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Molecular modeling of mechanical stresses on proteins in glassy matrices: Formalism
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10.1063/1.4734007
/content/aip/journal/jcp/137/3/10.1063/1.4734007
http://aip.metastore.ingenta.com/content/aip/journal/jcp/137/3/10.1063/1.4734007

Figures

Image of FIG. 1.
FIG. 1.

Illustration of the local stress tensor calculation, Eq. (19) , for a group containing particles 2 and 5. The volume of the group, , is the sum of the Voronoi volumes of particles 2 and 5 shown by thick black lines. By definition of the group, Λ = Λ = 1 while Λ = Λ = Λ = 0. The dimensionless quantity, = 0.5, is the fraction of the line segment connecting particles 1 and 2 that is within , shown by the thick red line. Note that the double sum of Eq. (19) involves all pairs of particles, which may lead to contributions from particles not within the group (e.g., ≃ 0.4).

Image of FIG. 2.
FIG. 2.

The STRIDE algorithm 120 was used to make secondary structure assignments of ubiquitin, and a typical liquid configuration in water at ambient conditions is shown. The α-helix is the largest helical region shown in blue. The other two blue regions are 3 helices. β-strands are colored yellow. The C-terminus is the coil at the top right.

Image of FIG. 3.
FIG. 3.

The 1a coiled-coil region of α-keratin was simulated as a fragment solvated in water. The coiled-coil structure is stabilized by a stripe of hydrophobic side chains which run along the length of both α-helical monomers.

Image of FIG. 4.
FIG. 4.

(a) Atomic-level normal stresses on ubiquitin in glassy water at 1 bar. Colored squares represent the following hydrophilic side chain atoms: (red) nitrogen on ammonium (−N+H) groups in lysine and the N-terminus, and (green) carbon on carboxylate (−COO) groups in aspartic and glutamic acid. Backbone carbonyl carbons are represented by the dashed line, α-carbons by the solid line, and all other atoms appear as dots. Atoms are listed from N-terminus to C-terminus. (b) Atomic-level normal stresses on ubiquitin in liquid water at 1 bar and 300 K. Error bars are the standard deviation of the mean from 500 samples in both liquid and glass.

Image of FIG. 5.
FIG. 5.

Atomic-level normal stresses for keratin fragment in glassy water at 1 bar. Symbols are as in Figure 4 . Atoms are listed from the N-terminus to the C-terminus for both coils in succession. The first coil ends and the second coil begins in the middle of the figure, denoted by the vertical line. Error bars are the standard deviation of the mean from 500 samples.

Image of FIG. 6.
FIG. 6.

(a) Residue-level normal stresses for ubiquitin in glassy water at 1 bar. Colored squares represent (blue) aspartic acid and (red) glutamic acid. Residues are listed from N-terminus to C-terminus. Note that the C-terminus residues also possess large, tensile normal stresses, perhaps due to the carboxylate group which is also present in aspartic and glutamic acid. (b) Residue-level normal stresses for keratin fragment in glassy water at 1 bar. The first coil ends and the second coil begins in the middle of the figure, denoted by the vertical line. Error bars are the standard deviation of the mean from 500 samples.

Image of FIG. 7.
FIG. 7.

The instantaneous normal stress on ubiquitin at 1 bar in the glass (blue) and liquid at 300 K (red). On average, ubiquitin is under compression in the glass and under tension in the liquid (see Table II for ensemble averages).

Image of FIG. 8.
FIG. 8.

Atomic-level normal stresses on ubiquitin in glassy water at 1 bar calculated with the Coulomb sum, = ∞) = = 1) + . Symbols are as in Figure 4 . Error bars are the standard deviation of the mean from 100 samples.

Tables

Generic image for table
Table I.

Summary of simulations performed in this work.

Generic image for table
Table II.

Summary of the normal stress on whole proteins in the glass and liquid.

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/content/aip/journal/jcp/137/3/10.1063/1.4734007
2012-07-18
2014-04-16
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Molecular modeling of mechanical stresses on proteins in glassy matrices: Formalism
http://aip.metastore.ingenta.com/content/aip/journal/jcp/137/3/10.1063/1.4734007
10.1063/1.4734007
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