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Molecular dynamics analysis of apolipoprotein-D-lipid hydroperoxide interactions: mechanism for selective oxidation of Met-93.

Oakley AJ, Bhatia S, Ecroyd H, Garner B - PLoS ONE (2012)

Bottom Line: Recent studies suggest reduction of radical-propagating fatty acid hydroperoxides to inert hydroxides by interaction with apolipoprotein-D (apoD) Met93 may represent an antioxidant function for apoD.Models of 5s- 12s- and 15s-hydroperoxyeicosatetraenoic acids were created and the lipids found to wrap around Met93 thus providing a plausible mechanism by which eicosatetraenoic acids bearing hydroperoxides on different carbon atoms can interact with Met93 to yield Met93 sulfoxide (Met93SO).These studies provide novel insights into the mechanisms that may contribute to the antioxidant function of apoD and the structural consequences that result if Met93SO is not redox-cycled back to its native state.

View Article: PubMed Central - PubMed

Affiliation: Illawarra Health and Medical Research Institute, University of Wollongong, New South Wales, Australia. aarono@uow.edu.au

ABSTRACT

Background: Recent studies suggest reduction of radical-propagating fatty acid hydroperoxides to inert hydroxides by interaction with apolipoprotein-D (apoD) Met93 may represent an antioxidant function for apoD. The nature and structural consequences of this selective interaction are unknown.

Methodology/principal findings: Herein we used molecular dynamics (MD) analysis to address these issues. Long-timescale simulations of apoD suggest lipid molecules are bound flexibly, with the molecules free to explore multiple conformations in a binding site at the entrance to the classical lipocalin ligand-binding pocket. Models of 5s- 12s- and 15s-hydroperoxyeicosatetraenoic acids were created and the lipids found to wrap around Met93 thus providing a plausible mechanism by which eicosatetraenoic acids bearing hydroperoxides on different carbon atoms can interact with Met93 to yield Met93 sulfoxide (Met93SO). Simulations of glycosylated apoD indicated that a second solvent exposed Met at position 49 was shielded by a triantennerary N-glycan attached to Asn45 thereby precluding lipid interactions. MD simulations of apoD showed B-factors of the loop containing Met93SO were higher in the oxidized protein, indicating increased flexibility that is predicted to destabilize the protein and promote self-association.

Conclusions/significance: These studies provide novel insights into the mechanisms that may contribute to the antioxidant function of apoD and the structural consequences that result if Met93SO is not redox-cycled back to its native state.

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MD simulation of glycosylated apoD.(A) Schematic representation of glycosylation patten found at Asn45 and Asn78. Symbols are: sialic acid (diamonds), mannose (filled circles), galactose (open circles), N-acetylglucosamine (squares) and fucose (triangle). (B) Orthogonal views of apoD in ribbon form with progesterone and methionine residues are represented as van der Waals spheres. The conformation of the glycosylations, sampled at 1 ns intervals, are shown (black carbon atoms).
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pone-0034057-g007: MD simulation of glycosylated apoD.(A) Schematic representation of glycosylation patten found at Asn45 and Asn78. Symbols are: sialic acid (diamonds), mannose (filled circles), galactose (open circles), N-acetylglucosamine (squares) and fucose (triangle). (B) Orthogonal views of apoD in ribbon form with progesterone and methionine residues are represented as van der Waals spheres. The conformation of the glycosylations, sampled at 1 ns intervals, are shown (black carbon atoms).

Mentions: Data derived from our previous studies [15] and the simulations above clearly indicate that HpETEs can interact with Met93. The side-chain of Met157 is buried and a lack of interaction between this residue and L-OOHs is therefore expected. However, Met49 is relatively exposed in the crystal structure (Figure 2A) and was observed to interact with solvent in the simulations described above. It was therefore unclear why the interaction of HpETEs with apoD do not generate Met49SO. Given the location of N-glycan structures at Asn45 and Asn78[25], we hypothesized that the N-glycan moiety at Asn45 might shield Met49 and prevent L-OOH mediated Met oxidation. We therefore ran an extended MD simulation of glycosylated apoD. The N-glycan structures present at Asn45 and Asn78 have been previously characterized and found to be mostly represented by trisialo triantennary and fucosylated disialo biantennary oligosaccharides, respectively [25], as graphically represented in Figure 7A. The conformations of the N-glycan chains are represented in Figure 7B. Clearly, access to Met49 is partially blocked by the trisialo triantennary N-glycan at Asn45 whereas neither of the N-glycans obstruct access to the apoD ligand binding pocket (Figure 7B). This provides a plausible explanation for the previously reported lack of reactivity between the apoD Met49 side chain and various HpETEs [15].


Molecular dynamics analysis of apolipoprotein-D-lipid hydroperoxide interactions: mechanism for selective oxidation of Met-93.

Oakley AJ, Bhatia S, Ecroyd H, Garner B - PLoS ONE (2012)

MD simulation of glycosylated apoD.(A) Schematic representation of glycosylation patten found at Asn45 and Asn78. Symbols are: sialic acid (diamonds), mannose (filled circles), galactose (open circles), N-acetylglucosamine (squares) and fucose (triangle). (B) Orthogonal views of apoD in ribbon form with progesterone and methionine residues are represented as van der Waals spheres. The conformation of the glycosylations, sampled at 1 ns intervals, are shown (black carbon atoms).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3316614&req=5

pone-0034057-g007: MD simulation of glycosylated apoD.(A) Schematic representation of glycosylation patten found at Asn45 and Asn78. Symbols are: sialic acid (diamonds), mannose (filled circles), galactose (open circles), N-acetylglucosamine (squares) and fucose (triangle). (B) Orthogonal views of apoD in ribbon form with progesterone and methionine residues are represented as van der Waals spheres. The conformation of the glycosylations, sampled at 1 ns intervals, are shown (black carbon atoms).
Mentions: Data derived from our previous studies [15] and the simulations above clearly indicate that HpETEs can interact with Met93. The side-chain of Met157 is buried and a lack of interaction between this residue and L-OOHs is therefore expected. However, Met49 is relatively exposed in the crystal structure (Figure 2A) and was observed to interact with solvent in the simulations described above. It was therefore unclear why the interaction of HpETEs with apoD do not generate Met49SO. Given the location of N-glycan structures at Asn45 and Asn78[25], we hypothesized that the N-glycan moiety at Asn45 might shield Met49 and prevent L-OOH mediated Met oxidation. We therefore ran an extended MD simulation of glycosylated apoD. The N-glycan structures present at Asn45 and Asn78 have been previously characterized and found to be mostly represented by trisialo triantennary and fucosylated disialo biantennary oligosaccharides, respectively [25], as graphically represented in Figure 7A. The conformations of the N-glycan chains are represented in Figure 7B. Clearly, access to Met49 is partially blocked by the trisialo triantennary N-glycan at Asn45 whereas neither of the N-glycans obstruct access to the apoD ligand binding pocket (Figure 7B). This provides a plausible explanation for the previously reported lack of reactivity between the apoD Met49 side chain and various HpETEs [15].

Bottom Line: Recent studies suggest reduction of radical-propagating fatty acid hydroperoxides to inert hydroxides by interaction with apolipoprotein-D (apoD) Met93 may represent an antioxidant function for apoD.Models of 5s- 12s- and 15s-hydroperoxyeicosatetraenoic acids were created and the lipids found to wrap around Met93 thus providing a plausible mechanism by which eicosatetraenoic acids bearing hydroperoxides on different carbon atoms can interact with Met93 to yield Met93 sulfoxide (Met93SO).These studies provide novel insights into the mechanisms that may contribute to the antioxidant function of apoD and the structural consequences that result if Met93SO is not redox-cycled back to its native state.

View Article: PubMed Central - PubMed

Affiliation: Illawarra Health and Medical Research Institute, University of Wollongong, New South Wales, Australia. aarono@uow.edu.au

ABSTRACT

Background: Recent studies suggest reduction of radical-propagating fatty acid hydroperoxides to inert hydroxides by interaction with apolipoprotein-D (apoD) Met93 may represent an antioxidant function for apoD. The nature and structural consequences of this selective interaction are unknown.

Methodology/principal findings: Herein we used molecular dynamics (MD) analysis to address these issues. Long-timescale simulations of apoD suggest lipid molecules are bound flexibly, with the molecules free to explore multiple conformations in a binding site at the entrance to the classical lipocalin ligand-binding pocket. Models of 5s- 12s- and 15s-hydroperoxyeicosatetraenoic acids were created and the lipids found to wrap around Met93 thus providing a plausible mechanism by which eicosatetraenoic acids bearing hydroperoxides on different carbon atoms can interact with Met93 to yield Met93 sulfoxide (Met93SO). Simulations of glycosylated apoD indicated that a second solvent exposed Met at position 49 was shielded by a triantennerary N-glycan attached to Asn45 thereby precluding lipid interactions. MD simulations of apoD showed B-factors of the loop containing Met93SO were higher in the oxidized protein, indicating increased flexibility that is predicted to destabilize the protein and promote self-association.

Conclusions/significance: These studies provide novel insights into the mechanisms that may contribute to the antioxidant function of apoD and the structural consequences that result if Met93SO is not redox-cycled back to its native state.

Show MeSH