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Workshop / Seminar

CHE 598 Seminar

Spark Room 335 and Floyd 224 on the Tri-Cities campus
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a head shot of Dr. Katelyn Dahlke

About the event

Dr. Katelyn Dahlke is a postdoctoral research associate in the Gene and Linda Voiland School of Chemical Engineering and Bioengineering. Dr. Dahlke received her B.S. from Iowa State University in chemical engineering in 2013 and her M.S. and Ph.D in chemical engineering from the University of Illinois at Urbana-Champaign in 2019. Her Ph.D. research focused on the computational and theoretical modeling of biophysical interactions between prokaryotic architectural proteins known as nucleoid associated proteins (NAPs) and DNA. She developed hybrid Brownian dynamics-Monte Carlo coarse-grained computational models, built up from local interactions, to study the long-scale behavior of the NAP-DNA systems. In particular, she investigated how ambient concentration, force, and topology impacted the mesoscale behavior of a model NAP-DNA system using these computational tools. She also developed theoretical models in support of these observations. Dr. Dahlke currently works in the area of educational research, studying the dissemination and effectiveness of implementing hands-on modules in student understanding of core chemical engineering principles.

Interactions Between Nucleoid Associated Proteins and DNA in the Presence of Mechanical and Chemical Forces 

The way that DNA is organized within a cell controls its physiological behavior. DNA must be condensed in order to fit into the much smaller cell but must also be accessible to proteins responsible for biological processes. Architectural proteins assist with this large-scale arrangement of DNA to achieve the correct balance between these two competing requirements. The structural proteins that interact with DNA in prokaryotes are known as nucleoid associated proteins (NAPs). These proteins play a vital role in shaping and manipulating the DNA and assist in many cell processes, including gene expression, replication, and transcription. In this seminar, I will discuss a coarse-grained model of a typical NAP-DNA system that bridges the gap  between local interactions and long-scale DNA behavior that is inaccessible to typical experimental and computational techniques. The model is built up from local interactions, such as multivalent binding that allows for unintuitive dissociation kinetics, as well as physical deformations of DNA induced by protein binding. This methodical coarse-graining allows us to   investigate the effect that these short-range interactions have on the mesoscale behavior of the system. Specifically, I will discuss the cooperative and competing behavior of NAP-DNA interactions that result in concentration-, force-, and topology-dependent changes to both protein kinetics and physical DNA behavior. This model produces data that qualitatively matches existing experimental observations and provides a physical explanation for the observed behavior based on cooperative local interactions.