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Mobility-based prediction of hydration structures of protein surfaces
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
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2015 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 31, no 12, 1959-1965 p.Article in journal (Refereed) Published
Abstract [en]

Motivation: Hydration largely determines solubility, aggregation of proteins and influences interactions between proteins and drug molecules. Despite the importance of hydration, structural determination of hydration structure of protein surfaces is still challenging from both experimental and theoretical viewpoints. The precision of experimental measurements is often affected by fluctuations and mobility of water molecules resulting in uncertain assignment of water positions. Results: Our method can utilize mobility as an information source for the prediction of hydration structure. The necessary information can be produced by molecular dynamics simulations accounting for all atomic interactions including water-water contacts. The predictions were validated and tested by comparison to more than 1500 crystallographic water positions in 20 hydrated protein molecules including enzymes of biomedical importance such as cyclin-dependent kinase 2. The agreement with experimental water positions was larger than 80% on average. The predictions can be particularly useful in situations where no or limited experimental knowledge is available on hydration structures of molecular surfaces.

Place, publisher, year, edition, pages
2015. Vol. 31, no 12, 1959-1965 p.
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Biochemistry and Molecular Biology
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URN: urn:nbn:se:uu:diva-258773DOI: 10.1093/bioinformatics/btv093ISI: 000356625700054PubMedID: 25682067OAI: oai:DiVA.org:uu-258773DiVA: diva2:842473
Available from: 2015-07-20 Created: 2015-07-20 Last updated: 2017-12-04Bibliographically approved

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van der Spoel, David

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