pH effects on the conformational preferences of Amyloid B-peptide (1-40) in HFIP aqueos solution by NMR Spectroscopy

The structure and aggregation state of amyloid ?-peptide (A?) in membrane-like environments are important determinants of pathological events in Alzheimer’s disease. In fact, the neurotoxic nature of amyloid-forming peptides and proteins is associated with specific conformational transitions proximal to the membrane. Under certain conditions, the A? peptide undergoes a conformational change that brings the peptide in solution to a “competent state” for aggregation. Conversion can be obtained at medium pH (5.0–6.0), and in vivo this appears to take place in the endocytic pathway. The combined use of 1H NMR spectroscopy and molecular dynamics-simulated annealing calculations in aqueous hexafluoroisopropanol simulating the membrane environment, at different pH conditions, enabled us to get some insights into the aggregation process of A?, confirming our previous hypotheses of a relationship between conformational flexibility and aggregation propensity. The conformational space of the peptide was explored by means of an innovative use of principal component analysis as applied to residue-by-residue root-mean-square deviations values from a reference structure. This procedure allowed us to identify the aggregation-prone regions of the peptide.