Project Abstract

Proteins are one of four macromolecules essential to life. They catalyze reactions, transport molecules, and defend the body. Protein-folding determines the shape and function of these essential macromolecules. Errors in protein folding have been linked to degenerative diseases such as Alzheimer’s and Parkinson’s. If the errors can be understood and reversed, these debilitating diseases may be solved. However, scientists have struggled to properly model proteins. While it is understood, through computational analysis, that proteins are in constant dynamic motion, the precise means by which proteins fold are unknown. Specifically, questions surround conserved and nonconserved positions in proteins, or positions that were thought to be essential and nonessential to protein function, respectively. Professor Swint-Kruse, however, determined that nonconserved positions still affect the overall function of the protein, even without affecting the structure. To better understand why nonconserved positions affect the function of a protein, this study employed a computational analysis, REMD, of two Lac1 protein samples to identify the dynamics of nonconserved positions within proteins. The first sample was unaltered, while the second sample had a drastically changed nonconserved region to see how changes in position alter protein dynamics. Specifically, DFI (dynamic flexibility index) was used to reveal how protein structure affects function. Comparing the differences in dynamics between the two Lac1 samples will provide insight into the underlying protein-folding mechanisms that have confused scientists for decades. The ultimate goal of this information is to facilitate the curing of the aforementioned degenerative diseases.

From Gene to Protein: Unlocking the Relationship between Mutations and Protein Folding in the LacI Repressor