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Atomic decomposition of the protein solvation free energy and its application to amyloid-beta protein in water
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10.1063/1.3610550
/content/aip/journal/jcp/135/3/10.1063/1.3610550
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/3/10.1063/1.3610550
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

(a) NMR structure of Aβ42 monomer determined in hexafluoroisopropanol/water 80:20 (PDB code: 1IYT) (Ref. 36). (b) Unfolded structure in water at 43 ns from the MD simulation. Each structure is color-coded according to sequence, ranging from blue to red at the N- and C-termini, respectively. Side-chains of the residues K16 and V40 are drawn with sphere representation to indicate the positions of these residues (C, N, H: orange, blue, white).

Image of FIG. 2.
FIG. 2.

Solvation free energy change ΔΔμ (black solid curve) upon the conformational transitions of Aβ42 monomer in water from the initial organic-phase helical structure as a function of time and its decompositions (a) into non-electrostatic (red dashed curve) and electrostatic (blue dashed-dotted curve) contributions, (b) into contributions from hydrophobic (red dashed curve) and non-hydrophobic (blue dashed-dotted curve) residues, and (c) into contributions from main-chain (red dashed curve) and side-chain (blue dashed-dotted curve) atoms. In (b), A, F, L, M, I, and V are considered to be hydrophobic amino acids except for the C-terminal residue A42 possessing the charged COO group, and all the other amino acids are considered non-hydrophobic.

Image of FIG. 3.
FIG. 3.

(a) Each residue's contribution to the solvation free energy change ΔΔμ between the initial organic-phase helical structure and the unfolded structure in water at 43 ns of Aβ42 monomer as a function of the residue number. Large contributions to ΔΔμ come from hydrophilic as well as terminal residues E3, R5, E11, K16, and A42. (b) Stick representation of the main-chain and side-chain atoms of the residues D1, A2, E3, R5, E11, K16, G38, and A42 for the initial organic-phase helical structure and the unfolded structure in water at 43 ns from the MD simulation (C, O, N, H: magenta, red, blue, white). Polar side-chain side-chain and side-chain main-chain interactions are indicated by red dotted lines. (c) Radial distribution functions g αO(r) between the side-chain atom α and the water oxygen for the residues E3 (blue curve), E11 (green), and K16 (red) of the initial organic-phase helical structure. One of oxygens in the COO group is chosen as the side-chain atom α for E3 and E11, whereas nitrogen in the group is chosen for K16. (d) Corresponding results for g αO(r) of the unfolded structure in water at 43 ns.

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/content/aip/journal/jcp/135/3/10.1063/1.3610550
2011-07-20
2014-04-24
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Atomic decomposition of the protein solvation free energy and its application to amyloid-beta protein in water
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/3/10.1063/1.3610550
10.1063/1.3610550
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