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Structure and stability of chiral -tapes: A computational coarse-grained approach
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10.1063/1.1866012
    + View Affiliations - Hide Affiliations
    Affiliations:
    1 Theory and Computation Group, Centre for Synthesis and Chemical Biology, Conway Institute for Biomolecular and Biomedical Research, Department of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
    2 Computing Centre, University College Dublin, Belfield, Dublin 4, Ireland
    3 Theory and Computation Group, Centre for Synthesis and Chemical Biology, Conway Institute of Biomolecular and Biomedical Research, Department of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
    a) Electronic mail: Giovanni.Bellesia@ucd.ie
    b) Electronic mail: Maxim.Fedorov@ucd.ie
    c) Electronic mail: Yuri.Kuznetsov@ucd.ie
    d) Author to whom correspondence should be addressed; FAX: +353-1-7162536; Electronic mail: Edward.Timoshenko@ucd.ie; URL: http://darkstar.ucd.ie
    J. Chem. Phys. 122, 134901 (2005); http://dx.doi.org/10.1063/1.1866012
/content/aip/journal/jcp/122/13/10.1063/1.1866012
http://aip.metastore.ingenta.com/content/aip/journal/jcp/122/13/10.1063/1.1866012

Figures

Image of FIG. 1.
FIG. 1.

(a) A circular helicoid described in parametric form by Eq. (15). The constants used to generate the surface were obtained from Monte Carlo simulations of the system of size and chirality parameter using the potential energy model . The thick lines (helical curves) sweeping the two surface’s edges are described in parametric form by Eq. (16). (b) A schematic representation of the regular tape corresponding to the circular helicoid. Gray and black points represent the positions of the monomers and (with , ), respectively. The connecting lines correspond to the vectors (with , ), where the values for , , and are, once again, taken from Monte Carlo simulations and . The positions of the monomers and were used as the reference data in our fitting procedure.

Image of FIG. 2.
FIG. 2.

Plot of the average LDA [Eqs. (3) and (21)–(23)] vs the dihedral angle number along the strand, , obtained from Monte Carlo simulations. Data are related to systems of size within potential energy model . Different lines correspond (from top to bottom) to tapes with chiral equilibrium parameter [Eqs. (7) and (8)].

Image of FIG. 3.
FIG. 3.

Averaged structures obtained from Monte Carlo simulations (over the last Monte Carlo sweeps) for systems of size within the potential energy model . Here the values of the chirality parameter were , respectively.

Image of FIG. 4.
FIG. 4.

Averaged structures obtained from Monte Carlo simulations (over the last Monte Carlo sweeps) for systems of size within potential energy model . (a) Achiral system with . (b) Introduction of chirality in the force field leads to the stabilization of a regularly-twisted supramolecular tape. (c) A larger twist is obtained for .

Image of FIG. 5.
FIG. 5.

Histograms of the pitch wave number (expressed in degrees for better clarity) obtained from Monte Carlo simulations for systems with size (from top to bottom). These data relate to the potential energy model with . Similar results have been obtained for potential energy model also.

Tables

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Table I.

Values of the pitch wave number obtained from the experimental analysis on chiral supramolecular clusters formed from several synthetic and natural peptides.

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Table II.

Average value of the individual strand chirality angle and its standard deviation obtained from Monte Carlo simulations in the potential model .

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Table III.

Average value of the individual strand chirality angle and its standard deviation obtained from Monte Carlo simulations in the potential model .

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Table IV.

Average value and standard deviation , obtained from Monte Carlo simulations, for the helical parameters [Eqs. (19) and (24)], [Eq. (20)], and [Eq. (18)] for the potential energy model .

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Table V.

Average value and standard deviation , obtained from Monte Carlo simulations, for the helical parameters [Eqs. (19) and (24)], [Eq. (20)], and [Eq. (18)] for the potential energy model .

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Table VI.

Fitting results for potential energy model . is the mean displacement between the regular geometrical and simulated helical structures. A similar behavior for the potential energy model has also been found.

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/content/aip/journal/jcp/122/13/10.1063/1.1866012
2005-04-01
2014-04-18
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Structure and stability of chiral β-tapes: A computational coarse-grained approach
http://aip.metastore.ingenta.com/content/aip/journal/jcp/122/13/10.1063/1.1866012
10.1063/1.1866012
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