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Hydrogen bond perturbation in hen egg white lysozyme by external electromagnetic fields: A nonequilibrium molecular dynamics study
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10.1063/1.3518975
/content/aip/journal/jcp/133/23/10.1063/1.3518975
http://aip.metastore.ingenta.com/content/aip/journal/jcp/133/23/10.1063/1.3518975

Figures

Image of FIG. 1.
FIG. 1.

Histogram of persistence times (duration of life before breakage) of hydrogen bonds for (a) ALA|10|N–CYS|6|O, (b) THR|51|N–SER|60| OG, (c) ASP|101|N–LYS|97| O, and (d) ASN|113|N–VAL|109|O.

Image of FIG. 2.
FIG. 2.

Reduction in overall persistence percentage vis-à-vis the zero-field case for the zero-field conserved core of hydrogen bonds (of Tables I and II), Δτ, for 2.45, 20 and 100 GHz cases, in terms of the average of the absolute proportional perturbations in dipole moment of the residues i containing the donors and j containing the acceptors. The dipole moments of the residues are defined vis-à-vis their respective centers-of-mass.

Image of FIG. 3.
FIG. 3.

Reduction in overall persistence percentage vis-à-vis the zero-field case for the zero-field conserved core of hydrogen bonds (of Tables I and II), Δτ, for 2.45, 20 and 100 GHz cases, as a function of the average distance between the hydrogen bonds (the donor-acceptor midpoint) and the center-of-mass of the protein.

Tables

Generic image for table
Table I.

Percentage of duration (persistence) of 20 ns simulations in which particular hydrogen bonds were present. A “…” entry signifies that the particular hydrogen bond was not observed. The residues containing the donors and acceptors are listed with the donor first. ALA | 95 (H) | N–SER | 91 (H) | O refers to the hydrogen bond between the nitrogen of residue 95 (Alanine), as donor, and the oxygen of residue 91 (serine), as acceptor. The bracketed letter is the STRIDE (Ref. 25) structural attribute, where T = turn, E = extended structure (β-sheet), H = (α-helix), and C = coil. Persistences <50% are boldface for convenience. “No.” refers to the ordering in terms of persistence from 1 (greatest persistence) to 27 hydrogen bonds with the shortest persistence.

Generic image for table
Table II.

Average hydrogen bond energies (when present) for the hydrogen bonds in Table I, in kcal/mol. A “-” entry signifies that the particular hydrogen bond was not observed. The residues containing the donors and acceptors are listed with the donor first. ALA|95(H)|N–SER|91(H)|O refers to the hydrogen bond between the nitrogen of residue 95 (alanine), as donor, and the oxygen of residue 91 (serine), acceptor. The bracketed letter is the STRIDE (Ref. 25) structural attribute, where T = turn, E = extended structure (β-sheet), H = (α-helix) and C = coil. Average hydrogen bond energies < 3.0 kcal/mol are boldface for convenience. “No.” refers to the ordering in terms of persistence from 1 (greatest persistence) to 27 hydrogen bonds with the shortest persistence as in Table I.

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/content/aip/journal/jcp/133/23/10.1063/1.3518975
2010-12-21
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Hydrogen bond perturbation in hen egg white lysozyme by external electromagnetic fields: A nonequilibrium molecular dynamics study
http://aip.metastore.ingenta.com/content/aip/journal/jcp/133/23/10.1063/1.3518975
10.1063/1.3518975
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