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Reproducible polypeptide folding and structure prediction using molecular dynamics simulations
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
2005 In: J. Mol. Biol., Vol. 354, 173-183 p.Article in journal (Refereed) Published
Place, publisher, year, edition, pages
2005. Vol. 354, 173-183 p.
Identifiers
URN: urn:nbn:se:uu:diva-96398OAI: oai:DiVA.org:uu-96398DiVA: diva2:170962
Available from: 2007-11-09 Created: 2007-11-09 Last updated: 2014-09-26Bibliographically approved
In thesis
1. From Solution into Vacuum - Structural Transitions in Proteins
Open this publication in new window or tab >>From Solution into Vacuum - Structural Transitions in Proteins
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Information about protein structures is important in many areas of life sciences, including structure-based drug design. Gas phase methods, like electrospray ionization and mass spectrometry are powerful tools for the analysis of molecular interactions and conformational changes which complement existing solution phase methods. Novel techniques such as single particle imaging with X-ray free electron lasers are emerging as well. A requirement for using gas phase methods is that we understand what happens to proteins when injected into vacuum, and what is the relationship between the vacuum structure and the solution structure.

Molecular dynamics simulations in combination with experiments show that protein structures in the gas phase can be similar to solution structures, and that hydrogen bonding networks and secondary structure elements can be retained. Structural changes near the surface of the protein happen quickly (ns-µs) during transition from solution into vacuum. The native solution structure results in a reasonably well defined gas phase structure, which has high structural similarity to the solution structure.

Native charge locations are in some cases also preserved, and structural changes, due to point mutations in solution, can also be observed in vacuo. Proteins do not refold in vacuo: when a denatured protein is injected into vacuum, the resulting gas phase structure is different from the native structure.

Native structures can be protected in the gas phase by adjusting electrospray conditions to avoid complete evaporation of water. A water layer with a thickness of less than two water molecules seems enough to preserve native conditions.

The results presented in this thesis give confidence in the continued use of gas phase methods for analysis of charge locations, conformational changes and non-covalent interactions, and provide a means to relate gas phase structures and solution structures.

Place, publisher, year, edition, pages
Uppsala: Universitetsbiblioteket, 2007. viii, 44 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 360
Keyword
molecular dynamics, computer simulations, mass spectrometry, electrospray ionization, free-electron laser, vacuum structure of proteins, solvation, desolvation, single molecule imaging
National Category
Other Basic Medicine
Identifiers
urn:nbn:se:uu:diva-8300 (URN)978-91-554-7014-2 (ISBN)
Public defence
2007-12-01, B7:113a, BMC, Husargatan 3, Uppsala, 13:00
Opponent
Supervisors
Available from: 2007-11-09 Created: 2007-11-09 Last updated: 2016-08-24Bibliographically approved

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