The Goldilocks Scenario:
Just the Right pH May Be Key to Early Amyloid Plaque Formation

By Eric Sauter

With the tsunami of Alzheimer's gathering speed—as many as 16 million Americans may be afflicted by 2050—new understanding of the disease is welcome for efforts to help slow, or even stop, the disaster headed our way.

Now, a computer simulation study by a pair of Scripps Research Institute scientists has revealed a novel pH-dependent molecular mechanism for the early aggregation of β-amyloid peptides, something that may offer a tempting new target for attacking amyloid at its earliest stage, shutting off the disease at what many consider to be its source.

The study was published in an advance online edition of the Proceedings of the National Academy of Sciences on October 17, 2007.

"Our study opens the door to critical questions concerning pH-dependent amyloid aggregation, and may, ultimately, provide a means of arresting that process," said Charles L. Brooks III, a Scripps Research professor in molecular biology. "We are excited about the fact that a great deal of disparate data concerning pH levels and amyloid aggregation has now been made clearer and connectable."

The study, which was conducted by Brooks and Jana Khandogin, a Brooks lab alumnus who is now an assistant professor at the University of Oklahoma, strongly supports the current theory that pre-fibrilar species of β-amyloid peptide (Aβ) may be the culprit of Alzheimer's disease, and that a very specific pH level makes the initial development of this peptide species possible.

In Alzheimer's disease, it is hypothesized that small bits of β-amyloid peptide—called oligomers—form in endosomes (a membrane-bound compartment inside cells) and are then expelled into the extracellular fluid, where they may start to disrupt neuronal activity and develop into amyloid fibrils (clumps). Protein aggregation and fibril formation have also been implicated in at least 16 other diseases, including Parkinson's and Huntington's.

"We know that in biological systems and cell compartments molecules are constantly bathed in various pH values," Brooks said. "It seems obvious that changes in pH levels should have influence on conformational changes—and the functioning or misfunctioning of proteins like the β-amyloid peptides."

To explore the impact of pH on biological processes like amyloid aggregation, Brooks and Khandogin used computer simulation techniques to focus on a pair of model peptides, Aβ (1-28) and Aβ (10-42). The scientists found that the folding landscape of the peptides was strongly modulated by pH—and that the most favorable aggregation environment was pH 6; basically the same as milk.

"That pH is like the Goldilocks equivalent of porridge," Brooks said. "Not too hot, not too cold. At pH 6, the peptides adopt conformations that are very 'fibril-friendly'—that is, they're already poised to form larger sheet-based oligomers, the next step up the toxicity ladder. As a result, our theoretical findings substantiate the possibility that Aβ oligomers are formed first in endosomes."

To achieve these results, the scientists built on the Brooks laboratory's computer simulation work on molecular dynamics, which has provided detailed information on the fluctuations and conformational changes of proteins and nucleic acids—basically, a kind of time lapse record that sheds light on the relationship between motion, structure, and function. In the current study, the scientists introduced a method called continuous constant pH molecular dynamics (CPHMD), which enables scientists to couple conformational dynamics with changes in pH levels.

Previous to this technique, including pH levels as part of modern molecular simulations was a fairly ad hoc operation. The technique may lead to new insights for a range of scientific problems.

"Combining our CPHMD method with a state-of-the-art conformational sampling protocol, our own theoretical framework, and other factors, has allowed us to develop a general predictive methodology to help determine how conformational changes are influenced by pH," Brooks said. "And because it is general, our methodology can be used to define the role of pH in mediating any number of other biological processes."

The study, Linking Folding With Aggregation In Alzheimer's β-Amyloid Peptides, was supported by the National Institutes of Health. For more information, see PNAS at http://www.pnas.org/cgi/content/abstract/0703832104v1.

Send comments to: mikaono[at]scripps.edu

"We are excited about the fact that a great deal of disparate data concerning pH levels and amyloid aggregation has now been made clearer and connectable," said Professor Charles L. Brooks III.