دورية أكاديمية
Molecular movie of nucleotide binding to a motor protein.
| العنوان: | Molecular movie of nucleotide binding to a motor protein. |
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| المؤلفون: | Bondar AN; Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany. Electronic address: nbondar@zedat.fu-berlin.de., Mishima H; Department of Physics, Graduate School of Science, Nagoya University, Aichi 464-8602, Japan; JST-CREST, Nagoya, Aicihi 464-8602, Japan., Okamoto Y; Department of Physics, Graduate School of Science, Nagoya University, Aichi 464-8602, Japan; JST-CREST, Nagoya, Aicihi 464-8602, Japan. |
| المصدر: | Biochimica et biophysica acta. General subjects [Biochim Biophys Acta Gen Subj] 2020 Oct; Vol. 1864 (10), pp. 129654. Date of Electronic Publication: 2020 Jun 05. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: Elsevier Country of Publication: Netherlands NLM ID: 101731726 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1872-8006 (Electronic) Linking ISSN: 03044165 NLM ISO Abbreviation: Biochim Biophys Acta Gen Subj Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Amsterdam : Elsevier |
| مواضيع طبية MeSH: | Adenosine Triphosphatases/*metabolism , Adenosine Triphosphate/*metabolism , Escherichia coli/*metabolism , Escherichia coli Proteins/*metabolism , SecA Proteins/*metabolism, Binding Sites ; Cations, Divalent/metabolism ; Escherichia coli/chemistry ; Escherichia coli Proteins/chemistry ; Hydrogen Bonding ; Magnesium/metabolism ; Molecular Dynamics Simulation ; Protein Binding ; Protein Conformation ; Protein Domains ; SecA Proteins/chemistry |
| مستخلص: | Background: The SecA DEAD (Asp-Glu-Ala-Asp) motor protein uses binding and hydrolysis of adenosine triphosphate (ATP) to push secretory proteins across the plasma membrane of bacteria. The reaction coordinate of nucleotide exchange is unclear at the atomic level of detail. Methods: We performed multiple atomistic computations of the DEAD motor domain of SecA with different occupancies of the nucleotide and magnesium ion sites, for a total of ~1.7 μs simulation time. To characterize dynamics at the active site we analyzed hydrogen-bond networks. Results: ATP and ADP can bind spontaneously at the interface between the nucleotide binding domains, albeit at an intermediate binding site distinct from the native site. Binding of the nucleotide is facilitated by the presence of a magnesium ion close to the glutamic group of the conserved DEAD motif. In the absence of the magnesium ion, protein interactions of the ADP molecule are perturbed. Conclusions: A protein hydrogen-bond network whose dynamics couples to the occupancy of the magnesium ion site helps guide the nucleotide along the nucleotide exchange path. In SecA, release of magnesium might be required to destabilize the ADP binding site prior to release of the nucleotide. General Significance: We identified dynamic hydrogen-bond networks that help control nucleotide exchange in SecA, and stabilize ADP at an intermediate site that could explain slow release. The reaction coordinate of the protein motor involves complex rearrangements of a hydrogen-bond network at the active site, with perturbation of the magnesium ion site likely occurring prior to the release of ADP. Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. (Copyright © 2020 Elsevier B.V. All rights reserved.) |
| فهرسة مساهمة: | Keywords: ADP release; H-bond networks; Magnesium; Protein motor; SecA |
| المشرفين على المادة: | 0 (Cations, Divalent) 0 (Escherichia coli Proteins) 8L70Q75FXE (Adenosine Triphosphate) EC 3.6.1.- (Adenosine Triphosphatases) EC 3.6.3.- (SecA protein, E coli) EC 7.4.2.4 (SecA Proteins) I38ZP9992A (Magnesium) |
| تواريخ الأحداث: | Date Created: 20200609 Date Completed: 20201204 Latest Revision: 20201214 |
| رمز التحديث: | 20231215 |
| DOI: | 10.1016/j.bbagen.2020.129654 |
| PMID: | 32512170 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1872-8006 |
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| DOI: | 10.1016/j.bbagen.2020.129654 |