Conformational Motions and Water Networks at the α/β Interface in E. coli Ribonucleotide Reductase
© 2020 American Chemical Society. Ribonucleotide reductases (RNRs) catalyze the conversion of all four ribonucleotides to deoxyribonucleotides and are essential for DNA synthesis in all organisms. The active form of E. coli Ia RNR is composed of two homodimers that form the active α2β2 complex. Cata...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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American Chemical Society (ACS)
2021
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| Online Access: | https://hdl.handle.net/1721.1/133250 |
| _version_ | 1826203235977789440 |
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| author | Reinhardt, Clorice R Li, Pengfei Kang, Gyunghoon Stubbe, JoAnne Drennan, Catherine L Hammes-Schiffer, Sharon |
| author2 | Howard Hughes Medical Institute |
| author_facet | Howard Hughes Medical Institute Reinhardt, Clorice R Li, Pengfei Kang, Gyunghoon Stubbe, JoAnne Drennan, Catherine L Hammes-Schiffer, Sharon |
| author_sort | Reinhardt, Clorice R |
| collection | MIT |
| description | © 2020 American Chemical Society. Ribonucleotide reductases (RNRs) catalyze the conversion of all four ribonucleotides to deoxyribonucleotides and are essential for DNA synthesis in all organisms. The active form of E. coli Ia RNR is composed of two homodimers that form the active α2β2 complex. Catalysis is initiated by long-range radical translocation over a ∼32 Å proton-coupled electron transfer (PCET) pathway involving Y356β and Y731α at the interface. Resolving the PCET pathway at the α/β interface has been a long-standing challenge due to the lack of structural data. Herein, molecular dynamics simulations based on a recently solved cryogenic-electron microscopy structure of an active α2β2 complex are performed to examine the structure and fluctuations of interfacial water, as well as the hydrogen-bonding interactions and conformational motions of interfacial residues along the PCET pathway. Our free energy simulations reveal that Y731 is able to sample both a flipped-out conformation, where it points toward the interface to facilitate interfacial PCET with Y356, and a stacked conformation with Y730 to enable collinear PCET with this residue. Y356 and Y731 exhibit hydrogen-bonding interactions with interfacial water molecules and, in some conformations, share a bridging water molecule, suggesting that the primary proton acceptor for PCET from Y356 and from Y731 is interfacial water. The conformational flexibility of Y731 and the hydrogen-bonding interactions of both Y731 and Y356 with interfacial water and hydrogen-bonded water chains appear critical for effective radical translocation along the PCET pathway. These simulations are consistent with biochemical and spectroscopic data and provide previously unattainable atomic-level insights into the fundamental mechanism of RNR. |
| first_indexed | 2024-09-23T12:33:28Z |
| format | Article |
| id | mit-1721.1/133250 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T12:33:28Z |
| publishDate | 2021 |
| publisher | American Chemical Society (ACS) |
| record_format | dspace |
| spelling | mit-1721.1/1332502023-11-08T22:06:02Z Conformational Motions and Water Networks at the α/β Interface in E. coli Ribonucleotide Reductase Reinhardt, Clorice R Li, Pengfei Kang, Gyunghoon Stubbe, JoAnne Drennan, Catherine L Hammes-Schiffer, Sharon Howard Hughes Medical Institute Massachusetts Institute of Technology. Department of Biology Massachusetts Institute of Technology. Department of Chemistry © 2020 American Chemical Society. Ribonucleotide reductases (RNRs) catalyze the conversion of all four ribonucleotides to deoxyribonucleotides and are essential for DNA synthesis in all organisms. The active form of E. coli Ia RNR is composed of two homodimers that form the active α2β2 complex. Catalysis is initiated by long-range radical translocation over a ∼32 Å proton-coupled electron transfer (PCET) pathway involving Y356β and Y731α at the interface. Resolving the PCET pathway at the α/β interface has been a long-standing challenge due to the lack of structural data. Herein, molecular dynamics simulations based on a recently solved cryogenic-electron microscopy structure of an active α2β2 complex are performed to examine the structure and fluctuations of interfacial water, as well as the hydrogen-bonding interactions and conformational motions of interfacial residues along the PCET pathway. Our free energy simulations reveal that Y731 is able to sample both a flipped-out conformation, where it points toward the interface to facilitate interfacial PCET with Y356, and a stacked conformation with Y730 to enable collinear PCET with this residue. Y356 and Y731 exhibit hydrogen-bonding interactions with interfacial water molecules and, in some conformations, share a bridging water molecule, suggesting that the primary proton acceptor for PCET from Y356 and from Y731 is interfacial water. The conformational flexibility of Y731 and the hydrogen-bonding interactions of both Y731 and Y356 with interfacial water and hydrogen-bonded water chains appear critical for effective radical translocation along the PCET pathway. These simulations are consistent with biochemical and spectroscopic data and provide previously unattainable atomic-level insights into the fundamental mechanism of RNR. 2021-10-27T19:51:47Z 2021-10-27T19:51:47Z 2020 2021-08-13T14:33:42Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/133250 en 10.1021/JACS.0C04325 Journal of the American Chemical Society Creative Commons Attribution-Noncommercial-Share Alike http://creativecommons.org/licenses/by-nc-sa/4.0/ application/pdf American Chemical Society (ACS) PMC |
| spellingShingle | Reinhardt, Clorice R Li, Pengfei Kang, Gyunghoon Stubbe, JoAnne Drennan, Catherine L Hammes-Schiffer, Sharon Conformational Motions and Water Networks at the α/β Interface in E. coli Ribonucleotide Reductase |
| title | Conformational Motions and Water Networks at the α/β Interface in E. coli Ribonucleotide Reductase |
| title_full | Conformational Motions and Water Networks at the α/β Interface in E. coli Ribonucleotide Reductase |
| title_fullStr | Conformational Motions and Water Networks at the α/β Interface in E. coli Ribonucleotide Reductase |
| title_full_unstemmed | Conformational Motions and Water Networks at the α/β Interface in E. coli Ribonucleotide Reductase |
| title_short | Conformational Motions and Water Networks at the α/β Interface in E. coli Ribonucleotide Reductase |
| title_sort | conformational motions and water networks at the α β interface in e coli ribonucleotide reductase |
| url | https://hdl.handle.net/1721.1/133250 |
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