Molecular Dynamics Simulation Studies on Interfacial Dynamics of Proteins

Clusters of water molecules embedded in proteins or at the interface between globules mediate protein dynamics, allostery and charge transfer. Confined clusters of water molecules exhibit dynamics distinct from dynamics of water in the bulk or in the hydration layer around biomolecules. Here, we describe and compare the dynamics of water in the hydration layer around antifreeze proteins, the dynamics of a cluster of water molecules at the interface between the globules of a homodimeric hemoglobin, and the dynamics of water molecules within green fluorescent protein (GFP) and the hydration water in the vicinity of photoactive yellow protein (PYP), all studied by molecular dynamics simulations. The water dynamics in these systems span a wide range of time scales and are closely related to function, ranging from relatively fast hydration water dynamics to tightly bound water clusters that mediate protein conformational change during ligand binding. Subsequent quantum mechanical studies on energy relaxation in proteins GFP and PYP provide insights into the microenvironment of the chromophore and identify energy flow channels that may mediate the kinetics of photochemical reactions such as charge transfer and conformational isomerization.

Level thesis:degree_level

Doctorate Degree

Year dc:date.issued

2013

Author dc:creator

• Xu, Yao

Advisor dc:contributor.advisor

• Leitner, David M.

Committee members dc:contributor.committeemember

• Varganov, Sergey A
• Winkler, Peter
• Derevianko, Andrei
• Pinsky, Mark

• Molecular Dynamics
• Molecular Dynamics Simulation
• Protein Dynamics
• Protein-water Interactions
• Vibrational Energy Flow
• Water Dynamics

Statement dc:rights

• In Copyright(All Rights Reserved)

Handle dc:identifier.uri

http://hdl.handle.net/11714/3115

OAI identifier oai:identifier

oai:scholarwolf.unr.edu:11714/3115