2025 Summer Undergraduate Research Program (SURP) symposium
Location
Dr. Ken Budke Family Auditorium, Schindler Education Center, University of Nothern Iowa
Presentation Type
Poster Presentation (UNI Access Only)
Document Type
poster
Abstract
- Understanding how proteins oligomerize and their binding affinities is key to studying macromolecular interactions. In particular, RAD51 is a nucleoprotein critical to DNA repair through homologous recombination. Its ability to form dynamic oligomers on single-stranded DNA directly impacts its biological function. In this project, mass photometry is used as the experimental tool to measure the mass distributions of RAD51- DNA complexes. This allows us to resolve the relative populations of polymer sizes. In order to interpret this data, a combination of stochastic simulation and data fitting methods were used:
- Stochastic Simulation of RAD51 Binding: A Dynamical Monte Carlo simulation was developed to model how RAD51 proteins bind to and unbind from a DNA. Monomers assemble into dimers, trimers, and tetramers, and the model tracks polymer formation, dissociation, and the spatial distribution of unbound gaps.
- Gaussian Mixture Model Fitting (EM): Experimental distributions of RAD51- DNA complexes were analyzed using the Expectation-Maximization (EM) algorithm to estimate the means, variances, and proportions of Gaussian components corresponding to different polymer sizes.
- Nonlinear Least Squares (NLS) Fitting: NLS was used to fit analytical models (e.g., sums of Gaussians, sigmoidal curves) to both experimental and simulated data. This approach extracts interpretable parameters and enables comparison between simulation results and experimental trends to validate model accuracy.
Start Date
1-8-2025 11:00 AM
End Date
1-8-2025 1:30 PM
Event Host
Summer Undergraduate Research Program, University of Northern Iowa
Faculty Advisor
Ali Tabei
Department
Department of Physics
Copyright
©2025 Addison Cunningham, Clare Wright, Sander Tompkins, and Ali Tabei
File Format
application/pdf
Recommended Citation
Cunningham, Addison; Wright, Clare; Tompkins, Sander; and Tabei, Ali, "Stochastic Modeling of Nucleoprotein Oligomerization and Parameter Estimation from Mass Photometry Data" (2025). Summer Undergraduate Research Program (SURP) Symposium. 33.
https://scholarworks.uni.edu/surp/2025/all/33
Stochastic Modeling of Nucleoprotein Oligomerization and Parameter Estimation from Mass Photometry Data
Dr. Ken Budke Family Auditorium, Schindler Education Center, University of Nothern Iowa
- Understanding how proteins oligomerize and their binding affinities is key to studying macromolecular interactions. In particular, RAD51 is a nucleoprotein critical to DNA repair through homologous recombination. Its ability to form dynamic oligomers on single-stranded DNA directly impacts its biological function. In this project, mass photometry is used as the experimental tool to measure the mass distributions of RAD51- DNA complexes. This allows us to resolve the relative populations of polymer sizes. In order to interpret this data, a combination of stochastic simulation and data fitting methods were used:
- Stochastic Simulation of RAD51 Binding: A Dynamical Monte Carlo simulation was developed to model how RAD51 proteins bind to and unbind from a DNA. Monomers assemble into dimers, trimers, and tetramers, and the model tracks polymer formation, dissociation, and the spatial distribution of unbound gaps.
- Gaussian Mixture Model Fitting (EM): Experimental distributions of RAD51- DNA complexes were analyzed using the Expectation-Maximization (EM) algorithm to estimate the means, variances, and proportions of Gaussian components corresponding to different polymer sizes.
- Nonlinear Least Squares (NLS) Fitting: NLS was used to fit analytical models (e.g., sums of Gaussians, sigmoidal curves) to both experimental and simulated data. This approach extracts interpretable parameters and enables comparison between simulation results and experimental trends to validate model accuracy.
