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Journal of Chemical Physics / Volume 132 / Issue 6 / ARTICLES / Biological Molecules, Biopolymers, and Biological Systems

J. Chem. Phys. 132, 065103 (2010); http://dx.doi.org/10.1063/1.3314309 (7 pages)

Sequence dependent self-assembly of β-peptides: Insights from a coarse-grained model

Jagannath Mondal1, Bong June Sung2, and Arun Yethiraj3

1Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
2Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
3Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA

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(Received 13 July 2009; accepted 20 January 2010; published online 12 February 2010)

The sequence-directed self-assembly of amphiphilic β-peptides is studied using Monte Carlo simulations. A phenomenological model is employed where each molecule is modeled as a rigid nanorod with side groups located at positions to mimic globally amphiphilic (GA) and nonglobally amphiphilic (non-GA) isomers of β-peptides. The strength and the range of interactions between side groups are chosen based on the types of residues. The simulations show that the aggregation of β-peptides is sensitive to the sequence and the residue types. For one type of β-peptide the GA isomer has a greater tendency to aggregate while for the other the non-GA isomer has a greater tendency to aggregate. The trends observed in the simulations are consistent with recent experiments [ Pomerantz et al., J. Am. Chem. Soc. 128, 8730 (2006) ; Pomerantz et al., Angew. Chem., Int. Ed. 47, 1 (2008) ], although the molecules do not spontaneously form the hollow fibers seen in experiment. Simulations with initial configurations as hollow fibers show that the stability of the fibers follows the same trend as the tendency for aggregation. The simulations demonstrate that the details matter: the self-assembly of the molecules is sensitive to the strength of the short-ranged interactions and the size of the side groups, in addition to the global amphiphilicity of the molecules. This suggests the possibility of designing molecules for desired nanostructures.

© 2010 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. MODEL AND METHODS
    1. Molecular model
    2. Monte Carlo simulation method
  3. RESULTS AND DISCUSSION
    1. Tendency for aggregation
    2. Stability of hollow fibers
  4. SUMMARY AND CONCLUSIONS

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KEYWORDS and PACS

Keywords

aggregation, fibres, isomerism, macromolecules, molecular biophysics, proteins, self-assembly

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3314309

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

For access to fully linked references, you need to log in.
    C. L. Pizzey, W. C. Pomerantz, B. J. Sung, V. M. Yuwono, S. H. Gellman, J. D. Hartgernik, A. Yethiraj, and N. L. Abbott, J. Chem. Phys. 129, 095103 (2008)JCPSA6000129000009095103000001.

    C. A. Miller, J. P. Hernandez-Ortiz, N. L. Abbott, S. H. Gellman, and J. J. de Pablo, J. Chem. Phys. 129, 015102 (2008)JCPSA6000129000001015102000001.

    S. Whitelam and P. L. Geissler, J. Chem. Phys. 127, 154101 (2007)JCPSA6000127000015154101000001.

    J. Liu and E. Luijten, Phys. Rev. Lett. 92, 035504 (2004).


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