Onuchic, José N.2019-05-162019-05-162017-122017-10-13December 2Sun, Li. "Probing Mechanical Properties of Proteins by Molecular Dynamics Simulations." (2017) Diss., Rice University. <a href="https://hdl.handle.net/1911/105550">https://hdl.handle.net/1911/105550</a>.https://hdl.handle.net/1911/105550Many proteins have force-related functions, such as force transducers and force sensors. Experimental efforts, such as protein structure determination, mutagenesis studies, single-molecule force experiments, fluorescent molecular probes, and traction force microscopy, have provided an insightful understanding of the mechanical properties of force-related proteins. Molecular dynamics simulations have also been widely performed and have become an increasingly useful technique for understanding the mechanisms of force regulation at the molecular level. By means of molecular simulations, one often aims to obtain a global picture of the free energy landscape and relevant kinetic data in an effort to understand the thermodynamic properties of the molecular system and kinetic pathways of reaction processes. However, the complete free energy landscape of a molecular system requires sufficient sampling of the multi-dimensional configuration space, which often involves applications of enhanced sampling techniques, such as umbrella sampling. This dissertation presents applications of molecular simulations and free energy landscape theory to biomolecular systems of different complexities. The first study investigates the force-dependent unfolding rates of an immunoglobulin-like domain ddFLN4. When constant forces of opposite directions are applied on the two terminal residues to mimic a physiological context, we observe distinct relations between the unfolding rate and applied force at different force levels, indicating that the force-induced unfolding behavior of ddFLN4 can be characterized into three force regimes. More detailed insights are obtained by making connections between unfolding kinetics and the underlying free energy landscape. The second study applies molecular dynamics techniques to a multidomain protein vinculin, an important force sensor and force transducer in focal adhesion mechanotransduction. This study aims to provide a molecular mechanism for vinculin activation, an important conformational change in focal adhesion assembly. Using constant forces applied on the experimentally determined ligand binding sites to mimic the in vivo mechanical context of vinculin, we propose a force-sensitive activation mechanism, and provide detailed analyses on the kinetic bottleneck and order of events in a physiological context.application/pdfengCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.ProteinsMolecular dynamicsFree energy landscapeUmbrella samplingForce-induced unfoldingVinculin activationThesis2019-05-16