Topological aspects of DNA function and protein folding

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Workshop theme

This meeting will provide a forum for biological scientists, physicists and mathematicians to discuss recent developments in the application of topology to the study of DNA and protein structure.

The structure and function of DNA and proteins are affected by the topology of the DNA strands or polypeptide chains, respectively. During DNA replication, transcription or recombination, DNA molecules become supercoiled, knotted or catenated. These processes are dynamic and are modulated by the activity of site-specific recombinases, which break double stranded DNA at a specific locations, and re-assort and rejoin the ends, and DNA topoisomerases, which permit intra- or inter-molecular strand passages by mechanisms also involving the breaking and rejoining of the DNA backbone. The transient DNA breaks induced by topoisomerases have made them a fruitful target for cytotoxic antibacterial and anti-tumour drugs. Recent structural and biochemical studies have elucidated many mechanistic details of both topoisomerases and recombinases.

While supercoiling, knotting and catenation have been intensively studied for over 40 years, the realization that proteins can also be knotted dates back just one decade. The number of known proteins that form knots in their native structure is growing and we are beginning to understand how knotted proteins can fold, and the potential structural advantages of knotted proteins.

Subjects to be covered will include:

Modelling of DNA molecules subject to topological constraints.
Mechanism of action of DNA topoisomerases.
DNA recombination and its mechanisms.
Chromosomal architecture.
Folding mechanisms of knotted proteins.
Function of knots in proteins.

Note: over 10 slots are reserved for 15 min talks that will be selected based on submitted abstracts.

An Independent Meeting of the Biochemical Society

Nucleic Acids Research
NAR awards for the best student presentations and posters

Background image: 110bp minicircle and counter ions (NAR, 39, 3928-38, 2011). Courtesy of Jonathan S Mitchell and Sarah A Harris.

Timetable

Monday 3rd September 2012
08:30 to 09:00	Registration	No Room Required
09:00 to 09:10	Welcome from John Toland	Room 1
09:10 to 09:50	Tamar Schlick New York University Chromatin Compaction: A Modeling Exploration of Fiber Hetergeoneity and Linker Histone Influence	Room 1
09:50 to 10:10	Morning Coffee	No Room Required
10:10 to 10:50	Makkuni Jayaram Japan Atomic Energy Agency & University of Texas at Austin The topological equivalence of the yeast chromosome centromere and the yeast plasmid partitioning locus	Room 1
10:50 to 11:30	Erez Lieberman Aiden Harvard University How the genome folds	Room 1
11:30 to 12:10	Leonid Mirny Massachusetts Institute of Technology The role of topological constraints on condensed polymers and DNA in human cells	Room 1
12:30 to 13:30	Lunch at Wolfson Court	Room 1
13:30 to 14:10	Mario Nicodemi Università degli Studi di Napoli Federico II Large scale organization of chromatin	Room 1
14:10 to 14:50	Stephen D Levene University of Texas at Dallas All Good Things Must Bend: the Energetics of DNA Shape and Flexibility in Biological Assemblies	Room 1
14:50 to 15:20	Afternoon Tea and Poster Session	No Room Required
15:20 to 15:40	Luca Giorgetti Institut Curie Structure meets function at the mouse X chromosome inactivation center	Room 1
15:40 to 16:00	Francesca Maggioni Università degli studi di Bergamo Modeling chromatin fibre folding for human embryonic stem cells and cancer cells	Room 1
16:00 to 16:20	Angelo Rosa SISSA Three-dimensional conformations of entangled ring polymers in solution	Room 1
16:20 to 17:00	Nancy Kleckner Harvard University How E.coli organizes and segregates its chromosome	Room 1
17:00 to 18:00	Drinks Reception and Poster Session	No Room Required
18:00 to 18:30	Dinner at Wolfson Court	No Room Required

Tuesday 4th September 2012
08:30 to 09:10	Sophie Jackson University of Cambridge A tangled problem: the structure,function and folding of knotted proteins	Room 1
09:10 to 09:50	Christian Micheletti SISSA Knotted and unknotted proteins: a comparative study (*)	Room 1
09:50 to 10:10	Morning Coffee	No Room Required
10:10 to 10:50	Marek Cieplak Polish Academy of Sciences Topological features in stretching of proteins	Room 1
10:50 to 11:30	Joanna Sulkowska University of California, San Diego Conservation of complex knotting and slipknotting patterns in proteins	Room 1
11:30 to 11:50	Alexander Kister Rutgers, The State University of New Jersey Amino acid patterns for protein folding	Room 1
11:50 to 12:10	Piotr Szymczak Uniwersytet Warszawski How to untie it-translocation of a knotted protein through a pore	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
13:30 to 14:10	Peter Virnau Johannes Gutenberg-Universität Mainz Computer simulations of knotted DNA and proteins	Room 1
14:10 to 14:50	Kai Ishihara Yamaguchi University Knots confined to tubes in the simple cubic lattice	Room 1
14:50 to 15:20	Afternoon Tea and Poster Session	No Room Required
15:20 to 15:40	Peter Cifra Slovak Academy of Sciences Simulations of cyclic and linear DNA chains moderately and strongly confined in nanochannels	Room 1
15:40 to 16:00	Tetsuo Deguchi Ochanomizu University Diffusion dynamics of circular DNA mini-rings in solution	Room 1
16:00 to 16:20	Influence of topology in coarse-graining of polymer solutions	Room 1
16:20 to 17:00	Kenneth Millett University of California, Santa Barbara Locating knots and slipknots in open and closed macromolecules	Room 1
17:00 to 17:40	Eric Rawdon University of St. Thomas, Minnesota Knotting of open chains, closed chains and proteins	Room 1
18:00 to 18:30	Dinner at Wolfson Court	No Room Required

Wednesday 5th September 2012
08:30 to 09:10	Craig Benham University of California, Davis Superhelically Driven Structural Transitions in Genomic DNA - Theoretical Analyses, Genomic Distributions and Roles in Regulation	Room 1
09:10 to 09:50	Charles Dorman Trinity College Dublin Co-operative roles for DNA supercoiling and nucleoid-associated proteins in the regulation of bacterial transcription	Room 1
09:50 to 10:10	Morning Coffee	No Room Required
10:10 to 10:50	Andrew Travers University of Cambridge Chromosomes as topological machines-the role of DNA thermodynamics	Room 1
10:50 to 11:30	Lynn Zechiedrich Baylor College of Medicine How DNA topology and DNA length affect the body's defense against nucleic acids of invading organisms in the blood	Room 1
11:30 to 11:50	Greg Chirikjian Johns Hopkins University Twisted paths in Euclidean groups: Keeping track of total orientation while traversing DNA	Room 1
11:50 to 12:10	Ruggero Cortini Imperial College London Chiral effects in DNA supercoiling	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
13:30 to 14:10	Lucy Lifschitz University of Virginia Sequence-Dependent Coarse-Grain Descriptions of DNA: models, methods and simulations	Room 1
14:10 to 14:50	Krystyna Zakrzewska Université Paris 7 - Denis-Diderot DNA recognition studied by molecular simulations	Room 1
14:50 to 15:20	Afternoon Tea and Poster Session	No Room Required
15:20 to 15:40	Jonathan Baxter University of Sussex The yeast Pif1 family helicase RRM3 promotes DNA unwinding during replisome swivelling	Room 1
15:40 to 16:00	Andreas Hanke University of Texas at Brownsville Denaturation transition of stretched DNA in the presence of DNA-binding ligands	Room 1
16:00 to 16:20	Jakob Bohr Technical University of Denmark Twist neutrality and topological aspects of nucleosomal DNA	Room 1
16:20 to 17:00	David Swigon University of Pittsburgh Dynamics of DNA supercoiling and knotting	Room 1
17:00 to 17:40	Wilma Olson Rutgers, The State University of New Jersey Simulated looping propensities of protein-decorated DNA	Room 1
17:40 to 19:00	Poster Session	Discussion Room
19:30 to 22:00	Conference Dinner at Christ's College	No Room Required

Thursday 6th September 2012
09:10 to 09:50	Tony Maxwell John Innes Centre, Norwich DNA topology and the mechanism of type II DNA topoisomerases	Room 1
09:50 to 10:10	Morning Coffee	No Room Required
10:10 to 10:50	Alfonso Mondragón Northwestern University Mechanistic studies of type IA topoisomerases	Room 1
10:50 to 11:30	Chris Soteros University of Saskatchewan Knot statistics and knot reduction for a lattice polygon model of local strand passage	Room 1
11:30 to 11:50	Topo IV is the topoisomerase that knots and unknots sister duplexes during DNA replication	Room 1
11:50 to 12:10	Piotr Sulkowski Universiteit van Amsterdam Topological recursion and classification of multi-stranded biopolymer configurations	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
13:30 to 14:10	Giovanni Dietler Centre de Physique Théorique de l’Ecole Polytechnique (CPHT) DNA in confined geometries: topology effects	Room 1
14:10 to 14:50	Chris Brackley University of Edinburgh A generic non-specific mechanism for the clustering of DNA and chromosome binding proteins	Room 1
14:50 to 17:40	Free Afternoon	No Room Required
18:00 to 18:30	Dinner at Wolfson Court	No Room Required

Friday 7th September 2012
08:30 to 09:10	Sean Colloms University of Glasgow Topology of Xer site-specific recombination	Room 1
09:10 to 09:50	Ian Grainge University of Newcastle, Australia Simplification of topology during Xer-mediated recombination	Room 1
09:50 to 10:10	Morning Coffee	No Room Required
10:10 to 10:50	Isabel Darcy University of Iowa Tangle analysis of protein-DNA complexes	Room 1
10:50 to 11:30	Mariel Vazquez San Francisco State University DNA unknotting and unlinking	Room 1
11:30 to 11:50	Rob Scharein Hypnagogic Software TopoICE and other software tools for investigating topological problems in DNA	Room 1
11:50 to 12:10	Summary/Closing Remarks	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
18:00 to 18:30	Dinner at Wolfson Court	No Room Required

Topological aspects of DNA function and protein folding

Speakers

Jonathan Baxter University of Sussex
Craig Benham University of California, Davis
Jakob Bohr Technical University of Denmark
Chris Brackley University of Edinburgh
Greg Chirikjian Johns Hopkins University
Marek Cieplak Polish Academy of Sciences
Peter Cifra Slovak Academy of Sciences
Sean Colloms University of Glasgow
Ruggero Cortini Imperial College London
Isabel Darcy University of Iowa
Tetsuo Deguchi Ochanomizu University
Giovanni Dietler Centre de Physique Théorique de l’Ecole Polytechnique (CPHT)
Charles Dorman Trinity College Dublin
Luca Giorgetti Institut Curie
Ian Grainge University of Newcastle, Australia
Andreas Hanke University of Texas at Brownsville
Kai Ishihara Yamaguchi University
Sophie Jackson University of Cambridge
Makkuni Jayaram Japan Atomic Energy Agency & University of Texas at Austin
Alexander Kister Rutgers, The State University of New Jersey
Nancy Kleckner Harvard University
Stephen D Levene University of Texas at Dallas
Erez Lieberman Aiden Harvard University
Lucy Lifschitz University of Virginia
Francesca Maggioni
Tony Maxwell John Innes Centre, Norwich
Christian Micheletti SISSA
Kenneth Millett University of California, Santa Barbara
Leonid Mirny Massachusetts Institute of Technology
Alfonso Mondragón Northwestern University
Mario Nicodemi Università degli Studi di Napoli Federico II
Wilma Olson Rutgers, The State University of New Jersey
Eric Rawdon University of St. Thomas, Minnesota
Angelo Rosa SISSA
Rob Scharein Hypnagogic Software
Tamar Schlick New York University
Chris Soteros University of Saskatchewan
Joanna Sulkowska University of California, San Diego
Piotr Sulkowski Universiteit van Amsterdam
David Swigon University of Pittsburgh
Piotr Szymczak Uniwersytet Warszawski
Andrew Travers University of Cambridge
Mariel Vazquez San Francisco State University
Peter Virnau Johannes Gutenberg-Universität Mainz
Krystyna Zakrzewska Université Paris 7 - Denis-Diderot
Lynn Zechiedrich Baylor College of Medicine

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Topological aspects of DNA function and protein folding

Workshop theme

Timetable

Speakers

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