Chemistry and Chemical Biology ETDs

Publication Date

Spring 5-12-2024

Abstract

All-atom molecular dynamics (MD) simulations are essential for examining the structural and dynamic aspects of proteins at high resolution, complementing experiments limited by resolution, size, and complexity. Advancements in algorithms and hardware have enhanced the role of computational tools in scientific research, allowing for more accurate simulations of proteins with standard residues. However, simulating real biological systems, which include non-standard residues such as lipid membranes, remains challenging despite the assistance of tools like CHARMM-GUI. My research initially focused on simulating the PICK1 BAR dimer using steered MD simulations to investigate its structure and dynamics. Simulation works expanded to include systems involving protein complexes with other molecules, demonstrating that MD simulations effectively describe both standard and nonstandard residues. Further studies on inorganic-organic aerosols showed that computational methods provide valuable insights into atomic details inaccessible to experiments, underscoring their potential to advance our understanding of biological complex systems.

Language

English

Keywords

Molecular dynamics simulation, standard residue, nonstandard residue, protein, biological complex system.

Document Type

Dissertation

Degree Name

Chemistry

Level of Degree

Doctoral

Department Name

Department of Chemistry and Chemical Biology

First Committee Member (Chair)

Yi He

Second Committee Member

Hua Guo

Third Committee Member

Susan R. Atlas

Fourth Committee Member

Eva Y. Chi

Comments

Newly revised version

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