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European Biophysics Journal

, Volume 43, Issue 2–3, pp 81–95 | Cite as

Probing the wild-type HRas activation mechanism using steered molecular dynamics, understanding the energy barrier and role of water in the activation

  • Neeru Sharma
  • Uddhavesh SonavaneEmail author
  • Rajendra JoshiEmail author
Original Paper

Abstract

Ras is one of the most common oncogenes in human cancers. It belongs to a family of GTPases that functions as binary conformational switches by timely switching of their conformations from GDP to GTP and vice versa. It attains the final active state structure via an intermediate GTP-bound state. The transition between these states is a millisecond-time-scale event. This makes studying this mechanism beyond the scope of classical molecular dynamics. In the present study, we describe the activation pathway of the HRas protein complex along the distance-based reaction coordinate using steered molecular dynamics. Approximately ~720 ns of MD simulations using CMD and SMD was performed. We demonstrated the change in orientation and arrangement of the two switch regions and the role of various hydrogen bonds during the activation process. The weighted histogram analysis method was also performed, and the potential of mean force was calculated between the inactive and active via the intermediate state (state 1) of HRas. The study indicates that water seems to play a crucial role in the activation process and to transfer the HRas protein from its intermediate state to the fully active state. The implications of our study hereby suggest that the HRas activation mechanism is a multistep process. It starts from the inactive state to an intermediate state 1 followed by trapping of water molecules and flipping of the Thr35 residue to form a fully active state (state 2). This state 2 also comprises Gly60, Thr35, GTP, Mg2+ and water-forming stable interactions.

Keywords

HRas activation mechanism GTP GDP Energy barrier Steered molecular dynamics Classical molecular dynamics 

Abbreviations

RAS

RAt Sarcoma

HRas

Harvey Rat sarcoma

MD

Molecular Dynamics

CMD

Classical Molecular Dynamics

SMD

Steered Molecular Dynamics

GTP

Guanosine tri-Phosphate

GDP

Guanosine di-Phosphate

PMF

Potential of Mean Force

Sw I

Switch-1

Sw II

Switch-2

P-loop

Phosphate-binding loop

Notes

Acknowledgments

The authors gratefully acknowledge the Department of Electronics and Information Technology (DeitY), Government of India, New Delhi, for providing financial support. This work was performed using the “Bioinformatics Resources and Applications Facility (BRAF)” and “National PARAM Supercomputing Facility (NPSF)” at C-DAC, Pune.

Supplementary material

249_2014_942_MOESM1_ESM.pdf (1.9 mb)
Supplementary material 1 (PDF 1924 kb)

Supplementary material 2 (MPG 51787 kb)

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Copyright information

© European Biophysical Societies' Association 2014

Authors and Affiliations

  1. 1.Bioinformatics Group, Centre for Development of Advanced ComputingPune University CampusPuneIndia

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