How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: An ab Initio QM/MM study

Yuhui Cheng, Yingkai Zhang, J. Andrew McCammon

Research output: Contribution to journalArticle

Abstract

We have carried out density functional theory QM/MM calculations on the catalytic subunit of cAMP-dependent protein kinase (PKA). The QM/MM calculations indicate that the phosphorylation reaction catalyzed by PKA is mainly dissociative, and Asp166 serves as the catalytic base to accept the proton delivered by the substrate peptide. Among the key interactions in the active site, the Mg2+ ions, glycine rich loop, and Lys72 are found to stabilize the transition state through electrostatic interactions. On the other hand, Lys168, Asn171, Asp184, and the conserved waters bound to Mg2+ ions do not directly contribute to lower the energy barrier of the phosphorylation reaction, and possible roles for these residues are proposed. The QM/MM calculations with different QM/MM partition schemes or different initial structures yield consistent results. In addition, we have carried out 12 ns molecular dynamics simulations on both wild type and K168A mutated PKA, respectively, to demonstrate that the catalytic role of Lys168 is to keep ATP and substrate peptide in the near-attack reactive conformation.

Original languageEnglish (US)
Pages (from-to)1553-1562
Number of pages10
JournalJournal of the American Chemical Society
Volume127
Issue number5
DOIs
StatePublished - Feb 9 2005

Fingerprint

Phosphorylation
Cyclic AMP-Dependent Protein Kinases
Protein Kinases
Catalytic Domain
Ions
Proteins
Peptides
Molecular Dynamics Simulation
Static Electricity
Glycine
Protons
Adenosine Triphosphate
Adenosinetriphosphate
Energy barriers
Substrates
Coulomb interactions
Density functional theory
Conformations
Molecular dynamics
Water

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction : An ab Initio QM/MM study. / Cheng, Yuhui; Zhang, Yingkai; McCammon, J. Andrew.

In: Journal of the American Chemical Society, Vol. 127, No. 5, 09.02.2005, p. 1553-1562.

Research output: Contribution to journalArticle

@article{d2f73173e3a64119a0687d746df8e843,
title = "How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: An ab Initio QM/MM study",
abstract = "We have carried out density functional theory QM/MM calculations on the catalytic subunit of cAMP-dependent protein kinase (PKA). The QM/MM calculations indicate that the phosphorylation reaction catalyzed by PKA is mainly dissociative, and Asp166 serves as the catalytic base to accept the proton delivered by the substrate peptide. Among the key interactions in the active site, the Mg2+ ions, glycine rich loop, and Lys72 are found to stabilize the transition state through electrostatic interactions. On the other hand, Lys168, Asn171, Asp184, and the conserved waters bound to Mg2+ ions do not directly contribute to lower the energy barrier of the phosphorylation reaction, and possible roles for these residues are proposed. The QM/MM calculations with different QM/MM partition schemes or different initial structures yield consistent results. In addition, we have carried out 12 ns molecular dynamics simulations on both wild type and K168A mutated PKA, respectively, to demonstrate that the catalytic role of Lys168 is to keep ATP and substrate peptide in the near-attack reactive conformation.",
author = "Yuhui Cheng and Yingkai Zhang and McCammon, {J. Andrew}",
year = "2005",
month = "2",
day = "9",
doi = "10.1021/ja0464084",
language = "English (US)",
volume = "127",
pages = "1553--1562",
journal = "Journal of the American Chemical Society",
issn = "0002-7863",
publisher = "American Chemical Society",
number = "5",

}

TY - JOUR

T1 - How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction

T2 - An ab Initio QM/MM study

AU - Cheng, Yuhui

AU - Zhang, Yingkai

AU - McCammon, J. Andrew

PY - 2005/2/9

Y1 - 2005/2/9

N2 - We have carried out density functional theory QM/MM calculations on the catalytic subunit of cAMP-dependent protein kinase (PKA). The QM/MM calculations indicate that the phosphorylation reaction catalyzed by PKA is mainly dissociative, and Asp166 serves as the catalytic base to accept the proton delivered by the substrate peptide. Among the key interactions in the active site, the Mg2+ ions, glycine rich loop, and Lys72 are found to stabilize the transition state through electrostatic interactions. On the other hand, Lys168, Asn171, Asp184, and the conserved waters bound to Mg2+ ions do not directly contribute to lower the energy barrier of the phosphorylation reaction, and possible roles for these residues are proposed. The QM/MM calculations with different QM/MM partition schemes or different initial structures yield consistent results. In addition, we have carried out 12 ns molecular dynamics simulations on both wild type and K168A mutated PKA, respectively, to demonstrate that the catalytic role of Lys168 is to keep ATP and substrate peptide in the near-attack reactive conformation.

AB - We have carried out density functional theory QM/MM calculations on the catalytic subunit of cAMP-dependent protein kinase (PKA). The QM/MM calculations indicate that the phosphorylation reaction catalyzed by PKA is mainly dissociative, and Asp166 serves as the catalytic base to accept the proton delivered by the substrate peptide. Among the key interactions in the active site, the Mg2+ ions, glycine rich loop, and Lys72 are found to stabilize the transition state through electrostatic interactions. On the other hand, Lys168, Asn171, Asp184, and the conserved waters bound to Mg2+ ions do not directly contribute to lower the energy barrier of the phosphorylation reaction, and possible roles for these residues are proposed. The QM/MM calculations with different QM/MM partition schemes or different initial structures yield consistent results. In addition, we have carried out 12 ns molecular dynamics simulations on both wild type and K168A mutated PKA, respectively, to demonstrate that the catalytic role of Lys168 is to keep ATP and substrate peptide in the near-attack reactive conformation.

UR - http://www.scopus.com/inward/record.url?scp=13444303958&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=13444303958&partnerID=8YFLogxK

U2 - 10.1021/ja0464084

DO - 10.1021/ja0464084

M3 - Article

VL - 127

SP - 1553

EP - 1562

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

SN - 0002-7863

IS - 5

ER -