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Comparative study of the prereactive protein kinase A Michaelis complex with Kemptide substrate

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Abstract

In the present work we have modeled the Michaelis complex of the cyclic-Adenosine Monophosphate Dependent (cAMD) Protein Kinase A (PKA) with Mg2ATP and the heptapeptide substrate Kemptide by classical molecular dynamics. The chosen synthetic substrate is relevant for its high efficiency and small size, and it has not been used in previous theoretical studies. The structural analysis of the data generated along the 6 ns simulation indicates that the modeled substrate–enzyme complex mimics the substrate binding pattern known for PKA. The values of the average prereactive distances obtained from the simulation do not exclude any of the two limiting situations proposed as mechanisms in the literature for the phosphorylation reaction (dissociative and associative) because the system oscillates between configurations compatible with each of them. Furthemore, the results obtained for the average interaction distances between active site residues concord in suggesting the plausability of an alternative third reaction mechanism.

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Notes

  1. From now on, with the name PKA we will refer solely to the catalytic subunit of the enzyme and not to the entire tetramer.

  2. The numbers of the residues of the substrates or inhibitor are referred to the peptide bound to the enzyme in the crystallographic structures. Thus the first residue of PKI(5–24), of SP20, and of the model substrate is Thr1, and the last one is Asp20 in place of Thr5 and Asp24, respectively. In the same way the first residue of Kemptide is Leu13 and the last one is Gly19.

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Acknowledgments

We are grateful for financial support from the Spanish “Ministerio de Educación y Ciencia” and the “Fondo Europeo de Desarrollo Regional” through projects CTQ2005-07115/BQU and BIO2004-05879-C02-01, the “Generalitat de Catalunya” (2005SGR00400), and the “Universitat Autònoma de Barcelona” (EME2006-18). M.G.-V. thanks the “Ramon y Cajal” program for financial support.

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Authors and Affiliations

  1. Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain

    Manuel Montenegro, Mireia Garcia-Viloca, Àngels González-Lafont & José M. Lluch

  2. Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain

    Àngels González-Lafont & José M. Lluch

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  1. Manuel Montenegro
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  2. Mireia Garcia-Viloca
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Correspondence to Mireia Garcia-Viloca.

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Montenegro, M., Garcia-Viloca, M., González-Lafont, À. et al. Comparative study of the prereactive protein kinase A Michaelis complex with Kemptide substrate. J Comput Aided Mol Des 21, 603–615 (2007). https://doi.org/10.1007/s10822-007-9143-x

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  • DOI: https://doi.org/10.1007/s10822-007-9143-x

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