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Title: Solitons and protein folding: An In Silico experiment

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 Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ 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 importancemore » 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.« less
Authors:
 [1] ;  [2] ;  [3] ;  [4] ;  [5]
  1. Institute of Information and Communication Technologies, Bulgarian Aacademy of Sciences, Sofia (Bulgaria)
  2. School of Physics, Beijing Institute of Technology, Beijing (China)
  3. Faculty of Chemistry, University of Gdańsk, Gdańsk (Poland)
  4. Department of Physics and Astronomy, Uppsala University, Uppsala (Sweden)
  5. (France)
Publication Date:
OSTI Identifier:
22492605
Resource Type:
Journal Article
Resource Relation:
Journal Name: AIP Conference Proceedings; Journal Volume: 1684; Journal Issue: 1; Conference: AMiTaNS'15: 7. international conference for promoting the application of mathematics in technical and natural sciences, Albena (Bulgaria), 28 Jun - 3 Jul 2015; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; AIDS VIRUS; AMINO ACID SEQUENCE; AMINO ACIDS; COMPUTERIZED SIMULATION; FORECASTING; GLYCOPROTEINS; MATHEMATICAL SOLUTIONS; MOLECULAR DYNAMICS METHOD; NONLINEAR PROBLEMS; RANDOMNESS; SCHROEDINGER EQUATION; SHAPE; SOLITONS; THREE-DIMENSIONAL CALCULATIONS