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Role of Counterions in Constant-pH Molecular Dynamics Simulations of PAMAM Dendrimers

2018-02-28Artigo científico Desconhecido
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dc.contributor.authorReis, Pedro B.P.S.
dc.contributor.authorVila-Viçosa, Diogo
dc.contributor.authorCampos, Sara R.R.
dc.contributor.authorBaptista, António M.
dc.contributor.authorMacHuqueiro, Miguel
dc.contributor.institutionMolecular, Structural and Cellular Microbiology (MOSTMICRO)
dc.contributor.institutionInstituto de Tecnologia Química e Biológica António Xavier (ITQB)
dc.contributor.pblACS - American Chemical Society
dc.date.accessioned2019-05-03T22:15:54Z
dc.date.available2019-05-03T22:15:54Z
dc.date.issued2018-02-28
dc.description.abstractElectrostatic interactions play a pivotal role in the structure and mechanism of action of most biomolecules. There are several conceptually different methods to deal with electrostatics in molecular dynamics simulations. Ionic strength effects are usually introduced using such methodologies and can have a significant impact on the quality of the final conformation space obtained. We have previously shown that full system neutralization can lead to wrong lipidic phases in the 25% PA/PC bilayer (J. Chem. Theory Comput. 2014, 10, 5483-5492). In this work, we investigate how two limit approaches to the ionic strength treatment (implicitly with GRF or using full system neutralization with either GRF or PME) can influence the conformational space of the second-generation PAMAM dendrimer. Constant-pH MD simulations were used to map PAMAM's conformational space at its full pH range (from 2.5 to 12.5). Our simulations clearly captured the coupling between protonation and conformation in PAMAM. Interestingly, the dendrimer conformational distribution was almost independent of the ionic strength treatment methods, which is in contrast to what we have observed in charged lipid bilayers. Overall, our results confirm that both GRF with implicit ionic strength and a fully neutralized system with PME are valid approaches to model charged globular systems, using the GROMOS 54A7 force field.en
dc.description.versionpublishersversion
dc.description.versionpublished
dc.format.extent9
dc.format.extent2127837
dc.identifier.doi10.1021/acsomega.7b01708
dc.identifier.issn2470-1343
dc.identifier.otherPURE: 12439635
dc.identifier.otherPURE UUID: b8040c6a-6a04-4848-b059-4e92e44e509a
dc.identifier.otherScopus: 85048407364
dc.identifier.urihttp://www.scopus.com/inward/record.url?scp=85048407364&partnerID=8YFLogxK
dc.identifier.urlhttps://www.scopus.com/pages/publications/85048407364
dc.language.isoeng
dc.peerreviewedyes
dc.subjectGeneral Chemistry
dc.subjectGeneral Chemical Engineering
dc.titleRole of Counterions in Constant-pH Molecular Dynamics Simulations of PAMAM Dendrimersen
dc.typejournal article
degois.publication.firstPage2001
degois.publication.issue2
degois.publication.lastPage2009
degois.publication.titleACS Omega
degois.publication.volume3
dspace.entity.typePublication
rcaap.rightsopenAccess

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