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Ligand binding and aggregation of pathogenic SOD1.

Wright GS, Antonyuk SV, Kershaw NM, Strange RW, Samar Hasnain S - Nat Commun (2013)

Bottom Line: Superoxide dismutase-1 mutations decrease protein stability and promote aggregation.We find both compounds interact with superoxide dismutase-1 at a key region identified at the core of the superoxide dismutase-1 fibrillar aggregates, β-barrel loop II-strand 3, rather than the proposed dimer interface site.This illustrates the need for direct structural observations when developing compounds for protein-targeted therapeutics.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK.

ABSTRACT
Mutations in the gene encoding Cu/Zn superoxide dismutase-1 cause amyotrophic lateral sclerosis. Superoxide dismutase-1 mutations decrease protein stability and promote aggregation. The mutant monomer is thought to be an intermediate in the pathway from the superoxide dismutase-1 dimer to aggregate. Here we find that the monomeric copper-apo, zinc-holo protein is structurally perturbed and the apo-protein aggregates without reattainment of the monomer-dimer equilibrium. Intervention to stabilize the superoxide dismutase-1 dimer and inhibit aggregation is regarded as a potential therapeutic strategy. We describe protein-ligand interactions for two compounds, Isoproterenol and 5-fluorouridine, highlighted as superoxide dismutase-1 stabilizers. We find both compounds interact with superoxide dismutase-1 at a key region identified at the core of the superoxide dismutase-1 fibrillar aggregates, β-barrel loop II-strand 3, rather than the proposed dimer interface site. This illustrates the need for direct structural observations when developing compounds for protein-targeted therapeutics.

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Epinephrine and dopamine bound to I113T SOD1.(a) Epinephrine with respect to the SOD1 dimer (4A7U) in grey and light grey; strands 2, 3 and 6 of the SOD1 β-barrel are coloured yellow, purple and green, respectively. (b) 2Fo-Fc electron density map of epinephrine contoured at 1σ at the Trp32-binding site with the SOD1 surface coloured by amino acid hydrophobicity. Average B factor of the catechol head is 16.6 Å2 in comparison with 21.7 Å2 for the Glu21 and Glu100 side chain carboxylates. (c) Hydrogen bonding between I113T SOD1 and epinephrine shown with black dashed line. (d) Dopamine with respect to the SOD1 dimer (4A7U) coloured as above. (e) 2Fo-Fc electron density map of dopamine contoured at 1σ at the Trp32-binding site coloured as above. Average B factor of the catechol head is 25.0 Å2 compared with 32.8 Å2 for the Glu21 and Glu100 carboxylates when refined at full occupancy. (f) Hydrogen bonding between I113T SOD1 and dopamine shown with black dashed line. Omit maps of epinephrine and dopamine bound to I113T SOD1 can be found in Supplementary Fig. S10.
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f6: Epinephrine and dopamine bound to I113T SOD1.(a) Epinephrine with respect to the SOD1 dimer (4A7U) in grey and light grey; strands 2, 3 and 6 of the SOD1 β-barrel are coloured yellow, purple and green, respectively. (b) 2Fo-Fc electron density map of epinephrine contoured at 1σ at the Trp32-binding site with the SOD1 surface coloured by amino acid hydrophobicity. Average B factor of the catechol head is 16.6 Å2 in comparison with 21.7 Å2 for the Glu21 and Glu100 side chain carboxylates. (c) Hydrogen bonding between I113T SOD1 and epinephrine shown with black dashed line. (d) Dopamine with respect to the SOD1 dimer (4A7U) coloured as above. (e) 2Fo-Fc electron density map of dopamine contoured at 1σ at the Trp32-binding site coloured as above. Average B factor of the catechol head is 25.0 Å2 compared with 32.8 Å2 for the Glu21 and Glu100 carboxylates when refined at full occupancy. (f) Hydrogen bonding between I113T SOD1 and dopamine shown with black dashed line. Omit maps of epinephrine and dopamine bound to I113T SOD1 can be found in Supplementary Fig. S10.

Mentions: Isoproterenol is structurally related to the neurotransmitters dopamine and epinephrine. In view of the findings above, X-ray crystal structures of both compounds bound to I113T SOD1 were subsequently obtained (4A7U and 4A7V, respectively, Figure 6, Supplementary Figs. S8, S9 and S10, and Table 1). Both were clearly visible in the same binding site as Isoproterenol and with comparable conformations, although the plane of the catechol head group is rotated in the case of dopamine. In this case, no hydrogen-bonding interactions can take place with Glu100, because of the absence of a tail hydroxyl.


Ligand binding and aggregation of pathogenic SOD1.

Wright GS, Antonyuk SV, Kershaw NM, Strange RW, Samar Hasnain S - Nat Commun (2013)

Epinephrine and dopamine bound to I113T SOD1.(a) Epinephrine with respect to the SOD1 dimer (4A7U) in grey and light grey; strands 2, 3 and 6 of the SOD1 β-barrel are coloured yellow, purple and green, respectively. (b) 2Fo-Fc electron density map of epinephrine contoured at 1σ at the Trp32-binding site with the SOD1 surface coloured by amino acid hydrophobicity. Average B factor of the catechol head is 16.6 Å2 in comparison with 21.7 Å2 for the Glu21 and Glu100 side chain carboxylates. (c) Hydrogen bonding between I113T SOD1 and epinephrine shown with black dashed line. (d) Dopamine with respect to the SOD1 dimer (4A7U) coloured as above. (e) 2Fo-Fc electron density map of dopamine contoured at 1σ at the Trp32-binding site coloured as above. Average B factor of the catechol head is 25.0 Å2 compared with 32.8 Å2 for the Glu21 and Glu100 carboxylates when refined at full occupancy. (f) Hydrogen bonding between I113T SOD1 and dopamine shown with black dashed line. Omit maps of epinephrine and dopamine bound to I113T SOD1 can be found in Supplementary Fig. S10.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3644087&req=5

f6: Epinephrine and dopamine bound to I113T SOD1.(a) Epinephrine with respect to the SOD1 dimer (4A7U) in grey and light grey; strands 2, 3 and 6 of the SOD1 β-barrel are coloured yellow, purple and green, respectively. (b) 2Fo-Fc electron density map of epinephrine contoured at 1σ at the Trp32-binding site with the SOD1 surface coloured by amino acid hydrophobicity. Average B factor of the catechol head is 16.6 Å2 in comparison with 21.7 Å2 for the Glu21 and Glu100 side chain carboxylates. (c) Hydrogen bonding between I113T SOD1 and epinephrine shown with black dashed line. (d) Dopamine with respect to the SOD1 dimer (4A7U) coloured as above. (e) 2Fo-Fc electron density map of dopamine contoured at 1σ at the Trp32-binding site coloured as above. Average B factor of the catechol head is 25.0 Å2 compared with 32.8 Å2 for the Glu21 and Glu100 carboxylates when refined at full occupancy. (f) Hydrogen bonding between I113T SOD1 and dopamine shown with black dashed line. Omit maps of epinephrine and dopamine bound to I113T SOD1 can be found in Supplementary Fig. S10.
Mentions: Isoproterenol is structurally related to the neurotransmitters dopamine and epinephrine. In view of the findings above, X-ray crystal structures of both compounds bound to I113T SOD1 were subsequently obtained (4A7U and 4A7V, respectively, Figure 6, Supplementary Figs. S8, S9 and S10, and Table 1). Both were clearly visible in the same binding site as Isoproterenol and with comparable conformations, although the plane of the catechol head group is rotated in the case of dopamine. In this case, no hydrogen-bonding interactions can take place with Glu100, because of the absence of a tail hydroxyl.

Bottom Line: Superoxide dismutase-1 mutations decrease protein stability and promote aggregation.We find both compounds interact with superoxide dismutase-1 at a key region identified at the core of the superoxide dismutase-1 fibrillar aggregates, β-barrel loop II-strand 3, rather than the proposed dimer interface site.This illustrates the need for direct structural observations when developing compounds for protein-targeted therapeutics.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK.

ABSTRACT
Mutations in the gene encoding Cu/Zn superoxide dismutase-1 cause amyotrophic lateral sclerosis. Superoxide dismutase-1 mutations decrease protein stability and promote aggregation. The mutant monomer is thought to be an intermediate in the pathway from the superoxide dismutase-1 dimer to aggregate. Here we find that the monomeric copper-apo, zinc-holo protein is structurally perturbed and the apo-protein aggregates without reattainment of the monomer-dimer equilibrium. Intervention to stabilize the superoxide dismutase-1 dimer and inhibit aggregation is regarded as a potential therapeutic strategy. We describe protein-ligand interactions for two compounds, Isoproterenol and 5-fluorouridine, highlighted as superoxide dismutase-1 stabilizers. We find both compounds interact with superoxide dismutase-1 at a key region identified at the core of the superoxide dismutase-1 fibrillar aggregates, β-barrel loop II-strand 3, rather than the proposed dimer interface site. This illustrates the need for direct structural observations when developing compounds for protein-targeted therapeutics.

Show MeSH
Related in: MedlinePlus