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Thermal-response of a protein (hHv1) by a coarse-grained MC and all-atom MD computer simulations

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  • Boonamnaj, Panisak
  • Paudel, Sunita Subedi
  • Jetsadawisut, Warin
  • Kitjaruwankul, Sunan
  • Sompornpisut, Pornthep
  • Pandey, R.B.

Abstract

A Monte Carlo simulation with a coarse-grained (CGMC) model of protein involving a phenomenological residue–residue interaction potential, augmented by a Molecular Dynamics simulation is used to investigate local and global structures of a protein (hHv1) as a function of temperature. Data from both all-atom MD and a coarse-grained MC simulations show that the radius of gyration of the protein (the cytoplasmic domain of hHv1 monomer and dimer) decreases on increasing the temperature, i.e. it becomes more globular on heating in its native phase in contrast to its thermal expansion in denatured phase. The globularization of the protein is quantified by analyzing the scaling of the structure factor. The crossover from globular to random-coil structure involving segmental reorganizations is found to depend on the length scale and the temperature.

Suggested Citation

  • Boonamnaj, Panisak & Paudel, Sunita Subedi & Jetsadawisut, Warin & Kitjaruwankul, Sunan & Sompornpisut, Pornthep & Pandey, R.B., 2019. "Thermal-response of a protein (hHv1) by a coarse-grained MC and all-atom MD computer simulations," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 527(C).
    • Handle: RePEc:eee:phsmap:v:527:y:2019:i:c:s0378437119307757
    DOI: 10.1016/j.physa.2019.121310
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    Cited by:

    1. Pandey, R.B., 2021. "A Monte Carlo simulation of a protein (CoVE) in a matrix of random barriers," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 572(C).

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