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Topological solitons and folded proteins

Maxim Chernodub (UGent) , Shuangwei Hu and Antti J Niemi
(2010) PHYSICAL REVIEW E. 82(1).
Author
Organization
Abstract
We argue that protein loops can be described by topological domain-wall solitons that interpolate between ground states which are the alpha helices and beta strands. We present an energy function that realizes loops as soliton solutions to its equation of motion, and apply these solitons to model a number of biologically active proteins including 1VII, 2RB8, and 3EBX (Protein Data Bank codes). In all the examples that we have considered we are able to numerically construct soliton solutions that reproduce secondary structural motifs such as alpha-helix-loop-alpha-helix and beta-sheet-loop-beta-sheet with an overall root-mean-square-distance accuracy of around 1.0 angstrom or less for the central alpha-carbons, i.e., close to the limits of current experimental accuracy.

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Citation

Please use this url to cite or link to this publication:

MLA
Chernodub, Maxim, et al. “Topological Solitons and Folded Proteins.” PHYSICAL REVIEW E, vol. 82, no. 1, 2010, doi:10.1103/PhysRevE.82.011916.
APA
Chernodub, M., Hu, S., & Niemi, A. J. (2010). Topological solitons and folded proteins. PHYSICAL REVIEW E, 82(1). https://doi.org/10.1103/PhysRevE.82.011916
Chicago author-date
Chernodub, Maxim, Shuangwei Hu, and Antti J Niemi. 2010. “Topological Solitons and Folded Proteins.” PHYSICAL REVIEW E 82 (1). https://doi.org/10.1103/PhysRevE.82.011916.
Chicago author-date (all authors)
Chernodub, Maxim, Shuangwei Hu, and Antti J Niemi. 2010. “Topological Solitons and Folded Proteins.” PHYSICAL REVIEW E 82 (1). doi:10.1103/PhysRevE.82.011916.
Vancouver
1.
Chernodub M, Hu S, Niemi AJ. Topological solitons and folded proteins. PHYSICAL REVIEW E. 2010;82(1).
IEEE
[1]
M. Chernodub, S. Hu, and A. J. Niemi, “Topological solitons and folded proteins,” PHYSICAL REVIEW E, vol. 82, no. 1, 2010.
@article{2119120,
  abstract     = {{We argue that protein loops can be described by topological domain-wall solitons that interpolate between ground states which are the alpha helices and beta strands. We present an energy function that realizes loops as soliton solutions to its equation of motion, and apply these solitons to model a number of biologically active proteins including 1VII, 2RB8, and 3EBX (Protein Data Bank codes). In all the examples that we have considered we are able to numerically construct soliton solutions that reproduce secondary structural motifs such as alpha-helix-loop-alpha-helix and beta-sheet-loop-beta-sheet with an overall root-mean-square-distance accuracy of around 1.0 angstrom or less for the central alpha-carbons, i.e., close to the limits of current experimental accuracy.}},
  articleno    = {{011916}},
  author       = {{Chernodub, Maxim and Hu, Shuangwei and Niemi, Antti J}},
  issn         = {{1539-3755}},
  journal      = {{PHYSICAL REVIEW E}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{5}},
  title        = {{Topological solitons and folded proteins}},
  url          = {{http://doi.org/10.1103/PhysRevE.82.011916}},
  volume       = {{82}},
  year         = {{2010}},
}
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