Daily Schedule

Jump to
September 17
September 18
September 19
September 20
September 21

Wednesday, September 17

6:00 PM - 6:50 PM Registration                     
6:50 PM - 8:00 PM Opening Talks
Jane Clarke, University of Cambridge, United Kingdom
Unfolded, but not Knotted! Mechanistic Studies of IDP Folding Upon Binding
Ada Yonath, Weizmann Institute of Science, Israel
Ribosomes: An RNA Machines for Protein Production that Withstand Evolution Pressures
8:00 PM - 9:30 PM Welcome Reception

Thursday, September 18 

8:00 AM - 8:45 AMRegistration
 Session: Structure of Proteins - Theory 
8:30 AM - 9:00 AM Alexey Murzin, Medical Research Council Center, United Kingdom 
Geometrical and Topological Aspects of Protein Structures
9:00 AM - 9:30 AM Wladek Minor, University of Virginia, USA
Experiment and Modeling: Competitive or Complementary Approaches to Structural Biology?
9:30 AM - 10:00 AM Kenneth C. Millett, University of California, Santa Barbara, USA
Knots and Slipknots in Proteins
10:00 AM - 10:30 AM Robert Jernigan, Iowa State University, USA
Extracting Protein Dynamics from Experimental Structures
10:30 AM - 10:45 AMCoffee Break

Session: Proteins - Experiment
10:45 AM - 11:15 AM Sophie Jackson, University of Cambridge, United Kingdom
Folding of Nascent Chains of Knotted Proteins
11:15 AM - 11:45 AMPatricia Jennings, University of California, San Diego, USA
Exploring the Coordinated Functional and Folding Landscapes of Knotted Proteins
11:45 AM - 12:15 PMYa-Ming Hou, Thomas Jefferson University, USA
Methyl Transfer from AdoMet by a Knotted Protein Fold
12:15 PM - 12:30 PMShort Talk
12:30 PM - 1:30 PMLunch
 Session: Energy Landscape of Biomolecules
1:30 PM - 2:00 PMPeter Wolynes, Rice University, USA
2:00 PM -  2:30 PMShoji Takada, Kyoto University, Japan
Knotted Structures in Refolding and Cotranslational Folding of Multi-domain Protein
2:30 PM - 3:00 PMAndrzej Kolinski, University of Warsaw, Poland
Coarse Grained Modeling of Protein Structure, Dynamics and Interactions
3:00 PM - 3:15 PMShort Talk
3:15 PM - 3:40 PMCoffee Break
 Session: Evolution Approach to Proteins, RNA
3:40 PM - 4:10 PM Alexander Grosberg, New York University, USA
Significance, Complexity, and Beauty of Knot-avoiding Structures
4:10 PM - 4:40 PMJanusz Bujnicki, International Institute of Molecular and Cell Biology, Poland
Simulations of Folding and Unfolding of Pseudoknots in RNA
4:40 PM - 8:00 PMFree Time
8:00 PM  - 9:30 PMPoster Session

Back to Top 

Friday, September 19

Session: Mathematical Perspectives on Knotting
8:30 AM - 9:00 AM Stuart Whittington, University of Toronto, Canada
Defining and Identifying Knots in Linear Polymers
9:00 AM - 9:30 AM Chris Soteros, University of Saskatchewan, Canada
The Knot Complexity of Compressed Polygons in a Lattice Tube
9:30 AM - 10:00 AM Eric Rawdon, University of St. Thomas, USA
Knotting in Subchains of Proteins and Other Entangled Chains
10:00 AM - 10:15 AM Short Talk
10:15 AM - 10:45 AM Coffee Break
 Session: Puling Knots and Slipknots
10:45 AM - 11:15 AM Michael Woodside, University of Alberta, Canada  
Mechanical Unfolding of Single RNA Pseudoknots Reveals that Conformational Plasticity, Not Resistance to Unfolding, is a Determinant of Programmed −1 Frameshifting
11:15 AM - 11:45 AM Hongbin Li, University of British Columbia, Canada
Mechanically Tightening a Protein Slipknot into a Trefoil Knot
11:45 AM - 12:15 PM Piotr Szymczak, University of Warsaw, Poland
Untying a Protein Knot - Translocation of Knotted Proteins Through a Pore
12:15 PM - 12:30 PM Short Talk
12:30 PM - 1:30 PM Lunch

Session: RNA Dynamics
1:30 PM - 2:00 PM Dave Thirumalai, University of Maryland, USA
Crowding Promotes the Switch from Hairpin to Pseudoknot Conformation in Human Telomerase RNA
2:00 PM - 2:30 PM Paul Whitford, Northeastern University, USA
Parallels Between Protein Folding and Ribosome Dynamics
2:30 PM - 3:00 PM Joanna Trylska, Center of New Technologies, Poland
Conformational Dynamics of RNA Functional Motifs: Ribosomal A-site and Thermosensing Hairpin
3:00 PM - 3:20 PM Coffee Break

Session: DNA-Protein Interaction
3:20 PM - 3:50 PM Sarah Harris, University of Leeds, United Kingdom
Closing the Loop: Comparing the Results of Experiment and Computer Simulations in the Study of DNA Minicircles
3:50 PM - 4:20 PM Dorothy Buck, Imperial College of London, United Kingdom
Knotted DNA: Mathematical Models and Biological Consequences
4:20 PM - 4:50 PM Nicolas Clauvelin, Rutgers University, USA
Protein-induced Entanglement on DNA: Connecting and Organizing Chromosomes via Multiple Loops
4:50 PM - 5:10 PM Open Discussion
Mattias Rief, Technical University of Munich, Germany
Jose Onuchic, Rice University, USA
Joanna Sulkowska, University of Warsaw, Poland
5:10 PM - 6:10 PM Trip to Old Town
8:00 PM - 9:30 PM Poster Session

Saturday, September 20


Session: DNA Topology and Topoisomerase
8:30 AM - 9:00 AM Tony Maxwell, John Innes Center, Norwich Research Park,
United Kingdom
DNA Topology, DNA Topoisomerases, and Small DNA Circles
9:00 AM - 9:30 AM Stephen Levene, University of Texas, Dallas, USA
Conformational Free-energy Calculations for Complex Biopolymer Structures
9:30 AM - 10:00 AM Phoebe Rice, University of Chicago, USA
Structural Basis for Regulation of Site-specific DNA Recombinases by DNA Topology
10:00 AM - 10:30 AM Anjum Ansari, University of Illinois at Chicago, USA
Unveiling the Molecular Trajectory During Binding Site Recognition by DNA-bending Proteins
10:30 AM - 10:45 AM Coffee Break

Session: DNA/RNA, Nanorobots, DNA Origami - Theory/Experiment
10:45 AM - 11:15 AM Giovanni Dietler, École Polytechnique Fédérale de Lausanne, Switzerland
Sedimentation of Macroscopic Rigid Knots and its Relation to Gel Electrophoretic Mobility of DNA Knots
11:15 AM - 11:45 AM Juli Feigon, University of California, Los Angeles, USA
RNA Pseudoknots in Telomerase and Riboswitches
11:45 AM - 12:15 PM Ebbe Andersen, Aarhus University, Denmark
Single-stranded Architecture for Cotranscriptional Folding of RNA Nanostructures
12:15 PM - 12:30 PM Short Talk
12:30 PM - 3:30 PM Lunch and Free Time (on one's own)
3:30 PM - 4:00 PM Lynn Zechiedrich, Baylor College of Medicine, USA
How Positive or Negative Supercoiling Affects the Structure and Reactivity of DNA
4:00 PM - 4:30 PM Andrzej Stasiak, University of Lausanne, Switzerland
Tightening of DNA Knots by Supercoiling Facilitates their Unknotting by Type II DNA Topoisomerases 
4:30 PM - 5:00 PM Remus Dame, Leiden Institute of Chemistry, The Netherlands
Fine-tuning the Activity of DNA Bridging Proteins
5:00 PM - 5:15 PM Coffee Break
5:15 PM - 5:45 PM Tamar Schlick, New York University, USA
Chromatin Looping and Interdigitation Mechanisms: Insights from Mesoscale

Session: Energy Landscape Proteins
5:45 PM - 6:15 PMJose Onuchic, Rice University, USA
Knotting a Protein in the Computer - From Simple Models to Explicit Solvent Simulations
6:15 PM - 7:00 PM Break
7:00 PM - 10:00 PM Banquet

Sunday, September 21


Session: DNA Knots and Viral Topology
8:30 AM - 9:00 AM Todd Yeates, University of California, Los Angeles, USA
9:00 AM - 9:30 AM Marek Cieplak, Polish Academy of Sciences, Poland
Knotted Proteins under Tension
9:30 AM - 10:00 AM Peter Virnau, Johannes Gutenberg University, Germany
Molecular Simulations of Knotted Proteins and DNA
10:00 AM - 10:30 AM Tetsuo Deguchi, Ochanomizu University, Japan
Probability of DNA Knots and the Effective Diameter of DNA Double Helix
10:30 AM - 10:45 AMCoffee Break
10:45 AM - 11:15 AMJohn Maddocks, École Polytechnique Fédérale de Lausanne, Switzerland
11:45 AM - 12:15 PMMariel Vazquez, San Francisco State University, USA
DNA Unlinking in Bacteria
12:15 PM - 12:45 PMPublic Talk - De Witt Sumners, Florida State University
DNA Knots Reveal Enzyme Mechanism and Viral Capsid Packing Geometry
 1:00 PMEnd of Meeting


Quick Links