Molecular Dynamics Simulations for Three-Dimensional Structures of Orotate Phosphoribosyltransferases Constructed from a Simplified Amino Acid Set
| العنوان: | Molecular Dynamics Simulations for Three-Dimensional Structures of Orotate Phosphoribosyltransferases Constructed from a Simplified Amino Acid Set |
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| المؤلفون: | Eiji Kurimoto, Koichi Kato, Akifumi Oda, Tomoki Nakayoshi, Mizuha Sato |
| المصدر: | ACS Omega, Vol 5, Iss 22, Pp 13069-13076 (2020) ACS Omega |
| بيانات النشر: | American Chemical Society, 2020. |
| سنة النشر: | 2020 |
| مصطلحات موضوعية: | chemistry.chemical_classification, Chemistry, General Chemical Engineering, General Chemistry, medicine.disease_cause, Article, Amino acid, Set (abstract data type), Molecular dynamics, Biochemistry, Helix, medicine, Orotate phosphoribosyltransferase, Escherichia coli, QD1-999, Function (biology) |
| الوصف: | Proteins of modern terrestrial organisms are composed of nearly 20 amino acids; however, the amino acid sets of primitive organisms may have contained fewer than 20 amino acids. Furthermore, the full set of 20 amino acids is not required by some proteins to encode their function. Indeed, simplified variants of Escherichia coli (E. coli) orotate phosphoribosyltransferase (OPRTase) constructed by Akanuma et al. and composed of a limited amino acid set exhibit significant catalytic activity for the growth of E. coli. However, its structural details are currently unclear. Here, we predict the structures of simplified variants of OPRTase using molecular dynamics (MD) simulations and evaluate the accuracy of the MD simulations for simplified proteins. The three-dimensional structure of the wild-type was largely maintained in the simplified variants, but differences in the catalyst loop and C-terminal helix were observed. These results are considered sufficient to elucidate the differences in catalytic activity between the wild-type and simplified OPRTase variants. Thus, using MD simulations to make structural predictions appears to be a useful strategy when investigating non-wild-type proteins composed of reduced amino acid sets. |
| اللغة: | English |
| تدمد: | 2470-1343 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::08fd4a6855901cbfd1e57698ef4719d9 https://doaj.org/article/51c684ffd46c470c9f12f3c6e4f6c493 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....08fd4a6855901cbfd1e57698ef4719d9 |
| قاعدة البيانات: | OpenAIRE |
Find this issue from the American Chemical Society | تدمد: | 24701343 |
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