Understanding the structural and assembly dynamics of the amyloid -protein (A) has direct relevance to the development of therapeutic agents for Alzheimer disease. To elucidate these dynamics, we combined scanning amino acid substitution with a method for quantitative determination of the A oligomer frequency distribution, photo-induced cross-linking of unmodified proteins (PICUP), to perform "scanning PICUP." Tyr, a reactive group in PICUP, was substituted at position 1, 10, 20, 30, or 40 (for A40) or 42 (for A42). The effects of these substitutions were probed using circular dichroism spectroscopy, thioflavin T binding, electron microscopy, PICUP, and mass spectrometry. All peptides displayed a random coil 3 ␣/ 3  transition, but substitution-dependent alterations in assembly kinetics and conformer complexity were observed. Tyr 1 -substituted homologues of A40 and A42 assembled the slowest and yielded unusual patterns of oligomer bands in gel electrophoresis experiments, suggesting oligomer compaction had occurred. Consistent with this suggestion was the observation of relatively narrow [Tyr 1 ]A40 fibrils. Substitution of A40 at the C terminus decreased the population conformational complexity and substantially extended the highest order of oligomers observed. This latter effect was observed in both A40 and A42 as the Tyr substitution position number increased. The ability of a single substitution (Tyr 1 ) to alter A assembly kinetics and the oligomer frequency distribution suggests that the N terminus is not a benign peptide segment, but rather that A conformational dynamics and assembly are affected significantly by the competition between the N and C termini to form a stable complex with the central hydrophobic cluster.Alzheimer disease (AD) 4 is the most common cause of latelife dementia (1) and is estimated to afflict more than 27 million people worldwide (2). An important etiologic hypothesis is that amyloid -protein (A) oligomers are the proximate neurotoxins in AD. Substantial in vivo and in vitro evidence supports this hypothesis (3)(4)(5)(6)(7)(8)(9)(10)(11)(12). Neurotoxicity studies have shown that A assemblies are potent neurotoxins (5,(13)(14)(15)(16)(17)(18)(19)(20), and the toxicity of some oligomers can be greater than that of the corresponding fibrils (21). Soluble A oligomers inhibit hippocampal long term potentiation (4,5,13,15,17,18,22) and disrupt cognitive function (23). Compounds that bind and disrupt the formation of oligomers have been shown to block the neurotoxicity of A (24,25). Importantly, recent studies in higher vertebrates (dogs) have shown that substantial reduction in amyloid deposits in the absence of decreases in oligomer concentration has little effect on recovery of neurological function (26).Recent studies of A oligomers have sought to correlate oligomer size and biological activity. Oligomers in the supernatants of fibril preparations centrifuged at 100,000 ϫ g caused sustained calcium influx in rat hippocampal neurons, leading to calpain activati...