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Peptide salt bridge stability: From gas phase via microhydration to bulk water simulations
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10.1063/1.4765052
/content/aip/journal/jcp/137/18/10.1063/1.4765052
http://aip.metastore.ingenta.com/content/aip/journal/jcp/137/18/10.1063/1.4765052

Figures

Image of FIG. 1.
FIG. 1.

Atom labeling of the Ac-Lys-Glu-NHMe model peptide, restricted just to groups that can form hydrogen bonds.

Image of FIG. 2.
FIG. 2.

Details of the model peptide Ac-Lys-Glu-NHMe side chain termini. Top: Dipeptide in neutral form with one (left: contact) and with two water (right: solvent shared) molecules attached. Center: Zwitterionic contact pair with one (left) or two (right) water molecules attached. Bottom: Solvent shared ion pairs involving one (left) or two (right) oxygen atoms of the carboxyl group.

Image of FIG. 3.
FIG. 3.

Proton transfer mechanisms from a 4 ps part of a BOMD trajectory for Ac-Lys-Glu-NHMe(HO). The figure shows the heavy-heavy atom distance vs. the corresponding proton asymmetry variable δ (see text) for three different transfer scenarios: Proton transferred between amino nitrogen and carboxylic oxygen (black) or water oxygen (red), or between water and carboxylic oxygen (green).

Image of FIG. 4.
FIG. 4.

Smeared number of hydrogen bonds additionally stabilizing the side chain termini and proton asymmetry coordinate δ = r−r.

Image of FIG. 5.
FIG. 5.

Normalized distributions of CN distances for the COO⋅⋅⋅NH + side chain termini from 200 ns/300 K simulation for Ac-Lys-Glu-NHMe dipeptide solvated in water clusters of different sizes.

Image of FIG. 6.
FIG. 6.

Fractions of contact, solvent shared, and solvent separated ion pairs obtained from 200 ns/300 K direct MD simulations as a function of the number of water molecules attached to the Ac-Lys-Glu-NHMe dipeptide. Dashed lines serve to guide the eye.

Image of FIG. 7.
FIG. 7.

Free energy profile of NH +⋅⋅⋅HCOO ion pair dissociation in water clusters of different sizes obtained by umbrella sampling.

Image of FIG. 8.
FIG. 8.

Free energy profile of Ac-Lys-Glu-NHMe dipeptide salt bridge opening in water clusters of different sizes obtained by umbrella sampling.

Tables

Generic image for table
Table I.

Lifetimes (ps) from linear fitting of logarithm of probability of staying in particular state. The lifetime is calculated as τ = −1/, where is the slope of the line, the shortest times were omitted from the fit in order to reduce the influence of recrossings. For details see Fig. S4. 28

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/content/aip/journal/jcp/137/18/10.1063/1.4765052
2012-11-08
2014-04-17
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Peptide salt bridge stability: From gas phase via microhydration to bulk water simulations
http://aip.metastore.ingenta.com/content/aip/journal/jcp/137/18/10.1063/1.4765052
10.1063/1.4765052
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