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Protein Sci. 2019 Mar;28(3):543-560. doi: 10.1002/pro.3556. Epub 2018 Dec 30.

Long-range molecular dynamics show that inactive forms of Protein Kinase A are more dynamic than active forms.

Author information

1
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
2
INSERM, U 1134, DSIMB, F-75739, Paris, France.
3
Univ Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, F-75739, Paris, France.
4
Institut National de la Transfusion Sanguine (INTS), F-75739, Paris, France.
5
Laboratoire d'Excellence GR-Ex, F-75739, Paris, France.

Abstract

Many protein kinases are characterized by at least two structural forms corresponding to the highest level of activity (active) and low or no activity, (inactive). Further, protein dynamics is an important consideration in understanding the molecular and mechanistic basis of enzyme function. In this work, we use protein kinase A (PKA) as the model system and perform microsecond range molecular dynamics (MD) simulations on six variants which differ from one another in terms of active and inactive form, with or without bound ligands, C-terminal tail and phosphorylation at the activation loop. We find that the root mean square fluctuations in the MD simulations are generally higher for the inactive forms than the active forms. This difference is statistically significant. The higher dynamics of inactive states has significant contributions from ATP binding loop, catalytic loop, and αG helix. Simulations with and without C-terminal tail show this differential dynamics as well, with lower dynamics both in the active and inactive forms if C-terminal tail is present. Similarly, the dynamics associated with the inactive form is higher irrespective of the phosphorylation status of Thr 197. A relatively stable stature of active kinases may be better suited for binding of substrates and detachment of the product. Also, phosphoryl group transfer from ATP to the phosphosite on the substrate requires precise transient coordination of chemical entities from three different molecules, which may be facilitated by the higher stability of the active state.

KEYWORDS:

STY kinases; active and inactive states; functional state; molecular dynamics; protein kinase A; protein kinases; structural flexibility in active and inactive state kinases

PMID:
30468265
PMCID:
PMC6371217
[Available on 2020-03-01]
DOI:
10.1002/pro.3556

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