Using Flory effect to improve protein unfolding pathway visualization

Abstract

The problem of protein folding is listed as an important issue in 21st century biophysics. It is a fundamental problem in the central dogma of molecular biology. Predicting the tertiary structure of protein molecules from primary sequences and further predicting their functions are challenging tasks. Knowledge of protein folding pathways can give us insight into how proteins function, how they cause diseases, and even how they can be improved. In the Bystroff lab, a program GeoFold is developed for predicting protein unfolding pathways, the reverse of folding pathways and kinetics. In this thesis, we develop an algorithm to find effecitve Loop Length in GeoFold. To begin with, we show why Flory effect is an entropic component when energy of GeoFold hierarchical partitions are measured. Then we will perform an algorithm of Shortest Path based on Dijkstra for calculating effective loop length in Fortran. To demonstrate the result of Flory effect in GeoFold, it will be used in the analysis of a test case including a mini protein of Trp-Cage.