sciences on 1.1.2016.