Daily Schedule

Jump to
Day
Wednesday,
September 17
 
Thursday, 
September 18
Friday, 
September 19
Saturday,
September 20
Sunday, 
September 21

Wednesday, September 17

6:00 PM - 8:00 PM Registration                     
6:50 PM - 8:05 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: RNA Machines for Protein Production that Withstand Evolution Pressures
8:10 PM - 9:30 PM Welcome Reception

Thursday, September 18 

8:00 AM - 5:00 PMRegistration
 Session: Structure of Proteins - Theory 
Chair: Jose Onuchic, Rice University, USA
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
Chair: Jane Clarke, University of Cambridge, United Kingdom
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 - 1:30 PMLunch
 Session: Energy Landscape of Biomolecules, Part I
Chair: Dave Thirumalai, University of Maryland, USA
1:30 PM - 2:00 PMPeter Wolynes, Rice University, USA
Harvesting the Fruits of the Energy Landscape Theory of Protein Folding
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 PMJeffrey Noel, Rice University, USA*
Connecting Simplified Models with Explicit-solvent Forcefields: Slipknotting during the Folding of the Smallest Knotted Protein
3:15 PM - 3:40 PMCoffee Break
 Session: Energy Landscape of Biomolecules, Part II
Chair: Alexey Murzin, Medical Research Council Center, United Kingdom
3:40 PM - 4:10 PM Alexander Grosberg, New York University, USA
Significance, Complexity, and Beauty of Knot-avoiding Structures
4:10 PM - 4:25 PM Sebastian Kmiecik, University of Warsaw, Poland*
Multiscale Modeling of Protein Flexibility
4:25 PM - 4:55 PMJanusz Bujnicki, International Institute of Molecular and Cell Biology, Poland
Simulations of Folding and Unfolding of Pseudoknots in RNA
4:55 PM - 8:00 PMFree Time
8:00 PM  - 9:30 PMPoster Session I

Back to Top 


Friday, September 19


Session: Mathematical Perspectives on Knotting
Chair: Kenneth C. Millett, University of California, Santa Barbara, USA
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 - 10:30 AM Coffee Break
 Session: Puling Knots and Slipknots
Chair: Matthias Rief, Technical University of Munich, Germany
10:30 AM - 11:00 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
11:00 AM - 11:30 AM Hongbin Li, University of British Columbia, Canada
Mechanically Tightening a Protein Slipknot into a Trefoil Knot
11:30 AM - 12:00 PM Piotr Szymczak, University of Warsaw, Poland
Untying a Protein Knot - Translocation of Knotted Proteins Through a Pore
12:00 PM - 12:15 PM Katrina Forest, University of Wisconsin-Madison, USA*
Why are Phytochromes Knotted?
12:15 PM - 1:30 PM Lunch

Session: RNA Dynamics
Chair: Sarah Woodson, Johns Hopkins University, USA
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, Knotted DNA
Chair: Mariel Vazquez, University of California, Davis, USA
3:20 PM - 3:50 PM Tamar Schlick, New York University, USA
Chromatin Looping and Interdigitation Mechanisms: Insights from Mesoscale
Simulations

3:50 PM - 4:20 PM Nicolas Clauvelin, Rutgers University, USA
Protein-induced Entanglement on DNA: Connecting and Organizing Chromosomes via Multiple Loops
4:20 PM - 4:50 PM Dorothy Buck, Imperial College of London, United Kingdom
Knotted DNA: Mathematical Models and Biological Consequences
4:50 PM - 5:10 PM Open Discussion
Wilma Olson, Rutgers University, USA
Jose Onuchic, Rice University, USA
Matthias Rief, Technical University of Munich, Germany
Joanna Sulkowska, University of Warsaw, Poland
Sarah Woodon, Johns Hopkins University, USA
5:10 PM - 8:00 PM Free Time
8:00 PM - 9:30 PM Poster Session II
 

Saturday, September 20

 

Session: DNA Topology and Topoisomerase
Chair: Lynn Zechiedrich, Baylor College of Medicine, USA
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, Origami - Theory/Experiment, Part I
Chair: Remus Dame, Leiden Institute of Chemistry, The Netherlands
10:45 AM - 11:15 AM Giovanni Dietler, Swiss Federal Institute of Technology (EPFL), 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 Zbyszek Otwinowski, UT Southwestern Medical Center, USA*
Single-stranded DNA Topology in Eukaryotes
12:30 PM - 3:30 PM Lunch and Free Time
 Session: DNA/RNA, Nanorobots, Origami - Theory/Experiment, Part II
Chair: Giovannia Dietler, Swiss Federal Institute of Technology (EPFL), Switzerland
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 - 4:15 PM Pawel Zawadzki, Oxford University, United Kingdom*
Escherichia coli Live Cell Super-resolution Analysis of Topoisomerase IV Action
4:15 PM - 4:45 PM Remus Dame, Leiden Institute of Chemistry, The Netherlands
Fine-tuning the Activity of DNA Bridging Proteins
4:45 PM - 5:00 PM Coffee Break
5:00 PM - 5:30 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

Session: Energy Landscape Proteins
Chair: Joanna Sulkowska, University of Warsaw, Poland
5:30 PM - 6:00 PMJose Onuchic, Rice University, USA
Knotting a Protein in the Computer - From Simple Models to Explicit Solvent Simulations
 

Sunday, September 21

 

Session: DNA Knots and Viral Topology, Part I
Chair: Alexander Grosberg, New York University, USA
8:30 AM - 9:00 AM Todd Yeates, University of California, Los Angeles, USA
Discoveries, Implications and Utilities of Proteins with Barriers, Knots, Slipknots, and Links
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
 Session: DNA Knots and Viral Topology, Part II
Chair: Wilma Olson, Rutgers University, USA
10:45 AM - 11:15 AMJohn Maddocks, Swiss Federal Institute of Technology (EPFL), Switzerland
Coarse-grain Models of DNA Free Energy and Sequence-dependent Minicircle Shapes
11:15 AM - 11:45 AMMariel Vazquez, University of California, Davis, USA
DNA Unlinking in Bacteria
11:45 AM - 12:15 PMPublic Talk - De Witt Sumners, Florida State University
DNA Knots Reveal Enzyme Mechanism and Viral Capsid Packing Geometry
12:15 PMEnd of Meeting
 

*Short talks selected from among submitted abstracts 

Quick Links