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Dynamic information for cardiotoxin protein desorption from a methyl-terminated self-assembled monolayer using steered molecular dynamics simulation
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10.1063/1.3592559
/content/aip/journal/jcp/134/19/10.1063/1.3592559
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/19/10.1063/1.3592559
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

The molecular model system consisting of a single CTX protein, SAM surface of S(CH2)5CH3 molecules, and the medium of the solvent with explicit water molecules and counter ions (blue spheres). The sizes of the different molecules are not in scale. The yellow dashed lines indicate the disulfide bonds. The molecule images in this paper were created by PyMOL (Ref. 62).

Image of FIG. 2.
FIG. 2.

(a)–(d) CTX conformations at Z CTX = 2.0, 2.5, 3.0, and 3.8 nm, respectively. (e) Z Loop , positions of the three loop tips of CTX (black solid line: Loop I; red dashed line: Loop II; blue dashed-dotted line: Loop III) and (f) adsorption force vs. Z CTX, center of mass of CTX, when pulling with velocity v = 0.25 nm/ns. Red triangles mark the positions of the snapshots in (a)–(d).

Image of FIG. 3.
FIG. 3.

(a)–(d) CTX conformations at Z CTX = 2.0, 2.5, 3.0, and 3.8 nm, respectively. (e) Z Loop , positions of the three loop tips of CTX (black solid line: Loop I; red dashed line: Loop II; blue dashed-dotted line: Loop III) and (f) adsorption force vs. Z CTX, center of mass of CTX, when pulling with velocity v = 1.0 nm/ns. Red triangles mark the positions of the snapshots in (a)–(d).

Image of FIG. 4.
FIG. 4.

(a) Average adsorption force curves with various pulling velocities, i.e., v = 0.125 (blue solid line), 0.25 (red dashed line), 0.5 (cyan dotted line), and 1 nm/ns (green dashed-dotted line). (b) Average rupture force vs. pulling velocity from SMD simulations (squares). Blue circle indicates the rupture force obtained from the derivation of the PMF calculated using umbrella sampling. The green dashed-dotted and red dashed lines represent the best linear and logarithm fits to the average rupture forces, respectively.

Image of FIG. 5.
FIG. 5.

(a) Components of the interaction energy acting on the CTX protein, i.e., the CTX-SAM vdW (black solid line), the CTX-solvent vdW (red dashed line), and the CTX-solvent electrostatic interaction (blue dotted-dashed line), when pulling with velocity v = 0.25 nm/ns. (b) The total vdW interaction acting on the CTX protein.

Image of FIG. 6.
FIG. 6.

(a) PMF profile calculated using umbrella sampling. Red triangles mark the positions of the snapshots in (c)–(f). (b) Mean force profile obtained from the derivative of the PMF with respect to Z CTX. (c)–(f) CTX conformations at Z CTX = 2.0, 2.4, 2.7, and 3.4 nm, respectively.

Image of FIG. 7.
FIG. 7.

Root-mean-square deviation (RMSD) of the resultant PMF between umbrella sampling and SMD estimators vs. the pulling velocity. RMSD values are indicated by red squares connected by a solid line (mean work estimator), green circles connected by a dashed line (Jarzynski's equality estimator), and blue triangles connected by a dotted line (fluctuation-dissipation estimator).

Image of FIG. 8.
FIG. 8.

PMF profiles with v = 0.25 nm/ns calculated using mean work (red), Jarzynski's equality (green), and fluctuation-dissipation (blue) estimators. The PMF profile calculated using umbrella sampling is shown in black.

Image of FIG. 9.
FIG. 9.

Histograms of dissipated work distribution at Z CTX = 2.6 nm with four pulling velocities (blue: v = 0.125 nm/ns; red: v = 0.25 nm/ns; cyan: v = 0. 5 nm/ns; green: v = 1 nm/ns). The histograms were fitted to a Gaussian distribution.

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/content/aip/journal/jcp/134/19/10.1063/1.3592559
2011-05-19
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Dynamic information for cardiotoxin protein desorption from a methyl-terminated self-assembled monolayer using steered molecular dynamics simulation
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/19/10.1063/1.3592559
10.1063/1.3592559
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