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Steered Molecular Dynamics for Investigating the Interactions Between Insulin Receptor Tyrosine Kinase (IRK) and Variants of Protein Tyrosine Phosphatase 1B (PTP1B)

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Abstract

The aim of this study is to use steered molecular dynamics to investigate the dissociation process between IRK and PTP1Bs for wild type and five mutants (consisting of p.D181E, p.D181A, p.Q262A, p.D181A-Y46F, and p.D181A-Q262A). The gained results are observed not only the unbinding mechanism of IRK-PTP1B complexes came from pulling force profile, number of hydrogen bonds, and interaction energy between IRK and PTP1Bs but also described PTP1B’s point mutations could variably change its binding affinity towards IRK. Additionally, the binding free energy calculated by Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) is also revealed that electrostatic energy and polar solvation energy mainly made up the binding free energy of PTP1B-IRK complexes.

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Acknowledgments

The computing resources were provided by the Institute for Computational Science and Technology, Ho Chi Minh City, and are gratefully acknowledged. The authors would like to express their gratitude to Mr. Linh Nguyen for valuable advice.

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Authors and Affiliations

  1. Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam

    Hung Nguyen, Tuyn Phan & Tri Pham

  2. Department of Medical Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam

    Nhat Do

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  1. Hung Nguyen
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  2. Nhat Do
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  3. Tuyn Phan
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  4. Tri Pham
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Contributions

Hung Nguyen designed the research, analyzed the data, and wrote the manuscript. Nhat Do and Tuyn Phan and Tri Pham analyzed the data. All authors reviewed the manuscript.

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Correspondence to Hung Nguyen.

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Nguyen, H., Do, N., Phan, T. et al. Steered Molecular Dynamics for Investigating the Interactions Between Insulin Receptor Tyrosine Kinase (IRK) and Variants of Protein Tyrosine Phosphatase 1B (PTP1B). Appl Biochem Biotechnol 184, 401–413 (2018). https://doi.org/10.1007/s12010-017-2549-6

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