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Solitons And Protein Folding: An In Silico Experiment
Bulgarian Aacademy Sci, Inst Informat & Commun Technol, Sofia, Bulgaria..
Beijing Inst Technol, Sch Phys, Beijing 100081, Peoples R China..
Univ Gdansk, Fac Chem, PL-80952 Gdansk, Poland..
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
2015 (English)In: Application of Mathematics in Technical and Natural Sciences (AMiTaNS'15), 2015, 030006Conference paper (Refereed)Text
Abstract [en]

Protein folding [1] is the process of formation of a functional 3D structure from a random coil - the shape in which amino-acid chains leave the ribosome. Anfinsen's dogma states that the native 3D shape of a protein is completely determined by protein's amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrodinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles kappa and tau provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. 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. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics.

Place, publisher, year, edition, pages
2015. 030006
Series
, AIP Conference Proceedings, ISSN 0094-243X ; 1684
National Category
Physical Sciences Mathematics
Identifiers
URN: urn:nbn:se:uu:diva-296921DOI: 10.1063/1.4934290ISI: 000371826600009ISBN: 978-0-7354-1331-3OAI: oai:DiVA.org:uu-296921DiVA: diva2:946876
Conference
7th International Conference on Application of Mathematics in Technical and Natural Sciences (AMiTaNS), JUN 28-JUL 03, 2015, Albena, BULGARIA
Available from: 2016-07-06 Created: 2016-06-20 Last updated: 2016-07-06Bibliographically approved

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Niemi, Antti
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