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Please use this identifier to cite or link to this item: http://dspace.utalca.cl/handle/1950/10072

Title: Study of the Affinity between the Protein Kinase PKA and Peptide Substrates Derived from Kemptide Using Molecular Dynamics Simulations and MM/GBSA
Authors: Mena-Ulecia, K.
Vergara-Jaque, A.
Poblete, H.
Tiznado, W.
Caballero, J.
Keywords: DRUG-RESISTANCE
INHIBITORS
ARABIDOPSIS
RECTIFICATION
MECHANISM
SPECIFICITY
PHOSPHORYLATION
BINDING
K+ CHANNEL
FREE-ENERGY
Issue Date: 2-Oct-2014
Publisher: PUBLIC LIBRARY SCIENCE
Citation: PLOS ONE 9 (10)
Abstract: We 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 (DDGERES) 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 (DDGERTS) 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.
Description: Vergara-Jaque, A (Vergara-Jaque, Ariela); Poblete, H (Poblete, Horacio); Caballero, J (Caballero, Julio) Univ Talca, Fac Ingn, Ctr Bioinformat & Simulac Mol, Talca, Chile
URI: http://dspace.utalca.cl/handle/1950/10072
ISSN: 1932-6203
Appears in Collections:Artículos en publicaciones ISI - Universidad de Talca

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