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Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling

Devaurs, Didier and Papanastasiou, Malvina and Antunes, Dinler A. and Abella, Jayvee R. and Moll, Mark and Ricklin, Daniel and Lambris, John D. and Kavraki, Lydia E.. (2018) Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling. International journal of computational biology and drug design, 11 (1-2). pp. 90-113.

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Official URL: https://edoc.unibas.ch/69162/

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Abstract

Hydrogen/deuterium exchange detected by mass spectrometry (HDXMS) provides valuable information on protein structure and dynamics. Although HDX-MS data is often interpreted using crystal structures, it was suggested that conformational ensembles produced by molecular dynamics simulations yield more accurate interpretations. In this paper, we analyse the complement protein C3d by performing an HDX-MS experiment, and evaluate several interpretation methodologies using an existing prediction model to derive HDX-MS data from protein structure. To interpret and refine C3d's HDX-MS data, we look for a conformation (or conformational ensemble) of C3d that allows computationally replicating this data. We confirm that crystal structures are not a good choice and suggest that conformational ensembles produced by molecular dynamics simulations might not always be satisfactory either. Finally, we show that coarse-grained conformational sampling of C3d produces a conformation from which its HDX-MS data can be replicated and refined.
Faculties and Departments:05 Faculty of Science > Departement Pharmazeutische Wissenschaften > Pharmazie > Molekulare Pharmazie (Ricklin)
UniBasel Contributors:Ricklin, Daniel
Item Type:Article, refereed
Article Subtype:Research Article
ISSN:1756-0756
Note:Publication type according to Uni Basel Research Database: Journal article
Identification Number:
Last Modified:10 Apr 2020 17:03
Deposited On:10 Apr 2020 17:03

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