PROJECT ABSTRACT

This project in its present form is an investigation of the accuracy of the ff14SB force field and its 
ability to produce adequate secondary structure calculations using the Snow Flea Antifreeze Protein 
(sfAFP). The snow flea antifreeze protein is unique in that the protein lacks a hydrophobic core and side 
chain burial . These properties are found in stable proteins, making the fact that the sfAFP can remain 
stable and fold cooperatively an anomaly. To find the origins of the protein’s stability, a computational 
approach needs to be used. This research sought to ensure that the newly developed ff14SB, which is the 
basis of protein MD simulations, was accurate enough to describe the sfAFP. The protein was simulated 
using the AMBER simulation package, under parameters intended to limit secondary structure 
development. The 800 frame trajectory was analyzed using the DSSP algorithm to determine if elements 
of secondary structure were created. The analysis found that the simulation only created transient 
secondary structure, and no significant permanent conformational changes. Thus, the ff14SB force field 
was confirmed to be a new and adequate model that can be applied to a variety of issues such as 
determining the origins of the stability of the sfAFP.