European Biophysics Journal

, Volume 28, Issue 6, pp 457–467 | Cite as

Poisson-Boltzmann model studies of molecular electrostatic properties of the cAMP-dependent protein kinase

  • Elżbieta Błachut-Okrasińska
  • Bogdan Lesyng
  • James M. Briggs
  • J. Andrew McCammon
  • J. M. Antosiewicz

Abstract

Protonation equilibria of residues important in the catalytic mechanism of a protein kinase were analyzed on the basis of the Poisson-Boltzmann electrostatic model along with a cluster-based treatment of the multiple titration state problem. Calculations were based upon crystallographic structures of the mammalian cAMP-dependent protein kinase, one representing the so called closed form of the enzyme and the other representing an open conformation. It was predicted that at pH 7 the preferred form of the phosphate group at the catalytically essential threonine 197 (P-Thr197) in the closed form is dianionic, whereas in the open form a monoanionic ionization state is preferred. This dianionic state of P-Thr197, in the closed form, is stabilized by interactions with ionizable residues His87, Arg165, and Lys189. Our calculations predict that the hydroxyl of the Ser residue in the peptide substrate is very difficult to ionize, both in the closed and open structures of the complex. Also, the supposed catalytic base, Asp166, does not seem to have a pKa appropriate to remove the hydroxyl group proton of the peptide substrate. However, when Ser of the peptide substrate is forced to remain ionized, the predicted pKa of Asp166 increases strongly, which suggests that the Asp residue is a likely candidate to attract the proton if the Ser residue becomes deprotonated, possibly during some structural change preceding formation of the transition state. Finally, in accord with suggestions made on the basis of the pH-dependence of kinase kinetics, our calculations predict that Glu230 and His87 are the residues responsible for the molecular pKa values of 6.2 and 8.5, observed in the experiment.

Key words Poisson-Boltzmann model Protein kinases 

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Copyright information

© Springer-Verlag Berlin Heidelberg 1999

Authors and Affiliations

  • Elżbieta Błachut-Okrasińska
    • 1
  • Bogdan Lesyng
    • 2
  • James M. Briggs
    • 3
  • J. Andrew McCammon
    • 4
  • J. M. Antosiewicz
    • 1
  1. 1.Department of Biophysics, University of Warsaw, Z˙wirki i Wigury 93, PL-02-089 Warsaw, Poland e-mail: jantosi@asp.biogeo.uw.edu.plPL
  2. 2.Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawińskiego 5A, PL-02-106 Warsaw, PolandPL
  3. 3.Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5513, USAUS
  4. 4.Department of Pharmacology and Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093-0365, USAUS

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