annual summer school in molecular biophysics and...

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


JOSEF LAZAR, Ph.D.


BABAK MINOFAR, Ph.D.


DAVID REHA, Ph.D.


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

mailto:[email protected]

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



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


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


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: Ievgenia Iermak, PhD, iermak @nh.cas.cz



University, USA

2002 – 2005



University, USA

2001

1996






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: Olga Rybakova, [email protected]

STILL STUDYING



University, USA

2002 – 2005



University, USA

2001

1996







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

[email protected]

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

http://www.chateau-novehrady.cz/

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.

annual summer school in molecular biophysics and...

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