Folding events in the 21-30 region of amyloid β-protein (Aβ) studied in silico

Abstract

Oligomeric assemblies of the amyloid ␤-protein (A␤) have been implicated in the pathogenesis of Alzheimer's disease as a primary source of neurotoxicity. Recent in vitro studies have suggested that a 10-residue segment, Ala-21-Ala-30, forms a turn-like structure that nucleates the folding of the full-length A␤. To gain a mechanistic insight, we simulated A␤(21-30) folding by using a discrete molecular dynamics algorithm and a united-atom model incorporating implicit solvent and a variable electrostatic interaction strength (EIS). We found that A␤(21-30) folds into a loop-like conformation driven by an effective hydrophobic attraction be- Amyloid fibrils were shown to be neurotoxic (1), but subsequent biophysical, biological, and clinical data indicated that smaller assemblies also were neurotoxic (2-4). More recent studies addressed the toxicity of soluble oligomeric A␤ assemblies (5-9). Taken together, these data suggest that small oligomers, not fibrils, may be the proximate toxin that causes neurodegeneration. An attractive strategy for drug development suggests itself: Prevent the formation of toxic oligomers. To do so, knowledge of the structure and dynamics of A␤ monomer under conditions that favor oligomerization is necessary.Recent limited proteolysis experiments on A␤(1-40) and A␤(1-42) identified protease-resistant segments under conditions favoring oligomerization (10). A 10-residue segment, Ala-21-Ala-30, was highly resistant to proteolytic attack, indicating the presence of a folded structure. Lazo et al. (10) postulated that this structure nucleates the intramolecular folding of A␤ monomer. Notably, the homologous decapeptide A␤(21-30) showed similar protease resistance when studied in monomeric solution, lending support to the hypothesis. Determination of the solution structure of A␤(21-30) by NMR yielded two families of structures containing a turn-like motif centered at residues Gly-25-Ser-26. Putative stabilization factors are (i) intrinsic turn propensities of Gly-25, Ser-25, and Asn-27; (ii) hydrophobic interaction between Val-24 and the butyl portion of the Lys-28 side chain; and (iii) electrostatic interactions (EI) between Glu-22 and Lys-28 or between Asp-23 and Lys-28. These latter interactions defined the two families and led to the question, Which of the two families of structures is preferred? Lazo et al. also postulated that partial unfolding of the Ala-21-Ala-30 region may be necessary for the subsequent fibrillization of A␤. How might this unfolding occur?To address these questions, we used an in silico approach to visualize the folding͞unfolding of A␤(21-30). Computer simulations, particularly molecular dynamics (MD) simulations, can provide information that cannot be obtained by experimental methods, including conformational transitions that occur at every step along the folding͞unfolding pathway. MD simulations also can contribute to a better understanding of the forces (e.g., electrostatic versus hydrophobic) controlling protein folding. Discrete MD (DMD) combined with a coarse...

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

“…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.…”

“…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°.…”

“…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. Recent MD simulations26-28 and solid-state NMR experiments29 on the Aβ [21][22][23][24][25][26][27][28][29][30] -peptide revealed a highly fluctuating structure of this decapeptide, with relatively low-probability of intra-peptide E22-K28 and D23-K28 saltbridges and the V24-K28 hydrophobic interaction also supporting the role of the VGSN (24)(25)(26)(27) in higher ordered structures.…”