Simulating the first steps of amyloid peptides aggregation

Jessica Nasica

Département de physique - Université de Montréal

GEPROM – 2ième réunion scientifique

May 27th, 2009

Overview of the presentation Medical interest

Problem of amyloid fibril formation

Our simulations & results

Protein misfolding and aggregationMany protein-misfolding diseases include conditions where a protein

forms insoluble aggregates, amyloid fibrils, that deposit toxically Amyloid diseases

e.g. : - Alzheimer’s- Parkinson’s- Huntington- type II diabetes

Dobson et al. (2003), Nature 426

Amyloid fibril formationAmyloid fibrils insoluble fibrous aggregates with a highly organized Macrostructure made of β-sheets.

Mechanism of formation 3 steps:1. Alignment of the molecules to form β-sheets fastest stage

involves H-bonds

2. Formation of the cross-β structure slower than step 1 involves Van-der-Waals forces interdigitation of residues side chains “steric zipper” structure

3. Fibril formation involves non-covalent bonds

Amyloid fibril formation is a nucleated-growth process stabilized by the protein concentration and by the formation of steric zippers

Nelson et al. (2005), Nature 435

Amyloid fibril polymorphism

Petkova et al. (2006), Biochemistry 45Paravastu et al. (2008), PNAS 105 &

For the Aβ40 sequence, they construct a full molecular model showing 2 distinct possible morphologies for the fibril structure.

Amyloid oligomers

intermediate states during the formation of amyloid fibrils

thought to be more toxic than the fibrils themselves

Different types of soluble amyloid oligomers share a common structure suggests they share a common toxicity mechanism

Lashuel et al. (2002), Nature 418

Kayed et al. (2003), Science 300

Theories on intermediate oligomer states Oligomers as protofibrils

Oligomers as pores may form annular pore-like structures to go through the cell membranes : β-barrel

Irbäck et al. (2007), Proteins 71

Esposito et al. (2006), PNAS 103

Lashuel et al. (2008), Nature 418

Amyloid oligomer pore structure observed experimentally (left) & numerically (right)

The “short peptides” approach

The gain-of-interaction model for amyloid structure suggests that

only a small portion of a native protein is responsible for amyloid fibrils.

Under conformational changes

this small portion is exposed & binds to an identical portion on another molecule

builds up a fibril

or

Cross-β spine (no domain swapping) Cross-β spine with domain swapping

The essential element involved in the fibril structure is the small portion

Nelson et al. (2006), Current opinion in structural biology 16

GNNQQNY GNNQQNY

For the budding yeast Sup35p fibril-forming protein

Experiments done on GNNQQNY

Nelson et al. (2005), Nature 435

Atomic structure of cross-β spine constructed from X-ray diffraction analysis

Fomation of a double β-sheet with parallel β-stands

Side chains form a self-complementing steric zipper

Interdigitation of the side-chains would stabilize the sheets

Our short-term goals

To understand the aggregation process of short peptides Kinetics of aggregation Final structures (morphologies accessible)

To study different sizes of systems Trimer GNNQQNY Pentamer GNNQQNY 20-mer GNNQQNY 50-mer GNNQQNY

Our simulation methodsReplica exchange MD

1. launch n molecular dynamical simulations in parallel, at n different temperatures

2. at regular intervals, try an exchange of configurations between two adjacent temperatures using a Metropolis accept-reject criterion

REMD accelerates sampling (in some cases) for the cost of losing dynamical information.

REMD still provides thermodynamical information

Final structures of simulations tested with an all-atom potential (GROMACS)

Our simulations : small aggregates

GNNQQNY trimer

GNNQQNY pentamer

We observe a strong tendency to form planar β-sheets

Our simulations : bigger aggregates GNNQQNY 20-mer – 300 ns simulation

Formation of twisted pair-of-sheet “protofibril-like” structuresFormation of β-barrel-like structures

Similar to the atomic structure described by Nelson et al. (2005)

GNNQQNY 20-mer results

We observe a nucleated-growth aggregation process

a clear loss of entropy as the energy of the system drops rapidly

&

GNNQQNY 20-mer results β-sheets favor a parallel orientation of the β-strands Consistent with the atomic description given by Nelson et al. (2005)

Statistics over 300 ns

Conclusions

We have described the first steps of aggregation of GNNQQNY. The results are consistent with experimental results on that sequence.

Polymorphism exists and we already see a clear separation between 2 different semi-organized structures.

The obtained β-barrel-like structures might not be on the fibril formation pathway. It seems it is a separate possible morphology.

For small aggregates (trimers, pentamers), the study of 2 other sequences (SSTSAA,SNQNNF) shows similar features compatible with the GNNQQNY results.

Future work Lots of statistics obtained from our 20-mer

simulations a lot of the analysis is still being done to understand

The formation process The triggering of the nucleated-growth process

Simulation of the GNNQQNY 50-mer

Simulation on other short sequences (SSTSAA, SNQNNF,…)

Acknowledgments

Collaborators

MONTREAL- Normand Mousseau

PARIS- Philippe Derreumaux

MILAN- Giorgio Colombo- Massimiliano Meli (Ph.D.)

Funding

- GEPROM- CRSNG- FESP

Resources

- Réseau québécois de calcul de haute performance

Special thanks to:Rozita Laghaei (post-doc), Lilianne Dupuis (Ph.D.) and Jean-François St-Pierre (Ph.D.)