All-atom molecular dynamics simulations of lung surfactant protein B : Structural features of SP-B promote lipid reorganization
Copyright © 2016 Elsevier B.V. All rights reserved..
Lung surfactant protein B (SP-B), a 79 residue, hydrophobic protein from the saposin superfamily, plays an essential role in breathing. Because of the extreme hydrophobicity of SP-B, the experimental structure of this protein has not yet been determined. Here, we run all-atom molecular dynamics simulations using the OPLS-AA force field in GROMACS to study SP-B's structure and mechanisms for promoting lipid reorganization. Firstly, we find that the final structures indicate the need for some fine-tuning of the homology-based secondary structure predictions. Secondly, we find energetically feasible structures 1) with SP-B's helices in the plane of the bilayer, 2) with SP-B's helices inclined with respect to the bilayer, and 3) with SP-B in a closed structure interacting peripherally with the bilayer. Interestingly, SP-B structures that were bent at the hinge region between the pairs of helices promoted and/or stabilized defects in the lipid bilayer. Finally, particular salt bridge patterns and structural plasticity in the central loop and adjacent region of SP-B appeared to be involved in SP-B's lipid reorganization abilities.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2016 |
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| Erschienen: |
2016 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:1858 |
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| Enthalten in: |
Biochimica et biophysica acta - 1858(2016), 12 vom: 27. Dez., Seite 3082-3092 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Khatami, Mohammad Hassan [VerfasserIn] |
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| Links: |
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| Themen: |
Bilayer diffusion |
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| Anmerkungen: |
Date Completed 26.10.2017 Date Revised 29.04.2018 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1016/j.bbamem.2016.09.018 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM264723236 |
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| 100 | 1 | |a Khatami, Mohammad Hassan |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a All-atom molecular dynamics simulations of lung surfactant protein B |b Structural features of SP-B promote lipid reorganization |
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| 500 | |a Date Completed 26.10.2017 | ||
| 500 | |a Date Revised 29.04.2018 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2016 Elsevier B.V. All rights reserved. | ||
| 520 | |a Lung surfactant protein B (SP-B), a 79 residue, hydrophobic protein from the saposin superfamily, plays an essential role in breathing. Because of the extreme hydrophobicity of SP-B, the experimental structure of this protein has not yet been determined. Here, we run all-atom molecular dynamics simulations using the OPLS-AA force field in GROMACS to study SP-B's structure and mechanisms for promoting lipid reorganization. Firstly, we find that the final structures indicate the need for some fine-tuning of the homology-based secondary structure predictions. Secondly, we find energetically feasible structures 1) with SP-B's helices in the plane of the bilayer, 2) with SP-B's helices inclined with respect to the bilayer, and 3) with SP-B in a closed structure interacting peripherally with the bilayer. Interestingly, SP-B structures that were bent at the hinge region between the pairs of helices promoted and/or stabilized defects in the lipid bilayer. Finally, particular salt bridge patterns and structural plasticity in the central loop and adjacent region of SP-B appeared to be involved in SP-B's lipid reorganization abilities | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a Bilayer diffusion | |
| 650 | 4 | |a GROMACS | |
| 650 | 4 | |a Lung surfactant protein | |
| 650 | 4 | |a Molecular dynamics | |
| 650 | 4 | |a POPC | |
| 650 | 4 | |a SP-B | |
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| 650 | 7 | |a Pulmonary Surfactant-Associated Protein B |2 NLM | |
| 700 | 1 | |a Saika-Voivod, Ivan |e verfasserin |4 aut | |
| 700 | 1 | |a Booth, Valerie |e verfasserin |4 aut | |
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