Experimental Evidence for the Reorganization of β-Strands within Aggregates of the Aβ(16−22) Peptide

Abstract

Amyloidogenic deposits that accumulate in brain tissue with the progression of Alzheimer's disease contain large amounts of the amyloid beta-peptide. A small fragment of this peptide, comprising residues 16-22 (Abeta(16-22)), forms beta-sheets in isolation, which then aggregate into amyloid fibrils. Here, using isotope edited infrared spectroscopy to probe the secondary structure of the peptide with residue level specificity, we are able to show conclusively that the beta-sheets formed are antiparallel and, following an anneal cycle or prolonged incubation, are in register with the central residue (Phe19) in alignment across all strands. The alignment of strands proceeds via a rapid interchange from one sheet to another. This realignment of the peptide strands into a more favorable registry may have important implications for therapeutics since previous work has shown that well aligned beta-sheets form more stable amyloid fibrils.

Computational Simulations of the Early Steps of Protein Aggregation

“…For example, a reptation mechanism first identified numerically, 22,23 seems to be dominant in the rearrangement of amyloid chains. 24 These results, and others presented below, show that simulations can complement and even guide experimental measurements in the study of amyloid aggregation. In this review, we limit ourselves to coarse-grained protein aggregation simulations taken largely from our work.…”

“…Activated approaches, such as the activation-relaxation technique (ART nouveau) for example, 55,56 explores the space of conformations, through well-defined transition states. Coupled with the implicit solvent coarse-grained protein OPEP force field, 57,58 this method has provided the best fit with the NMR data of the fragment Ab (21)(22)(23)(24)(25)(26)(27)(28)(29)(30) in solution 59 and has allowed to monitor the aggregation of various amyloid peptides with 4 to 15 amino-acids, in settings ranging from dimer to dodecamer. 22,23,[60][61][62][63][64][65][66] Because it lacks detailed balance ART cannot provide solid thermodynamic information.…”

Experimental characterization of disordered and ordered aggregates populated during the process of amyloid fibril formation

“…Several mechanisms have been proposed to explain amyloid fibril formation (24); among them, the nucleated conformational conversion (NCC) mechanism (25) is supported by a range of experimental and theoretical observations (26)(27)(28). In the NCC mechanism, a group of monomers initially present in solution coalesce to form amorphous oligomers.…”

Surface FTIR Techniques to Analyze the Conformation of Proteins/ Peptides in H2O Environment

“…Lots of FTIR spectra of proteins/peptides were obtained in D 2 O [15][16][17][18][19][20], not H 2 O, because the intensive IR absorption of H 2 O between 1500 to 1800 cm -1 overlaps the position of the amide I band [21,22]. Thus, the amide I band in the FTIR spectra of proteins/peptides can be clearly detected in D 2 O with the background IR absorption around 1200 cm -1 [21,22] …”

“…The 13 C amide I band which is in the range from 1585-1610 cm -1 has been shown to depend on the conformation of the 13 C labeled residue (or amino acid) in D 2 O. For example, the 13 C amide I' band (i.e., the amide I band in D 2 O) of α-helix has been shown to be around 1596 cm -1 and that of anti-parallel β-sheet was at either 1590 cm -1 or 1600 cm -1 [19,20]. Interestingly, the 13 C amide I band was not detected when the 13 C labeled residue was in unstructured conformation [20].…”