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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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Creation of a lipid-free apoA-I monomer modelfrom a combinationof the C-terminally truncated (Δ185–243)apoA-I27 and N-terminally truncated (Δ1–43)apoA-I18 crystal structures. (a and b) Depth-cued ribbonimages showing the creation of a monomer from the crystal structureof the (Δ185–243)apoA-I dimer of Mei and Atkinson:27 (a) crystal dimer27 and (b) monomeric (Δ185–243)apoA-I created by forminga hairpin from H5. Because residues 1 and 2 were missing from thecrystal structure, they were added from a previous MD simulation.(c–i) Development of the initial crystal model. Color codesfor ribbon models: H5, green; other helical domains, red; nonhelicaldomains, green; prolines in panels a–c, e–g, and i,space-filling yellow. Color codes for space-filling models: aromaticresidues, magenta; nonaromatic hydrophobic residues, gold; prolines,yellow. (c) Reorientation of the ribbon model of the (Δ185–243)apoA-Imonomer in panel b. (d) Space-filling model of the structure in panelc showing its deep hydrophobic cleft. (e) Ribbon model of residues183–243 from the N-terminally truncated crystal structure.18 (f) Space-filling model of the structure inpanel e. (g) Alignment of aromatic and hydrophobic residues betweenthe (Δ185–243)apoA-I monomer model (1–182) andthe N-terminally truncated fragment. (h) Initial crystal model (space-filling)for the full-length monomer. (i) Ribbon model of the structure inpanel h. Residues 1–182 are colored cyan and residues 183–243red.
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fig1: Creation of a lipid-free apoA-I monomer modelfrom a combinationof the C-terminally truncated (Δ185–243)apoA-I27 and N-terminally truncated (Δ1–43)apoA-I18 crystal structures. (a and b) Depth-cued ribbonimages showing the creation of a monomer from the crystal structureof the (Δ185–243)apoA-I dimer of Mei and Atkinson:27 (a) crystal dimer27 and (b) monomeric (Δ185–243)apoA-I created by forminga hairpin from H5. Because residues 1 and 2 were missing from thecrystal structure, they were added from a previous MD simulation.(c–i) Development of the initial crystal model. Color codesfor ribbon models: H5, green; other helical domains, red; nonhelicaldomains, green; prolines in panels a–c, e–g, and i,space-filling yellow. Color codes for space-filling models: aromaticresidues, magenta; nonaromatic hydrophobic residues, gold; prolines,yellow. (c) Reorientation of the ribbon model of the (Δ185–243)apoA-Imonomer in panel b. (d) Space-filling model of the structure in panelc showing its deep hydrophobic cleft. (e) Ribbon model of residues183–243 from the N-terminally truncated crystal structure.18 (f) Space-filling model of the structure inpanel e. (g) Alignment of aromatic and hydrophobic residues betweenthe (Δ185–243)apoA-I monomer model (1–182) andthe N-terminally truncated fragment. (h) Initial crystal model (space-filling)for the full-length monomer. (i) Ribbon model of the structure inpanel h. Residues 1–182 are colored cyan and residues 183–243red.

Mentions: To build the initial crystalmodel, we formed a complete monomer by joining residues 3–182of our C-terminally truncated monomer to residues 183–243 fromour N-terminally truncated monomer. To insert residues 193–243into the hydrophobic cleft seen in residues 3–182 (Figure 1d), we repositioned residues 193–243 by bendingthem slightly and stretching them at several points along the backbone.This aligned them with the aromatic residues of the cleft, as explainedin more detail in Results. The hairpin betweenresidues 192 and 193 in the N-terminally truncated monomer was instrumentalin joining the long helix of residues 131–182 of the C-terminallytruncated monomer around the bottom of the hybrid crystal model toresidues 193–243 of the N-terminally truncated monomer viathe short helix of residues 183–192. Additionally, residues1 and 2 were taken from a previous simulation of ours of monomericapoA-I at 500 K. The two residues were in a random coil structureand were joined to residue 3.


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)

Creation of a lipid-free apoA-I monomer modelfrom a combinationof the C-terminally truncated (Δ185–243)apoA-I27 and N-terminally truncated (Δ1–43)apoA-I18 crystal structures. (a and b) Depth-cued ribbonimages showing the creation of a monomer from the crystal structureof the (Δ185–243)apoA-I dimer of Mei and Atkinson:27 (a) crystal dimer27 and (b) monomeric (Δ185–243)apoA-I created by forminga hairpin from H5. Because residues 1 and 2 were missing from thecrystal structure, they were added from a previous MD simulation.(c–i) Development of the initial crystal model. Color codesfor ribbon models: H5, green; other helical domains, red; nonhelicaldomains, green; prolines in panels a–c, e–g, and i,space-filling yellow. Color codes for space-filling models: aromaticresidues, magenta; nonaromatic hydrophobic residues, gold; prolines,yellow. (c) Reorientation of the ribbon model of the (Δ185–243)apoA-Imonomer in panel b. (d) Space-filling model of the structure in panelc showing its deep hydrophobic cleft. (e) Ribbon model of residues183–243 from the N-terminally truncated crystal structure.18 (f) Space-filling model of the structure inpanel e. (g) Alignment of aromatic and hydrophobic residues betweenthe (Δ185–243)apoA-I monomer model (1–182) andthe N-terminally truncated fragment. (h) Initial crystal model (space-filling)for the full-length monomer. (i) Ribbon model of the structure inpanel h. Residues 1–182 are colored cyan and residues 183–243red.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4263436&req=5

fig1: Creation of a lipid-free apoA-I monomer modelfrom a combinationof the C-terminally truncated (Δ185–243)apoA-I27 and N-terminally truncated (Δ1–43)apoA-I18 crystal structures. (a and b) Depth-cued ribbonimages showing the creation of a monomer from the crystal structureof the (Δ185–243)apoA-I dimer of Mei and Atkinson:27 (a) crystal dimer27 and (b) monomeric (Δ185–243)apoA-I created by forminga hairpin from H5. Because residues 1 and 2 were missing from thecrystal structure, they were added from a previous MD simulation.(c–i) Development of the initial crystal model. Color codesfor ribbon models: H5, green; other helical domains, red; nonhelicaldomains, green; prolines in panels a–c, e–g, and i,space-filling yellow. Color codes for space-filling models: aromaticresidues, magenta; nonaromatic hydrophobic residues, gold; prolines,yellow. (c) Reorientation of the ribbon model of the (Δ185–243)apoA-Imonomer in panel b. (d) Space-filling model of the structure in panelc showing its deep hydrophobic cleft. (e) Ribbon model of residues183–243 from the N-terminally truncated crystal structure.18 (f) Space-filling model of the structure inpanel e. (g) Alignment of aromatic and hydrophobic residues betweenthe (Δ185–243)apoA-I monomer model (1–182) andthe N-terminally truncated fragment. (h) Initial crystal model (space-filling)for the full-length monomer. (i) Ribbon model of the structure inpanel h. Residues 1–182 are colored cyan and residues 183–243red.
Mentions: To build the initial crystalmodel, we formed a complete monomer by joining residues 3–182of our C-terminally truncated monomer to residues 183–243 fromour N-terminally truncated monomer. To insert residues 193–243into the hydrophobic cleft seen in residues 3–182 (Figure 1d), we repositioned residues 193–243 by bendingthem slightly and stretching them at several points along the backbone.This aligned them with the aromatic residues of the cleft, as explainedin more detail in Results. The hairpin betweenresidues 192 and 193 in the N-terminally truncated monomer was instrumentalin joining the long helix of residues 131–182 of the C-terminallytruncated monomer around the bottom of the hybrid crystal model toresidues 193–243 of the N-terminally truncated monomer viathe short helix of residues 183–192. Additionally, residues1 and 2 were taken from a previous simulation of ours of monomericapoA-I at 500 K. The two residues were in a random coil structureand were joined to residue 3.

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