Biomolecules and Nanostructures 4

15-19 May 2013, Pultusk, Poland


Abstract Book


All lectures and poster sessions will take place in the Manez (Old Riding School) Conference Hall.

All posters will be viewed during the whole time of the conference. Please, place your poster in the Manez Lecture Room immediately after arrival and dismount it not earlier than after the CLOSING LECTURE.


Wednesday, 15 May 2013


15:00 - 22:00            REGISTRATION

18:00 - 19:30            WELCOME RECEPTION - GARDEN PARTY



chairperson: Marek Cieplak

19:30 - 20:15            Jane Clarke, University of Cambridge, Department of Chemistry, UK
                               Lessons that can be learned from studying the folding of protein families

20:15 - 20:25            Anna Niedzwiecka, Institute of Physics PAS; University of Warsaw, Poland
                               National Multidisciplinary Laboratory of Functional Nanomaterials POIG 2.2 - NanoFun

20:30 - 22:00            DINNER AT BONFIRE



Thursday, 16 May 2013


SESSION I               FOLDING

chairperson: Marek Cieplak

9:00 - 9:30                Jasna Brujic, New York University, USA
                               Views of protein folding from a statistical physics approach to single molecule experiments

9:30 - 10:00              Thomas Kiefhaber, Technical Univeristy Munich, Germany
The unlocked state: a clue to understand how proteins fold and unfold

10:00 - 10:30            Andrzej Kolinski, University of Warsaw, Poland
                               CABS - coarse grained modeling of protein structure assembly, dynamics and interactions

10:30 - 11:00            COFFEE BREAK

chairperson: Jasna Brujic

11:00 - 11:30            George Stan, University of Cincinnati, USA
                               Computer simulations of protein unfoldimg and translocation by AAA+ chaperones

11:30 - 12:00            Joan-Emma Shea, University of California Santa Barbara, USA
                               Effect of surfaces in modulating protein folding

12:00 - 12:30            Patricia Faisca, University of Lisboa, Portugal
                               Intermediate states for protein folding and aggregation

12:30 - 12:45            Roberto Covino, University of Trento, INFN, Italy
                               Protein folding pathways with realistic atomistic force fields

12:45 - 13:00            Annett Bachmann, Technical Univeristy Munich, Germany
                               The Mechanism of a Coupled Protein Folding and Binding Reaction: Folding Before Binding
                               or Binding Before Folding?

13:00 - 14:30            LUNCH



chairperson: Thomas Kiefhaber

14:30 - 15:00            Rebecca C. Wade, Heidelberg Institute for Theoretical Studies; Heidelberg University, Germany
                               Protein dynamics and molecular recognition: Insights from simulations

15:00 - 15:30            Joanna Trylska, CeNT, University of Warsaw, Poland
                               Ribosomal RNA as a target for sequence-specific inhibition

15:30 - 16:00            Adam Liwo, University of Gdansk, POLAND
                               Mean field dipole-dipole interactions as essential factors in the formation of biomolecular

16:00 - 16:30            COFFEE BREAK

16:30 - 17:00            Peter Hinterdorfer, Johannes Kepler University Linz, Austria
                               Molecular recognition force microscopy/spectroscopy

17:00 - 17:30            Ruxandra Dima, University of Cincinnati, USA
                               Multiscale simulations of the mechanics of filamentous proteins

17:30 - 18:00            Pawel Pomorski, Nencki Institute of Experimental Biology PAS, Warsaw, Poland
                               How cell adhesion can influence nucleotide-dependent calcium signal: the idea of
                               signalosome and it's practical implementation

18:00 - 18:15             Michal Toborek, University of Miami School of Medicine, USA
                                Autophagy is involved in nanoalumina-induced cerebrovascular toxicity

18:15 - 18:30            Juergen Schluetter, LOT-Quantum Design, Germany
                               Studying of protein aggregation onto surfaces using QCM-D

18:30 - 19:45            DINNER


20:00 - 22:00           POSTER SESSION I - odd numbers presenting authors



Friday, 17 May 2013



chaiperson: Anna Niedzwiecka

9:00 - 9:30                Marc Fabian, McGill University, Montreal, Canada
                               Structural insight into gene silencing programs that employ the CCR4-NOT deadenylase

9:30 - 10:00              Marek Tchorzewski, Maria Curie-Sklodowska University, Lublin, Poland
                               The ribosome action as transitions between different functional/structural states driven by
obtained from GTP hydrolysis

10:00 - 10:30            Piotr Zielenkiewicz, Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
                               Whole cell model of translation

10:30 - 11:00            COFFEE BREAK



chairperson: Giovanni Dietler

11:00 - 11:30             Andrzej Sienkiewicz, EPFL, Lausanne, Switzerland
                               Multifunctional magnetic-photoluminescent-photocatalytic nanostructures for biomedical

The European Physical Society Invited Lecture

11:30 - 12:00            Damien Thompson, Tyndall Institute, Cork, Ireland
                               Nanoscale computer-aided design of self-assembling materials for electronics and health

12:00 - 12:30            Piotr Garstecki, Institute of Physical Chemistry PAS, Warsaw, Poland
                               Automated droplet microfluidics for studies of emergence of drug resistance in bacteria

12:30 - 13:00            Robert Leheny, Johns Hopkins Univeristy, Baltimore, USA
                               Viscoelastic behavior of proteinic surfaces

13:00 - 16:30            LUNCH & FREE TIME

16:30 - 17:00            COFFEE BREAK

chairperson: Joan Emma Shea

17:00 - 17:30            Robert Holyst, Institute of Physical Chemistry PAS, Warsaw, Poland
                               Biologistics: mobility of ligands, proteins and plasmids in cytoplasm of the eukaryotic and
                               prokaryotic cells

17:30 - 18:00            Jaroslaw Stolarski, Institute of Paleobiology PAS, Warsaw, Poland
                               How meaningful is prefix "bio" for minerals formed by organisms: the nanoscale perspective

18:00 - 18:30            Boguslaw Baginski, University of Warsaw, Poland
                               Zircon - small but great

18:30 - 19:45            DINNER


20:00 - 22:00            POSTER SESSION II - even numbers presenting authors


Saturday, 18 May 2013



chairperson: Mariusz Jaskólski

9:00 - 9:30               Catherine Royer, Centre de Biochemie Structurale, Montpelier, France
                               Pressure effects on protein stability - the devil is in the details

9:30 - 10:00              Wladek Minor, University of Virginia, Charlottesville, USA
                               Experiment and modeling: competitive or complementary approaches to structural biology?

10:00 - 10:30            Andrzej Kloczkowski, Nationwide Children's Hospital, Columbus, OH, USA
                               New methods to improve protein structure prediction and refinement

10:30 - 10:45            Agnieszka J. Pietrzyk, Institute of Bioorganic Chemistry, PAS, Poznan, Poland
                               Structural studies on 30-kDa lipoproteins from mulberry silkworm

10:45 - 11:15            COFFEE BREAK



chairperson: Catherine Royer

11:15 - 11:45            Gijs Wuite, Vrije Universiteit, Amsterdam, Holland
                               The nanomechanics of viruses

11:45 - 12:15            Neil Ferguson, University College Dublin, Ireland
                               Molecular mimicry in hepatitis B virus: How a viral intrinsically disordered protein helps
the host membrane-trafficking machinery

12:15 - 12:45            Wouter Roos, Vrije Universiteit, Amsterdam, Holland
                               Dual structural role of the viral RNA: capsid stabilization vs. genome uncoating

12:45 - 13: 15           Cristian Micheletti, SISSA, Trieste, Italy
                               DNA knotting inside viral capsids: a computational approach

13:15 - 15:15            LUNCH



chairperson: Cristian Micheletti

15:15 - 15:45            Giovanni Dietler, EPFL, Lausanne, Switzerland
                               Knots: from the sailing boat down to the cell's nucleus illustrated by means of simple

15:45 - 16:15            Andrew Travers, LMB, Cambridge, UK
                               Chromosomes as topological machines

16:15 - 16:45            Joerg Rottler, University of British Columbia, Vancouver, Canada
                               Predictions of a systematically coarse grained model for DNA

16:45 - 17:15            COFFEE BREAK



chairperson: Chris Johnson

17:15 - 17:45            Amos Maritan, University of Padua, Italy
                               Emergence of criticality in living systems

17:45 - 18:15            Annalisa Pastore, National Institute for Medical Research, MRC, London, UK
Kaleidoscopic protein self-assembly: The AXH domain of ataxin-1 undergoes a complex
                               multiple equilibrium of species in solution

18:15 - 18:45            Mariusz Jaskolski, Institute of Bioorganic Chemistry, PAS; Adam Mickiewicz University, Poznan,
                               Modulated macromolecular crystal structure with 28 protein molecules in the asymmetric



18:45 - 19:30            Gerhard Hummer, NIH Bethesda, USA
                               Order and disorder in biomolecular assemblies

20:00                         CONFERENCE BANQUET



Sunday, 19 May 2013


7:30 - 10:00             BREAKFAST

8:30                          DEPARTURE I

10:00 or 11:00        DEPARTURE II