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Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes

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cris.lastimport.scopus2024-02-12T19:46:10Z
dc.abstract.enProtein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered molecular dynamics (SMD) to assess the strength of protein-peptide interactions. The idea behind using SMD simulations is that the mechanical stability can be used as a promising and an efficient alternative to computationally highly demanding estimation of binding affinity. However, mechanical stability defined as a peak in force-extension profile depends on the choice of the pulling direction. Here we propose an uncommon choice of the pulling direction along resultant dipole moment (RDM) vector, which has not been explored in SMD simulations so far. Using explicit solvent all-atom MD simulations, we apply SMD technique to probe mechanical resistance of ligand-receptor system pulled along two different vectors. A novel pulling direction—when ligand unbinds along the RDM vector—results in stronger forces compared to commonly used ligand unbinding along center of masses vector. Our observation that RDM is one of the factors influencing the mechanical stability of protein-peptide complex can be used to improve the ranking of binding affinities by using mechanical stability as an effective scoring function.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorKouza, Maksim
dc.contributor.authorKloczkowski, Andrzej
dc.contributor.authorBuhimschi, Irina
dc.contributor.authorKoliński, Andrzej
dc.contributor.authorBanerji, Anirban
dc.date.accessioned2024-01-25T19:28:09Z
dc.date.available2024-01-25T19:28:09Z
dc.date.copyright2018-08-10
dc.date.issued2018
dc.description.accesstimeAT_PUBLICATION
dc.description.financeNie dotyczy
dc.description.number8
dc.description.versionFINAL_PUBLISHED
dc.description.volume23
dc.identifier.doi10.3390/MOLECULES23081995
dc.identifier.issn1420-3049
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/118749
dc.languageeng
dc.pbn.affiliationchemical sciences
dc.relation.ispartofMolecules
dc.relation.pagesart.no. 1995
dc.rightsCC-BY
dc.sciencecloudnosend
dc.subject.ensteered molecular dynamics
dc.subject.enall-atom molecular dynamics simulation
dc.subject.enresultant dipole moment
dc.subject.enmechanical stability
dc.subject.enprotein-peptide interactions
dc.titleRole of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes
dc.typeJournalArticle
dspace.entity.typePublication