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Cited by 5Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsEnzyme Structure and Function

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Structural proteomics of a bacterial mega membrane protein complex: FtsH-HflK-HflC

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Akkulak, Hatice, İnce, H. Kerim, Goc, Gunce, Lebrilla, Carlito B., Kabasakal, Burak V., Ozcan, Sureyya·2024·International Journal of Biological Macromolecules
DOI 10.1016/j.ijbiomac.2024.131923

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Abstract

Recent advances in mass spectrometry (MS) yielding sensitive and accurate measurements along with developments in software tools have enabled the characterization of complex systems routinely. Thus, structural proteomics and cross-linking mass spectrometry (XL-MS) have become a useful method for structural modeling of protein complexes. Here, we utilized commonly used XL-MS software tools to elucidate the protein interactions within a membrane protein complex containing FtsH, HflK, and HflC, over-expressed in E. coli. The MS data were processed using MaxLynx, MeroX, MS Annika, xiSEARCH, and XlinkX software tools. The number of identified inter- and intra-protein cross-links varied among software. Each interaction was manually checked using the raw MS and MS/MS data and distance restraints to verify inter- and intra-protein cross-links. A total of 37 inter-protein and 148 intra-protein cross-links were determined in the FtsH-HflK-HflC complex. The 59 of them were new interactions on the lacking region of recently published structures. These newly identified interactions, when combined with molecular docking and structural modeling, present opportunities for further investigation. The results provide valuable information regarding the complex structure and function to decipher the intricate molecular mechanisms underlying the FtsH-HflK-HflC complex.

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Metadata

Authors
Akkulak, H., İnce, H. K., Goc, G., Lebrilla, C. B., Kabasakal, B. V., & Ozcan, S.
Affiliations
  • Middle East Technical University (TR)
  • University of California, Davis (US)
  • University of Bristol (GB)
Corresponding author
Kabasakal, Burak V.
ORCID
Venue
International Journal of Biological Macromolecules
Publisher
Elsevier BV
Published
2024-06
Volume
269
Issue
Pt 1
Pages
131923
ISSN
0141-8130 (ISSN-L)
DOI
10.1016/j.ijbiomac.2024.131923
OpenAlex
W4396521432
Cited by
5
References
3
Citations by year
2026: 1 · 2025: 3 · 2024: 1
FWCI
0.63
Type
journal article
Language
en
Open access
Licence
Locations
  • International Journal of Biological Macromolecules (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • OpenMETU (Middle East Technical University) (submittedVersion, cc-by-nc-nd)
  • Explore Bristol Research (submittedVersion, cc-by-nc-nd)
Funders
TÜBİTAK
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords
membrane protein complexes, cross-linking mass spectrometry, protein-protein interaction, protein complex structure, Escherichia coli, distance restraints, molecular docking, structural modeling
MeSH terms
Bacterial Proteins, Escherichia coli, Membrane Proteins, Models, Molecular, Protein Binding, Software, Escherichia coli Proteins, Proteomics, Multiprotein Complexes, Molecular Docking Simulation

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