Amyloid fibrils

Aldo Rampioni

Meeting EMBIO project, Vienna, May 2006

What is the signature of amyloid fibrils?

• Fibrils bind the dye Congo red, resulting in a green birefringence under polirized light

• Electron Microscopy and Atomic Force Microscopy reveal that fibrils are typically long, unbranched and ≈ 100 Å in diameter

• X-ray diffraction indicates an ordered cross-β structure which consists of β-sheets running parallel (and the peptides strands perpendicular) to the fibril axis

From cryo-EM:Ribbon-like structure whose height is always multiple of ≈ 21 Å

multiple layers

From X-ray diffraction:A characteristic distance of ≈ 5 Å between β-strands in the same β-sheetTwo distances around

1 nm that arise from face-to-face separation of β-sheetsImage from M.L. de la Paz et al. Proc. Natl. Acad. Sci. USA, vol 99, 2002

OPEN PROBLEMS:

• STRUCTURE AT ATOMIC DETAIL

• PROCESS OF FORMATION

• TOXICITY

Three-dimensional structure of the transthyretin-retinol-binding protein complex.

The tetrameric transthyretin is shown in blue, light blue, green and yellow.  The retinol binding protein is shown in red and the retinol is shown in grey. TTR is found in plasma and cerebrospinal fluid and is composed of four identical 127 aminoacid subunits.

Function: the tetrameric structure binds and transports thyrosine and retinol binding protein.

To develop a model of fibril I am performing the following simulations in explicit solvent:

•Improper Dihedral Restraints on one peptide (in order to let it assume the structure determined by using NMR)

•Distance Restrains among peptides (in order to bring them close, but still free to arrange)

The main idea is to restraint the system in order to get an amyloid-like structure (trying both parallel and antiparallel beta sheets) letting it free to arrange…

…Until we get a stable multi-layer fibril and we can remove the restraints

From NMR we have informations about the structure of the single peptide in the fibril:

Improper dihedrals (choosen such that the experimental error on dihedral angles is of the order of kT, i.e. stochatstic perturbation)

Image from C.P. Jaroniec et al. Proc. Natl. Acad. Sci. USA, vol 101, p.711, 2004

We introduce distance restraints compatible with X-ray diffraction data:

So far we have performed short simulations (5 or 10 ns) for systems composed by

2,3,4,5,6,12,24 peptides

parallel

antiparallel

On which we have changed restraints:

•applying improper dihedrals on all peptides or just one

•changing the window and the multiplicative constant of distance restraints

4 antiparallel peptides

K=0.26 antiparallel peptides

K=1

6 parallel peptidesk=1

5 parallel peptidesk=0.2

4 parallel peptides

k=2

4 layers of 6 antiparallel

peptides

Is it possible to simulate the Is it possible to simulate the -sheet -sheet aggregate? aggregate?

Molecular Dynamics simulations to investigate Molecular Dynamics simulations to investigate stability of suprastructures of SIVwt stability of suprastructures of SIVwt

peptide aggregates in DMSOpeptide aggregates in DMSO

Frame at TinitialDistance between chain#1 and #30: ~12 nm

Simulation box with 30 parallel chains of SIVwt peptide in DMSO.Amount of particles: ~ 30000

The simulations show the spontaneous helical twisting of the The simulations show the spontaneous helical twisting of the protofibrilprotofibril

Patrica Soto

Spontaneous twisting…Spontaneous twisting…

t = 35 ns

t = 10 ns t = 20

ns

t = 0 ns

t = 50 ns

•Parallel or antiparallel?

•Chirality

•Twisted ribbon as energetically more favorable geometry

Patrica Soto

SIVwt peptide spontaneously aggregates into SIVwt peptide spontaneously aggregates into stable clusters that exhibit high population of stable clusters that exhibit high population of

-sheet secondary structure-sheet secondary structure

Is it possible to simulate the spontaneous Is it possible to simulate the spontaneous aggregation into ordered aggregation into ordered -sheet aggregates?-sheet aggregates?

Solvent: hexaneSolvent: hexane

t = 0nst = 2 ns

t = 20ns t = 50ns

t = 75ns

t = 90ns

Patrica Soto

Is it possible to simulate the spontaneous Is it possible to simulate the spontaneous aggregation into ordered aggregation into ordered -sheet aggregates?-sheet aggregates?

Solvent: waterSolvent: water

SIVwt peptide spontaneously aggregates into SIVwt peptide spontaneously aggregates into stable clusters that exhibit high population of stable clusters that exhibit high population of

-sheet secondary structure-sheet secondary structure

t = 0ns

t = 2ns

t = 35ns

t = 50ns

Patrica Soto

System studied:

7-residue peptide from Sup35Gly Asn Asn Gln Gln Asn Tyr

Picture from Nelson R. et al., 2005, Nature, 435, 773-778

This project is in collaboration with:

• Xavier Periole, University of Groningen, The Netherlands

• Alan Mark, University of Queensland, Brisbane, Ausralia

• Michele Vendruscolo, University of Cambridge, UK

Image from H.D. Nguyen and C.K. Hall . Proc. Natl. Acad. Sci. USA, vol 101, 2004