Study of the affinity between the protein kinase PKA and peptide substrates derived from kemptide using molecular dynamics simulations and MM/GBSA

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dc.contributor.authorMena-Ulecia, Karel
dc.contributor.authorVergara-Jaque, Ariela
dc.contributor.authorPoblete, Horacio
dc.contributor.authorTiznado, William
dc.contributor.authorCaballero, Julio
dc.date.accessioned2023-01-03T19:14:00Z
dc.date.available2023-01-03T19:14:00Z
dc.date.issued2014
dc.descriptionIndexación: Scopuses
dc.description.abstractWe have carried out a protocol in computational biochemistry including molecular dynamics (MD) simulations and MM/GBSA free energy calculations on the complex between the protein kinase A (PKA) and the specific peptide substrate Kemptide (LRRASLG). We made the same calculations on other PKA complexes that contain Kemptide derivatives (with mutations of the arginines, and with deletions of N and C-terminal amino acids). We predicted shifts in the free energy changes from the free PKA to PKA-substrate complex (δδGE→ES) when Kemptide structure is modified (we consider that the calculated shifts correlate with the experimental shifts of the free energy changes from the free PKA to the transition states (δδGE→TS) determined by the catalytic efficiency (kcat/KM) changes). Our results demonstrate that it is possible to predict the kinetic properties of protein kinases using simple computational biochemistry methods. As an additional benefit, these methods give detailed molecular information that permit the analysis of the atomic forces that contribute to the affinity between protein kinases and their substrates. © 2014 Mena-Ulecia et al.es
dc.description.urihttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.0109639
dc.identifier.doi10.1371/journal.pone.0109639
dc.identifier.issn1932-6203
dc.identifier.urihttps://repositorio.unab.cl/xmlui/handle/ria/35779
dc.language.isoenes
dc.publisherPublic Library of Sciencees
dc.rights.licenseAtribución 4.0 Internacional (CC BY 4.0)
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/deed.es
dc.subjectCyclic AMP Dependent Protein Kinasees
dc.subjectProtein Kinasees
dc.subjectDFGes
dc.titleStudy of the affinity between the protein kinase PKA and peptide substrates derived from kemptide using molecular dynamics simulations and MM/GBSAes
dc.typeArtículoes
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PLoS ONE Volume 9, Issue 102 October 2014 Article number 0109639
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