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

Saturday Abstracts

Conformational Free-Energy Calculations for Complex Biopolymer Structures Stephen Levene . University of Texas at Dallas, Richardson, TX, USA. Quantitative knowledge of free-energy changes are central to understanding protein and RNA folding, motion and energy transduction in molecular machines, macromolecule-ligand interactions, genome organization, and many other biological phenomena. We focus here on problems related to DNA tertiary structure and topology, especially loop-mediated interactions involving protein molecules bound to sites separated by large linear distances along DNA. Computing the free-energy cost of forming DNA or chromatin loops entails a delicate and length-scale-dependent balance of enthalpic and entropic contributions and is a challenging problem in statistical mechanics. Moreover, the effects of chromatin organization on such interactions are poorly understood. However, new insights can come from novel experimental approaches and computational models of DNA flexibility and folding under geometric and/or topological constraints. Experimental studies of DNA looping in systems such as Cre-loxP recombination and lac-repressor-mediated gene regulation will be discussed in conjunction with a new method for computing the free energies of looped nucleoprotein assemblies.

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