Globular bundles and entangled network of proteins (CorA) by a coarse-grained Monte Carlo simulation

Warin Rangubpit; Sunan Kitjaruwankul; Panisak Boonamnaj; Pornthep Sompornpisut; R.B. Pandey; Warin Rangubpit; Sunan Kitjaruwankul; Panisak Boonamnaj; Pornthep Sompornpisut; R.B. Pandey

doi:10.3934/biophy.2019.2.68

AIMS Biophysics

2019, Volume 6, Issue 2: 68-82. doi: 10.3934/biophy.2019.2.68

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Research article Topical Sections

Globular bundles and entangled network of proteins (CorA) by a coarse-grained Monte Carlo simulation

1.
Center of Excellence in Computational Chemistry, Department of Chemistry, Chulalongkorn University, Bangkok 10330, Thailand
2.
Faculty of Science at Sriracha, Kasetsart University Sriracha Campus, Chonburi 20230, Thailand
3.
Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, MS 39406, USA

Received: 26 April 2019 Accepted: 24 June 2019 Published: 18 July 2019

Using a coarse-grained model, self-organized assembly of proteins (e.g., CorA and its inner segment iCorA) is studied by examining quantities such as contact profile, radius of gyration, and structure factor as a function of protein concentration at a range of low (native phase) to high (denature phase) temperatures. Visual inspections show distinct structures, i.e., isolated globular bundles to entangled network on multiple length scales in dilute to crowded protein concentrations. In native phase, the radius of gyration of the protein does not vary much with the protein concentration while that of its inner segment increases systematically. In contrast, the radius of gyration of the protein shows enormous growth with the concentration due to entanglement while that of the inner segment remains almost constant in denatured phase. The multi-scale morphology of the collective assembly is quantified by estimating the effective dimension D of protein from scaling of the structure factor: collective assembly from inner segments remains globular (D~3) at almost all length scales in its native phase while that from protein chains shows sparsely distributed morphology with D ≤ 2 in entire temperature range due to entanglement except in crowded environment at low temperature where D~2.6. Higher morphological response of chains with only the inner-segments due to selective interactions in its native phase may be more conducive to self-organizing mechanism than that of the remaining segments of the protein chains.

Keywords:

Self-organizing structure of proteins (CorA),
protein folding,
Coarse-grained model,
Monte Carlo simulation,
effective dimension of self-assembly

Citation: Warin Rangubpit, Sunan Kitjaruwankul, Panisak Boonamnaj, Pornthep Sompornpisut, R.B. Pandey. Globular bundles and entangled network of proteins (CorA) by a coarse-grained Monte Carlo simulation[J]. AIMS Biophysics, 2019, 6(2): 68-82. doi: 10.3934/biophy.2019.2.68

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Abstract

Acknowledgments

This research has been supported by the Ratchadaphiseksomphot Endowment Fund, Chulalongkorn University to PS, the Chulalongkorn university dusadi phipat scholarship to WR. Support from the Chulalongkorn University for a visiting professorship is gratefully acknowledged by RBP along with the warm hospitality by the Department of Chemistry. The authors acknowledge HPC at The University of Southern Mississippi supported by the National Science Foundation under the Major Research Instrumentation (MRI) program via Grant # ACI 1626217.

Conflict of interest

We do not have conflict of interest.

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