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Reproducible polypeptide folding and structure prediction using molecular dynamics simulations.
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology.
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology.
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology.
2005 (English)In: J Mol Biol, ISSN 0022-2836, Vol. 354, no 1, 173-83 p.Article in journal (Other scientific) Published
Place, publisher, year, edition, pages
2005. Vol. 354, no 1, 173-83 p.
Keyword [en]
Computer Simulation, Kinetics, Models; Chemical, Models; Molecular, Nuclear Magnetic Resonance; Biomolecular, Organic Chemicals/*chemistry, Peptides/*chemistry, Protein Conformation, Protein Folding, Reproducibility of Results, Research Support; Non-U.S. Gov't, Solvents, Temperature, Thermodynamics, Vacuum
Identifiers
URN: urn:nbn:se:uu:diva-76149PubMedID: 16236315OAI: oai:DiVA.org:uu-76149DiVA: diva2:104061
Available from: 2006-02-27 Created: 2006-02-27 Last updated: 2011-03-04
In thesis
1. Protein Folding and DNA Origami
Open this publication in new window or tab >>Protein Folding and DNA Origami
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In this thesis, the folding process of the de novo designed polypeptide chignolin was elucidated through atomic-scale Molecular Dynamics (MD) computer simulations. In a series of long timescale and replica exchange MD simulations, chignolin’s folding and unfolding was observed numerous times and the native state was identified from the computed Gibbs free-energy landscape. The rate of the self-assembly process was predicted from the replica exchange data through a novel algorithm and the structural fluctuations of an enzyme, lysozyme, were analyzed.

DNA’s structural flexibility was investigated through experimental structure determination methods in the liquid and gas phase. DNA nanostructures could be maintained in a flat geometry when attached to an electrostatically charged, atomically flat surface and imaged in solution with an Atomic Force Microscope. Free in solution under otherwise identical conditions, the origami exhibited substantial compaction, as revealed by small angle X-ray scattering. This condensation was even more extensive in the gas phase.

Protein folding is highly reproducible. It can rapidly lead to a stable state, which undergoes moderate fluctuations, at least for small structures. DNA maintains extensive structural flexibility, even when folded into large DNA origami.

One may reflect upon the functional roles of proteins and DNA as a consequence of their atomic-level structural flexibility. DNA, biology’s information carrier, is very flexible and malleable, adopting to ever new conformations. Proteins, nature’s machines, faithfully adopt highly reproducible shapes to perform life’s functions robotically.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2010. 43 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 724
Keyword
protein folding, Molecular Dynamics simulations, DNA origami
National Category
Biophysics
Research subject
Physics with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-121549 (URN)978-91-554-7756-1 (ISBN)
Public defence
2010-04-20, B21, Husargatan 3, 751 24 Uppsala, BMC, 10:15 (English)
Opponent
Supervisors
Available from: 2010-03-29 Created: 2010-03-25 Last updated: 2011-03-04

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Patriksson, Alexandravan der Spoel, David

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