Protein/Lipid Interactions

Title: Exploring the Atomistic Volumetric Structures of Protein/Lipid/Water Complexes using Regular and Weighted Voronoi Tessellations.

Students: Garner Cochran, Santona Tuli, Austin Workman, Hai Viet Duong (Fall 2012) Valeri Alexiev, Jeanna Goodrich and Vanessa Moreno (Spring 2013), Sara Cheng and Campbell Compton (Summer 2013), Molly Zumbro and Kendrick James (Fall 2013)

Advisors: Dr. Kwan Kelvin Cheng and Dr. Hoa Nguyen

Abstract:

The distribution statistics of the surface area, volume and voids of biological molecules are important parameters to characterize the structural dynamics of self‐assembling protein­‐containing lipid membranes in the field of atomistic molecular dynamics simulations. Traditional surface area calculation methods are mostly based on assumptions of the thickness of the membrane and the volumes of certain molecules. However, those methods usually lead to different surface area estimations and fail to estimate the voids. In the presence of protein, those methods are not applicable due to the presence of the conformal annular lipids surrounding the protein.
We have developed a Voronoi tessellation method (with/without weights) to calculate the distributions and kinetics of volume of different functional groups of lipid and protein molecules in various simulated protein‐containing lipid bilayers. The structural parameters of the annular lipids in close proximity to the embedded protein have also been determined. The results of this study will provide a solid mathematical approach to study the perturbation effects of protein on cell membranes that are important for understanding protein/lipid interactions in biological systems.

Student Final Presentations: Fall 2012 , Spring 2013, Summer 2013, Fall 2013
Student Final Reports: Fall 2012, Spring 2013 (Numerical Analysis - Final Report - Balreira and Moreno.pdf, valexiev_project_report.pdf), Fall 2013