Transformation between α‐helix and β‐sheet structures of one and two polyglutamine peptides in explicit water molecules by replica‐exchange molecular dynamics simulations |
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| Authors: | Hsin‐Lin Chiang Chun‐Jung Chen Hisashi Okumura Chin‐Kun Hu |
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| Affiliation: | 1. Department of Physics, National Tsing Hua University, Hsinchu, Taiwan;2. Institute of Physics, Academia Sinica, Taipei, Taiwan;3. Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan;4. Institute of Biotechnology and University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan City, Taiwan;5. Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi, Japan;6. Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi, Japan |
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| Abstract: | Aggregation of polyglutamine peptides with β‐sheet structures is related to some important neurodegenerative diseases such as Huntington's disease. However, it is not clear how polyglutamine peptides form the β‐sheets and aggregate. To understand this problem, we performed all‐atom replica‐exchange molecular dynamics simulations of one and two polyglutamine peptides with 10 glutamine residues in explicit water molecules. Our results show that two polyglutamine peptides mainly formed helix or coil structures when they are separated, as in the system with one‐polyglutamine peptide. As the interpeptide distance decreases, the intrapeptide β‐sheet structure sometimes appear as an intermediate state, and finally the interpeptide β‐sheets are formed. We also find that the polyglutamine dimer tends to form the antiparallel β‐sheet conformations rather than the parallel β‐sheet, which is consistent with previous experiments and a coarse‐grained molecular dynamics simulation. © 2014 Wiley Periodicals, Inc. |
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| Keywords: | molecular dynamics simulation neurodegenerative diseases protein aggregation polyglutamine |
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