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Towards quantitative classification of folded proteins in terms of elementary functions
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
2011 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 83, no 4, 041907- p.Article in journal (Refereed) Published
Abstract [en]

A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a classification scheme that describes a protein starting from its well-organized secondary structures and often involves direct human involvement, with an atomary-level physics-based approach where a protein is fundamentally nothing more than an ensemble of mutually interacting carbon, hydrogen, oxygen, and nitrogen atoms. In order to bridge these two complementary approaches to proteins, conceptually novel tools need to be introduced. Here we explain how an approach toward geometric characterization of entire folded proteins can be based on a single explicit elementary function that is familiar from nonlinear physical systems where it is known as the kink soliton. Our approach enables the conversion of hierarchical structural information into a quantitative form that allows for a folded protein to be characterized in terms of a small number of global parameters that are in principle computable from atomary-level considerations. As an example we describe in detail how the native fold of the myoglobin 1M6C emerges from a combination of kink solitons with a very high atomary-level accuracy. We also verify that our approach describes longer loops and loops connecting alpha helices with beta strands, with the same overall accuracy.

Place, publisher, year, edition, pages
2011. Vol. 83, no 4, 041907- p.
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-152823DOI: 10.1103/PhysRevE.83.041907ISI: 000289354500006OAI: oai:DiVA.org:uu-152823DiVA: diva2:414314
Available from: 2011-05-03 Created: 2011-05-02 Last updated: 2017-12-11
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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Peng, Xubiao

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