A1 Journal article (refereed)
Exploring Strategies for Labeling Viruses with Gold Nanoclusters through Non-equilibrium Molecular Dynamics Simulations (2017)

Pohjolainen, E., Malola, S., Groenhof, G., & Häkkinen, H. (2017). Exploring Strategies for Labeling Viruses with Gold Nanoclusters through Non-equilibrium Molecular Dynamics Simulations. Bioconjugate Chemistry, 28(9), 2327-2339. https://doi.org/10.1021/acs.bioconjchem.7b00367

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Publication details

All authors or editorsPohjolainen, Emmi; Malola, Sami; Groenhof, Gerrit; Häkkinen, Hannu

Journal or seriesBioconjugate Chemistry



Publication year2017


Issue number9

Pages range2327-2339

PublisherAmerican Chemical Society

Publication countryUnited States

Publication languageEnglish


Publication open accessNot open

Publication channel open access


Biocompatible gold nanoclusters can be utilized as contrast agents in virus imaging. The labeling of viruses can be achieved noncovalently but site-specifically by linking the cluster to the hydrophobic pocket of a virus via a lipid-like pocket factor. We have estimated the binding affinities of three different pocket factors of echovirus 1 (EV1) in molecular dynamics simulations combined with non-equilibrium free-energy calculations. We have also studied the effects on binding affinities with a pocket factor linked to the Au102pMBA44 nanocluster in different protonation states. Although the absolute binding affinities are over-estimated for all the systems, the trend is in agreement with recent experiments.3 Our results suggest that the natural pocket factor (palmitic acid) can be replaced by molecules pleconaril (drug) and its derivative Kirtan1 that have higher estimated binding affinities. Our results also suggest that including the gold nanocluster does not decrease the affinity of the pocket factor to the virus, but the affinity is sensitive to the protonation state of the nanocluster, i.e., to pH conditions. The methodology introduced in this work helps in the design of optimal strategies for gold-virus bioconjugation for virus detection and manipulation.

Free keywordslabeling viruses; gold nanoclusters; non-equilibrium molecular dynamics

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Reporting Year2017

JUFO rating1

Last updated on 2024-10-05 at 23:27