Kink Formation Dynamics in a Single О±-helical Protein

Authors

  • Nevena Ilieva* Institute of Information and Communication Technologies - Bulgarian Academy of Sciences
  • Antti Niemi Department of Physics and Astronomy, Uppsala University
  • Xubiao Peng Department of Physics and Astronomy, Uppsala University
  • Adam Sieradzan University of Gdansk & TU of Gdansk

DOI:

https://doi.org/10.11145/473

Abstract

Protein folding remains an open problem despite the progress in understanding the process rate and the success in folding prediction for some small proteins. The reason is the absence of a constructive theoretical framework, both general and specific enough.In earlier papers, we have argued that protein-folding dynamics can be described in terms of solitons of a generalized discrete non-linear Schrodinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles [1]. The soliton manifestation is the pattern helix--loop--helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins and the kink assignment to it [2]. We propose a new mechanism for this process based on the energy transmission along the chain---a disturbance in the latter leads to energy accumulation sufficient to form a kink. We present first insights into the process dynamics by all-atom molecular-dynamics analysis of unfolding of a single alpha-helical protein–--one chain of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK). We suggest an adequate quantification of the side-chain orientation dynamics and also identify some force-field related artefacts.

Author Biographies

Nevena Ilieva*, Institute of Information and Communication Technologies - Bulgarian Academy of Sciences

Associate Professor

Antti Niemi, Department of Physics and Astronomy, Uppsala University

Professor

Xubiao Peng, Department of Physics and Astronomy, Uppsala University

Project Associate

Adam Sieradzan, University of Gdansk & TU of Gdansk

Project Associate

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Published

2015-04-26

Issue

Section

Conference Contributions