Limits...
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.

Show MeSH

Related in: MedlinePlus

Plots of changes in properties of the initialcrystal model duringa 30 ns MD simulation at 500 K. The double-headed arrows mark the10–20 ns intervals. The filled arrowheads mark the simulationsat 15 ns. (a) Change in fraction helicity with time. The white dottedline is a linear trendline for changes in helicity between 10 and20 ns. (b) Sum of the distances between Cα atoms of the 15-residuepair combinations from an average center for the six spin-coupledresidues predicted by Lagerstedt et al.50 to define a central plane. (c). Total number of distances of >20Å from the 15 combinations of distances between the six spin-coupledresidues. In all panels, the empty diamonds represent the initialcrystal model.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4263436&req=5

fig2: Plots of changes in properties of the initialcrystal model duringa 30 ns MD simulation at 500 K. The double-headed arrows mark the10–20 ns intervals. The filled arrowheads mark the simulationsat 15 ns. (a) Change in fraction helicity with time. The white dottedline is a linear trendline for changes in helicity between 10 and20 ns. (b) Sum of the distances between Cα atoms of the 15-residuepair combinations from an average center for the six spin-coupledresidues predicted by Lagerstedt et al.50 to define a central plane. (c). Total number of distances of >20Å from the 15 combinations of distances between the six spin-coupledresidues. In all panels, the empty diamonds represent the initialcrystal model.

Mentions: Changes in the helicity of theinitial crystal model with simulation time decreased for the first10 ns and then reached a relatively steady state between 10 and 20ns (white dotted line in Figure 2a), indicatingthat the ensemble of structures reached some sort of conformationalstability. The simulation between 10 and 20 ns exhibited ∼58%helicity, in excellent agreement with the value of 55 ± 5% reportedin the literature for lipid-free monomeric apoA-I.25,39,40


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)

Plots of changes in properties of the initialcrystal model duringa 30 ns MD simulation at 500 K. The double-headed arrows mark the10–20 ns intervals. The filled arrowheads mark the simulationsat 15 ns. (a) Change in fraction helicity with time. The white dottedline is a linear trendline for changes in helicity between 10 and20 ns. (b) Sum of the distances between Cα atoms of the 15-residuepair combinations from an average center for the six spin-coupledresidues predicted by Lagerstedt et al.50 to define a central plane. (c). Total number of distances of >20Å from the 15 combinations of distances between the six spin-coupledresidues. In all panels, the empty diamonds represent the initialcrystal model.
© Copyright Policy
Related In: Results  -  Collection

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

fig2: Plots of changes in properties of the initialcrystal model duringa 30 ns MD simulation at 500 K. The double-headed arrows mark the10–20 ns intervals. The filled arrowheads mark the simulationsat 15 ns. (a) Change in fraction helicity with time. The white dottedline is a linear trendline for changes in helicity between 10 and20 ns. (b) Sum of the distances between Cα atoms of the 15-residuepair combinations from an average center for the six spin-coupledresidues predicted by Lagerstedt et al.50 to define a central plane. (c). Total number of distances of >20Å from the 15 combinations of distances between the six spin-coupledresidues. In all panels, the empty diamonds represent the initialcrystal model.
Mentions: Changes in the helicity of theinitial crystal model with simulation time decreased for the first10 ns and then reached a relatively steady state between 10 and 20ns (white dotted line in Figure 2a), indicatingthat the ensemble of structures reached some sort of conformationalstability. The simulation between 10 and 20 ns exhibited ∼58%helicity, in excellent agreement with the value of 55 ± 5% reportedin the literature for lipid-free monomeric apoA-I.25,39,40

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