STRUCTURE, DYNAMICS, AND INHIBITION OF ALZHEIMER'S AMYLOID PEPTIDES A

276 Pages·2012·8.45 MB·English

STRUCTURE, DYNAMICS, AND INHIBITION OF ALZHEIMER’S AMYLOID
PEPTIDES

A Dissertation
Presented to
The Gradaute Faculty of The University of Akron

In Partial Fulfillment
of the Requirements for the Degree
Doctor of Philosophy

Xiang Yu
August, 2012
STRUCTURE, DYNAMICS, AND INHIBITION OF ALZHEIMER’S AMYLOID
PEPTIDES

Xiang Yu
Dissertation

Approved: Accepted:

_____________________________ _____________________________
Advisor Department Chair
Dr. Jie Zheng Dr. Lu-Kwang Ju

_____________________________ _____________________________
Committee Member Dean of the College
Dr. Edward A. Evans Dr. George K. Haritos

_____________________________ _____________________________
Committee Member Dean of the Graduate School
Dr. Steven S.C. Chuang Dr. George R. Newkome

_____________________________ _____________________________
Committee Member Date
Dr. Ernian Pan

_____________________________
Committee M ember
Dr. Gang Cheng

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ABSTRACT
Alzheimer’s disease (AD) is the most common age-related neurodegenerative
disorder, pathologically linked to the abnormal self-aggregation of amyloid peptides (Aβ
and tau) into amyloid fibrils. Accumulating evidence supports the “toxic oligomer
hypothesis” that small soluble amyloid oligomers (intermediate species), rather than
monomers (initial species) and insoluble fibrils (final species), are major toxic species
responsible for neuron dysfunction and death. However, due to the polymorphic and
transit nature of amyloid oligomers, atomic structures of amyloid oligomers are not
available to date, causing the difficulty in the fundamental understanding of the
mechanisms of amyloid formation and toxicity and in the rational design of structural-
based inhibitors to treat AD.
In this dissertation, we develop a multiscale computational framework to (1)
determine atomic structures of amyloid oligomers; (2) investigate the conformation,
orientation, and aggregation of amyloid oligomers upon adsorption on biological and
artificial surfaces; (3) probe binding and inhibitory ability of organic ligands to amyloid
oligomers. Throughout this work, we for the first time determine a series of atomic
structures of Aβmicelles (Chapter II), Aβ globulomers (Chapter III), and tau fibrillar-like

oligomers (Chapter IV). These oligomers vary considerably in overall structural
morphologies, reflecting a highly polymorphic nature of amyloid oligomers in a rugged
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energy landscape. We also study the effects of cholesterol level on the mutual structure,
dynamics, and interaction of Aβ and lipid bilayer (Chapter V). Increased cholesterol level
greatly enhances Aβ binding to the bilayer, which provides atomic-level explanation as to
why high-level cholesterol may have a higher risk for AD development. In parallel to
lipid bilayer, molecular dynamics simulations of Aβ peptides on graphite reveal the
important role of hydrophobic interactions in facilitating Aβ adsorption, reorientation,
structural transition, and aggregation (Chapter VI). With the assistance of atomic
structures of Aβ oligomers, we computationally examine binding events between
tanshinones and Aβ oligomer (Chapter VII). Strong binding affinity of tanshinone-I,
rather tanshinone-IIA, to Aβ is well correlated with inhibitory activity to Aβ aggregation.
Combination of our computational and experimental results represent an important step
towards a better understanding of the aggregation, toxicity, and inhibition mechanisms of
amyloid peptides at atomic level.

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ACKNOWLEDGEMENTS
First of all, I would like to express my sincere appreciation to my advisor
Dr. Jie Zheng for his consistent advise, support, and encouragement over the last four
years. Dr. Zheng introduces me to access and explore a fantastic and nanoscale world
using computational tools. He is boundlessly enthusiastic and eager to train and help me
to become a good researcher in every aspect, starting from literature search, critical
reading and thinking, model design, hand-on coding, preparation of slides and papers,
advices for oral presentations and conversations with other colleagues, and so on. I would
also like to extend my thanks to Dr. Steven Chuang, Dr. Edward A. Evans, Dr. Gang
Cheng, and Dr. Ernian Pan for serving on my supervising committee. Their insightful
suggestions and guidance direct me to complete this dissertation.
I would like to thank all faculty and staffs in the Department of Chemical
& Biomolecular Engineering of the University of Akron for their constant education and
supports. Particularly, thanks are also due to my group members, friends, and visiting
scholars for sharing their knowledge and for numerous helpful discussions, including
Qiuming Wang, Chao Zhao, Jun Zhao, Yin Luo, Dr. Jingdai Wang, Dr. Guizhao Liang,
and Dr. Qiang Chen.
Finally, I would like to express my sincere gratitude to my parents Fengying
Qin and Shiguang Yu for their unconditional support and inspiration throughout my life.
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TABLE OF CONTENTS
Page
LIST OF TABLES ............................................................................................................ xii
LIST OF FIGURES ......................................................................................................... xiii
CHAPTER
I. RESEARCH OVERVIEW .............................................................................................. 1
1.1. Background .............................................................................................................. 1
1.2. Fundamental and Technical Challenges ................................................................... 4
1.3. Specific Tasks .......................................................................................................... 7
II. STRUCTURAL DETERMINATION OF Aβ MICELLES BY MOLECULAR
25-35
DYNAMICS SIMULATIONS ........................................................................................... 9
2.1. Introduction .............................................................................................................. 9
2.2. Computational Models and Methods ..................................................................... 11
2.2.1. Model Construction of Aβ Micelles .......................................................... 11
25-35
2.2.2. MD Simulation Protocol .................................................................................. 15
2.3. Result and Discussion ............................................................................................ 17
2.3.1. Conformational Search for Stable Aβ Micelle-like Oligomers ................. 17
25-35
2.3.2. Structural Stability and Dynamics of Four Micelle Models with Distinct
Peptide Organizations ................................................................................................ 20
2.3.3. Effect of Lys28 on the Stability of Aβ Micelles .............................................. 23
vi
2.3.4. Peptide-Peptide and Peptide-Water Interactions ............................................. 26
2.3.5. Biological Implications.................................................................................... 29
2.4. Conclusions ............................................................................................................ 33
III. POLYMORPHIC STRUCTURES OF ALZHEIMER’S Aβ GLOBULOMERS ....... 36
3.1. Introduction ............................................................................................................ 36
3.2. Material and Methods ............................................................................................. 39
3.2.1. Model Construction ......................................................................................... 39
3.2.2. Explicit-Solvent MD Simulation ..................................................................... 42
3.3. Results .................................................................................................................... 43
3.3.1. Conformation Search for Monomer-Based and Dimer-Based Aβ Globulomers
................................................................................................................................... 44
3.3.2. Aβ Globulomers Display Different Structure Stabilities and Organizations .. 46
3.3.3. Heterogeneous Structures Suggest the Polymorphilc Nature of Aβ
Globulomers .............................................................................................................. 51
3.3.4. Stable Aβ Globulomers Are Assembled by Several Dynamic Subunits with a
Hydrophobic Core ..................................................................................................... 57
3.3.5. Solvation and VDW Interactions Control the Structure and Dynamics of Aβ
Globulomers .............................................................................................................. 59
3.3.6. Dimer Is a Basic Building Block for Aβ Globulomers ................................... 64
3.3.7. Lys28Ala Mutation Suggests the Importance of Dimerization on the Stability
of Aβ globulomers ..................................................................................................... 67
3.4. Conclusions ............................................................................................................ 70
IV. CROSS-SEEDING AND CONFORMATIONAL SELECTION BETWEEN THREE-
AND FOUR-REPEAT HUMAN TAU PROTEINS ........................................................ 72
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4.1. Introduction ............................................................................................................ 72
4.2. Materials and Methods ........................................................................................... 75
4.2.1. Explicit-Solvent Molecular Dynamics (MD) Simulation Protocol ................. 80
4.2.2. Structural Population Analysis ........................................................................ 81
4.2.3. Seeded Filament Growth and Sedimentation .................................................. 82
4.3. RESULTS ............................................................................................................... 83
4.3.1. K18 and K19 Octamers Display Different Structure Stabilities but Share Some
Common Features ...................................................................................................... 83
4.3.2. β-Structure Locates at Specific Regions in K18 and K19 Octamers ............... 87
4.3.3. Heterogeneous Structures Suggest the Polymorphic Nature of K18 and K19
Oligomers .................................................................................................................. 91
4.3.4. K18 and K19 Have Different Core Repeats for Conformational Selection .... 93
4.3.5. K18/K19 Cross-Seeding Can Magnify the Structural Polymorphism ........... 100
4.4. DISCUSSION ...................................................................................................... 103
V. CHOLESTEROL PROMOTES THE INTERACTION OF Aβ MONOMER WITH
LIPID BILAYER ............................................................................................................ 107
5.1. Introduction .......................................................................................................... 107
5.2. Materials and Methods ......................................................................................... 109
5.2.1. Initial Conformations of Aβ monomer .......................................................... 109
5.2.2. Aβ-Lipid Bilayer Systems ............................................................................. 110
5.2.3. Explicit-Solvent MD Simulation Protocol .................................................... 111
5.3. Results and Discussion ......................................................................................... 112
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5.3.1. Cholesterol Enhances the Binding of Aβ to Lipid Bilayer ....................... 112
1-42
5.3.2. Electrostatic Interactions are Dominant Forces Contributing to Aβ-Lipid
Interactions .............................................................................................................. 117
5.3.3. Cholesterol Alters the Structure and Dynamics of Lipid Bilayer .................. 120
5.3.4. Ca2+ Bridges Enhance Binding Events Between Aβ and POPC Bilayer ...... 124
5.3.5. Aβ Monomer Predominantly Adopts α-Helical or Unstructured Conformation
on the POPC bilayer ................................................................................................ 127
5.3.6. Repeated MD Simulations Confirms the Role of Cholesterol in Aβ Adsorption
on Lipid Bilayer ....................................................................................................... 131
5.3.7. Moderate Cholesterol in the Cell Membrane is Necessary to Balance the
Equilibrium between Aβ Adsorption on the Lipid Bilayer and Aβ Clearance Pathway
................................................................................................................................. 133
5.4. Conclusions .......................................................................................................... 134
VI. STRUCTURE, ORIENTATION, AND SURFACE INTERACTION OF AMYLOID
β PEPTIDES ON THE GRAPHITE ............................................................................... 136
6.1. Introduction .......................................................................................................... 136
6.2. Materials and Methods ......................................................................................... 139
6.2.1. Molecular Models of Aβ Aggregates ........................................................ 139
1-42
6.2.2. Graphite Surface ............................................................................................ 141
6.2.3. Aβ-Graphite Systems ..................................................................................... 142
6.2.4. MD Simulation Protocol ................................................................................ 144
6.2.5. AFM Images of Aβ Aggregation in Bulk Solution and on the Graphite
1-42
Surface ..................................................................................................................... 145
6.3. Results and Discussion ......................................................................................... 147
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6.3.1. Structural Stability of Aβ Peptides in Bulk Solution ..................................... 147
6.3.2. Aβ Ddsorption on the Graphite Surface ........................................................ 149
6.3.3. Aβ Orientation on the Graphite Surface ........................................................ 155
6.3.4. Interactions of Aβ Peptides with the Graphite Surface ................................. 158
6.3.5. Effect of Surface Hydration on Aβ Adsorption on the Graphite Surface ...... 162
6.3.6. AFM Studies of the Surface-Induced Aβ Aggregation ................................. 163
6.3.7. Adsorption Mechanism of Aβ Peptides on Graphite Surface ....................... 166
6.4 Conclusions ........................................................................................................... 170
VII. INTERACTION COMPARISON BETWEEN TANSHINONE-I AND
TANSHINON-IIA WITH AMYLOID-β OLIGOMER.................................................. 171
7.1. Introduction .......................................................................................................... 171
7.2. Materials and Methods ......................................................................................... 177
7.2.1. Aβ-Tanshinone Simulation Systems ............................................................. 177
7.2.2. MD Simulation Protocol ................................................................................ 178
7.2.3. Aβ-Tanshinone Binding Energy .................................................................... 179
7.3. Results and Discussion ......................................................................................... 180
7.3.1. The Behaviors of Tanshinones at Low Ligand:Aβ Pentamer Mole Ratio .... 181
7.3.2. Mole Ratio Effect on the Tanshinone Binding Behavior .............................. 186
7.3.3. Clustering and Energy Analysis .................................................................... 190
7.3.4. Biological Implications.................................................................................. 196
7.4. Conclusions .......................................................................................................... 199
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