dorsal/arxiv
View SchemaInfluence of subunit structure on the oligomerization state of light harvesting complexes: a free energy calculation study
| Authors | Lorant Janosi, Harindar Keer, Ioan Kosztin, Thorsten Ritz |
|---|---|
| Categories | |
| ArXiv ID | physics/0504213 |
| URL | https://arxiv.org/abs/physics/0504213 |
| DOI | 10.1016/j.chemphys.2005.08.038 |
| Journal | Chemical Physics (2005) |
Abstract
Light harvesting complexes 2 (LH2) from Rhodospirillum (Rs.) molischianum and Rhodopseudomonas (Rps.) acidophila form ring complexes out of eight or nine identical subunits, respectively. Here, we investigate computationally what factors govern the different ring sizes. Starting from the crystal structure geometries, we embed two subunits of each species into their native lipid-bilayer/water environment. Using molecular dynamics simulations with umbrella sampling and steered molecular dynamics, we probe the free energy profiles along two reaction coordinates, the angle and the distance between two subunits. We find that two subunits prefer to arrange at distinctly different angles, depending on the species, at about 42.5 deg for Rs. molischianum and at about 38.5 deg for Rps. acidophila, which is likely to be an important factor contributing to the assembly into different ring sizes. Our calculations suggest a key role of surface contacts within the transmembrane domain in constraining these angles, whereas the strongest interactions stabilizing the subunit dimers are found in the C-, and to a lesser extent, N-terminal domains. The presented computational approach provides a promising starting point to investigate the factors contributing to the assembly of protein complexes, in particular if combined with modeling of genetic variants.
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"abstract": "Light harvesting complexes 2 (LH2) from Rhodospirillum (Rs.) molischianum and\nRhodopseudomonas (Rps.) acidophila form ring complexes out of eight or nine\nidentical subunits, respectively. Here, we investigate computationally what\nfactors govern the different ring sizes. Starting from the crystal structure\ngeometries, we embed two subunits of each species into their native\nlipid-bilayer/water environment. Using molecular dynamics simulations with\numbrella sampling and steered molecular dynamics, we probe the free energy\nprofiles along two reaction coordinates, the angle and the distance between two\nsubunits. We find that two subunits prefer to arrange at distinctly different\nangles, depending on the species, at about 42.5 deg for Rs. molischianum and at\nabout 38.5 deg for Rps. acidophila, which is likely to be an important factor\ncontributing to the assembly into different ring sizes. Our calculations\nsuggest a key role of surface contacts within the transmembrane domain in\nconstraining these angles, whereas the strongest interactions stabilizing the\nsubunit dimers are found in the C-, and to a lesser extent, N-terminal domains.\nThe presented computational approach provides a promising starting point to\ninvestigate the factors contributing to the assembly of protein complexes, in\nparticular if combined with modeling of genetic variants.",
"arxiv_id": "physics/0504213",
"authors": [
"Lorant Janosi",
"Harindar Keer",
"Ioan Kosztin",
"Thorsten Ritz"
],
"categories": [
"physics.bio-ph",
"q-bio.BM"
],
"doi": "10.1016/j.chemphys.2005.08.038",
"journal_ref": "Chemical Physics (2005)",
"title": "Influence of subunit structure on the oligomerization state of light harvesting complexes: a free energy calculation study",
"url": "https://arxiv.org/abs/physics/0504213"
},
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