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The mechanism of antiparallel β-sheet formation based on conditioned self-avoiding walk

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Abstract

By introducing an additional hydrogen bond to hydrogen bond interaction in the force field of the CSAW (Conditioned Self-Avoiding Walk) model, we investigate into the mechanism of antiparallel β-sheet formation based on the folding of a short polyalanine in gas phase. Through our numerical simulation, we detect the possible presence of a transient helix during β-sheet formation, whose presence is shown to have slowed the formation of β-sheets by an order of magnitude. While we observe the mechanisms of nucleation, zipping and induction that drives the formation of a β-sheet, we uncover a new mechanism that involves transient β-turns and short β-sheets during the formation of long β-sheets. Our results have enabled us to provide an overview on the mechanisms of β-sheet formation via two main folding pathways: slow folding through the intermediate state of transient helix, and fast folding from the nucleation of β-turn.

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Author notes

  1. Boon Chong Goh

    Present address: Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

Authors and Affiliations

  1. Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore, Singapore

    Boon Chong Goh, Hon Wai Leong, Xiaohui Qu & Lock Yue Chew

  2. High Performance Computing Centre, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore, Singapore

    Hon Wai Leong

Authors
  1. Boon Chong Goh
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  2. Hon Wai Leong
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  3. Xiaohui Qu
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  4. Lock Yue Chew
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Correspondence to Lock Yue Chew.

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Goh, B.C., Leong, H.W., Qu, X. et al. The mechanism of antiparallel β-sheet formation based on conditioned self-avoiding walk. Eur. Phys. J. E 35, 27 (2012). https://doi.org/10.1140/epje/i2012-12027-8

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  • DOI: https://doi.org/10.1140/epje/i2012-12027-8

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