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An experimentally robust model of monomeric apolipoprotein A-I created from a chimera of two X-ray structures and molecular dynamics simulations.

Segrest JP, Jones MK, Shao B, Heinecke JW - Biochemistry (2014)

Bottom Line: Consequently, we combined these crystal structures into an initial model that was subjected to molecular dynamics simulations.We tested the initial and simulated models and the two previously published models in three ways: against two published data sets (domains predicted to be helical by H/D exchange and six spin-coupled residues) and against our own experimentally determined cross-linking distance constraints.We note that the best fit simulation model, superior by all tests to previously published models, has dynamic features of a molten globule with interesting implications for the functions of apoA-I.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, Atherosclerosis Research Unit, and Center for Computational and Structural Dynamics, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States.

ABSTRACT
High-density lipoprotein (HDL) retards atherosclerosis by accepting cholesterol from the artery wall. However, the structure of the proposed acceptor, monomeric apolipoprotein A-I (apoA-I), the major protein of HDL, is poorly understood. Two published models for monomeric apoA-I used cross-linking distance constraints to derive best fit conformations. This approach has limitations. (i) Cross-linked peptides provide no information about secondary structure. (ii) A protein chain can be folded in multiple ways to create a best fit. (iii) Ad hoc folding of a secondary structure is unlikely to produce a stable orientation of hydrophobic and hydrophilic residues. To address these limitations, we used a different approach. We first noted that the dimeric apoA-I crystal structure, (Δ185-243)apoA-I, is topologically identical to a monomer in which helix 5 forms a helical hairpin, a monomer with a hydrophobic cleft running the length of the molecule. We then realized that a second crystal structure, (Δ1-43)apoA-I, contains a C-terminal structure that fits snuggly via aromatic and hydrophobic interactions into the hydrophobic cleft. Consequently, we combined these crystal structures into an initial model that was subjected to molecular dynamics simulations. We tested the initial and simulated models and the two previously published models in three ways: against two published data sets (domains predicted to be helical by H/D exchange and six spin-coupled residues) and against our own experimentally determined cross-linking distance constraints. We note that the best fit simulation model, superior by all tests to previously published models, has dynamic features of a molten globule with interesting implications for the functions of apoA-I.

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Goodness of fit of modelsto the helical regions predicted by Chettyet al.40 and the spin-coupled residuespredicted by Lagerstedt et al.50 proposedto define a central plane. (a) Bar graph showing the goodness of fitof helicity of five models (initial crystal, 10–20 ns, 15 ns,Silva, and Pollard) to the position of the five helical regions (designated1–5) predicted by Chetty et al.40 using H/D exchange. (b and c) Relaxed-eyed stereo ribbon imagesillustrating distances and positions of the six spin-coupled residues(Cα, magenta spheres) predicted by Lagerstedt et al.50 to define a central plane: (b) initial crystalmodel and (c) 15 ns model. Distances between residues are denotedby dotted lines. Color code: H5 (residues 121–143), green;prolines, yellow spheres; H10 (residues 221–243), red; remainderof the helical residues, cyan; remainder of random coil residues,orange.
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fig3: Goodness of fit of modelsto the helical regions predicted by Chettyet al.40 and the spin-coupled residuespredicted by Lagerstedt et al.50 proposedto define a central plane. (a) Bar graph showing the goodness of fitof helicity of five models (initial crystal, 10–20 ns, 15 ns,Silva, and Pollard) to the position of the five helical regions (designated1–5) predicted by Chetty et al.40 using H/D exchange. (b and c) Relaxed-eyed stereo ribbon imagesillustrating distances and positions of the six spin-coupled residues(Cα, magenta spheres) predicted by Lagerstedt et al.50 to define a central plane: (b) initial crystalmodel and (c) 15 ns model. Distances between residues are denotedby dotted lines. Color code: H5 (residues 121–143), green;prolines, yellow spheres; H10 (residues 221–243), red; remainderof the helical residues, cyan; remainder of random coil residues,orange.

Mentions: Using site-directed spin-label electron paramagneticresonance spectroscopy (EPR), Lagerstedt et al.41 identified six spin-coupled residues (G26, L44, L64, S167,G217, and K226) in lipid-free human apoA-I. In the initial crystalmodel, all but G26 are exposed to solvent and four (L44, L64, G217,and K226) are in loops on the surface of our 15 ns model (Figure 3c); the two that are not, G26 and S167, are smalland in physical contact with each other.


An experimentally robust model of monomeric apolipoprotein A-I created from a chimera of two X-ray structures and molecular dynamics simulations.

Segrest JP, Jones MK, Shao B, Heinecke JW - Biochemistry (2014)

Goodness of fit of modelsto the helical regions predicted by Chettyet al.40 and the spin-coupled residuespredicted by Lagerstedt et al.50 proposedto define a central plane. (a) Bar graph showing the goodness of fitof helicity of five models (initial crystal, 10–20 ns, 15 ns,Silva, and Pollard) to the position of the five helical regions (designated1–5) predicted by Chetty et al.40 using H/D exchange. (b and c) Relaxed-eyed stereo ribbon imagesillustrating distances and positions of the six spin-coupled residues(Cα, magenta spheres) predicted by Lagerstedt et al.50 to define a central plane: (b) initial crystalmodel and (c) 15 ns model. Distances between residues are denotedby dotted lines. Color code: H5 (residues 121–143), green;prolines, yellow spheres; H10 (residues 221–243), red; remainderof the helical residues, cyan; remainder of random coil residues,orange.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4263436&req=5

fig3: Goodness of fit of modelsto the helical regions predicted by Chettyet al.40 and the spin-coupled residuespredicted by Lagerstedt et al.50 proposedto define a central plane. (a) Bar graph showing the goodness of fitof helicity of five models (initial crystal, 10–20 ns, 15 ns,Silva, and Pollard) to the position of the five helical regions (designated1–5) predicted by Chetty et al.40 using H/D exchange. (b and c) Relaxed-eyed stereo ribbon imagesillustrating distances and positions of the six spin-coupled residues(Cα, magenta spheres) predicted by Lagerstedt et al.50 to define a central plane: (b) initial crystalmodel and (c) 15 ns model. Distances between residues are denotedby dotted lines. Color code: H5 (residues 121–143), green;prolines, yellow spheres; H10 (residues 221–243), red; remainderof the helical residues, cyan; remainder of random coil residues,orange.
Mentions: Using site-directed spin-label electron paramagneticresonance spectroscopy (EPR), Lagerstedt et al.41 identified six spin-coupled residues (G26, L44, L64, S167,G217, and K226) in lipid-free human apoA-I. In the initial crystalmodel, all but G26 are exposed to solvent and four (L44, L64, G217,and K226) are in loops on the surface of our 15 ns model (Figure 3c); the two that are not, G26 and S167, are smalland in physical contact with each other.

Bottom Line: Consequently, we combined these crystal structures into an initial model that was subjected to molecular dynamics simulations.We tested the initial and simulated models and the two previously published models in three ways: against two published data sets (domains predicted to be helical by H/D exchange and six spin-coupled residues) and against our own experimentally determined cross-linking distance constraints.We note that the best fit simulation model, superior by all tests to previously published models, has dynamic features of a molten globule with interesting implications for the functions of apoA-I.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, Atherosclerosis Research Unit, and Center for Computational and Structural Dynamics, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States.

ABSTRACT
High-density lipoprotein (HDL) retards atherosclerosis by accepting cholesterol from the artery wall. However, the structure of the proposed acceptor, monomeric apolipoprotein A-I (apoA-I), the major protein of HDL, is poorly understood. Two published models for monomeric apoA-I used cross-linking distance constraints to derive best fit conformations. This approach has limitations. (i) Cross-linked peptides provide no information about secondary structure. (ii) A protein chain can be folded in multiple ways to create a best fit. (iii) Ad hoc folding of a secondary structure is unlikely to produce a stable orientation of hydrophobic and hydrophilic residues. To address these limitations, we used a different approach. We first noted that the dimeric apoA-I crystal structure, (Δ185-243)apoA-I, is topologically identical to a monomer in which helix 5 forms a helical hairpin, a monomer with a hydrophobic cleft running the length of the molecule. We then realized that a second crystal structure, (Δ1-43)apoA-I, contains a C-terminal structure that fits snuggly via aromatic and hydrophobic interactions into the hydrophobic cleft. Consequently, we combined these crystal structures into an initial model that was subjected to molecular dynamics simulations. We tested the initial and simulated models and the two previously published models in three ways: against two published data sets (domains predicted to be helical by H/D exchange and six spin-coupled residues) and against our own experimentally determined cross-linking distance constraints. We note that the best fit simulation model, superior by all tests to previously published models, has dynamic features of a molten globule with interesting implications for the functions of apoA-I.

Show MeSH
Related in: MedlinePlus