Solvent and mutation effects on the nucleation of amyloid β-protein folding

Abstract

Experimental evidence suggests that the folding and aggregation of the amyloid ␤-protein (A␤) into oligomers is a key pathogenetic event in Alzheimer's disease. Inhibiting the pathologic folding and oligomerization of A␤ could be effective in the prevention and treatment of Alzheimer's disease. Here, using all-atom molecular dynamics simulations in explicit solvent, we probe the initial stages of folding of a decapeptide segment of A␤, A␤21-30, shown experimentally to nucleate the folding process. In addition, we examine the folding of a homologous decapeptide containing an amino acid substitution linked to hereditary cerebral hemorrhage with amyloidosis-Dutch type, [Gln-22]A␤ 21-30. We find that: (i) when the decapeptide is in water, hydrophobic interactions and transient salt bridges between Lys-28 and either Glu-22 or Asp-23 are important in the formation of a loop in the Val-24 -Lys-28 region of the wild-type decapeptide; (ii) in the presence of salt ions, salt bridges play a more prominent role in the stabilization of the loop; (iii) in water with a reduced density, the decapeptide forms a helix, indicating the sensitivity of folding to different aqueous environments; and (iv) the ''Dutch'' peptide in water, in contrast to the wild-type peptide, fails to form a long-lived Val-24 -Lys-28 loop, suggesting that loop stability is a critical factor in determining whether A␤ folds into pathologic structures. molecular dynamics ͉ Alzheimer's disease ͉ hydrophobic interactions ͉ salt bridges T he amyloid cascade hypothesis, first proposed in the early 1990s, posits that the deposition of amyloid fibrils is the seminal event in the pathogenesis of Alzheimer's disease (1, 2). However, recent biophysical, biological, and clinical data indicate that the formation of oligomeric assemblies much smaller than fibrils may be a key pathologic event (3-10). This paradigm shift suggests an attractive therapeutic approach: prevent or disrupt the assembly of amyloid ␤-protein (A␤) monomer into toxic oligomers. To do so requires an understanding of the molecular dynamics (MD) involved in the transition from nontoxic monomeric to toxic oligomeric states.Elucidation of the initial events in A␤ monomer folding and assembly is complicated by the solvent dependence of the process (11). Monomeric A␤ is largely helical in a membrane or membrane-mimicking environment such as ionic detergents (12-15). In contrast, A␤ monomers in aqueous solution show negligible ␣-helix or ␤-sheet content (11,16,17). Studies of A␤ 10 -35 -amide at micromolar concentrations in water show a pH-dependent folding transition in which the conformation is not helical but contains several turns and at least two short strands (18). Solution-state NMR combined with diffusionordered spectroscopy indicate that variation of the anionic strength in the buffer shifts the equilibrium between monomeric and oligomeric states, possibly allowing for the stabilization of intermediate structures (19). MD studies of A␤ 16 -22 monomer in aqueous urea solution show that increasin...

A polymer physics perspective on driving forces and mechanisms for protein aggregation

“…Additionally, as Wu and coworkers have demonstrated, the use of scattering-based techniques [73], including X-ray / neutron scattering and light scattering, combined with theory and simulation should be very useful in the study of aggregation-prone IDPs. Several groups in the amyloid field are already pursuing these types of multi-faceted approaches [5,84,[94][95][96][97][98][99][100][101][102][103][104][105][106][107]. However, we remain blind to interactions and conformational fluctuations that occur at low concentrations.…”

Structures and Free-Energy Landscapes of the Wild Type and Mutants of the Aβ21–30 Peptide Are Determined by an Interplay between Intrapeptide Electrostatic and Hydrophobic Interactions

“…Kirschner and coworkers12 used theoretical predictors of β-turn propensity13 to show that the region of sequence centered about residue 26 (as well as residue 8) as having high β-turn potential. Limited proteolysis studies14 identified β-turn in the SNKG (26)(27)(28)(29) region of the full length peptide. NMR and CD spectroscopy15 for the full length Aβ-protein and fragments in a trifluoroethanol and water solution to show that the VGSN (24)(25)(26)(27)) region forms stable turn structures.…”

“…Limited proteolysis studies14 identified β-turn in the SNKG (26)(27)(28)(29) region of the full length peptide. NMR and CD spectroscopy15 for the full length Aβ-protein and fragments in a trifluoroethanol and water solution to show that the VGSN (24)(25)(26)(27)) region forms stable turn structures. Several other studies16-19 also identified a helix-turn-helix structure for the Aβ-peptide in non-polar or membrane mimicking environments.…”

“…The aqueous solution phase NMR structure of the Aβ congener peptide20, 21 shows that, in addition to the LVFFA(17-21) "central hydrophobic cluster" region, a turn centered at the VGSN (24)(25)(26)(27) region of the peptide is a key structural motif. Subsequent studies of the Aβ -peptide demonstrated that the C α proton chemical shift in the VGSNKG(24-29) region does not change over a range of temperature, which suggests that the peptide structure surrounding the VGSN (24)(25)(26)(27) region is stable in the temperature range from 5°-35°.…”

“…Subsequent studies of the Aβ -peptide demonstrated that the C α proton chemical shift in the VGSNKG(24-29) region does not change over a range of temperature, which suggests that the peptide structure surrounding the VGSN (24)(25)(26)(27) region is stable in the temperature range from 5°-35°. 21,22 Simulation studies21,23,24 lent support for the stability of the proposed structure of the LVFFA(17-21) central hydrophobic cluster and VGSN (24)(25)(26)(27) turn regions on the nanosecond time scale. 21 The conservation of the VGSN (24)(25)(26)(27) turn region in the putative β-fibril25 and the "collapsed coil" structures leads to the conjecture that the VGSN (24)(25)(26)(27) may nucleate the formation of Aβ aggregates.…”