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 II

38 – POS Board 10 Binding of Fullerene to Amyloid Beta Fibrils: Size Matters Dinh Quoc Huy Pham 1,2 , Mai Suan Li 2 . 1 Institute for Computational Sciences and Technology, Ho Chi Minh City, Viet Nam, 2 Institute of Physics, Polish Academy of Science, Warsaw, Poland. Carbon based nanomaterials, such as fullerene, nanotube and graphene have been found to recently interact with and influence assemblies of proteins and peptides. Their applicability and usage in biology and medicine is increasingly being considered. In this report the binding affinity of fullerenes C20, C36, C60, C70 and C84 to Aβ40 and Aβ42 fibrils is studied by docking and all-atom molecular dynamics simulations with the Amber 99SB force field and water model TIP3P. Using the molecular mechanic-Poisson Boltzmann surface area method one can show that the binding free energy linearly decreases with the number of carbon atoms of fullerene, i.e. the larger is the fullerene size, the higher is binding affinity. Overall, fullerenes bind to Aβ9-40 fibrils stronger than to Aβ17-42. The number of water molecules trapped in the interior of Aβ9- 40 fibrils was found to be lower than inside pentamer 5Aβ17-42. C60 destroys 5Aβ17-42 structure to a greater extent compared to other fullerenes. Our study revealed that the van der Waals interaction dominates over the electrostatic interaction and non-polar residues of amyloid beta peptides play the significant role in interaction with fullerenes providing novel insight into the development of drug candidates against Alzheimer's disease. Board 11 Study of DNA Knots with Solid-State Nanopores Calin Plesa 1 , Daniel V. Verschueren 1 , Menno J. Witteveen 1 , Justus W. Ruitenberg 1 , Magnus P. Jonsson 1 , Alexander Y. Grosberg 2 , Yitzhak Rabin 3 , Cees Dekker 1 . 1 Delft University of Technology, Delft, Netherlands, 2 New York University, New York, NY, USA, 3 Bar Ilan University, Ramat Gan, Israel. Knots play an important role in biology, particularly in the context of DNA molecules. Experimental techniques to observe DNA knots rely primarily on gel electrophoresis and are limited to circular molecules below 10 kbp in length. Here we show that solid-state nanopores can be used to directly observe DNA knots in both linear and circular single molecules with lengths above 10 kbp under high ionic strength conditions, something which has not been possible before. We use this technique to study the percentage of knots for different length molecules up to 165.5 kbp in length and compare these values to theoretical predictions for long polymers. We vary buffers and voltages to find how the measurement’s resolution limit influences the amount of knots observed. We demonstrate that the solid-state nanopore technique can provide information about the position, the size, and the number of DNA strands inside the knot. 39 – POS

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