Biophysical Society Thematic Meeting| Les Houches 2019

Multiscale Modeling of Chromatin: Bridging Experiment with Theory

Wednesday Speaker Abstracts

TRANSFER-MATRIX CALCULATION OF THE EFFECTS OF PHYSICAL CONSTRAINTS APPLIED TO DNA ON DNA-PROTEIN INTERACTIONS Jie Yan 1,2 ; 1 National University of Singapore, Mechanobiology Institute, Singapore, South-West, Singapore 2 National University of Singapore, Department of Physics, Singapore, South-West, Singapore Organization of the chromosomal DNA and numerous biological processes taking place on chromosomes depends on the DNA interaction with a plethora of DNA-binding proteins. These interactions are subject to a variety of physical constraints, such as volume exclusion, finite binding size, force and torque, applied to the DNA. Recent development of single-molecule manipulation technologies has made it possible to quantify the interactions between DNA and proteins under these physical constraints, however, the exact effect of these constraints on the DNA-protein interactions is not completely understood. To fill this gap, we have developed a systematic theoretical framework based on the transfer-matrix calculation method that can be used to accurately describe the effects of these physical constraints on the behaviour of DNA- binding proteins. Potential applications of the developed theoretical approach are demonstrated by predicting how such constraints affect the DNA-binding properties of different types of architectural proteins, which have been found in living cells. Obtained results also provide important insights into potential physiological functions of physical constraints in the chromosomal DNA organization and transcription regulation by architectural proteins as well as into single-DNA manipulation studies of DNA-protein interactions.

FOLDING GENES AT NUCLEOSOME RESOLUTION Tamar Schlick New York University, USA No Abstract

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