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Soliton concepts and protein structure
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics. Univ Tours, Lab Math & Phys Theor, CNRS, UMR 6083, F-37200 Tours, France.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
2012 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 85, no 3, 031906Article in journal (Refereed) Published
Abstract [en]

Structural classification shows that the number of different protein folds is surprisingly small. It also appears that proteins are built in a modular fashion from a relatively small number of components. Here we propose that the modular building blocks are made of the dark soliton solution of a generalized discrete nonlinear Schrödinger equation. We find that practically all protein loops can be obtained simply by scaling the size and by joining together a number of copies of the soliton, one after another. The soliton has only two loop-specific parameters, and we compute their statistical distribution in the Protein Data Bank (PDB). We explicitly construct a collection of 200 sets of parameters, each determining a soliton profile that describes a different short loop. The ensuing profiles cover practically all those proteins in PDB that have a resolution which is better than 2.0 Å, with a precision such that the average root-mean-square distance between the loop and its soliton is less than the experimental B-factor fluctuation distance. We also present two examples that describe how the loop library can be employed both to model and to analyze folded proteins.

Place, publisher, year, edition, pages
APS , 2012. Vol. 85, no 3, 031906
National Category
Biophysics
Research subject
Theoretical Physics
Identifiers
URN: urn:nbn:se:uu:diva-196716DOI: 10.1103/PhysRevE.85.031906ISI: 000209132200002PubMedID: 22587122OAI: oai:DiVA.org:uu-196716DiVA: diva2:610847
Available from: 2013-03-13 Created: 2013-03-13 Last updated: 2017-12-06Bibliographically approved
In thesis
1. Protein Folding Simulations in Kink Model
Open this publication in new window or tab >>Protein Folding Simulations in Kink Model
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The structure of protein is essentially important for life activities. Proteins can perform their functions only by specific structures. In this thesis, the kink and multi-kink model for protein description are reviewed. It is shown that most of the loop parts in Protein Databank (PDB) can be described by very limited number of kinks within the experimental precision. Furthermore, by applying the model into two well studied real proteins (myoglobin and villin headpiece HP35), it is shown that the multi-kink model gives correct folding pathway and thermal dynamical properties compared with the experimental results for both proteins. In particular, the kink model is computationally inexpensive compared with other existing models. In the last chapter, a new visualization method for the heavy atoms in the side-chain is presented.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2014. 56 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1184
Keyword
protein folding, kink model, soliton
National Category
Biophysics
Research subject
Physics with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-232562 (URN)978-91-554-9043-0 (ISBN)
Public defence
2014-11-07, 80101, Ångström Laboratory, Lägerhyddsvägen 1, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2014-10-14 Created: 2014-09-22 Last updated: 2015-01-23

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Niemi, Antti J.Peng, Xubiao

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