The Effect of Amino Acid Sequence Patterning on Protein Phase Transitions

Abstract

Protein phase transitions provide a mechanism for cells to compartmentalize and spatiotemporally regulate biochemical reactions. At the same time, irreversible protein phase transitions have been implicated in various disorders like amyotrophic lateral sclerosis (ALS), Huntington’s disease and some forms cancer. Amino acid sequences have been shown to play a significant role in modulating protein phase transition dynamics. Here, we use computational and experimental approaches to investigate the role of amino acid sequence in two different modes of protein phase transition: liquid-liquid phase separation of intrinsically disordered proteins (IDP) and the irreversible aggregation of the Huntingtin protein. For IDPs, we characterize how the sequence charge patterning and polymer length impacts the surface tension in binary phase. We use molecular dynamics (MD) simulations, polymer physics theory and neural networks to create a framework that predicts the surface tension using only the sequence. For the Huntingtin protein, we study the role of the 10 amino acids-long polyproline stretch at the C-terminus in modulating the protein aggregation propensity. We create sequence modifications at the C-terminus to change the identity of this amino acid block, making it either strongly negatively charged or much more flexible than proline, and we quantify the changes in the aggregation propensity. Taken together, this work is part of a larger effort to understand how the amino acid sequences impact protein phase transition in cellular compartmentalization and disease states.