Significance of Knotted Structures for Function of Proteins and Nucleic Acids - September 17-21, 2014

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. 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. 17 – POS Board 17 Direct Coupling Analysis in Study of Knotted Proteins

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