Intrinsic Determinants of Aβ12–24 pH-Dependent Self-Assembly Revealed by Combined Computational and Experimental Studies

Weixin Xu,Astrid Gräslund,Philippe Derreumaux,Yuguang Mu,Ce Zhang,Ludmilla Morozova-Roche,Jie Zheng

doi:10.1371/journal.pone.0024329

Abstract

The propensity of amyloid- (A) peptide to self-assemble into highly ordered amyloid structures lies at the core of their accumulation in the brain during Alzheimer's disease. By using all-atom explicit solvent replica exchange molecular dynamics simulations, we elucidated at the atomic level the intrinsic determinants of the pH-dependent dimerization of the central hydrophobic segment A and related these with the propensity to form amyloid fibrils measured by experimental tools such as atomic force microscopy and fluorescence. The process of A dimerization was evaluated in terms of free energy landscape, side-chain two-dimensional contact probability maps, -sheet registries, potential mean force as a function of inter-chain distances, secondary structure development and radial solvation distributions. We showed that dimerization is a key event in A amyloid formation; it is highly prompted in the order of pH 5.02.98.4 and determines further amyloid growth. The dimerization is governed by a dynamic interplay of hydrophobic, electrostatic and solvation interactions permitting some variability of -sheets at each pH. These results provide atomistic insight into the complex process of molecular recognition detrimental for amyloid growth and pave the way for better understanding of the molecular basis of amyloid diseases.

Highlights

Alzheimer’s disease (AD) or Alzheimer’s is the most common form of dementia in aging people
The chilled powdered peptide was initially dissolved in 10 mM NaOH just above 1 mg/ml concentration, sonicated in an ice cold water bath for 1 min, and ca. 10–20ml of 1 M NaH2PO4 buffer was added to adjust the environmental condition to a final buffer concentration of 20 mM and corresponding pH: 2.9; 5.0 and 8.4; after dilution pH was controlled by pH meter
The kinetics of amyloid formation was monitored by ThT binding as the specific interaction of ThT dye with cross-b sheet containing amyloids leads to an increase of its fluorescence emission (Fig. 1a, upper panel)

Summary

Introduction

Alzheimer’s disease (AD) or Alzheimer’s is the most common form of dementia in aging people. The toxic agents include soluble oligomers [1,2,3,4] as small as dimers [4], protofibrils [5,6,7,8] and mature fibrils [9], the etiology of amyloidoses is still poorly understood. Knowledge of the polymerization at the molecular level, the structural details of fibrils, as well as the effects of external perturbations on fibrillation should facilitate the design of inhibitors. It is known that the predominant morphology is influenced by a variety of competing factors, including rates of spontaneous nucleation, fibril elongation, and fibril fragmentation. The morphologies of the fibrillar structures and the aggregation kinetics are highly sensitive to the pH values at which the protein solutions are incubated [15]. We would like to gain insights into the effects of pH variations on the initial stages of Ab self-assembly at atomic resolution

Methods

Results

Conclusion