Emulation of the structure of the Saposin protein fold by a lung surfactant peptide construct of surfactant Protein B
Abstract
The three-dimensional structure of the synthetic lung Surfactant Protein B Peptide Super Mini-B was determined using an integrative experimental approach, including mass spectrometry and isotope enhanced Fourier-transform infrared (FTIR) spectroscopy. Mass spectral analysis of the peptide, oxidized by solvent assisted region-specific disulfide formation, confirmed that the correct folding and disulfide pairing could be facilitated using two different oxidative structure-promoting solvent systems. Residue specific analysis by isotope enhanced FTIR indicated that the N-terminal and C-terminal domains have well defined α-helical amino acid sequences. Using these experimentally derived measures of distance constraints and disulfide connectivity, the ensemble was further refined with molecular dynamics to provide a medium resolution, residue-specific structure for the peptide construct in a simulated synthetic lung surfactant lipid multilayer environment. The disulfide connectivity combined with the α-helical elements stabilize the peptide conformationally to form a helical hairpin structure that resembles critical elements of the Saposin protein fold of the predicted full-length Surfactant Protein B structure.
Additional Information
© 2022 Waring et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. This work was supported by the Bill & Melinda Gates Foundation [grants OPP1112090 and INV-001227 to FW]. Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission. JW received support from the National Institutes of Health (grant P30 DK063491). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Data Availability: Protocols and data are deposited in the ModelArchive depository (https://modelarchive.org). S1. Mass Spectral derterminations, CD data and iTasser homology modeling protocols and data: ModelArchive repository, accession code: ma-axqi2. S2. Protocols and data for AlphaFold predictive modeling: ModelArchive repository, accession code: ma-scodz. S3. FTIR measurements and structural protein refinement with molecular dynamics: ModelArchive repository, accession code: ma-abz44. S4. Protocol and data for the AlphaFold SMB molecular dynamics refined structure: ModelArchive repository, accession code: ma-p57c0. S5. Supporting raw data for the predictive structure of human SP-B and overlay of the SMB refined structure: ModelArchive repository, accession code: ma-6jm8t. Competing interests: FW, AW, LG and the Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center hold a patent on Super Mini-B (US 8,563,683).Attached Files
Published - pone.0276787.pdf
Supplemental Material - journal.pone.0276787.s001.docx
Supplemental Material - journal.pone.0276787.s002.docx
Supplemental Material - journal.pone.0276787.s003.docx
Supplemental Material - journal.pone.0276787.s004.docx
Supplemental Material - journal.pone.0276787.s005.docx
Files
Name | Size | Download all |
---|---|---|
md5:8a18a7c453cbfafbe41d0299397d72fd
|
423.4 kB | Download |
md5:457a536ed017ba78afbb20cd01432370
|
2.0 MB | Preview Download |
md5:001be2ed2bf313fd943f904615add1a9
|
245.1 kB | Download |
md5:754349d7b9f49264880a84ce16b4e65e
|
362.5 kB | Download |
md5:bdb93370963106bd0a7c2c4045093634
|
186.3 kB | Download |
md5:25ed45c9c46a9a73276671bcbb052b5e
|
467.0 kB | Download |
Additional details
- PMCID
- PMC9632872
- Eprint ID
- 119637
- Resolver ID
- CaltechAUTHORS:20230302-365334800.5
- OPP1112090
- Bill and Melinda Gates Foundation
- P30 DK063491
- NIH
- INV-001227
- Bill and Melinda Gates Foundation
- Created
-
2023-05-17Created from EPrint's datestamp field
- Updated
-
2023-05-17Created from EPrint's last_modified field