Depth of S-palmitoylated Cysteines on the Transmembrane Protein Governs Palmitoylation-induced Changes in Protein-lipid Interface

Date of Award

Winter 12-22-2021

Degree Type

Thesis

Degree Name

Master of Science (MS)

Department

Biomedical and Chemical Engineering

Advisor(s)

Nangia, Shikha

Keywords

Coarse-grained simulations, Lipid Membranes, Palmitoyl chains' behaviors, Palmitoyl chains' depth, S-palmitoylation, Tansmembrane proteins

Subject Categories

Biomedical Engineering and Bioengineering | Chemical Engineering | Chemistry | Computational Chemistry | Engineering | Physical Sciences and Mathematics

Abstract

S-Palmitoylation is a post-translational modification that attaches palmitic acid to proteins at cysteine residues via a thioester bond. Though palmitoylations are believed to be associated with regulatory functions of transmembrane proteins in bilayer lipids, molecular-level understanding of their behavior in different membrane and their impact on both lipids and proteins remain elusive. In this project, we investigate the behavior of various sites of palmitoyl chains on four different proteins: peripheral myelin protein 22 (PMP22), rhodopsin (RH), linker for activation of T-cells (LAT), and claudin-14 (CLD14), in three different membrane systems: an asymmetric one, a phase-separated one and a pure POPC one, via coarse-grained simulation. With the simulation results, we built simplified but visualized 3D models. The results elucidate the great importance of palmitoyl chains' depths on their various behavior and opposite preference to saturated, unsaturated lipids and cholesterols. In contrast, the lipid environment does not significantly influence proteins' and palmitoyl chains' behavior. Overall, we believe the project provides an understanding of palmitoyl chains' behavior and their key influencing factor in the lipid bilayer systems. It also offers a potential guide of how palmitoylation works on the proteins and surrounding lipids which could help to further understand the palmitoylation modification of proteins.

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