Computational analysis of homo-dimerization of chloroplast-localized chaperonin from the alga Chlamydomonas reinhardtii

Authors

  • Rungdawan Wongsamart Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
  • Duangnapa Kiriwan Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
  • Chonticha Suwattanasophon Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna 1010 Austria
  • Kittisak Yokthongwattana Center for Excellence in Protein and Enzyme technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
  • Kiattawee Choowongkomon Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand

Keywords:

Binding free energy, Chlamydomonas reinhardtii, Cpn60, Homodimer, MD simulation

Abstract

Molecular chaperones are major groups of proteins responsible for proteostasis regulation. GroEL is a protein belonging to the chaperonin family of molecular chaperones. Unlike GroEL in prokaryotes, chloroplast chaperonin 60 (Cpn60) has distinct subunits. The chaperonin for the alga Chlamydomonas reinhardtii has one α and two β subunits (β1 and β2). Even though a crystal structure of homo-oligomer (Cpn60β1) has been reported, it is still unclear how these subunits assemble. This study modeled homo-subunit dimers of C. reinhardtii. Dimers αα, β1β1 and β2β2 were analyzed based on molecular dynamics simulation. Many hydrogen bonds presented in the same position among the three dimers, even though the amino acids were different. Charged amino acids were an important factor influencing the binding interface orientation. The binding free energy of the β1β1 dimer was the lowest, followed by β2β2 and αα, respectively. The results suggested that the β1β1 assembly was more favorable than β2β2 and αα.

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Published

2021-10-31

Issue

Section

Research Article