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Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
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2015 (English)In: PLoS ONE, ISSN 1932-6203, Vol. 10, no 5Article in journal (Refereed) Published
Abstract [en]

The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un) folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un) folding reaction has often been questioned. One of the most well studied (un) folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un) folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un) folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution.

Place, publisher, year, edition, pages
2015. Vol. 10, no 5
National Category
Biophysics Biochemistry and Molecular Biology
URN: urn:nbn:se:uu:diva-256130DOI: 10.1371/journal.pone.0125662ISI: 000354049700081PubMedID: 25946337OAI: diva2:824812
Available from: 2015-06-22 Created: 2015-06-22 Last updated: 2015-06-22Bibliographically approved

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Nasedkin, AlexandrJemth, Pervan der Spoel, David
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Physical ChemistryDepartment of Cell and Molecular BiologyScience for Life Laboratory, SciLifeLabDepartment of Medical Biochemistry and MicrobiologyComputational and Systems Biology
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