Significance of Knotted Structures for Function of Proteins and Nucleic Acids
Poster Session I
16 – POS
Board 16
Atomic Force Microscopy Study of DNA knots in Confined Geometry
Aleksandre Japaridze
1
, Kathleen Smith
1
, Francesco Valle
2
, Giovanni Dietler
1
.
1
EPFL, Lausanne, Switzerland,
2
Institute of nanostructured materials-CNR, Bologna, Italy.
DNA is a very important object of study for geneticists and biologists as well as for physicist. It
is important to understand the role of topology of DNA in confined geometry, to better
understand such processes as DNA migration in nanofluidics devices or DNA compaction in
Viral capsids.
By combining Microfluidics device with Atomic Force Microscopy technique we were able to
directly visualize and measure the effects of confining space on the statistical parameters of
DNA with various topology (Linear, Circular relaxed & Knotted DNA)
Our method enabled us to separate DNA based on its size and topology, as well as based on the
Knot complexity of DNA, with microfluidics device acting as a topological sieve.
17 – POS
Board 17
Direct Coupling Analysis in Study of Knotted Proteins
Aleksandra I. Jarmolińska
1
, Agata P. Perlińska
1
, Faruck Morcos
2
, Joanna I. Sulkowska
1,3
.
1
Centre of New Technologies, University of Warsaw, Poland,
2
Rice University, Houston, USA.
3
Faculty of Chemistry, University of Warsaw, Poland
One of the most defining characteristics of proteins, one that enables them to perform their
functions, is their structure. That holds especially true for the knotted proteins [1], since that
structure requires a considerable "effort" on part of the protein. Both the evolutionary origin and
the folding process of such molecule are still an unknown. One of the methods that holds the
most promise for extracting such information is the Direct Coupling Analysis [2]. By indicating
residue positions with high correlations it shows their conservation throughout the evolutionary
history and suggests probable contact maps for both final structure and folding process of a
protein.
Using direct information coefficient obtained from mean field DCA combined with structural
information from Protein Data Bank we compare evolutionary conservation of the knotted and
unknotted parts of the methyltransferases from the SPOUT clan with respect to the contacts
present in the folded molecule, with most results suggesting better (or at least similar)
correlations within the knot, which is nonetheless not reflected in the final protein structure.
[1] Sulkowska J.I., Rawdon E.J., Millett K.C., Onuchic J.N., Stasiak A. (2012)
Conservation of
complex knotting and slipknotting patterns in proteins
. PNAS (USA). 109, E1715–E1723.
[2] Sulkowska J.I., Marcos F., Hwa T., Onuchic J.N., (2012)
Genomics Aided Structure
Prediction (GASP)
, PNAS (USA), 109(26):10340-5.
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