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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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Ribbon comparison of the four alternatively open and closedstructures:15 ns (Closed1) → 20 ns (Open1) →25 ns (Closed2) → 28 ns (Open2). Colorcode: H10, red; H5, green; H4, cyan; H6, magenta; remainder of structure,gray; N-termini, yellow arrowheads; C-termini, red arrowheads. Inboth transitions from open to closed structures, H5 and H10 move awayfrom each other and from the main body of the protein exposing theH4–H5–H6 hairpin so that a second apoA-I rotated alongits long axis by 180° can dimerize with the first through intermolecularinteractions of the H4–H5–H6 region.
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fig6: Ribbon comparison of the four alternatively open and closedstructures:15 ns (Closed1) → 20 ns (Open1) →25 ns (Closed2) → 28 ns (Open2). Colorcode: H10, red; H5, green; H4, cyan; H6, magenta; remainder of structure,gray; N-termini, yellow arrowheads; C-termini, red arrowheads. Inboth transitions from open to closed structures, H5 and H10 move awayfrom each other and from the main body of the protein exposing theH4–H5–H6 hairpin so that a second apoA-I rotated alongits long axis by 180° can dimerize with the first through intermolecularinteractions of the H4–H5–H6 region.

Mentions: The experimentally determined helicity for monomeric lipid-freehuman apoA-I is 55 ± 5%.25,39,40 Our hybrid structure had significantly more helicity (74%). We thereforeused MD simulations of the initial crystal model to explore additionalconformational space. As MD simulations at 310 K produced only minorstructural changes, we subjected the initial crystal model to MD simulationsat 500 K for 30 ns. The rmsd of this simulation is shown in FigureS2 of the Supporting Information; the rmsdof the full model flattens out between 15 and 28 ns but increasesbetween 28 and 30 ns (Figure S2a of the SupportingInformation), suggesting at least a portion of the model isnot equilibrating. Restriction of the rmsd to the model’s corehelical domains 1, 4 and 5 (see Figure 6a forthe definition) shows that the core is equilibrated from 15 ns tothe 30 ns end (Figure S2b of the Supporting Information). The rmsd of the noncore domains, however, increased between 28and 30 ns (Figure S2c of the Supporting Information), and thus, these domains account for the corresponding increasein the rmsd of the full model.


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)

Ribbon comparison of the four alternatively open and closedstructures:15 ns (Closed1) → 20 ns (Open1) →25 ns (Closed2) → 28 ns (Open2). Colorcode: H10, red; H5, green; H4, cyan; H6, magenta; remainder of structure,gray; N-termini, yellow arrowheads; C-termini, red arrowheads. Inboth transitions from open to closed structures, H5 and H10 move awayfrom each other and from the main body of the protein exposing theH4–H5–H6 hairpin so that a second apoA-I rotated alongits long axis by 180° can dimerize with the first through intermolecularinteractions of the H4–H5–H6 region.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263436&req=5

fig6: Ribbon comparison of the four alternatively open and closedstructures:15 ns (Closed1) → 20 ns (Open1) →25 ns (Closed2) → 28 ns (Open2). Colorcode: H10, red; H5, green; H4, cyan; H6, magenta; remainder of structure,gray; N-termini, yellow arrowheads; C-termini, red arrowheads. Inboth transitions from open to closed structures, H5 and H10 move awayfrom each other and from the main body of the protein exposing theH4–H5–H6 hairpin so that a second apoA-I rotated alongits long axis by 180° can dimerize with the first through intermolecularinteractions of the H4–H5–H6 region.
Mentions: The experimentally determined helicity for monomeric lipid-freehuman apoA-I is 55 ± 5%.25,39,40 Our hybrid structure had significantly more helicity (74%). We thereforeused MD simulations of the initial crystal model to explore additionalconformational space. As MD simulations at 310 K produced only minorstructural changes, we subjected the initial crystal model to MD simulationsat 500 K for 30 ns. The rmsd of this simulation is shown in FigureS2 of the Supporting Information; the rmsdof the full model flattens out between 15 and 28 ns but increasesbetween 28 and 30 ns (Figure S2a of the SupportingInformation), suggesting at least a portion of the model isnot equilibrating. Restriction of the rmsd to the model’s corehelical domains 1, 4 and 5 (see Figure 6a forthe definition) shows that the core is equilibrated from 15 ns tothe 30 ns end (Figure S2b of the Supporting Information). The rmsd of the noncore domains, however, increased between 28and 30 ns (Figure S2c of the Supporting Information), and thus, these domains account for the corresponding increasein the rmsd of the full model.

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