Peptide sections taken out the context of the protein in which they are present are often too small to support enough intra-peptide noncovalent interactions for the formation of any stable structure. Thus, in CD spectroscopy, they show up as being unfolded. However, it remains possible that a small fraction of the population of such a peptide is actually folded, and even folded into the native structural format, but because the fraction is very small it cannot be detected by any physical-chemical technique. Still, if the theoretical possibility exists that such fractional subpopulations are folded into native-like structural format, it would be useful to examine whether they can bind to surfaces on partially-unfolded or partially-folded forms of their parent proteins (i.e., the proteins from which the peptides are derived), and interfere with protein aggregation. One way of ensuring that there would be enough numbers of peptide molecules in native format would be to use a huge molar excess of the peptide over the protein. For example, one could use 0.5 micromolar protein, and 50 or 100 micromolar peptide, so that the numbers of native-like peptide molecules could rise to such levels that they could compete with protein surfaces and affect aggregation. Based on this argument, we used 15 overlapping 14-mer synthetic peptides derived from the entire sequence of gammaB lens crystallin (human), to examine the effects of including each of these peptides, in 100- to 200-fold molar excess over protein, in thermal aggregation reactions involving gammaB crystalline. To our great satisfaction, we identified two peptides that elicited a very significant aggregation-blocking effect. Both peptides corresponded to the only two small helices present in gammaBcrystallin, one in each of its bi-lobed double-Greek-key motif domains. GammaBcrystallin is a nearly completely beta-sheet-based protein with only two small helices on its surface. That we should have identified peptides corresponding to these as aggregation-blocking suggested that these helices are involved in the protein’s thermal aggregation. We have presented reason to hold that these helices transform into beta strands and engender intermolecular beta sheet formation during protein aggregation.

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