Molecular Dynamics of Monomeric IAPP in Solution

Table of Contents

1 Introduction

1.1 Islet Amyloid Polypeptide

1.1.1 Diabetes Mellitus Type II

1.1.2 Mutations and Homologues

1.1.3 IAPP Properties

1.1.3.1 IAPP Aggregation

1.1.3.2 Proline

1.2 Hydrational Water

1.3 Overview

1.4 Thesis Objectives

2 Methods

2.1 Molecular Dynamics Simulation Methods in a Nutshell

2.2 Preparation of Initial Conformations

2.2.1 In vacuo hIAPP Simulations

2.2.2 Solvated Uncapped hIAPP

2.2.3 Solvated Amide Capped hIAPP

2.3 Scaling Charges

2.4 Software

2.4.1 Ramachandran Angles

2.4.2 Hydrogen Bond Definitions

2.4.3 Statistical Properties

2.4.3.1 Water box and Maximum Distance between Heavy Atoms

2.4.4 Data Crunching

2.4.4.1 Error Estimate

2.4.4.2 Savitzky-Golay Smoothing Filter

2.4.4.3 Scott’s Choice

2.4.4.3 Rounding Data - Taylor

2.5 Hydration Water

2.5.1 System Description

2.5.2 Water Shell Analysis Software

3 Preparation of the Initial Conformations

3.1 Random Conformations from Vacuum

3.1.1 Data Analysis

3.1.1.1 Initial Modeled α-Helix Conformation

3.1.1.2 Comparison of Independent Starting Conformations

3.1.1.3 Independent Concatenated Data

3.2 Extended Trajectories

3.3 Conclusions

4 Water Percolation

4.1 Hydration Water Properties

4.2 Hydration Water Analysis

4.2.1 Temperature-Induced Percolation Transition of Hydration Water

4.2.2 Effect of the Spanning Water Network on Peptide Properties

4.2.3 Effect of Peptide Structure on the Spanning Network of Hydration Water

4.3 Conclusions

5 Comparing hIAPP and rIAPP in Liquid Water

5.1 Conformational Changes of Oxidized hIAPP at 330 K

5.1.1 Conformational Properties Rg, reted, and SASA of IAPP

5.2 Compact hIAPP Conformation at 330 K

5.2.1 Aromatic-Aromatic Interactions

5.2.2 Secondary Structure

5.2.2.1 Ramachandran Angles

5.2.2.2 DSSPcont

5.2.3 Snapshots of IAPP

5.2.4 H-bond Patterns and Secondary Structure of Oxidized hIAPP at 330 K

5.2.5 System Perturbation

5.2.5.1 Thermal Induced “Unfolding”

5.2.5.2 In silico Point Mutations on Oxidized hIAPP at 330 K

5.3 Discussion and Conclusions

5.3.1 Compact, but not Entirely Disordered, Polypeptide

5.3.2 Effect of P28 on the C-Terminal Region

5.3.3 Effect of Aromatic Residues

5.3.4 Temperature Effect on Oxidized hIAPP

5.3.5 Effect of the Disulfide Bond

6 Outlook

Objectives and Topics

The primary research objective is to examine the conformational behavior and aggregation propensities of two highly homologous polypeptides, human IAPP (hIAPP) and rat IAPP (rIAPP), to determine the structural factors that induce amyloid formation in the human variant while preventing it in the rodent variant.

• Molecular Dynamics (MD) simulation of monomeric peptide conformations
• Impact of the natural disulfide bond on peptide flexibility and folding
• Role of specific amino acid residues, particularly proline, on secondary structure and stability
• Percolation transition of hydration water and its correlation with peptide conformational changes
• Comparative analysis of aromatic-aromatic interactions in hIAPP and rIAPP

Excerpt from the Book

Summary of Chapters

1 Introduction: Provides the historical context and biological importance of proteins, specifically introducing islet amyloid polypeptide (IAPP) and its role in type II diabetes.

2 Methods: Explains the theoretical foundations of Molecular Dynamics (MD) simulations, including force field parametrization, boundary conditions, and the specific software used to analyze the data.

3 Preparation of the Initial Conformations: Describes the methodology for generating starting conformations for the MD simulations, including vacuum equilibration and the subsequent solvation steps.

4 Water Percolation: Investigates the thermal stability of the hydration water network around the peptide and its quasi-2D percolation transition.

5 Comparing hIAPP and rIAPP in Liquid Water: Presents a detailed comparison of the conformational changes, secondary structure, and folding pathways of human and rat IAPP at physiological temperatures.

6 Outlook: Summarizes the key findings and suggests further investigations, such as studying oligomeric forms or interactions with lipid bilayers.

Keywords

Molecular Dynamics, IAPP, Amyloidosis, Protein Folding, Hydration Water, Percolation Transition, Secondary Structure, Disulfide Bond, Proline, Diabetes Mellitus, Conformational Stability, In silico simulation, Peptide Aggregation.

Frequently Asked Questions

What is the core subject of this doctoral dissertation?

The work investigates the structural and conformational properties of monomeric human and rat Islet Amyloid Polypeptide (IAPP) in liquid water using Molecular Dynamics simulations to understand the molecular basis of amyloid aggregation.

Which specific themes are addressed in the study?

The research focuses on the impact of the disulfide bond, the role of specific residues like proline (P28) and phenylalanine (F23), and the influence of the hydration shell on peptide folding and stability.

What is the primary goal of this research?

The goal is to pinpoint the conformational differences between amyloidogenic human IAPP and non-amyloidogenic rat IAPP that contribute to the distinct aggregation propensities observed in these homologs.

What scientific methods were employed?

The author uses Molecular Dynamics (MD) simulations with the GROMACS suite, utilizing force fields like OPLS-AA/L, and analyzes the data using custom Python programs to evaluate properties like radius of gyration, solvent-accessible surface area, and hydrogen bond patterns.

What topics are covered in the main body?

The main sections cover the preparation of valid initial peptide conformations, the analysis of the water percolation transition, a comparative conformational study of the hIAPP and rIAPP variants at physiological temperatures, and an investigation into in silico point mutations.

Which keywords define this work?

Key terms include Molecular Dynamics, IAPP, amyloidosis, hydration water, percolation transition, secondary structure, and peptide aggregation.

What is the significance of the water percolation transition in this work?

The percolation transition of the hydration shell, occurring at approximately 320 K, is shown to correlate with the conformational behavior of the peptide, suggesting it may play a role in the kinetics of aggregation.

How does the disulfide bond influence the peptide?

The study finds that the natural disulfide bond between residues C2 and C7 confers flexibility to the C-terminal region, which appears to be a necessary condition for the peptide to transition into a compact, amyloid-prone state.

What role does proline at position 28 play in rIAPP?

The presence of proline at residue 28 in rat IAPP is identified as a factor that stabilizes helical conformations in the C-terminal region, effectively acting as an inhibitor of the aggregation-prone folding pathways seen in human IAPP.