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Collective motions and structural self-organisation along the myoglobin folding pathway
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. Faculty of Chemistry, University of Gdansk.
Baker Laboratory of Chemistry and Chemical Biology, Cornell University.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
Abstract [en]

We develop a highly predictive energy function to describe the low temperature crystallographic structure of myoglobin with sub-\AA ngstr\"om precision. We use the energy function to investigate the way how myoglobin folds.For this we employ the Glauber protocol, with a variable ambient temperature. We first increase the temperature so that the structure unfolds into a random coil. We then lower thetemperature back to its original value, and monitor how the myoglobin folds towards its native state.We find that the folding proceeds by $\alpha$-helix nucleation, and that the ordering of helix formation parallels experimental observations. There is also a molten globule folding intermediate, with a radius of gyration that matches the experimentally measured value. We estimate the relative folding times between a random chain and molten globule, and between molten globule and the native state, and we find that the ratio is consistentwith the experimentally measured values. We also propose a number of novel experimental characteristics that could be measured in future experiments.

Biophysics
Identifiers
OAI: oai:DiVA.org:uu-232561DiVA: diva2:748721
Available from: 2014-09-22 Created: 2014-09-22 Last updated: 2015-01-23Bibliographically 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
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)
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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Cite
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