Study of the affinity between the protein kinase PKA and homoarginine-containing peptides derived from kemptide: Free energy perturbation (FEP) calculations

Karel Mena-Ulecia, Fabian Gonzalez-Norambuena, Ariela Vergara-Jaque, Horacio Poblete, William Tiznado, Julio Caballero

Resultado de la investigación: Article

2 Citas (Scopus)

Resumen

Protein kinases (PKs) discriminate between closely related sequences that contain serine, threonine, and/or tyrosine residues. Such specificity is defined by the amino acid sequence surrounding the phosphorylatable residue, so that it is possible to identify an optimal recognition motif (ORM) for each PK. The ORM for the protein kinase A (PKA), a well-known member of the PK family, is the sequence RRX(S/T)X, where arginines at the −3 and −2 positions play a key role with respect to the primed phosphorylation site. In this work, differential affinities of PKA for the peptide substrate Kemptide (LRRASLG) and mutants that substitute the arginine residues by the unnatural peptide homoarginine were evaluated through molecular dynamics (MD) and free energy perturbation (FEP) calculations. The FEP study for the homoarginine mutants required previous elaboration of a CHARMM “arginine to homoarginine” (R2B) hybrid topology file which is available in this manuscript as Supporting Information. Mutants substituting the arginine residues by alanine, lysine, and histidine were also considered in the comparison by using the same protocol. FEP calculations allowed estimating the free energy changes from the free PKA to PKA-substrate complex (ΔΔGE→ES) when Kemptide structure was mutated. Both ΔΔGS→ES values for homoarginine mutants were predicted with a difference below 1 kcal/mol. In addition, FEP correctly predicted that all the studied mutations decrease the catalytic efficiency of Kemptide for PKA.

Idioma originalEnglish
Páginas (desde-hasta)986-992
Número de páginas7
PublicaciónJournal of Computational Chemistry
Volumen39
N.º16
DOI
EstadoPublished - 15 jun 2018

Huella dactilar

kemptide
Homoarginine
Protein Kinase
Cyclic AMP-Dependent Protein Kinases
Peptides
Protein Kinases
Free energy
Affine transformation
Free Energy
Arginine
Proteins
Perturbation
Mutant
Phosphorylation
Substrates
Threonine
Histidine
Alanine
Serine
Substrate

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

Citar esto

Mena-Ulecia, Karel ; Gonzalez-Norambuena, Fabian ; Vergara-Jaque, Ariela ; Poblete, Horacio ; Tiznado, William ; Caballero, Julio. / Study of the affinity between the protein kinase PKA and homoarginine-containing peptides derived from kemptide : Free energy perturbation (FEP) calculations. En: Journal of Computational Chemistry. 2018 ; Vol. 39, N.º 16. pp. 986-992.
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abstract = "Protein kinases (PKs) discriminate between closely related sequences that contain serine, threonine, and/or tyrosine residues. Such specificity is defined by the amino acid sequence surrounding the phosphorylatable residue, so that it is possible to identify an optimal recognition motif (ORM) for each PK. The ORM for the protein kinase A (PKA), a well-known member of the PK family, is the sequence RRX(S/T)X, where arginines at the −3 and −2 positions play a key role with respect to the primed phosphorylation site. In this work, differential affinities of PKA for the peptide substrate Kemptide (LRRASLG) and mutants that substitute the arginine residues by the unnatural peptide homoarginine were evaluated through molecular dynamics (MD) and free energy perturbation (FEP) calculations. The FEP study for the homoarginine mutants required previous elaboration of a CHARMM “arginine to homoarginine” (R2B) hybrid topology file which is available in this manuscript as Supporting Information. Mutants substituting the arginine residues by alanine, lysine, and histidine were also considered in the comparison by using the same protocol. FEP calculations allowed estimating the free energy changes from the free PKA to PKA-substrate complex (ΔΔGE→ES) when Kemptide structure was mutated. Both ΔΔGS→ES values for homoarginine mutants were predicted with a difference below 1 kcal/mol. In addition, FEP correctly predicted that all the studied mutations decrease the catalytic efficiency of Kemptide for PKA.",
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Study of the affinity between the protein kinase PKA and homoarginine-containing peptides derived from kemptide : Free energy perturbation (FEP) calculations. / Mena-Ulecia, Karel; Gonzalez-Norambuena, Fabian; Vergara-Jaque, Ariela; Poblete, Horacio; Tiznado, William; Caballero, Julio.

En: Journal of Computational Chemistry, Vol. 39, N.º 16, 15.06.2018, p. 986-992.

Resultado de la investigación: Article

TY - JOUR

T1 - Study of the affinity between the protein kinase PKA and homoarginine-containing peptides derived from kemptide

T2 - Free energy perturbation (FEP) calculations

AU - Mena-Ulecia, Karel

AU - Gonzalez-Norambuena, Fabian

AU - Vergara-Jaque, Ariela

AU - Poblete, Horacio

AU - Tiznado, William

AU - Caballero, Julio

PY - 2018/6/15

Y1 - 2018/6/15

N2 - Protein kinases (PKs) discriminate between closely related sequences that contain serine, threonine, and/or tyrosine residues. Such specificity is defined by the amino acid sequence surrounding the phosphorylatable residue, so that it is possible to identify an optimal recognition motif (ORM) for each PK. The ORM for the protein kinase A (PKA), a well-known member of the PK family, is the sequence RRX(S/T)X, where arginines at the −3 and −2 positions play a key role with respect to the primed phosphorylation site. In this work, differential affinities of PKA for the peptide substrate Kemptide (LRRASLG) and mutants that substitute the arginine residues by the unnatural peptide homoarginine were evaluated through molecular dynamics (MD) and free energy perturbation (FEP) calculations. The FEP study for the homoarginine mutants required previous elaboration of a CHARMM “arginine to homoarginine” (R2B) hybrid topology file which is available in this manuscript as Supporting Information. Mutants substituting the arginine residues by alanine, lysine, and histidine were also considered in the comparison by using the same protocol. FEP calculations allowed estimating the free energy changes from the free PKA to PKA-substrate complex (ΔΔGE→ES) when Kemptide structure was mutated. Both ΔΔGS→ES values for homoarginine mutants were predicted with a difference below 1 kcal/mol. In addition, FEP correctly predicted that all the studied mutations decrease the catalytic efficiency of Kemptide for PKA.

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KW - cAMP-dependent kinase

KW - free energy perturbation

KW - homoarginine

KW - PKA

KW - protein kinases

KW - unnatural amino acid modeling

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