Date of Award


Degree Type


Degree Name

Master of Science (MS)


Biomedical and Chemical Engineering


Shikha Nangia


Anti-freeze proteins are a class of proteins present in various organisms to allow their cells to survive in sub-freezing temperatures. These proteins act by binding to the surface of ice crystals in the cell’s cytoplasm. Each protein has a characteristic flat face that is considered its ice binding site. Despite a common function and ice binding mechanism, the sequence and 3-D folded structure between each anti-freeze protein is vastly different and results in a knowledge gap as to the common feature in these sequences that allow them to exhibit this same function. Here I present the use of a novel computational method, named PARCH, that uses MD all-atom simulations to provide the characterization of amino acid residues based on their interactions at the protein surface. Understanding the hydropathic behavior of anti-freeze protein surfaces can provide greater insight into their functions and ice-binding mechanisms for future applications. Some of these applications could be in fields such as cryogenics, food technology, and genetic engineering. In this work I modelled 10 different anti-freeze proteins that are present in different organisms, such as, fish, insects, bacteria, yeast, and fungi.


Open Access

Available for download on Friday, June 13, 2025