Is it possible that amyloid formation of a proteins doesn't always happen even though I did the same process for replications? Sometimes they aggregate and form amyloid however sometimes there is no aggregation. Do you have anything that I have to be aware of aside from pH and incubation temperature?
When working with protein fibrillation, keep in mind that higher protein concentrations often boost fibrillation. The salt concentration in the solution affects how quickly aggregation occurs—higher salt, faster aggregation. Also, be cautious with freezing/thawing cycles of the protein you are working, as they can influence the fibrillation process. Good luck!
When performing amyloid aggregation assays, mechanical stress may also boost fibrillation. You can either use sonication or shaking. Also, be cautious that the frequency and time of sonication and the orientation (oribital/linear/double orbital etc), speed (rpm) and duration of shaking can influence the aggregation process. Also, addition of silica beads helps in maintaining homogeneity. All the best!
The factors that are important to amyloid formation will be somewhat specific to your protein. The suggestions above are good ones, but I would look into the literature for your protein to see what others have done to generate amyloid. Different approaches can produce different morphologies. It would be helpful to the people trying to help you to know:
1. what protein you are working with
2. what solution conditions you are currently attempting
3. what your goal is
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