Homing In on the Molecular Determinants of Aβ Assembly and Toxicity: Lessons from the Computer, Test Tube, and Fly

The paper by Luheshi et al. describes the direct comparison of in silico, in vitro, and in vivo analysis of Aβ aggregation. It builds on many years of computational modeling by Vendruscolo and Dobson and animal modelling by Crowthers and Lomas, and it strongly suggests that protofibrillar assemblies of Aβ are the primary neurotoxic species both in their fly models and perhaps in brains of patients suffering with Alzheimer disease.

Using a previously described algorithm, the authors estimated intrinsic aggregation propensities of all 419 possible single point mutations of Aβ1-42 and all 379 single point mutations of the more toxic Aβ1-42E22G. Based on these data, they selected 15 mutations predicted to produce peptides with a broad range of aggregation propensities. The authors then generated flies transgenic for each of the 15 mutant peptides, plus flies transgenic for wild-type Aβ40 and Aβ42. In each case four to six independent lines for each of...  Read more

Homing In on the Molecular Determinants of Aβ Assembly and Toxicity: Lessons from the Computer, Test Tube, and Fly

The paper by Luheshi et al. describes the direct comparison of in silico, in vitro, and in vivo analysis of Aβ aggregation. It builds on many years of computational modeling by Vendruscolo and Dobson and animal modelling by Crowthers and Lomas, and it strongly suggests that protofibrillar assemblies of Aβ are the primary neurotoxic species both in their fly models and perhaps in brains of patients suffering with Alzheimer disease.

Using a previously described algorithm, the authors estimated intrinsic aggregation propensities of all 419 possible single point mutations of Aβ1-42 and all 379 single point mutations of the more toxic Aβ1-42E22G. Based on these data, they selected 15 mutations predicted to produce peptides with a broad range of aggregation propensities. The authors then generated flies transgenic for each of the 15 mutant peptides, plus flies transgenic for wild-type Aβ40 and Aβ42. In each case four to six independent lines for each of the 17 Aβ sequences were generated, i.e., a total of 68-102 different individual transgenic fly lines. After completing this gigantic task, the authors then set about characterizing the transgenic flies.

Certain mutations, such as E22G, caused a dramatic reduction in both the life span and locomotor ability of flies, whereas other mutations had the opposite effect. Strikingly, comparison of intrinsic aggregation propensity versus longevity or locomotor activity revealed a strong correlation. This demonstrates a direct link between aggregation and decreased locomotion/longevity.

However, the correlation was not perfect, and one particular mutation, I31E/E22G, did not fit this trend. In vitro analysis of the fibril-forming propensity of the I31E/E22G confirmed that this peptide had a similar aggregation propensity as did the E22G peptide. Moreover, when the authors examined brain from flies expressing I31E/E22G and E22G, they found highly similar levels of amyloid deposits. So if I31E/E22G flies had abundant amyloid deposits, why did they not exhibit a phenotype similar to E22G flies?

The suggested answer came from careful immunohistochemical analysis, which indicated that the E22G flies had not only profound Aβ deposition, but also substantial vacuolation, whereas vacuoles were absent in brains of I31E/E22G flies. Since both the I31E/E22G and E22G flies had abundant amyloid deposits, this led the authors to speculate that something other than amyloid fibrils was precipitating vacuole formation. Mindful of the burgeoning evidence that non-fibrillar soluble forms of Aβ play an important role in cognitive impairment, the authors revised their approach and developed a second algorithm designed to predict the relative propensity of proteins to form protofibrils (PFs). Comparison of predicted propensity of different Aβ mutations to form PF with the relative change in longevity or locomotor ability yielded a substantially improved correlation between that predicted in silico and that observed in flies.

This is an impressive piece of work, but like all leaps forward it raises more questions than it answers. Specifically, while the second algorithm was designed to predict PF forming propensity, it is not clear what the authors actually define as PF. Also unclear is whether the algorithm can predict the formation of structures other than PFs; for instance, what if the algorithm predicts the formation of low-n oligomers? Whatever the answer, it will be extremely interesting to isolate Aβ species from brains of the different mutant flies and attempt to identify the Aβ assembly form that precipitates their impaired locomotion and untimely death.

View all comments by Dominic Walsh

Aggregation Propensity of Aβ Predicts Longevity of Fly Model of AD
AD pathology is strongly associated with initial stages of amyloid-β protein (Aβ) aggregation. At different stages of Aβ assembly, Aβ oligomers, protofibrils, and fibrils are observed which differ in structure as well as toxic function. In particular, earlier assemblies, oligomers, are known to be toxic to cells in cell cultures and in a transgenic mouse model. While Aβ oligomers seem to be involved in cell death, it is a lot less clear how Aβ oligomers mediate their toxic function. There is an ongoing debate on intra- versus extracellular assembly processes that are associated with toxicity. There are numerous studies indicating strong and potentially disruptive interactions between Aβ oligomers and lipid bilayers, some suggesting that Aβ assemblies form ion channels in the cell membrane, thereby inducing abnormal calcium transport and consequently cell death. It is quite possible that there is more than one potentially toxic pathway of Aβ assembly.

Given the complexity of Aβ...  Read more

Aggregation Propensity of Aβ Predicts Longevity of Fly Model of AD
AD pathology is strongly associated with initial stages of amyloid-β protein (Aβ) aggregation. At different stages of Aβ assembly, Aβ oligomers, protofibrils, and fibrils are observed which differ in structure as well as toxic function. In particular, earlier assemblies, oligomers, are known to be toxic to cells in cell cultures and in a transgenic mouse model. While Aβ oligomers seem to be involved in cell death, it is a lot less clear how Aβ oligomers mediate their toxic function. There is an ongoing debate on intra- versus extracellular assembly processes that are associated with toxicity. There are numerous studies indicating strong and potentially disruptive interactions between Aβ oligomers and lipid bilayers, some suggesting that Aβ assemblies form ion channels in the cell membrane, thereby inducing abnormal calcium transport and consequently cell death. It is quite possible that there is more than one potentially toxic pathway of Aβ assembly.

Given the complexity of Aβ oligomer-mediated toxicity in humans and in transgenic mouse models, it is thus quite surprising to encounter a study that shows a clear correlation between the protein's primary structure, which determines its aggregation propensity, and in vivo consequences of such aggregation. In an extensive in vivo-->in silico study, Leila Luheshi and colleagues link the aggregation propensity of full-length Aβ to the neuronal dysfunction in a Drosophila model of AD. Luheshi et al. used single point mutations of Aβ42 wild-type (WT) and its Arctic mutant E22G in combination with a previously reported algorithm to calculate intrinsic aggregation propensities based only on the amino acid sequence. They selected 17 mutational variants out of 798 total, and expressed them throughout the central nervous system of fruit flies. The longevity and locomotor ability of multiple lines of flies for each variant were compared to Aβ42-WT and Aβ42-E22G. Luheshi et al. found a statistically significant correlation between the propensity of a variant to aggregate and its effect on the longevity as well as locomotor ability.

There were a few exceptions, most notably Aβ42-I31E/E22G, where there was no correlation between the predicted aggregation propensity (which was found to be similar to that of Aβ42-E22G) and its effect on longevity and locomotor ability. Further examination of the Aβ42-I31E/E22G showed that while this variant has a high propensity to aggregate into fibrils (similar to Aβ42-E22G), it does not create vacuoles in the brain of flies, which translates into a lack of neurodegeneration. When Luheshi et al. adjusted their computational approach to calculation of propensity to form protofibrils instead of fibrils, they found a significantly stronger correlation between the protofibril formation propensity and locomotor activity/longevity.

As Dominic Walsh noted before me, the definition of a protofibril that Luheshi et al. use in their redesigned computational approach is not clearly explained, but that is crucial to a deeper understanding of processes leading to various longevities of different fly variants. It is not necessarily clear what the cause of death of the flies was. Was a reduced/enhanced longevity in all variants related to increased/decreased neuronal loss? Did Aβ soluble oligomers form at all or is Aβ oligomerization inhibited in this animal model? In a naturally occurring human mutation, i.e., the E22G Arctic, protofibril formation is enhanced [1]. However, recent work by Cheng et al. in Lennart Mucke's lab demonstrated in transgenic mice that overexpress Aβ with the Arctic mutation a significantly higher propensity to form fibrils compared to the wild-type, but reduced functional deficits and reduced levels of deficit-causing Aβ*56 oligomers [2].

We have to be cautious when extrapolating results from one species to another, in particular because Aβ is very sensitive to relatively small changes in the environment, such as pH, and has a high propensity to interact with other proteins. The present findings by Luheshi et al. provide important insights into aberrant Aβ aggregation and its deleterious effects. They also raise a series of questions that will hopefully be addressed in future studies.

References:
[1] Nilsberth C, Westlind-Danielsson A, Eckman CB, Condron MM, Axelman K, Forsell C, Stenh C, Luthman J, Teplow DB, Younkin SG, Näslund J, Lannfelt L. The 'Arctic' APP mutation (E693G) causes Alzheimer's disease by enhanced Abeta protofibril formation. Nat Neurosci. 2001 Sep 1;4(9):887-93. Abstract

[2] Cheng IH, Scearce-Levie K, Legleiter J, Palop JJ, Gerstein H, Bien-Ly N, Puoliväli J, Lesné S, Ashe KH, Muchowski PJ, Mucke L. Accelerating amyloid-beta fibrillization reduces oligomer levels and functional deficits in Alzheimer disease mouse models. J Biol Chem. 2007 Aug 17;282(33):23818-28. Abstract

View all comments by Brigita Urbanc

On Computers, Flies, and Alzheimer Disease
Two recently published papers address the fundamental question of how amyloid proteins form neurotoxic assemblies (see Luheshi et al., 2007 and Cheon et al., 2007). Pat McCaffrey has written an informative and insightful news report that summarizes their key findings and implications. The work reported extends efforts by the ”Cambridge group” (broadly defined, and including those in Firenze, Italy; Busan, Korea; and Jülich, Germany) to explore ”generic” protein folding pathways and their biological consequences. In these latest publications, the group extends the idea of generic protein structures to generic toxicity, meaning that protein assemblies that share structural features also share toxic activity. Importantly, algorithms have been developed that allow prediction of assembly state and neurotoxicity from protein primary structure.

The technical rigor of the two studies is excellent. Thus, within the contexts of the...  Read more

On Computers, Flies, and Alzheimer Disease
Two recently published papers address the fundamental question of how amyloid proteins form neurotoxic assemblies (see Luheshi et al., 2007 and Cheon et al., 2007). Pat McCaffrey has written an informative and insightful news report that summarizes their key findings and implications. The work reported extends efforts by the ”Cambridge group” (broadly defined, and including those in Firenze, Italy; Busan, Korea; and Jülich, Germany) to explore ”generic” protein folding pathways and their biological consequences. In these latest publications, the group extends the idea of generic protein structures to generic toxicity, meaning that protein assemblies that share structural features also share toxic activity. Importantly, algorithms have been developed that allow prediction of assembly state and neurotoxicity from protein primary structure.

The technical rigor of the two studies is excellent. Thus, within the contexts of the experimental systems employed, namely in silico and in vivo (in Drosophila), one may have great confidence in the results. However, now comes the more philosophical and difficult question of meaning. Specifically, how do these results contribute to our understanding of diseases of protein folding?

In this brief discussion, I consider this question and raise a number of others for consideration by the reader. My goal in playing the metaphorical ”Devil's advocate” is to stimulate scientific discourse.

”Meaning” is a nebulous and malleable term for which a definition invariably depends upon the system of evaluation one employs. The goal of the studies of Luheshi et al. and Cheon et al. is to answer the questions of “... the molecular basis of amyloid formation and the nature of the toxic species.” In this context, it is reasonable to ask whether simulating the self-association of Aβ(16-22) or Aβ(25-35) has any relevance (meaning) to Alzheimer disease (AD) or any other disease. Why? Neither peptide is found in vivo. Historically, the former has been a favorite of theorists (including this writer), as its size makes it amenable to in silico study and it forms fibrils in vitro. The latter has been studied since 1990, when the suggestion was made that it was homologous to the tachykinin family of neuropeptides (Yankner et al., 1990). However, the homology relationship was tenuous (as are many when sequence length is so short), authentic tachykinin peptides had no trophic or toxic effects on neurons, and significant evidence supporting the tachykinin connection has not emerged in the subsequent 17 years. Thus, without compelling biological precedent, one must ask what study of these peptides can reveal. For example, are these peptides proxies for holo-Aβ? Clearly, the answer must be ”no,” as the critical determinant of peptide pathogenicity lies at the Aβ C-terminus in the form of the Ile-Ala dipeptide.

Why are people studying what may be irrelevant peptides, and why is such irrelevance not recognized? An answer may come from what, until recently, has been one of the most controversial and contentious fields of modern biology, i.e., prions. The prion theory postulates that the causative agent of a variety of neurodegenerative diseases in animals and humans is composed entirely of protein (no nucleic acid). In the last three decades, the status of this ”protein only” hypothesis in the scientific community has moved from heresy to orthodoxy. However, questions about the scientific appropriateness of this changing perspective have led some, including Laura Manuelidis, to suggest that a re-examination is warranted of ”the objectivity of science and whether it is a myth vanished.” Manuelidis opines that the acceptance of the theory reflects "the peculiarly American sport of betting on popular momentum” (Manuelidis, 2000). A more apropos metaphor, considering that one prion disease is bovine spongiform encephalopathy (“Mad Cow” disease), might have been that of “following the herd.”

Much research on AD could be subject to the same type of criticism. Consider the example of what may be called the "generic” herd. This herd believes that amyloid structure is "generic” because many (most? all?) proteins form amyloids with some common structural organization. Although amyloids, by definition, do share a number of biophysical and spectroscopic features, great structural diversity may be found in the assemblies formed by classical and non-classical amyloid proteins and peptides (e.g., see Sawaya et al., 2007). Importantly, no generic structure outside of the cross-β core of the amyloid fibril has been shown to exist, for obvious reasons. Regions outside of the core, which can be quite extensive in protein, as opposed to peptide amyloids, are likely to influence the biological behavior of the assemblies significantly.

Now, Cheon and colleagues suggest that amyloid formation involves a second generic process, a two-step mechanism of “collapse” of monomers and their subsequent rearrangement into amyloid fibrils. This idea appears to invoke known processes of globular protein folding in the context of amyloid formation, specifically the classical idea of hydrophobic collapse into a molten globule followed by proper arrangement of secondary structure elements to form the native tertiary structure. The idea that some peptides bypass this two-step pathway if they can immediately form hydrogen bonds in their eventual cross-β organization is quite interesting. However, although plausible for short, disordered peptides of the sort studied here, what happens in the common case of natively folded proteins forming amyloid? Here, and as the authors themselves suggest implicitly, factors other than the intrinsic properties of the protein monomer likely moderate amyloid assembly. This increased complexity requires me to question the value of this suggestion of generic mechanisms. Scientists, especially medicinal chemists, need targets. Does a “generic amyloid target” exist? Could a single compound directed at such a target be of value in the treatment of the greater than two score amyloid diseases defined thus far?

Maybe a generic target does exist. In Luheshi et al., studies of the effects of expression of human Aβ42 in Drosophila suggest that protofibril formation correlates with neuronal dysfunction and neurodegeneration. In addition, in a kind of Anfinsen redux (Anfinsen, 1973), an algorithm has been created to predict from primary structure alone the propensity of a protein to form toxic protofibrils. My question: Does the experimental assessment of Aβ-induced locomotor and longevity effects in flies, and its correlation with the toxicity metric, have any relevance to the consideration of Aβ-induced disease in humans? Granted, the same question is sometimes raised as gratuitous criticism of work in a variety of non-human animal models, and it is an easy concern to raise, but that does not diminish the significance of the question.

In closing, it may appear to some that the answers to the questions I have asked are implicit in the construction of the questions themselves. This certainly was not my intention. From a purely academic perspective, I found the publications rigorous, enjoyable to read, and quite thought-provoking. It is the provocation aspect of the experience that operates here, particularly with respect to establishing the meaning of the results and their impact on our shared efforts to understand and treat diseases of aberrant protein folding and assembly.

View all comments by David Teplow

Reply by Leila M. Luheshi, Giorgio Favrin, Damian C. Crowther, Michele Vendruscolo, and Christopher M. Dobson to Teplow Comment
We are pleased to have the opportunity of adding further observations to a recent commentary by David Teplow about the “generic hypothesis” of amyloid fibril formation (1). According to this hypothesis, the ability to form amyloid structures is an inherent property of polypeptide chains, although the propensity to form such structures can vary dramatically with their sequences (2).

This hypothesis is supported by a growing body of experimental evidence that has been summarized in a number of recent reviews (3). The generic nature of amyloid fibrils resides in their core cross-β structure, which is stabilized predominantly by backbone hydrogen bonding interactions (4). It has also been recently discovered that the range of proteins capable of forming toxic oligomers, that may well be precursors to mature amyloid fibrils, is very large and includes those with no known association with disease (5-7). Of course, there are many additional...  Read more

Reply by Leila M. Luheshi, Giorgio Favrin, Damian C. Crowther, Michele Vendruscolo, and Christopher M. Dobson to Teplow Comment
We are pleased to have the opportunity of adding further observations to a recent commentary by David Teplow about the “generic hypothesis” of amyloid fibril formation (1). According to this hypothesis, the ability to form amyloid structures is an inherent property of polypeptide chains, although the propensity to form such structures can vary dramatically with their sequences (2).

This hypothesis is supported by a growing body of experimental evidence that has been summarized in a number of recent reviews (3). The generic nature of amyloid fibrils resides in their core cross-β structure, which is stabilized predominantly by backbone hydrogen bonding interactions (4). It has also been recently discovered that the range of proteins capable of forming toxic oligomers, that may well be precursors to mature amyloid fibrils, is very large and includes those with no known association with disease (5-7). Of course, there are many additional complexities involved in misfolding diseases, and it is also clear that the aggregation of different proteins in vitro does result in fibrils of different morphologies, and the aggregation of different proteins in vivo causes diseases with very different characteristics.

So far the generic hypothesis has provided the inspiration for a number of innovative studies, including the two mentioned by David Teplow (8, 9). We have been astonished by the way that the principles observed in the test tube and in the computer are able to explain the behavior and lifespan of living organisms such as Drosophila. We are therefore optimistic that the insights such studies have given us will lead, in the next few years, to the development of effective therapeutic strategies to combat the debilitating and increasingly prevalent diseases associated with protein misfolding.

References:
1. Dobson CM. Protein misfolding, evolution and disease. Trends Biochem Sci. 1999 Sep;24(9):329-32. Review. No abstract available. Abstract

2. Chiti F, Stefani M, Taddei N, Ramponi G, Dobson CM. Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature. 2003 Aug 14;424(6950):805-8. Abstract

3. Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem. 2006;75:333-66. Review. Abstract

4. Knowles, T. P. J. et al. The Role of Inter-Molecular Forces in Defining the Material Properties of Fibrillar Protein Nanostructures. Science (2007) in press.

5. Bucciantini M, Giannoni E, Chiti F, Baroni F, Formigli L, Zurdo J, Taddei N, Ramponi G, Dobson CM, Stefani M. Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature. 2002 Apr 4;416(6880):507-11. Abstract

6. Baglioni S, Casamenti F, Bucciantini M, Luheshi LM, Taddei N, Chiti F, Dobson CM, Stefani M. Prefibrillar amyloid aggregates could be generic toxins in higher organisms. J Neurosci. 2006 Aug 2;26(31):8160-7. Abstract

7. Kayed R, Glabe CG. Conformation-dependent anti-amyloid oligomer antibodies. Methods Enzymol. 2006;413:326-44. Abstract

8. Luheshi LM, Tartaglia GG, Brorsson AC, Pawar AP, Watson IE, Chiti F, Vendruscolo M, Lomas DA, Dobson CM, Crowther DC. Systematic in vivo analysis of the intrinsic determinants of amyloid Beta pathogenicity. PLoS Biol. 2007 Oct 30;5(11):e290. Abstract

9. Cheon M, Chang I, Mohanty S, Luheshi LM, Dobson CM, Vendruscolo M, Favrin G. Structural reorganisation and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils. PLoS Comput Biol. 2007 Sep 14;3(9):1727-38. Abstract

View all comments by Leila Luheshi