The amyloid pharmacophore

Binding of Small Molecules to Fibers associated with Alzheimer's disease


In this website you can find crystal structures of amyloid-like peptide segments complexed with small molecule binders.

The structures were determined by Meytal Landau at David Eisenberg's Lab at UCLA.


Primary citation:

Towards a Pharmacophore for Amyloid.  
Meytal Landau, Michael R. Sawaya, Kym F. Faull, Arthur Laganowsky, Lin Jiang, Stuart Sievers, Jie Liu, Jorge R. Barrio and David Eisenberg.
PLoS Biol 9(6):e1001080. (2011)
doi:10.1371/journal.pbio.1001080



Available structures:

  1. A crystal structure of the KLVFFA segment from Aβ complexed with orangeG

  2. Negative Control - A crystal structure of the KLVFFA segment from Aβ grown under the same crystallization conditions as the KLVFFA complexed with orangeG

  3. A crystal structures of the VQIVYK segment from the tau protein complexed with orange-G

  4. *** Note - Crystals of the VQIVYK segment from the tau protein grown under the same crystallization conditions as the VQIVYK complexed with orange-G are colorless, fibrous, and show poor x-ray diffraction.


  5. A crystal structure of the VQIVYK segment from the tau protein complexed with curcumin

  6. Negative Control - A crystal structure of the VQIVYK segment from the tau protein grown under the same crystallization conditions as the VQIVYK complexed with curcumin

  7. A crystal structure of the VQIVYK segment from the tau protein complexed with DDNP

  8. Negative Control - A crystal structure of the VQIVYK segment from the tau protein grown under the same crystallization conditions as the VQIVYK complexed with DDNP

  9. Positive Control - A crystal structure of the VQIVYK segment from the tau protein complexed with DDNP grown under alternative crystallization conditions





A crystal structure of the KLVFFA segment from Aβ complexed with orangeG

PDB ID:3OVJ

The KLVFFA segment (residues 16-21) from Aβ contains apolar residues that are believed to participate in a hydrophobic core in Aβ fibers [1], and, like whole Aβ, interacts with orange G.
Orange-G, a synthetic azo dye used in histological staining, was shown to inhibit the formation of Aβ fibers and attenuate their toxic effects [2, 3].


Here you can find:

Coordinate file

Structure-Factor file (MTZ)

Fiber structure

Crystallographic Table



KLVFFA with orange G

The crystal structure of the KLVFFA segment from Amyloid-β complexed with orangeG.

A-B.The KLVFFA segments are packed as pairs of β-sheets forming the basic unit of the fiber, namely the steric zipper [4, 5]. Here 10 layers are depicted; actual fibers contain ~100,000 layers. Orange-G (orange carbons) opens the zipper and binds between the pair of β-sheets. KLVFFA and orange-G are shown as sticks with non-carbon atoms colored by atom type. The β-sheets are composed of anti-parallel strands (represented as cartoon arrows and sticks), alternately colored white and blue. In panel A the view looks down the fiber axis. In panel B the view is perpendicular to the fiber axis; the β-strands run horizontally. The sulfonic acid groups of orange-G form salt links (dashed pink lines) with four lysine residues, two protruding from each facing β-sheet and with a water molecule shown as an aqua sphere. Only side chain atoms are shown. The unit cell dimension of the crystal along the fiber axis (9.54Å) is indicated. D. Micro-crystals of KLVFFA co-crystallized with orange-G.




Negative Control - A crystal structure of the KLVFFA segment from Aβ grown under the same crystallization conditions as the KLVFFA complexed with orangeG


Here you can find:

Coordinate file

Structure-Factor file (MTZ)

Fiber structure

Crystallographic Table



Neg ctrl xtals to KLVFFA with orange G

Crystals of the KLVFFA segment from Aβ grown with and without orange-G.

A-B.Micro-crystals of the KLVFFA segment of Amyloid-β grown under identical conditions with (A) and without (B) orange-G.




A crystal structure of the VQIVYK segment from the tau protein complexed with orange-G

PDB ID:3OVL

The VQIVYK segment was suggested to contain the minimal interaction motif in the fiber formation of the tau protein, a random-coil protein [6].


Here you can find:

Coordinate file

Structure-Factor file (MTZ)

Fiber structure

Crystallographic Table



VQIVYK with orange G

The crystal structure of the VQIVYK segment from the tau protein complexed with orange-G.

A-C.The VQIVYK segments pack in parallel, in-register β-sheets (represented as cartoon arrows) that form steric zippers (two are shown in panel A). Nine layers of the fiber are depicted. VQIVYK and orange-G are shown as sticks with non-carbon atoms colored by atom type. The carbons of VQIVYK are colored white for one steric zipper and blue for the other. Two orange-G molecules (orange carbons) mediate contacts between two pairs of steric zippers; that is, orange-G is located between the protofilaments composing the fiber. In panel A, the view looks down the fiber axis. In panels B, the view is perpendicular to the fiber axis. Only the two sheets that are in contact with orange-G are shown. Backbone atoms are not shown. The unit cell dimension of the crystal along the fiber axis (4.83Å) is indicated. The length of orange-G spans multiple unit cells of the fibril; that is, the dimensions of the small molecule and the fibril unit cell were incommensurate (supporting online text). Panel C is an inset of panel B, focusing on the network of salt links (dashed pink lines) between the sulfonic acid groups of two orange-G molecules and six lysine residues and with zinc cations (brown spheres). D. Micro-crystals of VQIVYK co-crystallized with orange-G.




Negative Control - Crystals of the VQIVYK segment from the tau protein grown in the same crystallization conditions as the VQIVYK complexed with orange-G are colorless, fibrous, and show poor x-ray diffraction.

VQIVYK with orange G xtals

Crystals of the VQIVYK segment from the tau protein grown with and without orange-G.

A-B. Micro-crystals of the VQIVYK segment of the tau protein grown under identical conditions with (A) and without (B) orange-G.




A crystal structure of the VQIVYK segment from the tau protein complexed with curcumin

Curcumin, the active ingredient in the plant turmeric (Curcuma Longa), was shown to inhibit amyloid fiber formation and to protect neuronal cells against toxicity [7-9].


Here you can find:

Coordinate file

Structure-Factor file (MTZ)

Fiber structure

Crystallographic Table



VQIVYK with CUR

Models of curcumin bound to the VQIVYK fiber based on undifferentiated electron density.

Panel A is micro-crystals of VQIVYK co-crystallized with curcumin. B-C. In the structure of the complexes with curcumin, VQIVYK is packed in a unique form having a steric zipper with one β-sheet shifted in relation to the other β-sheet. Six layers of the fiber are depicted. VQIVYK and curcumin are shown as sticks with non-carbon atoms colored by atom type. The carbons of VQIVYK are colored white for one steric zipper and blue for the other. In panel B, the view looks down the fiber axis. In panels C, the view is perpendicular to the fiber axis. Only the VQIVYK segment is modelled into the electron density; there is an apparent difference electron density Fo-Fc map (shown as mesh, +3σ in green and -3σ in red) located in the void formed by the shift of the steric zipper. The positive density (part of the structure that has not been modelled, green mesh) displays a continuous tube-like shape, running along the fiber axis. We attribute this density to the presence of the small molecule, yet it is too undifferentiated to fit atoms in detail. curcumin (magenta carbons) have been computationally docked [10, 11] into the structures and fit the location of the positive density. The length of curcumin spans multiple unit cells of the fibril; that is, the dimensions of the small molecule and the fibril unit cell were incommensurate (supporting online text).




Negative Control - A crystal structure of the VQIVYK segment from the tau protein grown under the same crystallization conditions as the VQIVYK complexed with curcumin


Here you can find:

Coordinate file

Structure-Factor file (MTZ)

Fiber structure

Crystallographic Table



VQIVYK with CUR

Crystal structures used as controls for the complex of the VQIVYK segment from the tau protein with curcumin.

A. Micro-crystals of VQIVYK co-crystallized with curcumin; the structure is shown in panel B.
D. Micro-crystals of VQIVYK crystallized under identical conditions to the crystals in panel A, lacking curcumin. The structure is shown in panel C.
In panels B-C, six layer of the VQIVYK fiber are depicted. The VQIVYK segment pack in parallel β-sheets (represented as cartoon arrows with white carbons). The view is perpendicular to the fiber axis, with β-strands running horizontally. Only the VQIVYK segment was modelled into the electron density. The difference electron density Fo-Fc map is shown as mesh (+3σ in green and -3σ in red).
The crystals grown without curcumin (panel D), are colorless, whereas the co-crystals are yellow (panel A). Moreover, the VQIVYKapo structure (panel C) also lack the positive density (part of the structure that has not been modelled, panel B - green mesh) that we attribute to the presence of the curcumin.




A crystal structure of the VQIVYK segment from the tau protein complexed with DDNP

DDNP[10], and its analogs, synthetic diagnostics, were shown to bind Alzheimer’s-associated neurofibrillary tangles and β-amyloid senile plaques, and are used for the in vitro and in vivo detection of plaques in the brains of Alzheimer's disease patients [11,12].


Here you can find:

Coordinate file

Structure-Factor file (MTZ)

Fiber structure

Crystallographic Table



VQIVYK with DDNP

Models of DDNP bound to the VQIVYK fiber based on undifferentiated electron density.

Panel A is micro-crystals of VQIVYK co-crystallized with DDNP. B-C. In the structure of the complexe with DDNP, VQIVYK is packed in a unique form having a steric zipper with one β-sheet shifted in relation to the other β-sheet. Six layers of the fiber are depicted. VQIVYK and DDNP are shown as sticks with non-carbon atoms colored by atom type. The carbons of VQIVYK are colored white for one steric zipper and blue for the other. In panel B, the view looks down the fiber axis. In panel C, the view is perpendicular to the fiber axis. Only the VQIVYK segment is modelled into the electron density; there is an apparent difference electron density Fo-Fc map (shown as mesh, +3σ in green and -3σ in red) located in the void formed by the shift of the steric zipper. The positive density (part of the structure that has not been modelled, green mesh) displays a continuous tube-like shape, running along the fiber axis. We attribute this density to the presence of the small molecule, yet it is too undifferentiated to fit atoms in detail. DDNP (two molecules are shown, magenta carbons) have been computationally docked [10, 11] into the structures and fit the location of the positive density. The length of DDNP spans multiple unit cells of the fibril; that is, the dimensions of the small molecule and the fibril unit cell were incommensurate (supporting online text).




Negative Control - A crystal structure of the VQIVYK segment from the tau protein grown under the same crystallization conditions as the VQIVYK complexed with DDNP


Here you can find:

Coordinate file

Structure-Factor file (MTZ)

Fiber structure

Crystallographic Table



Positive Control - A crystal structure of the VQIVYK segment from the tau protein complexed with DDNP grown under alternative crystallization conditions


Here you can find:

Coordinate file

Structure-Factor file (MTZ)

Fiber structure

Crystallographic Table



VQIVYK with DDNP Xtals

Crystal structures used as controls for the complexe of the VQIVYK segment from the tau protein with DDNP.

A. Micro-crystals of VQIVYK co-crystallized with DDNP; the structure is shown in panel C. B. Micro-crystals of VQIVYK crystallized under identical conditions to the crystals in panel A, lacking DDNP (see Methods). The structure is shown in panel E. D. The structure of VQIVYK co-crystallized with DDNP, grown under different crystallization conditions than the structure shown in panel C.
In panels C-E, six layer of the VQIVYK fiber are depicted. The VQIVYK segment pack in parallel β-sheets (represented as cartoon arrows with white carbons). The view is perpendicular to the fiber axis, with β-strands running horizontally. Only the VQIVYK segment was modelled into the electron density. The difference electron density Fo-Fc map is shown as mesh (+3σ in green and -3σ in red).
The crystals grown without DDNP (panel B), are colorless, whereas the co-crystals are yellow (panel A). Moreover, the VQIVYKapo structure (panel E) also lack the positive density (part of the structure that has not been modelled, panel C - green columns) that we attribute to the presence of DDNP.
Both structures of VQIVYK complexed with DDNP, grown under different crystallization conditions (panels C and D), show a similar, tube-like, positive electron density map, supporting the attribution of DDNP to this density.



References

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  2. M. Necula, R. Kayed, S. Milton, C. G. Glabe, Small molecule inhibitors of aggregation indicate that amyloid beta oligomerization and fibrillization pathways are independent and distinct. J. Biol. Chem. 282, 10311 (2007).

  3. S. J. Pollack, Sadler, II, S. R. Hawtin, V. J. Tailor, M. S. Shearman, Sulfonated dyes attenuate the toxic effects of beta-amyloid in a structure-specific fashion. Neurosci. Lett. 197, 211 (1995).

  4. R. Nelson, D. Eisenberg, Recent atomic models of amyloid fibril structure. Curr. Opin. Struct. Biol. 16, 260 (2006).

  5. M. R. Sawaya et al., Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature 447, 453 (2007).

  6. M. von Bergen et al., Assembly of tau protein into Alzheimer paired helical filaments depends on a local sequence motif ((306)VQIVYK(311)) forming beta structure. Proc. Natl. Acad. Sci. U. S. A. 97, 5129 (2000).

  7. Q. L. Ma et al., Beta-amyloid oligomers induce phosphorylation of tau and inactivation of insulin receptor substrate via c-Jun N-terminal kinase signaling: suppression by omega-3 fatty acids and curcumin. J. Neurosci. 29, 9078 (2009).

  8. R. Narlawar et al., Curcumin-derived pyrazoles and isoxazoles: Swiss army knives or blunt tools for Alzheimer's disease? ChemMedChem 3, 165 (2008).

  9. F. Yang et al., Curcumin inhibits formation of amyloid beta oligomers and fibrils, binds plaques, and reduces amyloid in vivo. J. Biol. Chem. 280, 5892 (2005).

  10. M. Jackson, H. H. Mantsch, The use and misuse of FTIR spectroscopy in the determination of protein structure. Crit. Rev. Biochem. Mol. Biol. 30, 95 (1995).M. Jackson, H. H. Mantsch, The use and misuse of FTIR spectroscopy in the determination of protein structure. Crit. Rev. Biochem. Mol. Biol. 30, 95 (1995).

  11. E. D. Agdeppa et al., 2-Dialkylamino-6-acylmalononitrile substituted naphthalenes (DDNP analogs): novel diagnostic and therapeutic tools in Alzheimer's disease. Mol. Imaging Biol. 5, 404 (2003).

  12. K. Shoghi-Jadid et al., Localization of neurofibrillary tangles and beta-amyloid plaques in the brains of living patients with Alzheimer disease. Am. J. Geriatr. Psychiatry 10, 24 (2002).