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Soliton driven relaxation dynamics and protein collapse in the villin headpiece
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.
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.
2013 (English)In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 25, no 32, 325103- p.Article in journal (Refereed) Published
Abstract [en]

Protein collapse from a random chain to the native state involves a dynamical phase transition. During the process, new scales and collective variables become excited while old ones recede and fade away. The presence of different phases and many scales causes formidable computational bottle-necks in approaches that are based on full atomic scale scrutiny. Here we propose a way to describe the folding and unfolding processes effectively, using only the biologically relevant time and distance scales. We merge a coarse grained Landau theory that models the static collapsed protein in the low-temperature limit with a Glauber protocol that describes finite-temperature relaxation dynamics in a statistical system which is out of thermal equilibrium. As an example we inspect the collapse of a HP35 chicken villin headpiece subdomain, a paradigm specimen in protein folding studies. We simulate the folding and unfolding process by repeated heating and cooling cycles between a given low-temperature, i.e. bad solvent, environment where the protein is collapsed and various different high-temperature, i.e. good solvent, environments. We find that as long as the high temperature value stays below a value in the range that separates the random walk phase from the self-avoiding walk phase, we consistently recover the native state upon cooling. But, when heated to sufficiently high temperatures, the native state practically never recurs. Our result confirms Anfinsen's thermodynamical hypothesis and estimates a temperature range for its validity, in the case of villin.

Place, publisher, year, edition, pages
2013. Vol. 25, no 32, 325103- p.
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-207013DOI: 10.1088/0953-8984/25/32/325103ISI: 000322227600003OAI: oai:DiVA.org:uu-207013DiVA: diva2:647115
Available from: 2013-09-10 Created: 2013-09-09 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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