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

Relaxed-eyed stereo views of the 15 ns model. (a) Mappingof thelocation of the five helical domains predicted by Chetty et al. usingH/D exchange40 onto a relaxed-eyed stereoribbon representation of the 15 ns model. Helical domains [markedas 1–5 (see Figure 3a)] of the 15 nsmodel predicted to be helical are colored red and helical domainsof the 15 ns model predicted not to be helical are green. The remainderof the nonhelical structure is colored gray. Prolines are shown asyellow spheres. The N-terminus is marked with a yellow N and the C-terminuswith a red C. (b) Cartoon representation of the 15 ns model in sameorientation as panel a. Helical domains are represented as cylindersand nonhelical domains as random coils. Color code: H5, green; H10,red; N-terminal helical domain, yellow; other helical domains, magenta;K40 and Y192, cyan and magenta spheres, respectively. The N- and C-terminiare indicated as in panel a.
© Copyright Policy
Related In: Results  -  Collection

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

fig5: Relaxed-eyed stereo views of the 15 ns model. (a) Mappingof thelocation of the five helical domains predicted by Chetty et al. usingH/D exchange40 onto a relaxed-eyed stereoribbon representation of the 15 ns model. Helical domains [markedas 1–5 (see Figure 3a)] of the 15 nsmodel predicted to be helical are colored red and helical domainsof the 15 ns model predicted not to be helical are green. The remainderof the nonhelical structure is colored gray. Prolines are shown asyellow spheres. The N-terminus is marked with a yellow N and the C-terminuswith a red C. (b) Cartoon representation of the 15 ns model in sameorientation as panel a. Helical domains are represented as cylindersand nonhelical domains as random coils. Color code: H5, green; H10,red; N-terminal helical domain, yellow; other helical domains, magenta;K40 and Y192, cyan and magenta spheres, respectively. The N- and C-terminiare indicated as in panel a.

Mentions: Figure 5a is a stereo ribbon image of the15 ns model. The five domains predicted to be helical by H/D exchangeand the four domains that are helical in the 15 ns model but not helicalas predicted by H/D exchange40 are coloredred and green, respectively. Figure 5b illustratesthe general conformation of the 15 ns model in the form of a stereocartoon in which the 10 helical segments are shown as cylinders. Thefollowing are key features of the model. (i) The C-terminal H10 (red)is nestled under the folded H5 helical hairpin (green) covering theantiparallel H4–H6 array (residues 100–120 and 144–164).(ii) The C-terminal and N-terminal domains, residues 226–239(red) and 7–31 (yellow), respectively, are in contact, formingan antiparallel helical array. (iii) H5 and the N- and C-terminalsegments are in the proximity of each other on the side of the modelfacing the viewer, a feature also found in the Silva25 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)

Relaxed-eyed stereo views of the 15 ns model. (a) Mappingof thelocation of the five helical domains predicted by Chetty et al. usingH/D exchange40 onto a relaxed-eyed stereoribbon representation of the 15 ns model. Helical domains [markedas 1–5 (see Figure 3a)] of the 15 nsmodel predicted to be helical are colored red and helical domainsof the 15 ns model predicted not to be helical are green. The remainderof the nonhelical structure is colored gray. Prolines are shown asyellow spheres. The N-terminus is marked with a yellow N and the C-terminuswith a red C. (b) Cartoon representation of the 15 ns model in sameorientation as panel a. Helical domains are represented as cylindersand nonhelical domains as random coils. Color code: H5, green; H10,red; N-terminal helical domain, yellow; other helical domains, magenta;K40 and Y192, cyan and magenta spheres, respectively. The N- and C-terminiare indicated as in panel a.
© Copyright Policy
Related In: Results  -  Collection

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

fig5: Relaxed-eyed stereo views of the 15 ns model. (a) Mappingof thelocation of the five helical domains predicted by Chetty et al. usingH/D exchange40 onto a relaxed-eyed stereoribbon representation of the 15 ns model. Helical domains [markedas 1–5 (see Figure 3a)] of the 15 nsmodel predicted to be helical are colored red and helical domainsof the 15 ns model predicted not to be helical are green. The remainderof the nonhelical structure is colored gray. Prolines are shown asyellow spheres. The N-terminus is marked with a yellow N and the C-terminuswith a red C. (b) Cartoon representation of the 15 ns model in sameorientation as panel a. Helical domains are represented as cylindersand nonhelical domains as random coils. Color code: H5, green; H10,red; N-terminal helical domain, yellow; other helical domains, magenta;K40 and Y192, cyan and magenta spheres, respectively. The N- and C-terminiare indicated as in panel a.
Mentions: Figure 5a is a stereo ribbon image of the15 ns model. The five domains predicted to be helical by H/D exchangeand the four domains that are helical in the 15 ns model but not helicalas predicted by H/D exchange40 are coloredred and green, respectively. Figure 5b illustratesthe general conformation of the 15 ns model in the form of a stereocartoon in which the 10 helical segments are shown as cylinders. Thefollowing are key features of the model. (i) The C-terminal H10 (red)is nestled under the folded H5 helical hairpin (green) covering theantiparallel H4–H6 array (residues 100–120 and 144–164).(ii) The C-terminal and N-terminal domains, residues 226–239(red) and 7–31 (yellow), respectively, are in contact, formingan antiparallel helical array. (iii) H5 and the N- and C-terminalsegments are in the proximity of each other on the side of the modelfacing the viewer, a feature also found in the Silva25 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