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  4. HRD Motif as the Central Hub of the Signaling Network for Activation Loop Autophosphorylation in Abl Kinase
 
research article

HRD Motif as the Central Hub of the Signaling Network for Activation Loop Autophosphorylation in Abl Kinase

La Sala, Giuseppina
•
Riccardi, Laura
•
Gaspari, Roberto
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2016
Journal of chemical theory and computation

A number of structural factors modulate the activity of Abelson (Abl) tyrosine kinase, whose deregulation is often related to oncogenic processes. First, only the open conformation of the Abl kinase domain's activation loop (A-loop) favors ATP binding to the catalytic cleft. In this regard, the trans-autophosphorylation of the Y412 residue, which is located along the A-loop, favors the stability of the open conformation, in turn enhancing Abl activity. Another key factor for full Abl activity is the formation of active conformations of the catalytic DFG motif in the Abl kinase domain. Furthermore, binding of the SH2 domain to the N-lobe of the Abl kinase was recently demonstrated to have a long-range allosteric effect on the stabilization of the A-loop open state. Intriguingly, these distinct structural factors imply a complex signal transmission network for controlling the A-loop's flexibility and conformational preference for optimal Abl function. However, the exact dynamical features of this signal transmission network structure remain unclear. Here, we report on microsecond-long molecular dynamics coupled with enhanced sampling simulations of multiple Abl model systems, in the presence or absence of the SH2 domain and with the DFG motif flipped in two ways (in or out conformation). Through comparative analysis, our simulations augment the interpretation of the existing Abl experimental data, revealing a dynamical network of interactions that interconnect SH2 domain binding with A-loop plasticity and Y412 autophosphorylation in Abl. This signaling network engages the DFG motif and, importantly, other conserved structural elements of the kinase domain, namely, the EPK-ELK H-bond network and the HRD motif. Our results show that the signal propagation for modulating the A-loop spatial localization is highly dependent on the HRD motif conformation, which thus acts as the central hub of this (allosteric) signaling network controlling Abl activation and function.

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Type
research article
DOI
10.1021/acs.jctc.6b00600
Web of Science ID

WOS:000387519400031

Author(s)
La Sala, Giuseppina
Riccardi, Laura
Gaspari, Roberto
Cavalli, Andrea
Hantschel, Oliver  
De Vivo, Marco
Date Issued

2016

Publisher

Amer Chemical Soc

Published in
Journal of chemical theory and computation
Volume

12

Issue

11

Start page

5563

End page

5574

Editorial or Peer reviewed

REVIEWED

Written at

OTHER

EPFL units
UPHAN  
Available on Infoscience
January 24, 2017
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/133257
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