Computational investigations of protein dynamics and its implications for biological functions

Liu, Yanxin

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https://hdl.handle.net/2142/45294 Copy

Description

Title

Computational investigations of protein dynamics and its implications for biological functions

Author(s)

Liu, Yanxin

Issue Date

2013-08-22T16:35:08Z

Director of Research (if dissertation) or Advisor (if thesis)

Schulten, Klaus J.

Doctoral Committee Chair(s)

Dahmen, Karin A.

Committee Member(s)

• Schulten, Klaus J.
• Gruebele, Martin
• Stack, John D.

Department of Study

Physics

Discipline

Physics

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• molecular dynamics simulation
• protein folding
• enhanced sampling
• lambda-repressor
• glycoprotein
• flow-induced protein folding
• myosin VI
• motor protein

Abstract

Computer simulation is a powerful approach to study protein dynamics and functions. We employed molecular dynamics (MD) simulations to investigate large conformational changes in proteins, including folding, dimerization, and unfolding, and how these conformational changes help the proteins perform their biological functions. We first study protein folding, a process by which a protein acquires its functional structure and is related to many neurodegenerative diseases. A fast-folding five-helix bundle λ-repressor fragment is chosen as a model system. A length of 80 amino acid residues puts it on the large end among all known microsecond folders and its size poses a computational challenge for MD studies. We simulate the folding of a novel λ-repressor fast-folding mutant λ*HG) in explicit solvent using an all-atom description. By means of a recently developed tempering method, we observe reversible folding and unfolding of λ-repressor in a 10-μs trajectory. The folding kinetics is also investigated through a set of MD simulations run at different temperatures that together cover more than 125 μs. The protein is seen to fold into a native-like topology at intermediate temperature and a slow-folding pathway is identified. For two other lambda-repressor mutants, λ*YG and λ*YA, we study pressure effect on the protein dynamics. A short refolding time of 2 μs was reported for λ*YG in pressure-jump experiments. To investigate this pressure-jump induced fast folding behavior, MD simulations of more than 35 μs are carried out on the λ*YG mutant. High-pressure denatured states are found to contain a significant amount of helical structure. Upon pressure drop, the protein refolds into the native state in 20 μs. The simulations confirm the existence of pressure-jump induced fast folding pathway for λ*YG. We also perform over 50 μs pressure-jump simulations on λ*YA with four different force fields. Two of the force fields yield compact non-native states with misplaced α-helix content within a few microseconds of the pressure drop. We conclude that the pressure-denatured state of λ*YA contains mainly residual helix and little β-sheet; following a fast pressure-drop, at least some λ*YA forms misplaced helical structure within microseconds. We hypothesize that non-native helix at helix-turn interfaces traps the protein in compact non-native conformations. These traps delay the folding of at least some of the protein population to the native state, reflected as the millisecond slow folding phase in pressure jump experiments. Based on the simulations, we predict specific mutations at the helix-turn interfaces that should speed up refolding from the pressure-denatured state. In addition to being a spontaneous process, protein folding can also be modulated through external factors, such as flow, light, or mechanical force. Flow-induced shear has been identified as a regulatory driving force in blood clotting. Shear induces β-hairpin folding of the glycoprotein Ibα β-switch which increases affinity for binding to the von Willebrand factor, a key step in blood clot formation and wound healing. Through 2.1-μs MD simulations, we investigate the kinetics of flow-induced β-hairpin folding. Simulations sampling different flow velocities reveal that under flow, β-hairpin folding is initiated by hydrophobic collapse, followed by inter-strand hydrogen-bond formation and turn formation. Adaptive biasing force simulations are employed to determine the free energy required for extending the unfolded β-switch from a loop to an elongated state. Lattice and freely jointed chain models illustrate how the folding rate depends on the entropic and enthalpic energy, the latter controlled by flow. The results reveal that the free energy landscape of the β-switch has two stable conformations imprinted on it, namely, loop and hairpin -- with flow inducing a transition between the two. Finally, we investigate how the dimerization and unfolding of individual domain of myosin VI help this motor protein move on the actin filament with a large step size. The unconventional motor protein, myosin VI, is known to dimerize upon cargo binding to its C-terminal end. It has been shown that one of its tail domains, called the medial tail domain, is a dimerization region. MD simulations reveal the unknown dimerization mechanism of the medial tail domain. The results suggest that the formation of electrostatic-based inter-helical salt bridges between oppositely charged residues is a key dimerization factor. Calculations of the dimer-dissociation energy find the contribution of hydrophobic residues to the dimerization process to be minor; we also find that the asymmetric homodimer state is energetically favorable over a state of separate helices. Recent experimental work proposed that myosin VI dimerization triggers the unfolding of the protein's proximal tail domain which could help the protein realize a step size of 30~36 nm. Here, we demonstrate through steered molecular dynamics simulation the feasibility of sufficient extension arising from turning a three-helix bundle into a long α-helix. A key role is played by the known calmodulin binding that facilitates the extension by altering the strain path in myosin VI. Sequence analysis of the proximal tail domain suggests that further calmodulin binding sites open up when the domain's three-helix bundle is unfolded and that subsequent calmodulin binding stabilizes the extended lever arms.

Graduation Semester

2013-08

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http://hdl.handle.net/2142/45294

Copyright and License Information

Copyright 2013 Yanxin Liu

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