Article

Experimental Constraints on Quaternary Structure in Alzheimer's β-Amyloid Fibrils †

Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
Biochemistry (Impact Factor: 3.02). 02/2006; 45(2):498-512. DOI: 10.1021/bi051952q
Source: PubMed

ABSTRACT

We describe solid-state nuclear magnetic resonance (NMR) measurements on fibrils formed by the 40-residue beta-amyloid peptide associated with Alzheimer's disease (Abeta(1-40)) that place constraints on the identity and symmetry of contacts between in-register, parallel beta-sheets in the fibrils. We refer to these contacts as internal and external quaternary contacts, depending on whether they are within a single molecular layer or between molecular layers. The data include (1) two-dimensional 13C-13C NMR spectra that indicate internal quaternary contacts between side chains of L17 and F19 and side chains of I32, L34, and V36, as well as external quaternary contacts between side chains of I31 and G37; (2) two-dimensional 15N-13C NMR spectra that indicate external quaternary contacts between the side chain of M35 and the peptide backbone at G33; (3) measurements of magnetic dipole-dipole couplings between the side chain carboxylate group of D23 and the side chain amine group of K28 that indicate salt bridge interactions. Isotopic dilution experiments allow us to make distinctions between intramolecular and intermolecular contacts. On the basis of these data and previously determined structural constraints from solid-state NMR and electron microscopy, we construct full molecular models using restrained molecular dynamics simulations and restrained energy minimization. These models apply to Abeta(1-40) fibrils grown with gentle agitation. We also present evidence for different internal quaternary contacts in Abeta(1-40) fibrils grown without agitation, which are morphologically distinct.

Full-text preview

Available from: ncbi.nlm.nih.gov
  • Source
    • "We used an A fibrillar structure from a solid-state NMR fibril model of full-length Aβ (PDB entry: 2LMO) (Petkova et al. 2006). Each GSPE molecule was prepared for Rosetta docking simulations, as described previously (Jiang et al. 2013). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Epidemiological evidence that red wine consumption negatively correlates with risk of AD has led to experimental studies demonstrating that grape seed extracts inhibit the aggregation and oligomerization of Aβ in vitro and ameliorate neuropathology and behavioral deficits in a mouse model of AD. The active agent in the extracts is a mixed population of polyphenolic compounds. To evaluate the relative potency of each of these compounds, HPLC was used to fractionate the mixture into monomers, dimers, and oligomers. Each fraction was analyzed for its effect on Aβ conformational dynamics (circular dichroism), oligomerization (zero-length photochemical cross-linking), aggregation kinetics (Thioflavin T fluorescence), and morphology (electron microscopy). The relative activities of each fraction were determined on the basis of molar concentration (mol/L) or mass concentration (g/L). When molar concentration, the number concentration of each polyphenolic compound, was considered, the oligomer fraction was the most potent inhibitor of Aβ oligomerization and aggregation. However, when mass concentration, the number concentration of phenolic groups, was considered, monomers were the most potent inhibitors. To understand these ostensibly contradictory results, a model of polyphenol:Aβ complexation was developed. This model, which was found to be consistent with published X-ray crystallographic studies, offers an explanation for the effects of functional group polyvalency on inhibitor activity. Our data emphasize the importance of an in-depth understanding of the mechanism(s) underlying "concentration dependence" in inhibitor systems involving polyfunctional agents. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Full-text · Article · Jul 2015 · Journal of Neurochemistry
    • "Specific molecular architecture of amyloid assemblies is stabilized by the enthalpic contribution from the main-chain hydrogen bonding, ionic pairing, aromatic π-π interactions and hydrogen bonds between amino-acid side chains (Nelson et al. 2005; Makin et al. 2005; Petkova et al. 2006), as well as the entropic contribution originating from the release of structured water molecules from the tightly packed amyloid core (Sawaya et al. 2007; Williams et al. 2006). Clearly, all forces stabilizing fibril structure can be modulated by the environmental factors inherent to a lipid bilayer. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Amyloid fibrils are an intriguing class of protein aggregates with distinct physicochemical, structural and morphological properties. They display peculiar membrane-binding behavior, thus adding complexity to the problem of protein-lipid interactions. The consensus that emerged during the past decade is that amyloid cytotoxicity arises from a continuum of cross-β-sheet assemblies including mature fibrils. Based on literature survey and our own data, in this chapter we address several aspects of fibril-lipid interactions, including (i) the effects of amyloid assemblies on molecular organization of lipid bilayer; (ii) competition between fibrillar and monomeric membrane-associating proteins for binding to the lipid surface; and (iii) the effects of lipids on the structural morphology of fibrillar aggregates. To illustrate some of the processes occurring in fibril-lipid systems, we present and analyze fluorescence data reporting on lipid bilayer interactions with fibrillar lysozyme and with the N-terminal 83-residue fragment of amyloidogenic mutant apolipoprotein A-I, 1-83/G26R/W@8. The results help understand possible mechanisms of interaction and mutual remodeling of amyloid fibers and lipid membranes, which may contribute to amyloid cytotoxicity.
    No preview · Article · Jul 2015 · Advances in Experimental Medicine and Biology
  • Source
    • "Comparison of these two ensembles suggested a statistically significant, tenfold increase in the relative stability of a hairpin conformation in the Aβ42 isoform versus its shorter counterpart and correlates well with findings from unbiased molecular dynamics simulations of these two peptides[175]. While the strand segments within each hairpin correspond to segments that are also in a strand conformation in the fibrillar state, the tertiary structural arrangement of these strands is different since they are involved in intramolecular hydrogen bonds with each other[162], in contrast to the fibrillar conformations which contain intermolecular hydrogen bonds[146,168169170. Hairpin-type structures containing intramolecular hydrogen bonds would therefore have to undergo structural rearrangements to form amyloid protofibrils. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Proteins are heteropolymers that play important roles in virtually every biological reaction. While many proteins have well-defined three-dimensional structures that are inextricably coupled to their function, intrinsically disordered proteins (IDPs) do not have a well-defined structure, and it is this lack of structure that facilitates their function. As many IDPs are involved in essential cellular processes, various diseases have been linked to their malfunction, thereby making them important drug targets. In this review we discuss methods for studying IDPs and provide examples of how computational methods can improve our understanding of IDPs. We focus on two intensely studied IDPs that have been implicated in very different pathologic pathways. The first, p53, has been linked to over 50% of human cancers, and the second, Amyloid-beta (A beta), forms neurotoxic aggregates in the brains of patients with Alzheimer's disease. We use these representative proteins to illustrate some of the challenges associated with studying IDPs and demonstrate how computational tools can be fruitfully applied to arrive at a more comprehensive understanding of these fascinating heteropolymers.
    Full-text · Article · Oct 2014 · Polymers
Show more