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

Friday Abstracts

Chromatin Looping and Interdigitation Mechanisms: Insights from Mesoscale Simulations Antoni Luque, Tamar Schlick . NYU, New York, USA. In all eukaryotic organisms, the chromatin fibers, composed of DNA complexed with core histones and linker histone proteins, store a vast amount of information. The chromatin building blocks, namely nucleosomes -- nanometric beads made of DNA and eight core histones -- connect to one another by DNA linkers and form hierarchical structures whose folds are essential for the nderstanding of basic regulatory processes in the cell. However, the precise organization of chromatin remains elusive. In particular, it is not clear whether chromatin organizes in independent or inter-digitated fibers. To address this question, we have developed and applied a mesoscale computational model in collaboration with experiments to probe structural, energetic, and dynamical questions associated with chromatin as a function of various internal and external factors. We will describe several mechanisms that affect fiber architecture, including the size of the linker DNAs and the presence of linker histones. Depending on the conditions, these molecular mechanisms favor the formation of segregated fibers, inter-digitated fibers, and chromatin loops. The modeling thus helps interpret the variation in chromatin fibers for different cell types and represents a reference framework to investigate local and global mechanisms that regulate chromatin structure in the nucleus. Protein-induced Entanglement on DNA: Connecting and Organizing Chromosomes via Multiple Loops. Nicolas Clauvelin 1 , Wilma K. Olson 1,2 . 1 Rutgers University, Piscataway, NJ, USA, 2 Rutgers University, Piscataway, NJ, USA. The control of gene expression sometimes entails the folding of DNA into looped structures mediated by the binding of protein. Although the literature abounds with examples of single DNA loops induced by the attachment of sequentially distant genetic elements on a common protein core, recent studies have demonstrated the occurrence of multiple loops formed by three or more remote, protein-anchored sites. The direct physical connections between these DNA sites stem from the capability of protein, such as the Escherichia coli Gal repressor, to form oligomeric structures. Structure-based genetic analyses have shown that dimeric units of the Gal repressor stack one above the other in a V-shaped tetrameric assembly. Repeated dimeric associations of the same type lead to higher-order helical protein pathways that can secure multiple chromosomal connections. We are examining the entanglement of DNA loops that attach to such proteins with the help of a novel energy minimization method. Our method makes it possible to optimize DNA pathways at the base-pair level under various constraints, such as imposed end-to-end displacement and rotation. We focus on the multiple loops that can be induced by oligomeric Gal assemblies and compute the relevant energy landscapes and topological properties as functions of the number of Gal repressors and the chain lengths of the different loops. The binding of the less stacked Lac repressor to a DNA minicircle, which segregates the double helix in two loops, is also investigated. In addition, we take advantage of the fact that our optimization method accounts for the presence along DNA of bound ligands to study how the binding of architectural proteins ( e.g. , the Escherichia coli histone-like HU protein) can ease or suppress the formation of such loops.

- 33 -