Solution structure of multi-domain protein ER-60 studied by aggregation-free SAXS and coarse-grained-MD simulation
Multi-domain proteins (MDPs) show a variety of domain conformations under physiological conditions, regulating their functions through such conformational changes. One of the typical MDPs, ER-60 which is a protein folding enzyme, has a U-shape with four domains and is thought to have different domai...
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| Published in | Scientific reports Vol. 11; no. 1; pp. 5655 - 13 |
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| Main Authors | , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
11.03.2021
Nature Publishing Group Nature Portfolio |
| Subjects | |
| Online Access | Get full text |
| ISSN | 2045-2322 2045-2322 |
| DOI | 10.1038/s41598-021-85219-0 |
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| Abstract | Multi-domain proteins (MDPs) show a variety of domain conformations under physiological conditions, regulating their functions through such conformational changes. One of the typical MDPs, ER-60 which is a protein folding enzyme, has a U-shape with four domains and is thought to have different domain conformations in solution depending on the redox state at the active centres of the edge domains. In this work, an aggregation-free small-angle X-ray scattering revealed that the structures of oxidized and reduced ER-60 in solution are different from each other and are also different from those in the crystal. Furthermore, structural modelling with coarse-grained molecular dynamics simulation indicated that the distance between the two edge domains of oxidized ER-60 is longer than that of reduced ER-60. In addition, one of the edge domains has a more flexible conformation than the other. |
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| AbstractList | Abstract Multi-domain proteins (MDPs) show a variety of domain conformations under physiological conditions, regulating their functions through such conformational changes. One of the typical MDPs, ER-60 which is a protein folding enzyme, has a U-shape with four domains and is thought to have different domain conformations in solution depending on the redox state at the active centres of the edge domains. In this work, an aggregation-free small-angle X-ray scattering revealed that the structures of oxidized and reduced ER-60 in solution are different from each other and are also different from those in the crystal. Furthermore, structural modelling with coarse-grained molecular dynamics simulation indicated that the distance between the two edge domains of oxidized ER-60 is longer than that of reduced ER-60. In addition, one of the edge domains has a more flexible conformation than the other. Multi-domain proteins (MDPs) show a variety of domain conformations under physiological conditions, regulating their functions through such conformational changes. One of the typical MDPs, ER-60 which is a protein folding enzyme, has a U-shape with four domains and is thought to have different domain conformations in solution depending on the redox state at the active centres of the edge domains. In this work, an aggregation-free small-angle X-ray scattering revealed that the structures of oxidized and reduced ER-60 in solution are different from each other and are also different from those in the crystal. Furthermore, structural modelling with coarse-grained molecular dynamics simulation indicated that the distance between the two edge domains of oxidized ER-60 is longer than that of reduced ER-60. In addition, one of the edge domains has a more flexible conformation than the other. Multi-domain proteins (MDPs) show a variety of domain conformations under physiological conditions, regulating their functions through such conformational changes. One of the typical MDPs, ER-60 which is a protein folding enzyme, has a U-shape with four domains and is thought to have different domain conformations in solution depending on the redox state at the active centres of the edge domains. In this work, an aggregation-free small-angle X-ray scattering revealed that the structures of oxidized and reduced ER-60 in solution are different from each other and are also different from those in the crystal. Furthermore, structural modelling with coarse-grained molecular dynamics simulation indicated that the distance between the two edge domains of oxidized ER-60 is longer than that of reduced ER-60. In addition, one of the edge domains has a more flexible conformation than the other.Multi-domain proteins (MDPs) show a variety of domain conformations under physiological conditions, regulating their functions through such conformational changes. One of the typical MDPs, ER-60 which is a protein folding enzyme, has a U-shape with four domains and is thought to have different domain conformations in solution depending on the redox state at the active centres of the edge domains. In this work, an aggregation-free small-angle X-ray scattering revealed that the structures of oxidized and reduced ER-60 in solution are different from each other and are also different from those in the crystal. Furthermore, structural modelling with coarse-grained molecular dynamics simulation indicated that the distance between the two edge domains of oxidized ER-60 is longer than that of reduced ER-60. In addition, one of the edge domains has a more flexible conformation than the other. |
| ArticleNumber | 5655 |
| Author | Sato, Nobuhiro Okuda, Aya Sugiyama, Masaaki Shimizu, Masahiro Urade, Reiko Inoue, Rintaro Morishima, Ken |
| Author_xml | – sequence: 1 givenname: Aya surname: Okuda fullname: Okuda, Aya organization: Institute for Integrative Radiation and Nuclear Science, Kyoto University – sequence: 2 givenname: Masahiro surname: Shimizu fullname: Shimizu, Masahiro organization: Institute for Integrative Radiation and Nuclear Science, Kyoto University – sequence: 3 givenname: Ken surname: Morishima fullname: Morishima, Ken organization: Institute for Integrative Radiation and Nuclear Science, Kyoto University – sequence: 4 givenname: Rintaro surname: Inoue fullname: Inoue, Rintaro organization: Institute for Integrative Radiation and Nuclear Science, Kyoto University – sequence: 5 givenname: Nobuhiro surname: Sato fullname: Sato, Nobuhiro organization: Institute for Integrative Radiation and Nuclear Science, Kyoto University – sequence: 6 givenname: Reiko surname: Urade fullname: Urade, Reiko email: urade.reiko.8w@kyoto-u.ac.jp organization: Institute for Integrative Radiation and Nuclear Science, Kyoto University – sequence: 7 givenname: Masaaki surname: Sugiyama fullname: Sugiyama, Masaaki email: sugiyama@rri.kyoto-u.ac.jp organization: Institute for Integrative Radiation and Nuclear Science, Kyoto University |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33707747$$D View this record in MEDLINE/PubMed |
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| Title | Solution structure of multi-domain protein ER-60 studied by aggregation-free SAXS and coarse-grained-MD simulation |
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