CBE Seminar: Gaurav Chauhan
Title: "Effects of crowding and confinement on the spatial organization of biopolymers and dynamics of gene expression."
Abstract
The intracellular environment is crowded with macromolecules that can occupy a significant fraction of the cellular volume. This can give rise to attractive depletion interactions that impact the conformations and interactions of biopolymers, as well as their interactions with confining surfaces. We used computer simulations to study the effects of crowding on biologically inspired models of polymers. We showed that crowding can lead to attractive interactions between two flexible ring polymers, and we further characterized the adsorption of both flexible and semiflexible polymers onto confining surfaces. These results indicate that crowding-induced depletion interactions could play a role in the spatial organization of biopolymers in cells, and they also suggest that macromolecular crowding could be used to alter the spatial organization of cell-free synthetic systems. A major limitation of cell-free expression systems, which are widely used to study gene expression, is the lack of means to achieve spatial control of gene expression components. With a coarse-grained model of DNA plasmids and crowders, we showed that plasmids were uniformly distributed at low levels of crowding but, due to depletion interactions, became strongly adsorbed to confining surfaces at high levels of crowding. These results were experimentally validated by our collaborators using DNA and crowders in cell-sized vesicles. We used kinetic Monte Carlo simulations to study the effect of crowding and confinement on gene expression dynamics and noise, giving insight into experiments. Our work provides insights into the role of crowding and confinement on the spatial organization and dynamics of gene expression in cellular and cell-free systems.
Bio
Gaurav Chauhan is a fifth-year PhD student in the research group of Steve Abel in the Department of Chemical and Biomolecular Engineering at UT. Gaurav received his bachelor’s degree in chemical engineering from the Indian Institute of Technology, Dhanbad, India. In his PhD work, Gaurav is using computer simulations to study the effect of macromolecular crowding on gene expression.
Dial-In Information
Zoom Meeting ID: 98699166529
Tuesday, April 13, 2021 at 4:00pm to 5:00pm
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