Replica exchange molecular dynamics simulation study on the mechanism of desiccation-induced structuralization of an intrinsically disordered peptide as a model of LEA proteins
| Autor: | Minoru Sakurai, Shohei Miyama, Yuta Takahashi, Tatsushi Nishimoto, Tadaomi Furuta |
|---|---|
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Peptide late embryogenesis abundant proteins Intrinsically disordered proteins lcsh:Physiology desiccation protectant 03 medical and health sciences Molecular dynamics Late embryogenesis abundant proteins α-helical coiled coil Tandem repeat Amphiphile Peptide sequence lcsh:QH301-705.5 chemistry.chemical_classification Coiled coil 030102 biochemistry & molecular biology lcsh:QP1-981 Chemistry Regular Article General Medicine lcsh:QC1-999 030104 developmental biology lcsh:Biology (General) Biophysics lcsh:Physics |
| Zdroj: | Biophysics and Physicobiology Biophysics and Physicobiology, Vol 16 (2019) |
| ISSN: | 2189-4779 |
| Popis: | Group 3 late embryogenesis abundant (G3LEA) proteins, which act as a well-characterized desiccation protectant in anhydrobiotic organisms, are structurally disordered in solution, but they acquire a predominantly α-helical structure during drying. Thus, G3LEA proteins are now accepted as intrinsically disordered proteins (IDPs). Their functional regions involve characteristic 11-mer repeating motifs. In the present study, to elucidate the origin of the IDP property of G3LEA proteins, we applied replica exchange molecular dynamics (REMD) simulation to a model peptide composed of two tandem repeats of an 11-mer motif and its counterpart peptide whose amino acid sequence was randomized with the same amino acid composition as that of the 11-mer motif. REMD simulations were performed for a single α-helical chain of each peptide and its double-bundled strand in a wide water content ranging from 5 to 78.3 wt%. In the latter case, we tested different types of arrangement: 1) the dipole moments of the two helices were parallel or anti-parallel and 2) due to the amphiphilic nature of the α-helix of the 11-mer motif, two types of the side-to-side contact were tested: hydrophilic-hydrophilic facing or hydrophobic-hydrophobic facing. Here, we revealed that the single chain alone exhibits no IDP-like properties, even if it involves the 11-mer motif, and the hydrophilic interaction of the two chains leads to the formation of a left-handed α-helical coiled coil in the dry state. These results support the cytoskeleton hypothesis that has been proposed as a mechanism by which G3LEA proteins work as a desiccation protectant. |
| Databáze: | OpenAIRE |
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