Atomistic Insights into Disordered Proteins and Condensates via Molecular Simulations
Name
wang-congwang-phd-chemistry-2025-thesis.pdf
Description
Thesis PDF
Size
92.61 MB
Format
Adobe PDF
Checksum (MD5)
e78e7b1f21dc2c3d2772d9328da2bc05
Author(s)
Wang, Cong
Advisor(s)
Zhang, Bin
Date Issued
September 2025
Publisher
Massachusetts Institute of Technology
Abstract
Biomolecular condensates formed by intrinsically disordered proteins (IDPs) play essential roles in cellular organization and function, attracting broad scientific interest. In addition to experimental approaches, molecular dynamics simulations—particularly atomistic simulations—serve as powerful tools for gaining mechanistic insights into IDP conformations and inter- and intramolecular interactions within condensates. In this work, we developed a multiscale simulation strategy that balances efficiency and accuracy by combining coarse-grained and atomistic modeling. We further applied dimensionality reduction techniques to extract meaningful features from high-dimensional simulation data. Using this integrated framework, we investigated three scientific problems: (1) the sequence-dependent conformational ensembles of IDPs, (2) nonspecific yet selective condensate–drug interactions, and (3) the mechanism of formation of monocomponent, multiphasic condensates formed by tetrapeptide sequences.
MIT Department
Massachusetts Institute of Technology. Department of Chemistry
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In Copyright - Educational Use Permitted
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